AbstractHydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.
AbstractThe in situ production of necromass and its role as a power source in sustaining heterotrophic microorganisms in natural settings has never been quantified. Here, we quantify the power availability from necromass oxidation to living microorganisms buried in marine sediments over millions of years, first in the oligotrophic South Pacific Gyre (SPG), and second on a global scale. We calculate that power from autochthonously produced necromass in the upper meter of sediment at SPG provides only a small fraction (~0.02%) of the maintenance power demand of the living community (1.9×10-19 W cell-1). Power from necromass oxidation diminishes considerably with increasing sediment depth (and thus sediment age). Alternatively, the oxidation of allochthonous organic matter, and of radiolytic H2, provides power equivalent to or in excess of the maintenance demands of living microorganisms at SPG. On a global scale, necromass may support the maintenance power demand of 2 to 13% of the microbial community in relatively young sediments (<10,000 years) when it is oxidized with SO42- and O2 respectively. However, in older sediments, the power supplied by necromass is negligible (<0.01%). Nevertheless, the oxidation of a single dead cell per year provides sufficient power to support the maintenance demands of dozens to thousands of cells in low-energy marine sediments. This raises the possibility that the production and oxidation of necromass may provide a mechanism for non-growing microorganisms to endure unfavorable, low-energy settings over geological timescales.
AbstractMarine sediments constitute one of the most energy-limited habitats on Earth, in which microorganisms persist over extraordinarily long timescales with very slow metabolisms. This habitat provides an ideal environment in which to study the energetic limits of life. However, the bioenergetic factors that can determine whether microorganisms will grow, lie dormant, or die, as well as the selective environmental pressures that determine energetic trade-offs between growth and maintenance activities, are not well understood. Numerical models will be pivotal in addressing these knowledge gaps. However, models rarely account for the variable physiological states of microorganisms and their demand for energy. Here, we review established modeling constructs for microbial growth rate, yield, maintenance, and physiological state, and then provide a new model that incorporates all of these factors. We discuss this new model in context with its future application to the marine subsurface. Understanding the factors that regulate cell death, physiological state changes, and the provenance of maintenance energy (i.e., endogenous versus exogenous metabolism), is crucial to the design of this model. Further, measurements of growth rate, growth yield, and basal metabolic activity will enable bioenergetic parameters to be better constrained. Last, biomass and biogeochemical rate measurements will enable model simulations to be validated. The insight provided from the development and application of new microbial modeling tools for marine sediments will undoubtedly advance the understanding of the minimum power required to support life, and the ecophysiological strategies that organisms utilize to cope under extreme energy limitation for extended periods of time.
AbstractThe microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the Caribbean Sea were characterized using microscopy, phylogenetic analyses, and a metagenomic approach. The present study adds new evidence that tubeworm endosymbionts can potentially switch from autotrophic to heterotrophic metabolism, or may be mixotrophic, presumably while free-living, and also suggests their versatile metabolic potential may enable both the host and symbionts to exploit a wide range of environmental conditions. Together, the marked gene content and sequence dissimilarity at the rRNA operon and whole genome level between vent and seep symbionts suggest these newly described endosymbionts from the MCR belong to a novel tubeworm endosymbiont genera, introduced as Candidatus Vondammii.
AbstractThe emplacement of subaqueous gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro-organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the buried La Jolla Canyon sediment–water interface reflect turbidite-induced changes to the geochemical environment. Species-level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1-cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low-energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.
AbstractMicroorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7.2 million contigs ≥2 kb in length. Approximately 1 million of these contigs were binned to reconstruct draft genomes. In total, 2,631 draft genomes with an estimated completion of ≥50% were generated (1,491 draft genomes >70% complete; 603 genomes >90% complete). A majority of the draft genomes were manually assigned phylogeny based on sets of concatenated phylogenetic marker genes and/or 16S rRNA gene sequences. The draft genomes are now publically available for the research community at-large.
AbstractThe deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi.
AbstractAt deep-sea hydrothermal vents, microbial communities thrive across geochemical gradients above, at, and below the seafloor. In this study, we determined the gene content and transcription patterns of microbial communities and specific populations to understand the taxonomy and metabolism both spatially and temporally across geochemically different diffuse fluid hydrothermal vents. Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and geochemical analyses from Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge in the NE Pacific Ocean, from 2013 to 2015 at three different vents: Anemone, Marker 33, and Marker 113. Results showed that individual vent sites maintained microbial communities and specific populations over time, but with spatially distinct taxonomic, metabolic potential, and gene transcription profiles. The geochemistry and physical structure of each vent both played important roles in shaping the dominant organisms and metabolisms present at each site. Genomic binning identified key populations of SUP05, Aquificales and methanogenic archaea carrying out important transformations of carbon, sulfur, hydrogen, and nitrogen, with groups that appear unique to individual sites. This work highlights the connection between microbial metabolic processes, fluid chemistry, and microbial population dynamics at and below the seafloor and increases understanding of the role of hydrothermal vent microbial communities in deep ocean biogeochemical cycles.
AbstractIODP Expedition 357 utilized seabed drills for the first time in the history of the ocean drilling program, with the aim of collecting intact sequences of shallow mantle core from the Atlantis Massif to examine serpentinization processes and the deep biosphere. This novel drilling approach required the development of a new remote seafloor system for delivering synthetic tracers during drilling to assess for possible sample contamination. Here, we describe this new tracer delivery system, assess the performance of the system during the expedition, provide an overview of the quality of the core samples collected for deep biosphere investigations based on tracer concentrations, and make recommendations for future applications of the system.
AbstractAncient putative microbial structures that appear in the rock record commonly serve as evidence of early life on Earth, but the details of their formation remain unclear. The study of modern microbial mat structures can help inform the properties of their ancient counterparts, but modern mineralizing mat systems with morphological similarity to ancient structures are rare. Here, we characterize partially lithified microbial mats containing cm-scale dendrolitic coniform structures from a geothermal pool (“Cone Pool”) at Little Hot Creek, California, that if fully lithified, would resemble ancient dendrolitic structures known from the rock record. Light and electron microscopy revealed that the cm-scale ‘dendrolitic cones’ were comprised of intertwined microbial filaments and grains of calcium carbonate. The degree of mineralization (carbonate content) increased with depth in the dendrolitic cones. Sequencing of 16S rRNA gene libraries revealed that the dendrolitic cone tips were enriched in OTUs most closely related to the genera Phormidium, Leptolyngbya, and Leptospira, whereas mats at the base and adjacent to the dendrolitic cones were enriched in Synechococcus. We hypothesize that the consumption of nutrients during autotrophic and heterotrophic growth may promote movement of microbes along diffusive nutrient gradients, and thus microbialite growth. Hour-glass shaped filamentous structures present in the dendrolitic cones may have formed around photosynthetically-produced oxygen bubbles—suggesting that mineralization occurs rapidly and on timescales of the lifetime of a bubble. The dendrolitic-conical structures in Cone Pool constitute a modern analog of incipient microbialite formation by filamentous microbiota that are morphologically distinct from any structure described previously. Thus, we provide a new model system to address how microbial mats may be preserved over geological timescales.
AbstractInternational Ocean Discovery Program (IODP) Expedition 370 aimed to explore the limits of life in the deep subseafloor biosphere at a location where temperature increases with depth at an intermediate rate and exceeds the known temperature maximum of microbial life (~120°C) at the sediment/basement interface ~1.2 km below the seafloor. Drilling Site C0023 is located in the vicinity of Ocean Drilling Program (ODP) Sites 808 and 1174 at the protothrust zone in the Nankai Trough off Cape Muroto at a water depth of 4776 m. ODP Leg 190 in 2000, revealed the presence of microbial cells at Site 1174 to a depth of ~600 meters below seafloor (mbsf), which corresponds to an estimated temperature of ~70°C, and reliably identified a single zone of higher cell concentrations just above the décollement at around 800 mbsf, where temperature presumably reached 90°C; no cell count data was reported for other sediment layers in the 70°–120°C range, because the limit of manual cell count for low-biomass samples was not high enough. With the establishment of Site C0023, we aimed to detect and investigate the presence or absence of life and biological processes at the biotic–abiotic transition with unprecedented analytical sensitivity and precision. Expedition 370 was the first expedition dedicated to subseafloor microbiology that achieved time-critical processing and analyses of deep biosphere samples by simultaneous shipboard and shore-based investigations. Our primary objectives during Expedition 370 were to study the relationship between the deep subseafloor biosphere and temperature. We aimed to comprehensively study the factors that control biomass, activity, and diversity of microbial communities in a subseafloor environment where temperatures increase from ~2°C at the seafloor to ~120°C at the sediment/basement interface and thus likely encompasses the biotic–abiotic transition zone. We also aimed to determine geochemical, geophysical, and hydrogeological characteristics in sediment and the underlying basaltic basement and elucidate if the supply of fluids containing thermogenic and/or geogenic nutrient and energy substrates may support subseafloor microbial communities in the Nankai accretionary complex. To address these primary scientific objectives and questions, we penetrated 1180 m and recovered 112 cores across the sediment/basalt interface. More than 13,000 samples were collected, and selected samples were transferred to the Kochi Core Center by helicopter for simultaneous microbiological sampling and analysis in laboratories with a super-clean environment. Following the coring operations, a temperature observatory with 13 thermistor sensors was installed in the borehole to 863 mbsf.
AbstractWater radiolysis is the dissociation of water molecules by ionizing radiation from the decay of radionuclides. Primary products of water radiolysis include reactive chemicals, such as H2 and H2O2. For this reason, radiolysis is studied in many domains, including nuclear waste, microbiology and planetary evolution. In order to understand the importance of radiolysis in many of these environments, accurate quantification of radiolytic production rates is vital. In this dissertation, I present a new quantitative model calculating radiolytic production rates at solid-water interfaces and apply it to understand the role that radiolysis plays in various environments. ^ This radiolytic model is the first to explicitly calculate radiolytic production due to α-, β- and γ-radiation near solid-water interfaces. We use this model to investigate the effects of radiolytic compounds on the dissolution rate of spent nuclear fuel. The production of rate of H2 and H2O2, which control the dissolution rate of the fuel, depends on the amount and type of radiation surrounding breached nuclear spent fuel rods. Understanding the distribution of radiolytic products is important in assessing different hazards associated with spent fuel storage and the potential release of radionuclides into the environment. We find that in old (1000-year-old) spent fuel α-radiation dominates radiolysis, while β- and γ-radiation control the production rates near young (20-year-old) spent fuel.^ Radiolysis also is an important process in understanding the extent of life on Earth, as well as possibly providing a means for life on Mars. We investigate the significance of water radiolysis in sustaining microbial communities in Earth’s oceanic crust and the potential extent of radiolysis in wet martian environments (such as the ancient martian surface and the present martian subsurface). These two studies focus specifically on the production of radiolytic H2 as an electron donor. H2 is an important source of energy in these two environments where there other resources for microbes are limited. In the oceanic basaltic aquifer of the South Pacific Gyre, we find that radiolytic H2 production yields depend largely on the width of fractures in basalt and on radionuclide concentrations. We show that in old seafloor (>10 Ma), where there are no other readily available electron donors, radiolytic H2 may dominate and is able to support up to 103 cells in the water adjacent to a square cm of basaltic fracture.^ The extent of water radiolysis on Mars can be determined for water-saturated martian environments, such as the ancient martian surface or the present martian subsurface. Using the fractured rock radiolytic model as well as a previously developed sediment radiolytic model, we calculate potential H2 production rates for eleven martian lithologies assuming contact with water. The highest rates on Mars are for water-saturated material with the radionuclide concentrations of Acidalia Planitia, a region with surface materials that are enriched in uranium and thorium. We also calculate production rates for the eight proposed Mars 2020 landing sites, assuming water-saturated porosity. Radiolytic H2 production rates calculated for wet martian sediment and water-filled microfractured rock are comparable to the range of rates calculated for Earth’s South Pacific basement basalt which is known to harbor low concentrations of microbial life.
AbstractWeathered crude oil sank to the seafloor following the Deepwater Horizon disaster in 2010, removing this oil from further physical and photo-chemical degradation processes and leaving benthic processes as the mechanisms for altering and remediating this hydrocarbon source. To quantify potential microbial oil degradation rates at the seafloor, and associated changes in sediment microbial community structure and pore fluid composition, we used a benthic lander system to deploy novel sediment flow-through chambers at a natural hydrocarbon seep in the Gulf of Mexico (at a depth of 1226 m in lease block GC600) roughly 265 km southwest of the Deepwater Horizon wellhead (at 1500 m depth). Sediment amended with 20% unweathered crude oil had elevated rates of sulfate reduction over the course of the 5-month-long experiment as compared to an unamended control, yielding potential rates of sulfate reduction (600–800 mmol m–2 d–1) among the highest measured in hydrocarbon-influenced seafloor sediment. Oil amendment also stimulated methane production towards the end of the experiment, and led to slightly higher cell densities without significant changes in microbial community structure, based on 16S rRNA gene sequence libraries and fatty acid profiles. Assuming a link between sulfate reduction and hydrocarbon degradation, these results suggest that electron acceptor availability may become limiting in heavily oiled deep-sea environments, resulting in minimal degradation of deposited oil. This study provides unique data on seafloor sediment responses to oil deposition, and reveals the value of using observatories to fill the gap in understanding deep-sea microbial processes, especially for ephemeral and stochastic events such as oil spills.
AbstractGeothermobacter sp. strain EPR-M was isolated from a hydrothermal vent on the East Pacific Rise and has been shown to participate in the reduction of Fe(III) oxides. Here, we report its 3.73-Mb draft genome sequence.
In 1973, Christian Anfinsen and coworkers noted that accelerated protein folding in intact cells and cell extracts suggested that a “disulfide interchange enzyme” might be present in vivo. This concept of catalyzed folding foreshadowed the discovery of ubiquitous protein chaperones. The chaperonin GroEL/GroES was identified serendipitously when GroE mutants of E. coli failed to grow bacteriophage λ and were also temperature sensitive. The GroEL/GroES proved to be a ubiquitous chaperone and heat shock protein in bacteria and eukaryotic organelles, with two back-to-back rings of seven subunits each, forming a cavity that enclosed nonnative proteins, capped by the separate GroES lid complex. Group II chaperonins were subsequently discovered in all of the Archaea and in the Eukaryote cytoplasm with a similar cage-like shape, only with a “built-in” lid instead of the GroES module of Group I chaperonins. These chaperones have been intensely studied for three decades and have provided deep insights into protein-folding mechanisms. Despite this, some aspects of chaperonin-induced protein folding remain controversial.
The shared architecture and sequence similarity of two classes of chaperonins implies that they share a common ancestor. A recently identified, deeply branching clade of archaeal-like chaperonins encoded in bacteria may shed light on the early history of chaperonins. This clade shares many molecular properties with Group II chaperones; however, their phylogeny suggests that they arose early in prokaryotic evolution and may represent a vestige of the common ancestor of Group I and Group II chaperonins.
AbstractThe Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ≥50%, and an additional 2,786 bins, with estimated completion of 0–50%. We have submitted our results, including initial taxonomic and phylogenetic assignments, for the putative draft genomes to open-access repositories for the scientific community to use in ongoing research.
Since its inception, the Deep Carbon Observatory (DCO) has coalesced a multidisciplinary and international group of researchers focused on understanding and quantifying Earth's deep carbon budget. Carbon is the fourth most abundant element in the universe, and understanding carbon chemistry under a variety of environmental conditions impacts all aspects of planetary sciences. DCO recognizes that contributions of early career scientists are integral to the advancement of knowledge regarding the quantities, movements, origins, and forms of Earth's deep carbon. This research topic highlights the contributions of the DCO Early Career Scientist community.
AbstractThe rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.
This study investigates the morphology, mineralogy, and geochemistry of seafloor massive sulfide (SMS) deposits from six back-arc hydrothermal vent fields along the Eastern Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) in the context of endmember vent fluid chemistry and proximity to the Tonga Subduction Zone. To complement deposit geochemistry, vent fluid analyses of Cu, Zn, Ba, Pb and H2,(aq)were completed to supplement existing data and enable thermodynamic calculations of mineral saturation states at in situ conditions. Results document southward increases in the abundance of mantle-incompatible elements in hydrothermal fluids (Ba and Pb) and SMS deposits (Ba, Pb, As, and Sb), which is also expressed in the abundance of barite (BaSO4) and galena (PbS) in SMS deposits. These increases correspond to a decrease in distance between the ELSC/VFR and the Tonga Subduction Zone that correlates with a change in crustal lithology from back-arc basin basalt in the north to mixed andesite, rhyolite, and dacite in the south. Barite influences deposit morphology, contributing to the formation of horizontal flanges and squat terraces. Results are also consistent with a regional-scale lowering of hydrothermal reaction zone temperatures from north to south (except at the southernmost Mariner vent field) that leads to lower-temperature, higher-pH vent fluids relative to mid-ocean ridges of similar spreading rates (Mottl et al., 2011). These fluids are Cu- and Zn-poor and the deposits formed from these fluids are Cu-poor but Zn-rich. In contrast, at the Mariner vent field, higher-temperature and lower pH vent fluids are hypothesized to result from higher reaction zone temperatures and the localized addition of acidic magmatic volatiles (Mottl et al., 2011). The Mariner fluids are Cu- and Zn-rich and vent from SMS deposits that are rich in Cu but poor in Zn with moderate amounts of Pb. Thermodynamic calculations indicate that the contrasting metal contents of vent fluids and SMS deposits can be accounted for by vent fluid pH. Wurtzite/sphalerite ((Zn, Fe)S) and galena (PbS) are saturated at higher temperatures in higher-pH, Zn-, Cu-, and Pb-poor ELSC/VFR vent fluids, but are undersaturated at similar temperatures in low-pH, Zn-, Cu-, and Pb-rich vent fluids from the Mariner vent field.
Indicators of pH in the ELSC and VFR SMS deposits include the presence of co-precipitated wurtzite and chalcopyrite along conduit linings in deposits formed from higher pH fluids, and different correlations between concentrations of Zn and Ag in bulk geochemical analyses. Significant positive bulk geochemical Zn:Ag correlations occur for deposits at vent fields where hydrothermal fluids have a minimum pH (at 25 °C) < 3.3, while correlations of Zn:Ag are weak or negative for deposits at vent fields where the minimum vent fluid pH (at 25 °C) > 3.6. Data show that the compositions of the mineral linings of open conduit chimneys (minerals present, mol% FeS in (Zn,Fe)S) that precipitate directly from hydrothermal fluids closely reflect the temperature and sulfur fugacity of sampled hydrothermal fluids. These mineral lining compositions thus can be used as indicators of hydrothermal fluid temperature and composition (pH, metal content, sulfur fugacity).
AbstractDifficulty quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentration consistent with predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, for fraction of read abundance times cells), to estimate population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply-branching uncultured groups and ∼ 98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from quantitative PCR (qPCR) at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate reducing bacteria, Desulfovibrio sp., Desulfobacter sp., and Desulfobacterium sp. increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions only stimulates growth in a few clades directly involved in methanogenesis, rather than the whole microbial community.
AbstractThe past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of 13C- or 15N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.
AbstractLittle is known about evolutionary drivers of microbial populations in the warm subseafloor of deep-sea hydrothermal vents. Here we reconstruct 73 metagenome-assembled genomes (MAGs) from two geochemically distinct vent fields in the Mid-Cayman Rise to investigate patterns of genomic variation within subseafloor populations. Low-abundance populations with high intra-population diversity coexist alongside high-abundance populations with low genomic diversity, with taxonomic differences in patterns of genomic variation between the mafic Piccard and ultramafic Von Damm vent fields. Populations from Piccard are significantly enriched in nonsynonymous mutations, suggesting stronger purifying selection in Von Damm relative to Piccard. Comparison of nine Sulfurovum MAGs reveals two high-coverage, low-diversity MAGs from Piccard enriched in unique genes related to the cellular membrane, suggesting these populations were subject to distinct evolutionary pressures that may correlate with genes related to nutrient uptake, biofilm formation, or viral invasion. These results are consistent with distinct evolutionary histories between geochemically different vent fields, with implications for understanding evolutionary processes in subseafloor microbial populations.
AbstractDespite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica’s Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ13C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ13C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.
AbstractLife may have emerged on early Earth in serpentinizing systems, where ultramafic rocks react with aqueous solutions to generate high levels of dissolved H2 and CH4 and, on meeting seawater, steep redox, ionic, and pH gradients. Most extant life harnesses energy as ion (e.g., H+, Na+) gradients across membranes, and it seems reasonable to suggest that environments with steep ion gradients would have also been important for early life forms. The Strytan Hydrothermal Field (SHF) is a mid-ocean ridge–flank submarine hydrothermal (~70 °C) vent in Iceland that produces steep Na+ (<3–468 mM) and pH (8.1–10.2) gradients, concomitant with enrichments in methane (0.5–1.4 μM) and hydrogen (0.1–5.2 μM), relative to seawater. Large (up to 55 m) saponite towers create ideal "incubators" similar to other proposed origin-of-life analogs (e.g., Lost City hydrothermal field in the mid-Atlantic). However, the SHF is basalt hosted. We suggest that the observed conditions are generated by (1) plagioclase hydrolysis, coupled with calcite precipitation, and (2) hydration of Mg in pyroxene and olivine in basalt. Along with microbial activity, aqueous reactions of Fe in olivine and pyroxene are possible sources of the observed H2. Although the δ13C-CH4 values were highly variable (–53‰ to –8‰), isotopically heavy CH4 suggests possible abiotic formation or the imprint of methane oxidation. If environments similar to SHF occurred on the early Earth, they should be considered as potential origin-of-life environments.
AbstractGeothermal heat flux (GHF) is an important part of the basal heat budget of continental ice sheets. The difficulty of measuring GHF below ice sheets has directly hindered progress in understanding of ice sheet dynamics. We present a new GHF measurement from below the West Antarctic Ice Sheet, made in subglacial sediment near the grounding zone of the Whillans Ice Stream. The measured GHF is 88 ± 7 mW m-2, a relatively high value compared to other continental settings and to other GHF measurements along the eastern Ross Sea of 55 mW m-2 and 69 ± 21 mW m-2, but within the range of regional values indicated by geophysical estimates. The new GHF measurement was made ~100 km from the only other direct GHF measurement below the ice sheet, which was considerably higher at 285 ± 80 mW m-2, suggesting spatial variability that could be explained by shallow magmatic intrusions or the advection of heat by crustal fluids. Analytical calculations suggest that spatial variability in GHF exceeds spatial variability in the conductive heat flux through ice along the Siple Coast. Accurate GHF measurements and high-resolution GHF models may be necessary to reliably predict ice sheet evolution, including responses to ongoing and future climate change.
AbstractHydrothermal circulation within oceanic basement can have a profound influence on temperatures in the upper crust, including those close to the subduction thrust and in the overlying plate. Heat flow evidence for hydrothermal circulation in the volcanic basement of incoming plates includes: (1) values that are well below conductive predictions due to the advection of heat into the ocean, and (2) variability about conductive predictions that cannot be explained by variations in seafloor relief or thermal conductivity. In this review we summarize evidence for hydrothermal circulation in subducting oceanic basement from the Nankai, Costa Rica, south-central Chile, Haida Gwaii, and Cascadia margins and explore its influence on plate boundary temperatures. Models of these systems using a high Nusselt number proxy for hydrothermal circulation are used to illustrate the influence of this process on seafloor observations and thermal conditions at depth. We show that at these subduction zones, patterns of seafloor heat flow are best explained by thermal models that include the influence of hydrothermal circulation.
AbstractMicrobial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity, and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete, and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling, and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility, and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.
AbstractWe present geochemical data from the first samples of spring fluids from Dorado Outcrop, a basaltic edifice on 23 M.y. old seafloor of the Cocos Plate, eastern Pacific Ocean. These samples were collected from the discharge of a cool hydrothermal system (CHS) on a ridge flank, where typical reaction temperatures in the volcanic crust are low (2–20 °C) and fluid residence times are short. Ridge-flank hydrothermal systems extract 25% of Earth's lithospheric heat, with a global discharge rate equivalent to that of Earth's river discharge to the ocean; CHSs comprise a significant fraction of this global flow. Upper crustal temperatures around Dorado Outcrop are ∼15 °C, the calculated residence time is <3 y, and the composition of discharging fluids is only slightly altered from bottom seawater. Many of the major ions concentrations in spring fluids are indistinguishable from those of bottom seawater; however, concentrations of Rb, Mo, V, U, Mg, phosphate, Si and Li are different. Applying these observed differences to calculated global CHS fluxes results in chemical fluxes for these ions that are ≥15% of riverine fluxes. Fluxes of K and B also may be significant, but better analytical resolution is required to confirm this result. Spring fluids also have ∼50% less dissolved oxygen (DO) than bottom seawater. Calculations of an analytical model suggest that the loss of DO occurs primarily (>80%) within the upper basaltic crust by biotic and/or abiotic consumption. This calculation demonstrates that permeable pathways within the upper crust can support oxic water–rock interactions for millions of years.
AbstractChemosynthetic Fe-oxidizing communities are common at diffuse-flow hydrothermal vents throughout the world’s oceans. The foundational members of these communities are the Zetaproteobacteria, a class of Proteobacteria that is primarily associated with ecosystems fueled by ferrous iron, Fe(II). We report here the discovery of two new isolates of Zetaproteobacteria isolated from the Mid-Atlantic Ridge (TAG-1), and the Mariana back-arc (SV-108), that are unique in that they can utilize either Fe(II) or molecular hydrogen (H2) as sole electron donor and oxygen as terminal electron acceptor for growth. Both strains precipitated Fe-oxyhydroxides as amorphous particulates. The cell doubling time on H2 vs Fe(II) for TAG-1 was 14.1 vs 21.8 h, and for SV-108 it was 16.3 vs 20 h, and it appeared both strains could use either H2 or Fe(II) simultaneously. The strains were close relatives, based on genomic analysis, and both possessed genes for the uptake NiFe-hydrogenase required for growth on H2. These two strains belong to Zetaproteobacteria operational taxonomic unit 9 (ZetaOTU9). A meta-analysis of public databases found ZetaOTU9 was only associated with Fe(II)-rich habitats, and not in other environments where known H2-oxidizers exist. These results expand the metabolic repertoire of the Zetaproteobacteria, yet confirm that Fe(II) metabolism is the primary driver of their physiology and ecology.
AbstractAn anaerobic, nitrate-reducing, sulfur- and thiosulfate-oxidizing bacterium, designated strain 1812ET, was isolated from the vent polychaete Riftia pachyptila, which was collected from a deep-sea hydrothermal vent on the East Pacific Rise. Cells were Gram-stain-negative rods, measuring approximately 1.05±0.11 µm by 0.40±0.05 µm. Strain 1812ET grew at 25 – –45 °C (optimum 35 °C), with 1.5–4.0 % (w/v) NaCl (optimum 3.0 %) and at pH 5.0–8.0 (optimum pH 6.0). The generation time under optimal conditions was 3 h. Strain 1812ET was an anaerobic chemolithotroph that grew with either sulfur or thiosulfate as the energy source and carbon dioxide as the sole carbon source. Nitrate was used as a sole terminal electron acceptor. The predominant fatty acids were C16 : 1 ω7c, C18 : 1 ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 47.4 mol%. Phylogenetic analysis of the 16S rRNA gene of strain 1812ET showed that the isolate belonged to the Epsilonproteobacteria , and its closest relatives were Sulfurovum lithotrophicum 42BKTT and Sulfurovum aggregans Monchim 33T (98.3 and 95.7 % sequence similarity, respectively). DNA–DNA relatedness between strain 1812ET and the type strain of S. lithotrophicum was 29.7 %, demonstrating that the two strains are not members of the same species. Based on the phylogenetic, molecular, chemotaxonomic and physiological evidence, strain 1812ET represents a novel species within the genus Sulfurovum , for which the name Sulfurovum riftiae sp. nov. is proposed. The type strain is 1812ET (=DSM 101780T=JCM 30810T).
AbstractWe have analyzed the dissolved organic carbon, OC, in ocean basement fluids using Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS). The compounds identified at the two sites, near the Juan de Fuca and Mid-Atlantic Ridges (North Pond), differ substantially from each other and from seawater. Compared to Juan de Fuca, North Pond organics had a lower average molecular weight (349 vs. 372 g/mol), 50% more identifiable compounds (2181 vs. 1482), and demonstrably lower average nominal oxidation state of carbon (-0.70 vs. -0.57). The North Pond fluids were also found to have many more N- and S-bearing compounds. Based on our data, the marine subsurface can alter the types of dissolved OC, DOC, compounds in seawater.
AbstractThe anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors.
AbstractAt deep-sea hydrothermal vents, reduced, super-heated hydrothermal fluids mix with cold, oxygenated seawater. This creates temperature and chemical gradients that support chemosynthetic primary production and a biomass-rich community of invertebrates. In late 2005/early 2006 an eruption occurred on the East Pacific Rise at 9°50′N, 104°17′W. Direct observations of the post-eruptive diffuse-flow vents indicated that the earliest colonizers were microbial biofilms. Two cruises in 2006 and 2007 allowed us to monitor and sample the early steps of ecosystem recovery. The main objective of this work was to characterize the composition of microbial biofilms in relation to the temperature and chemistry of the hydrothermal fluids and the observed patterns of megafaunal colonization. The area selected for this study had local seafloor habitats of active diffuse flow (in-flow) interrupted by adjacent habitats with no apparent expulsion of hydrothermal fluids (no-flow). The in-flow habitats were characterized by higher temperatures (1.6–25.2 °C) and H2S concentrations (up to 67.3 µM) than the no-flow habitats, and the microbial biofilms were dominated by chemosynthetic Epsilonproteobacteria. The no-flow habitats had much lower temperatures (1.2–5.2 °C) and H2S concentrations (0.3–2.9 µM), and Gammaproteobacteria dominated the biofilms. Siboglinid tubeworms colonized only in-flow habitats, while they were absent at the no-flow areas, suggesting a correlation between siboglinid tubeworm colonization, active hydrothermal flow, and the composition of chemosynthetic microbial biofilms.
AbstractSedimenticola selenatireducens strain AK4OH1T (= DSM 17993T = ATCC BAA-1233T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. The draft genome comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report the main features of the genome of S. selenatireducensstrain AK4OH1T.
AbstractAll life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids—the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena.
AbstractPockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.
AbstractThe global scale of the biodiversity crisis has stimulated research into the relationship between biodiversity and ecosystem functioning (BEF). Even though the deep sea is the largest biome on Earth, BEF studies in deep-sea benthic ecosystems are scant. Moreover, the small number of recent studies, which mostly focus on meiobenthic nematodes, report conflicting results that range from a very clear positive relationship to none at all. In this BEF study, the deep-sea macrofauna were used as a model to investigate the structural and functional diversity of macrofauna assemblages at three depths (1,200, 1,900, and 3,000 m) in seven open-slope systems from the North-Eastern Atlantic Ocean to the Central-Eastern Mediterranean Sea. The presence and nature of BEF relationships were studied considering two spatial scales, the large and the basin scale, in different environmental settings. Total benthic biomass and macrofaunal predator biomass were used as proxies to assess ecosystem functioning. Ecosystem efficiency was expressed as macrofaunal biomass to biopolymeric carbon content ratio, macrofaunal biomass to prokaryotic biomass ratio, macrofaunal biomass to meiofaunal biomass ratio, and meiofaunal biomass to prokaryotic biomass ratio. On both large and basin spatial scales, some significant relationships between macrofaunal diversity and ecosystem functioning and efficiency were reported. When significant, the nature of BEF relations was positive and exponential or linear supporting the general idea that a higher diversity can enhance ecosystem functioning. Other BEF relationships were explained by the effect of environmental variables. More data from different deep-sea systems are needed, to better elucidate the consequences of biodiversity loss on the ocean floor.
AbstractMicrobial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.
AbstractAquatic habitats beneath ice masses contain active microbial ecosystems capable of cycling important greenhouse gases, such as methane (CH4). A large methane reservoir is thought to exist beneath the West Antarctic Ice Sheet, but its quantity, source and ultimate fate are poorly understood. For instance, O2 supplied by basal melting should result in conditions favourable for aerobic methane oxidation. Here we use measurements of methane concentrations and stable isotope compositions along with genomic analyses to assess the sources and cycling of methane in Subglacial Lake Whillans (SLW) in West Antarctica. We show that sub-ice-sheet methane is produced through the biological reduction of CO2 using H2. This methane pool is subsequently consumed by aerobic, bacterial methane oxidation at the SLW sediment–water interface. Bacterial oxidation consumes >99% of the methane and represents a significant methane sink, and source of biomass carbon and metabolic energy to the surficial SLW sediments. We conclude that aerobic methanotrophy may mitigate the release of methane to the atmosphere upon subglacial water drainage to ice sheet margins and during periods of deglaciation.
AbstractSelection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
AbstractEditorial on the Research Topic Recent Advances in Geomicrobiology of the Ocean Crust. Igneous oceanic crust is one of the largest potential habitats for life on earth (Orcutt et al., 2011), and microbial activity supported by rock-water-microbe reactions in this environment can impact global biogeochemical cycles (Bach and Edwards, 2003). However, our understanding of the microbiology of this system, especially the subsurface “deep biosphere” component of it, has traditionally been limited by sample availability and quality. Over the past decade, several major international programs (such as the Center for Dark Energy Biosphere Investigations, the current International Ocean Discovery Program, and its predecessor Integrated Ocean Drilling Program, and the Deep Carbon Observatory) have focused on advancing our understanding of life in this cryptic, yet globally relevant, biosphere. Additionally, many field and laboratory research programs are examining hydrothermal vent systems—a seafloor expression of seawater that has been thermally and chemically altered in subseafloor crust—and the microbial communities supported by these mineral-rich fluids. The papers in this special issue bring together recent discoveries of microbial presence, diversity, and activity in these dynamic ocean environments.
AbstractMarine shallow-water vents are ubiquitous but poorly studied geothermal environments located worldwide between the intertidal zone and 212 m depth. Important factors differentiating them from their deep-sea counterparts include sunlight, tidal/wave pumping, meteoric water sources, terrigenous inputs, elevated metal concentrations, and abundant free gas. Mixing of vent fluids with oxidized seawater generates multiple redox disequilibria readily exploited by microbes. Although highly diverse, two major groups include an Epsilonprotebacteria-dominated community sharing similarities with deep-sea analogs, and a community dominated by Gammaproteobacteria/Firmicutes. The distribution of different microbial taxa within each vent is primarily controlled by temperature and availability of suitable electron donors and acceptors. However, the coexistence of phototrophs, chemolithoautotrophs, and a high abundance of aerobic and anaerobic heterotrophs, suggests the presence of sunlight and high organic carbon loads define unique microbial habitats that are transitionary between terrestrial and deep-sea vents. We summarize here the current knowledge of shallow-sea vents worldwide, highlighting gaps on our understanding of these unique environments.
AbstractExcerpt: The USC Young Scientists Program (YSP) Director, and the National Marine Educators Association (NMEA) Expanded Audience Committee Chair Dieuwertje Kast, hosted a deep sea science workshop for 50 fourth and fifth grade students at Vermont Elementary on November 15, 2016. The event was a collaboration between YSP, Ocean Exploration Trust/Nautilus, Deezmaker, OpenROV, and the Center for Dark Energy Biosphere Investigations (C-DEBI, a National Science Foundation Science and Technology Center) and NMEA. C-DEBI provided YSP with an Educator Small Grant to make the event possible. C-DEBI research focuses on the discovery of the microbial life below the ocean floor, in rocks, and sediments (the deep biosphere). C-DEBI welcomed the proposal that engaged diverse and underserved populations and brought in scientists from ethnic minority backgrounds. Current: The Journal of Marine Education, is a journal produced by NMEA, the National Marine Educators Association.
AbstractCandidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential, and exclusive reliance on fermentation for energy acquisition. The study of new environmental niches, such as the marine versus terrestrial subsurface, often expands the understanding of the genetic potential of taxonomic groups. For this reason we analyzed twelve Parcubacteria single amplified genomes (SAGs) from sediment samples collected within the Challenger Deep of the Mariana Trench, obtained during the Deepsea Challenge (DSC) Expedition. Many of these SAGs are closely related to environmental sequences obtained from deep-sea environments based on 16S rRNA gene similarity and BLAST matches to predicted proteins. DSC SAGs encode features not previously identified in Parcubacteria obtained from other habitats. These include adaptation to oxidative stress, polysaccharide modification, and genes associated with respiratory nitrate reduction. The DSC SAGs are also distinguished by relative greater abundance of genes for nucleotide and amino acid biosynthesis, repair of alkylated DNA and the synthesis of mechanosensitive ion channels. These results present an expanded view of the Parcubacteria, among members residing in an ultra-deep hadal environment.
AbstractNO3- reduction is a metabolism that is widespread among ε-Proteobacteria and Aquificae, two abundant classes of microorganisms found at deep-sea vents. In this study, we used Sulfurovum lithotrophicum, Caminibacter mediatlanticus and Thermovibrio ammonificans as representatives of these groups to study ecophysiological, metabolic and biogeochemical parameters associated with chemolithoautotrophic NO3- reduction under different temperature regimes. We observed that while S. lithotrophicum and C. mediatlanticus achieved higher cell densities than T. ammonificans, the overall NO3- consumption by the latter was on average ∼ 9 and ∼ 5 times faster on a per cell basis, respectively. Comparison with previously published data from other cultured vent ε-Proteobacteria and Aquificae suggests that the rate-yield trade-offs observed in our experiments are generally conserved between these two groups in line with their ecophysiologies. Kinetic isotope effects of N from NO3- reduction were 9.6 ± 2.7 ‰ for S. lithotrophicum, 6.4 ± 0.7 ‰ for C. mediatlanticus and 8.8 ± 0.6 ‰ for T. ammonificans. Our results help evaluate how metabolic partitioning between growth efficiency and reaction kinetics during chemolithoautotrophic NO3- reduction affect the concentration and isotope composition of N compounds at deep-sea hydrothermal vents.
AbstractAnaerobic thermophiles inhabit relic environments that resemble the early Earth. However, the lineage of these modern organisms co-evolved with our planet. Hence, these organisms carry both ancestral and acquired genes and serve as models to reconstruct early metabolism. Based on comparative genomic and proteomic analyses, we identified two distinct groups of genes in Thermovibrio ammonificans: the first codes for enzymes that do not require oxygen and use substrates of geothermal origin; the second appears to be a more recent acquisition, and may reflect adaptations to cope with the rise of oxygen on Earth. We propose that the ancestor of the Aquificae was originally a hydrogen oxidizing, sulfur reducing bacterium that used a hybrid carbon fixation pathway for CO2fixation. With the gradual rise of oxygen in the atmosphere, more efficient terminal electron acceptors became available and this lineage acquired genes that increased its metabolic flexibility while retaining ancestral metabolic traits.
AbstractIt is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.
AbstractReactive Fe(III) minerals can influence methane (CH4) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and CH4oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capacity for CH4 to warm the early Earth under the Faint Young Sun. We studied CH4 and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH4 oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4 production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4 oxidation, although some incubations displayed CH4-stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4 as a greenhouse gas throughout the first half of Earth history.
AbstractAquatic sediments harbor diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic-rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO2 production rates, as well as sequential sampling of isotopic signatures (δ13C, Δ14C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton-derived compounds were degraded first, followed by petroleum-derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations. This article is protected by copyright. All rights reserved.
AbstractThe recent retreat of glaciers and ice sheets as a result of global warming exposes forefield soils that are rapidly colonized by microbes. These ecosystems are dominant in high-latitude carbon and nutrient cycles as microbial activity drives biogeochemical transformations within these newly exposed soils. Despite this, little is known about the response of these emerging ecosystems and associated biogeochemical cycles to projected changes in environmental factors due to human impacts. Here, we applied the model SHIMMER to quantitatively explore the sensitivity of biogeochemical dynamics in the forefield of Midtre Lovénbreen, Svalbard, to future changes in climate and anthropogenic forcings including soil temperature, snow cover, and nutrient and organic substrate deposition. Model results indicated that the rapid warming of the Arctic, as well as an increased deposition of organic carbon and nutrients, may impact primary microbial colonizers in Arctic soils. Warming and increased snow-free conditions resulted in enhanced bacterial production and an accumulation of biomass that was sustained throughout 200 years of soil development. Nitrogen deposition stimulated growth during the first 50 years of soil development following exposure. Increased deposition of organic carbon sustained higher rates of bacterial production and heterotrophic respiration leading to decreases in net ecosystem production and thus net CO2 efflux from soils. Pioneer microbial communities were particularly susceptible to future changes. All future climate simulations encouraged a switch from allochthonously-dominated young soils (<40 years) to microbially-dominated older soils, due to enhanced heterotrophic degradation of organic matter. Critically, this drove remineralisation and increased nutrient availability. Overall, we show that human activity, especially the burning of fossil fuels and the enhanced deposition of nitrogen and organic carbon, has the potential to considerably affect the biogeochemical development of recently exposed Arctic soils in the present day and for centuries into the future. These effects must be acknowledged when attempting to make accurate predictions of the future fate of Arctic soils that are exposed over large expanses of presently ice-covered regions.
AbstractSerpentinization is a geologic process that produces highly reduced, hydrogen-rich fluids that support microbial communities under high pH conditions. We investigated the activity of microbes capable of extracellular electron transfer in a terrestrial serpentinizing system known as “The Cedars”. Measuring current generation with an on-site two-electrode system, we observed daily oscillations in current with the current maxima and minima occurring during daylight hours. Distinct members of the microbial community were enriched. Current generation in lab-scale electrochemical reactors did not oscillate, but was correlated with carbohydrate amendment in Cedars-specific minimal media. Gammaproteobacteria and Firmicutes were consistently enriched from lab electrochemical systems on δ-MnO2 and amorphous Fe(OH)3 at pH 11. However, isolation of an electrogenic strain proved difficult as transfer cultures failed to grow after multiple rounds of media transfer. Lowering the bulk pH in the media allowed us to isolate a Firmicutes strain (Paenibacillus sp.). This strain was capable of electrode and mineral reduction (including magnetite) at pH 9. This report provides evidence of the in situ activity of microbes using extracellular substrates as sinks for electrons at The Cedars, but also highlights the potential importance of community dynamics for supporting microbial life through either carbon fixation and/or moderating pH stress.
AbstractMajor radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.
AbstractThe global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.
AbstractMetagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
AbstractOrganic carbon (OC) preserved in marine sediments acts as a reduced carbon sink that balances the global carbon cycle. Understanding the biogeochemical mechanisms underpinning the balance between OC preservation and degradation is thus critical both to quantifying this carbon reservoir and to estimating the extent of life in the deep subsurface biosphere. This work utilizes bulk and spatially-resolved X-ray absorption spectroscopy to characterize the OC content and composition of various environmental systems in order to identify the role of minerals and surrounding geochemistry in organic carbon preservation in sediments. Biogenic manganese (Mn) oxides formed either in pure cultures of Mn-oxidizing microorganisms, in incubations of brackish estuarine waters, or as ferromanganese deposits in karstic cave systems rapidly associate with OC following precipitation. This association is stable despite Mn oxide structural ripening, suggesting that mineral-associated OC could persist during early diagenetic reactions. OC associated with bacteriogenic Mn oxides is primarily proteinaceous, including intact proteins involved in Mn oxidation and likely oxide nucleation and aggregation. Pelagic sediments from 16 sites underlying the South Pacific and North Atlantic gyres and spanning a gradient of sediment age and redox state were analyzed in order to contrast the roles of oxygen exposure, OC recalcitrance, and mineral-based protection of OC as preservation mechanisms. OC and nitrogen concentrations measured at these sites are among the lowest globally (<0.1%) and, to a first order, scale with sediment oxygenation. In the deep subsurface, however, molecular recalcitrance becomes more important than oxygen exposure time in protecting OC against remineralization. Deep OC consists of primarily amide and carboxylic carbon in a scaffolding of aliphatic and O-alkyl moieties, corroborating the extremely low C/N values observed. These findings suggest that microbes in oxic pelagic sediments are carbon-limited and may preferentially remove carbon relative to nitrogen from the organic matter pool. As a whole, this work documents how interactions with mineral surfaces and exposure to oxygen generate a reservoir of OC stabilized in sediments on at least 25-million year time scales.
AbstractA new approach for the preparation of marine sediment samples for solution 31P nuclear magnetic resonance spectroscopy (31P NMR) has been developed and tested. This approach addresses important aspects associated with sample pretreatments for marine sediments, including the effects of sample pretreatment on sedimentary P composition. The method increases the signals of low abundance P species in 31P NMR spectra by quantitatively and precisely removing up to 80% of inorganic P (orthophosphate) from sediment samples while causing minimal alteration of the chemical structure of organic P compounds. This method uses a reductive step to solubilize P bound to iron oxyhydroxides, followed by a low pH digestion to extract P from authigenic and biogenic apatite, as well as P bound to calcium carbonate. These P forms combined represent the most abundant inorganic P reservoir in marine sediments. The sample residue is then extracted in an alkaline solvent, 0.25 M NaOH with 0.05 M Na2EDTA, and processed for 31P NMR spectroscopy. The method was tested on natural marine sediment samples from different localities with high inorganic P content (>85% molybdate reactive P), and allowed for the detection of orthophosphate monoesters and pyrophosphate in samples for which only an orthophosphate signal could be resolved with an NaOH-EDTA extraction alone. This new approach will allow the use of 31P NMR on samples for which low organic P concentrations previously hindered the use of this tool, and will help answer longstanding question regarding the fate of organic P in marine sediments.
Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 105 to 2 × 105 ml−1 (n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome.
IMPORTANCE The hydrothermally active ocean basement is voluminous and likely provided conditions critical to the origins of life, but the microbiology of this vast habitat is not well understood. Viruses in particular, although integral to the origins, evolution, and ecology of all life on earth, have never been documented in basement fluids. This report provides the first estimate of free virus particles (virions) within fluids circulating through the extrusive basalt of the seafloor and describes the morphological and genetic signatures of basement viruses. These data push the known geographical limits of the virosphere deep into the ocean basement and point to a wealth of novel viral diversity, exploration of which could shed light on the early evolution of viruses.
This paper is dedicated to the late James P. Cowen, whose collegiality, infectious enthusiasm for science, and pioneering studies of the ocean basement microbiome inspired the work.
AbstractWe report measurements of resolved 12CH2D2 and 13CH3D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve 12CH2D2 from 13CH3D provides unprecedented insights into the origin and evolution of CH4. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ12CH2D2 and Δ13CH3D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH4/H2 D/H exchange, underscoring the importance of reliable thermometry based on the CH4 molecules themselves. Where Δ12CH2D2 and Δ13CH3D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide novel information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis vs. biological processes. Deficits in 12CH2D2 compared with equilibrium values in CH4 gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in 13CH3D that accompany the low 12CH2D2 abundances produced by abiotic reactions. The tunneling signature may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ12CH2D2 values are a key tracer of microbial recycling.
AbstractExtracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments.
AbstractTwo common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an inter-laboratory comparison: 1) proteinase K permeabilization of Archaeal cell walls increases CARD-FISH accuracy, and 2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 × 107 cells cm−3. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 ×106 to 2.34 ×109 16S rRNA gene copies cm−3 vs. 1.39 × 107 to 1.87 × 109 total cells cm−3. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.
To quantify the potential for biological contamination associated with the coring process, we conducted perfluorocarbon tracer (PFT) analysis on 556 sediment samples from Integrated Ocean Drilling Program (IODP) Expedition 329. The expedition cored deep-sea sediment at seven sites in the South Pacific Gyre (Sites U1365–U1371). We analyzed two types of sediment samples: (1) samples taken in the central part of the core (i.e., interior samples) and (2) samples taken near the core edge (i.e., exterior samples). We calculated the amount of potential drilling fluid intrusion from the mass of PFT that we measured in each sample. For the seven Expedition 329 sites (15 holes analyzed), PFT content ranges from below detection to levels where contamination is extremely apparent. The centers of the sediment cores (interior samples) contained generally less PFT than the core margins (exterior samples) and thus have lower potential drilling fluid (DF) contamination. The majority of sediment samples (interior) at Sites U1370 and U1371 have a contamination potential close to or below detection levels (i.e., 1.19 × 10–4 ngPFT/gsediment or 1.78 × 10–3 µLDF/gsediment on average). We observed higher contamination values (i.e., 7.28 × 10–3 ngPFT/gsediment or 6.98 × 10–2 µLDF/gsediment on average) at Sites U1365, U1366, and U1367. Finally, we measured much higher PFT concentrations throughout the sediment of Sites U1368 and U1369 (i.e., 5.48 × 10–2 ngPFT/gsediment or 6.60 × 10–1 µLDF/gsediment on average). We observe no apparent correlation of sample PFT content to sediment lithology, degree of sediment disturbance, core section number, or porosity.
- The oceans that cover 70% of the Earth's surface lie above 3×108 km3 of sediment containing an estimated 3×1029 microbial cells.
- The role played by spores in low-energy sedimentary ecosystems remains an enigma.
- Despite conflicting results from earlier analyses, archaea and bacteria apparently exist in similar abundances within deep-sea sediments.
- Within these sediments, anaerobic metabolisms dominate, especially those in which sulfate reduction and oxidation of organic matter are coupled.
- Modeling proves crucial when trying to connect sedimentary microorganisms to their appropriate geochemical environments.
AbstractSulfide mineral precipitation occurs at mid‐ocean ridge (MOR) spreading centers, both in the form of plume particles and seafloor massive sulfide structures. A common constituent of MOR is the iron‐bearing sulfide mineral pyrrhotite, which was chosen as a substrate for in‐situ incubation studies in shallow waters of Catalina Island, CA to investigate the colonization of iron‐oxidizing bacteria. Microbial community datasets were obtained from in‐situ incubated pyrrhotite, allowing for direct comparison to microbial communities of iron‐sulfides from active and inactive chimneys in deep‐sea environments. Unclassified Gammaproteobacteria and Alphaproteobacteria (Magnetovibrio) largely dominated the bacterial community on pyrrhotite samples incubated in the water column while samples incubated at the surface sediment showed more even dominance by Deltaproteobacteria (Desulfobulbus), Gammaproteobacteria (Piscirickettsiaceae), Alphaproteobacteria (Rhodobacteraceae), and Bacteroidetes (Flavobacteriia). Cultivations that originated from pyrrhotite samples resulted in the enrichment of both, sheath‐forming and stalk‐forming Zetaproteobacteria. Additionally, a putative novel species of Thiomicrospira was isolated and shown to grow autotrophically with iron, indicating a new biogeochemical role for this ubiquitous microorganism.
AbstractMarine sediments contribute significantly to global element cycles on multiple time scales. This is due in large part to microbial activity in the shallower layers and abiotic reactions resulting from increasing temperatures and pressures at greater depths. Quantifying the rates of these diagenetic changes requires a three-dimensional description of the physiochemical properties of marine sediments. In a step toward reaching this goal, we have combined global data sets describing bathymetry, heat conduction, bottom-water temperatures, and sediment thickness to quantify the three-dimensional distribution of temperature in marine sediments. This model has revealed that ∼35% of sediments are above 60 °C, conditions that are suitable for petroleum generation. Furthermore, significant microbial activity could be inhibited in ∼25% of marine sediments, if 80 °C is taken as a major thermal barrier for subsurface life. In addition to a temperature model, we have calculated new values for the total volume (3.01 × 108 km3) and average thickness (721 m) of marine sediments, and provide the only known determination of the volume of marine-sediment pore water (8.46 × 107 km3), equivalent to ∼6.3% of the volume of the ocean. The results presented here can be used to help quantify the rates of mineral transformations, lithification, catagenesis, and the extent of life in the subsurface on a global scale.
AbstractMid-Cayman Rise objectives were built on exciting results from a flurry of recent expeditions that investigated hydrothermal sites in the region (German et al., 2010, 2012). The 2013 E/V Nautilus cruise explored oceanic core complexes (OCCs), tall, smooth-sided hills that rise from the seafloor on the flanks of some mid-ocean ridges. Dives (Figure 1) explored the full extent and nature of life around the Von Damm hydrothermal field, previously discovered there, as well as the geology to further understanding of the vents’ origins, and to survey the OCC summits that had never before been investigated by a deep diving vehicle. This 2013 study was the first Nautilus cruise to have more scientists participating in the expedition from locations on shore than from the ship, tripling the size of the science party.
AbstractSediments within the Okinawa back-arc basin overlay a subsurface hydrothermal network, creating intense temperature gradients with sediment depth and potential limits for microbial diversity. We investigated taxonomic changes across 45 m of recovered core with a temperature gradient of 3°C/m from the dynamic Iheya North Hydrothermal System. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay at 10 meters below seafloor (mbsf). Here, we present taxonomic results from an analysis of the 16S rRNA gene that support a conceptual model in which common marine subsurface taxa persist into the subsurface, while high temperature adapted archaeal taxa show localized peaks in abundances in the hydrothermal clay horizons. Specifically, the bacterial phylum Chloroflexi accounts for a major proportion of the total microbial community within the upper 10 mbsf, whereas high temperature archaea (Terrestrial Hot Spring Crenarchaeotic Group and methanotrophic archaea) appear in varying local abundances in deeper, hydrothermal clay horizons with higher in situ temperatures (up to 55°C, 15 mbsf). In addition, geochemical evidence suggests that methanotrophy may be occurring in various horizons. There is also relict DNA (i.e., DNA preserved after cell death) that persists in horizons where the conditions suitable for microbial communities have ceased.
AbstractSubsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2. Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4 to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H2 oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface.
AbstractA genomic reconstruction belonging to the genus Methanosarcina was assembled from metagenomic data from a methane-producing enrichment of Antarctic permafrost. This is the first methanogen genome reported from permafrost of the Dry Valleys and can help shed light on future climate-affected methane dynamics.
AbstractThe hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed “Mat Mound”) were characterized by porewater geochemistry of methane, C2–C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas, and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.
AbstractMethane seeps are globally distributed geologic features in which reduced fluid from below the seafloor is advected upward and meets the oxidized bottom waters of Earth’s oceans. This redox gradient fuels chemosynthetic communities anchored by the microbially-mediated anaerobic oxidation of methane (AOM). Both today and in Earth’s past, methane seeps have supported diverse biological communities extending from microorgansisms to macrofauna and adding to the diversity of life on Earth. Simultaneously, the carbon cycling associated with methane seeps may have played a significant role in modulating ancient Earth’s climate, particularly by acting as a control on methane emissions. The AOM metabolism generates alkalinity and dissolved inorganic carbon (DIC) and at a 2:1 ratio, promoting the abiogenic, or authigenic, precipitation of carbonate minerals. Over time, these precipitates can grow into pavements covering hundreds of square meters on the seafloor and dominating the volumetric habitat space available in seep ecosystems. Importantly, carbonates are incorporated into the geologic record and therefore preserve an inorganic (i.e., d13C) and organic (i.e., lipid biomarker) history of methane seepage. However, the extent to which preserved biomarkers represent a snapshot of microorganisms present at the time of primary precipitation, a time-integrated history of microbial assemblages across the life cycle of a methane seep, or a view of the final microorganisms inhabiting a carbonate prior to incorporation in the sedimentary record is unresolved. This thesis addresses the ecology of carbonate-associated seep microorganisms. Chapters One and Two contextualize the extant microbial diversity on seep carbonates versus within seep sediments, as determined through 16S rRNA gene biomarkers. Small, protolithic carbonate “nodules” recovered from within seep sediments are observed to be capable of capturing surrounding sediment-hosted microbial diversity, but in some cases also diverge from sediments. Meanwhile, lithified carbonate blocks recovered from the seafloor host microbial assemblages demonstrably distinct from seep sediments (and seep nodules). Microbial 16S rRNA gene diversity within carbonate samples is well-differentiated by the extent of contemporary seepage. In situ seafloor transplantation experiments further demonstrated the microbial assemblages associated with seep carbonates to be sensitive to seep quiescence and activation on short (13-month) timescales. This was particularly true for organisms whose 16S rRNA genes imply physiologies dependent on methane or sulfur oxidation. With an improved understanding of the modern ecology of carbonate-associated microorganisms, Chapter Three applies intact polar lipid (IPL) and core lipid analyses to begin describing whether, and to what extent, geologically relevant biomarkers mimic short-term dynamics observed in 16S rRNA gene profiles versus archive a record of historic microbial diversity. Biomarker longevity is determined to increase from 16S rRNA genes to IPLs to core lipids, with IPLs preserving microbial diversity history on timescales more similar to 16S rRNA genes than core lipids. Ultimately, individual IPL biomarkers are identified which may be robust proxies for determining whether the biomarker profile recorded in a seep carbonate represents vestiges of active seepage processes, or the profile of a microbial community persisting after seep quiescence.
AbstractDespite mounting evidence for biogeochemical interactions between iron and nitrogen, our understanding of their environmental importance remains limited. Here we present an investigation of abiotic nitrite (NO2−) reduction by Fe(II) or ‘chemodenitrification’, and its relevance to the production of nitrous oxide (N2O), specifically focusing on dual (N and O) isotope systematics under a variety of environmental conditions. We observe a range of kinetic isotope effects that are regulated by reaction rates, with faster rates at higher pH (∼8), higher concentrations of Fe(II) and in the presence of mineral surfaces. A clear non-linear relationship between rate constant and kinetic isotope effects of NO2−reduction was evident (with larger isotope effects at slower rates) and is interpreted as reflecting the dynamics of Fe(II)–N reaction intermediates. N and O isotopic composition of product N2O also suggests a complex network of parallel and/or competing pathways. Our findings suggest that NO2− reduction by Fe(II) may represent an important abiotic source of environmental N2O, especially in iron-rich environments experiencing dynamic redox variations. This study provides a multi-compound, multi-isotope framework for evaluating the environmental occurrence of abiotic NO2− reduction and N2O formation, helping future studies constrain the relative roles of abiotic and biological N2O production pathways.
AbstractMethane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.
AbstractAt the broadest scale, this thesis is an investigation of how life modulates the movement of essential elements (carbon, sulfur, nitrogen, and silicon) on modern and geologic timescales. Chapters 1 and 2 explore carbon and sulfur cycling microbial communities found centimeters below the seafloor in hydrocarbon-rich methane seep ecosystems. At the Hydrate Ridge methane seep, we investigated how microbial partnerships direct the flow of methane and sulfide in these benthic oases by using identity-based physical separation methods developed in our lab (Magneto-FISH) in conjunction with community profiling and metagenomic sequencing. This method explores the middle ground between single cell and bulk sediment analysis by separating target microbes and their physically associated community for downstream sequencing applications. Magneto-FISH captures were done at a range of microbial taxonomic group specificities and sequenced with both clone library and next-gen iTag 16S rRNA gene methods. Chapter 1 provides a demonstration of how FISH probe taxonomic specificity correlates to resultant Archaeal taxonomic diversity in Magneto-FISHed seep sediments, with specific attention to preparation of Archaea-enriched samples for downstream metagenomic sequencing. In Chapter 2, a Bacteria-focused parallel environmental isolation and sequencing effort was subjected to co-occurrence analyses which suggested there may be far more microbial associations in methane seep systems than are currently appreciated, including partnerships that do not involve the canonical anaerobic methane oxidizing archaea and sulfate reducing bacteria. With samples from IODP Expedition 337 Shimokita coalbed biosphere, Chapter 3 provides evidence for an active microbial assemblage kilometers below the sea floor in the deepest samples ever collected by marine scientific ocean drilling. Using in situ temperature Stable Isotope Probing (SIP) incubations and NanoSIMS, we investigated whole community activity (with the passive tracer D2O) and substrate specific activity with C1-carbon compounds methylamine and methanol. We found deuterium-based turnover times to be faster (years) than previous deep biosphere estimates (hundreds to thousands of years), but methylotrophy rates to be slower than previous carbon metabolic rates.
AbstractIncreasing anthropogenic CO2 in the atmosphere causes global warming and subsequent environmental changes, which may lead to an increase in natural disasters jeopardizing human society. Prompt technological development for CO2 capture and sequestration is required in the international community. In this study, we performed CO2 emission and shallow-type methane hydrate decomposition experiments at the Joetsu Knoll, offshore Joetsu, Niigata, Japan, as pilot studies to test feasibility of CO2 sequestration and methane recovery using methane-CO2 replacement in shallow-type methane hydrates. An isobaric cylinder pump and probe with a built-in heater (“Heat sonde”) were developed to inject CO2 in deep-sea, high-pressure conditions. Before injecting CO2 into a methane hydrate located in deep-sea sediments, we attempted CO2 emission directly into deep-seafloor. In the experiment, liquid CO2 was emitted at the head of Heat sonde, however, the isobaric cylinder pump became clogged during operation. The result reveals that precipitates of CO2 hydrate, which are generated during mixing of inflow seawater and outflow liquid CO2, blocked flow lines of the isobaric cylinder pump and Heat sonde. This suggests that our developed instruments must be improved for future work. We also observed the collapse of an exposed methane hydrate layer at the seafloor upon contact with the Heat sonde in our experiment.
AbstractOne of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components.
AbstractSubglacial microbial habitats are widespread in glaciated regions of our planet. Some of these environments have been isolated from the atmosphere and from sunlight for many thousands of years. Consequently, ecosystem processes must rely on energy gained from the oxidation of inorganic substrates or detrital organic matter. Subglacial Lake Whillans (SLW) is one of more than 400 subglacial lakes known to exist under the Antarctic ice sheet; however, little is known about microbial physiology and energetics in these systems. When it was sampled through its 800 m thick ice cover in 2013, the SLW water column was shallow (~2 m deep), oxygenated, and possessed sufficient concentrations of C, N, and P substrates to support microbial growth. Here, we use a combination of physiological assays and models to assess the energetics of microbial life in SLW. In general, SLW microorganisms grew slowly in this energy-limited environment. Heterotrophic cellular carbon turnover times, calculated from 3H-thymidine and 3H-leucine incorporation rates, were long (60 to 500 days) while cellular doubling times averaged 196 days. Inferred growth rates (average ~0.006 d−1) obtained from the same incubations were at least an order of magnitude lower than those measured in Antarctic surface lakes and oligotrophic areas of the ocean. Low growth efficiency (8%) indicated that heterotrophic populations in SLW partition a majority of their carbon demand to cellular maintenance rather than growth. Chemoautotrophic CO2-fixation exceeded heterotrophic organic C-demand by a factor of ~1.5. Aerobic respiratory activity associated with heterotrophic and chemoautotrophic metabolism surpassed the estimated supply of oxygen to SLW, implying that microbial activity could deplete the oxygenated waters, resulting in anoxia. We used thermodynamic calculations to examine the biogeochemical and energetic consequences of environmentally imposed switching between aerobic and anaerobic metabolisms in the SLW water column. Heterotrophic metabolisms utilizing acetate and formate as electron donors yielded less energy than chemolithotrophic metabolisms when calculated in terms of energy density, which supports experimental results that showed chemoautotrophic activity in excess of heterotrophic activity. The microbial communities of subglacial lake ecosystems provide important natural laboratories to study the physiological and biogeochemical behavior of microorganisms inhabiting cold, dark environments.
AbstractHigh iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, CA, USA, for periods of 2 and 6 months. Substrates consisted of mild steel – a major constituent of maritime infrastructure – and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting “high-flux” conditions; a “stagnant” condition; an “active” flow-through condition with seawater slowly pumped over the substrates; and an “enrichment” condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the 2-month high flux incubations document coating of substrates with “twisted stalks,” resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria (FeOB). Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all 6 month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that (i) high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of marine neutrophilic FeOB and (ii) long-term nutrient stimulation results in substrate corrosion and biofilms with different bacterial community composition and structure relative to stagnant and non-nutritionally enhanced incubations. Similar microbial succession scenarios, involving increases in nutritional input leading to the proliferation of anaerobic iron and sulfur-cycling guilds, may occur at the nearby Port of Los Angeles and cause potential damage to maritime port infrastructure.
AbstractEnrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica(98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).
AbstractAmorphous orpiment-like As-sulfides (As2S3) are the most common As phases precipitating in hydrothermal systems, yet there is a lack of information regarding their solid-state characterization. Using a combination of optical, SEM–EDS, micro-Raman and XANES/EXAFS applications, we investigated yellow-orange As- and S-rich sediments occurring in the shallow-water hydrothermal system off the coast of Milos Island, Greece. The precipitates have several morphologies, but are dominantly colloidal. Intriguing “biological” morphologies also exist (e.g., cell-like (~ 10 μm), spirals (~ 20 μm), and rounded “cinnamon bun” shapes (~ 20 μm)). SEM–EDS data indicated that the precipitates have an As:S ratio similar to orpiment (average = 0.58, range 0.51–0.63; n = 8). Micro-Raman spectra indicated that orange colored precipitates appear to be dominated by poorly crystalline and/or amorphous arsenic sulfides with micro-amounts of more crystalline orpiment and impure sulfur. The yellow sediments also contained crystalline elemental sulfur in the form S8. Bulk As K-edge XANES spectra of the As-sulfide precipitates proved a valence of As corresponding to orpiment-type (As2S3) compounds (− 1 to + 3). EXAFS fitting results indicated that the studied material exhibits an amorphous orpiment-like structure with As ions coordinated by 3 sulfur atoms (CN = 3.0). The As–S interatomic distance of the first shell is calculated at 2.279 Å and the Debye–Waller factor (σ2) is 0.00427. These data suggest that the modeled structure of the studied precipitates is slightly S-deficient and ordered only in the first shell around As, resembling an orpiment-type structure, whereas higher shells are not present and must be disordered. The disorder phenomenon may be strictly produced either by the existence of occasional As–S–As bridges with As–As bonds or by the occurrence of As–O–As bridges, causing twisting of the AsS3 pyramids in the initial orpiment structure. This distortion in the higher coordination shells of the structural sheets creates the amorphous orpiment.
AbstractThe role of nitrogen cycling in submarine hydrothermal systems is far less studied than that of other biologically reactive elements such as sulfur and iron. In order to address this knowledge gap, we investigated nitrogen redox processes at Loihi Seamount, Hawaii, using a combination of biogeochemical and isotopic measurements, bioenergetic calculations and analysis of the prokaryotic community composition in venting fluids sampled during four cruises in 2006, 2008, 2009 and 2013. Concentrations of NH4+ were positively correlated to dissolved Si and negatively correlated to NO3-+NO2-, while NO2- was not correlated to NO3-+NO2-, dissolved Si or NH4+. This is indicative of hydrothermal input of NH4+ and biological mediation influencing NO2-concentrations. The stable isotope ratios of NO3- (δ15N and δ18O) was elevated with respect to background seawater, with δ18O values exhibiting larger changes than corresponding δ15N values, reflecting the occurrence of both production and reduction of NO3- by an active microbial community. δ15N-NH4+ values ranged from 0‰ to +16.7‰, suggesting fractionation during consumption and potentially N-fixation as well. Bioenergetic calculations reveal that several catabolic strategies involving the reduction of NO3- and NO2- coupled to sulfide and iron oxidation could provide energy to microbes in Loihi fluids, while 16S rRNA gene sequencing of Archaea and Bacteria in the fluids reveals groups known to participate in denitrification and N-fixation. Taken together, our data support the hypothesis that microbes are mediating N-based redox processes in venting hydrothermal fluids at Loihi Seamount.
Ultramafic rocks exposed on the continent serve as a window into oceanic and continental processes of water–peridotite interaction, so called serpentinization. In both environments there are active carbon and sulfur cycles that contain abiogenic and biogenic processes, which are eventually imprinted in the geochemical signatures of the basement rocks and the calcite and magnesite deposits associated with fluids that issue from these systems. Here, we present the carbon and sulfur geochemistry of ultramafic rocks and carbonate deposits from the Santa Elena ophiolite in Costa Rica. The aim of this study is to leverage the geochemistry of the ultramafic sequence and associated deposits to distinguish between processes that were dominant during ocean floor alteration and those dominant during low-temperature, continental water–peridotite interaction.
The peridotites are variably serpentinized with total sulfur concentrations up to 877 ppm that is typically dominated by sulfide over sulfate. With the exception of one sample the ultramafic rocks are characterized by positive δ34Ssulfide (up to + 23.1‰) and δ34Ssulfatevalues (up to + 35.0‰). Carbon contents in the peridotites are low and are isotopically distinct from typical oceanic serpentinites. In particular, δ13C of the inorganic carbon suggests that the carbon is not derived from seawater, but rather the product of the interaction of meteoric water with the ultramafic rocks. In contrast, the sulfur isotope data from sulfide minerals in the peridotites preserve evidence for interaction with a hydrothermal fluid. Specifically, they indicate closed system abiogenic sulfate reduction suggesting that oceanic serpentinization occurred with limited input of seawater. Overall, the geochemical signatures preserve evidence for both oceanic and continental water–rock interaction with the majority of carbon (and possibly sulfate) being incorporated during continental water–rock interaction. Furthermore, there is evidence for microbial activity that was possibly stimulated by carbon sourced from water–rock interaction with adjacent sediments or fluid inclusions. This study provides detailed insight into the complex hydrothermal history of continental serpentinization systems and adds to our understanding of the carbon and sulfur cycling within peridotite-hosted hydrothermal systems.
AbstractThe recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producingCandidatus Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, USA, we sequenced a single cell amplified genome (SAG), WOR_SM1_SCG, and used it to identify and refine two high-quality genomes from metagenomes, WOR_SM1_79 and WOR_SM1_86-2, from the same site. These three genomic reconstructions form a monophyletic group, which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, caused the protein to be encoded as two subunits at non-adjacent loci. Consistent with the terrestrial spring clades, our estuarine genomes contained a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H)-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identified two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which was more widespread, diverse, and not associated with visible mats. The core Alti-1 genome suggested Alti-1 is adapted for the stream environment with lipopolysaccharide production capacity and extracellular hami structures. The core Alti-2 genome suggested members of this clade are free-living with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These data suggested that the hamus structures found in Candidatus Altiarchaeum hamiconexum are not present outside of stream-adapted Altiarchaeales. Homologs to a Na+transporter and membrane bound coenzyme A disulfide reductase that were unique to the brackish sediment Alti-2 genomes, could indicate adaptations to the estuarine, sulfur-rich environment.
AbstractThe rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.
Numerous field, laboratory, and modeling studies have explored the flows of fluid, heat, and solutes during seafloor hydrothermal circulation, but it has been challenging to determine transport rates and flow directions within natural systems. Here we present results from the first cross-hole tracer experiment in the upper oceanic crust, using four subseafloor borehole observatories equipped with autonomous samplers to track the transport of a dissolved tracer (sulfur hexafluoride, SF6) injected into a ridge-flank hydrothermal system. During the first three years after tracer injection, SF6 was transported both north and south through the basaltic aquifer. The observed tracer transport rate of ∼2–3 m/day is orders of magnitude greater than bulk rates of flow inferred from thermal and chemical observations and calculated with coupled fluid-heat flow simulations. Taken together, these results suggest that the effective porosity of the upper volcanic crust through which much tracer was transported is <1%, with fluid flowing rapidly along a few well-connected channels. This is consistent with the heterogeneous (layered, faulted, and/or fractured) nature of the volcanic upper oceanic crust.
AbstractDNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given >150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y.
Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates to abundance-weighted community composition, but does not drive the vertical decrease in richness. Vertical patterns of richness at the open-ocean sites closely match organic degradation rates; both properties are highest near the seafloor and decline together as sediment depth increases. This relationship suggests that (i) total catabolic activity and/or electron donor diversity exerts a primary influence on bacterial richness in marine sediment, and (ii) many bacterial taxa that are poorly adapted for subseafloor sedimentary conditions are degraded in the geologically young sediment where respiration rates are high. Richness consistently takes a few hundred thousand years to decline from near-seafloor values to much lower values in deep anoxic subseafloor sediment, regardless of sedimentation rate, predominant terminal electron acceptor, or oceanographic context.
Importance Subseafloor sediment provides a wonderful opportunity to investigate drivers of microbial diversity in communities that may be isolated for millions of years. Our manuscript shows the impact of in situ conditions on bacterial community structure in subseafloor sediment. Specifically, it shows that bacterial richness in subseafloor sediment declines exponentially with sediment age, and in parallel with organic-fueled oxidation rate. This result suggests that subseafloor diversity ultimately depends on electron donor diversity and/or total community respiration. Despite the extraordinary nature of this ecosystem, we believe this is the first study of how and why biological richness changes over time in subseafloor sediment.
To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.
The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry.
IMPORTANCE This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium.
AbstractAlthough fluids within the upper oceanic basaltic crust harbor a substantial fraction of the total prokaryotic cells on Earth, the energy needs of this microbial population are unknown. In this study, a nanocalorimeter (sensitivity down to 1.2 nW ml-1) was used to measure the enthalpy of microbially catalyzed reactions as a function of temperature in samples from two distinct crustal fluid aquifers. Microorganisms in unamended, warm (63°C) and geochemically altered anoxic fluids taken from 292 meters sub-basement (msb) near the Juan de Fuca Ridge produced 267.3 mJ of heat over the course of 97 h during a step-wise isothermal scan from 35.5 to 85.0°C. Most of this heat signal likely stems from the germination of thermophilic endospores (6.66 × 104 cells ml-1FLUID) and their subsequent metabolic activity at temperatures greater than 50°C. The average cellular energy consumption (5.68 pW cell-1) reveals the high metabolic potential of a dormant community transported by fluids circulating through the ocean crust. By contrast, samples taken from 293 msb from cooler (3.8°C), relatively unaltered oxic fluids, produced 12.8 mJ of heat over the course of 14 h as temperature ramped from 34.8 to 43.0°C. Corresponding cell-specific energy turnover rates (0.18 pW cell-1) were converted to oxygen uptake rates of 24.5 nmol O2 ml-1FLUID d-1, validating previous model predictions of microbial activity in this environment. Given that the investigated fluids are characteristic of expansive areas of the upper oceanic crust, the measured metabolic heat rates can be used to constrain boundaries of habitability and microbial activity in the oceanic crust.
AbstractStudies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.
AbstractOceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement.
AbstractThe deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.
AbstractChloroflexi small-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylum Chloroflexi is represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurface Chloroflexi. Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurface Chloroflexi single amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nine Chloroflexi SAGs (seven of which are from the order Anaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of the Chloroflexi SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven Anaerolineales SAGs contains a distinct reductive dehalogenase homologous (rdhA) gene. IMPORTANCE Through the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, the Chloroflexi. These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examined Chloroflexi SAGs, our genomes (several are from the order Anaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (rdhA) has been directly linked to marine subsurface Chloroflexi, suggesting that reductive dehalogenation is not limited to the class Dehalococcoidia. This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group.
AbstractSubglacial Lake Whillans (SLW), West Antarctica, is an active component of the subglacial hydrological network located beneath 800 m of ice. The fill and drain behavior of SLW leads to long (years to decades) water residence times relative to those in mountain glacier systems. Here, we present the aqueous geochemistry of the SLW water column and pore waters from a 38-cm-long sediment core. Stable isotopes indicate that the water is primarily sourced from basal-ice melt with a minor contribution from seawater that reaches a maximum of ∼6% in pore water at the bottom of the sediment core. Silicate weathering products dominate the crustal (non-seawater) component of lake- and pore-water solutes, and there is evidence for cation exchange processes within the clay-rich lake sediments. The crustal solute component ranges from 6 meq L–1 in lake waters to 17 meq L–1 in the deepest pore waters. The pore-water profiles of the major dissolved ions indicate a more concentrated solute source at depth (>38 cm). The combination of significant seawater and crustal components to SLW lake and sediment pore waters in concert with ion exchange processes result in a weathering regime that contrasts with other subglacial systems. The results also indicate cycling of marine water sourced from the sediments back to the ocean during lake drainage events.
AbstractVolcanic ocean crust contains a global chemosynthetic microbial ecosystem that impacts ocean productivity, seawater chemistry, and geochemical cycling. We examined the mineralogical effect on community structure in the aquifer ecosystem by using a four-year in situ colonization experiment with igneous minerals and glasses in IODP Hole 1301A on the Juan de Fuca Ridge. Microbial community analysis and scanning electron microscopy revealed that olivine phases and iron-bearing minerals bore communities that were distinct from iron-poor phases. Communities were dominated by Archaeoglobaceae, Clostridia, Thermosipho, Desulforudis, and OP1 lineages. Our results suggest that mineralogy determines microbial composition in the subseafloor aquifer ecosystem.
AbstractThe hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.
AbstractSulfate reducing bacteria (SRB) oxidize a significant proportion of subseafloor organic carbon, but their metabolic activities and subsistence mechanisms are poorly understood. Here, we report in depth phylogenetic and metabolic analyses of SRB transcripts in the Peru Margin subseafloor and interpret these results in the context of sulfate reduction activity in the sediment. Relative abundance of overall SRB gene transcripts declines strongly whereas relative abundance of ribosomal protein transcripts from sulfate reducing δ‐Proteobacteria peak at 90 m below seafloor (mbsf) within a deep sulfate methane transition zone. This coincides with isotopically heavy δ34S values of pore water sulfate (70‰), indicating active subseafloor microbial sulfate reduction. Within the shallow sulfate reduction zone (0–5 mbsf), a transcript encoding the beta subunit of dissimilatory sulfite reductase (dsrB) was related to Desulfitobacterium dehalogenans and environmental sequences from Aarhus Bay (Denmark). At 159 mbsf we discovered a transcript encoding the reversely operating dissimilatory sulfite reductase α‐subunit (rdsrA), with basal phylogenetic relation to the chemolithoautotrophic SUP05 Group II clade. A diversity of SRB transcripts involved in cellular maintenance point toward potential subsistence mechanisms under low‐energy over long time periods, and provide a detailed new picture of SRB activities underlying sulfur cycling in the deep subseafloor.
AbstractSubsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H2ases to successively higher concentrations of H2 in successively deeper zones.
AbstractWe present three‐dimensional simulations of coupled fluid and heat transport in the ocean crust, to explore patterns and controls on ridge‐flank hydrothermal circulation on the eastern flank of the Juan de Fuca Ridge. Field studies have shown that there is large‐scale fluid flow in the volcanic ocean crust in this region, including local convection and circulation between two basement outcrops separated by ~50 km. New simulations include an assessment of crustal permeability and aquifer thickness, outcrop permeability, the potential influence of multiple discharging outcrops, and a comparison between two‐dimensional (profile) and three‐dimensional representations of the natural system. Field observations that help to constrain new simulations include a modest range of flow rates between recharging and discharging outcrops, secondary convection adjacent to the recharging outcrop, crustal permeability determinations made in boreholes, and the lack of a regional seafloor heat flux anomaly as a consequence of advective heat loss from the crust. Three‐dimensional simulations are most consistent with field observations when models use a crustal permeability of 3 × 10−13 to 2 × 10−12 m2, and the crustal aquifer is ≤300 m thick, values consistent with borehole observations. We find fluid flow rates and crustal cooling efficiencies that are an order of magnitude greater in three‐dimensional simulations than in two‐dimensional simulations using equivalent properties. Simulations including discharge from an additional outcrop can also replicate field observations but tend to increase the overall rate of recharge and reduce the flow rate at the primary discharge site.
AbstractThe deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.
AbstractOur knowledge of microbial life residing in the oceans- photic and aphoticand within the subseafloor sediment has grown exponentially within the last few decades. This is partly because of advances in next-generation sequencing technology, which has provided an opportunity to address previously unanswerable questions regarding microbial diversity and biogeography (Hamady & Knight, 2009; Petrosino, Highlander, Luna, Gibbs, & Versalovic, 2009). By utilizing a next-generation sequencing approach, I determined microbial community compositions and assessed their response to environmental and geographic variation within and between five different oceanic regimes (i) the South Pacific Gyre (SPG), (ii) the Eastern and Central Equatorial Pacific (EQP), (iii) the North Pacific Gyre (NPG), (iv) the Bering Sea (U1343), and (v) the Indian Ocean (NGHP-1-14). My first manuscript, “ The bacterial and archaeal biogeography of the deep chlorophyll maximum of the South Pacific Gyre”, examines the prokaryotic community composition at a continuous and biologically significant horizon, the deep chlorophyll maximum (DCM), across Earth’s largest oceanographic province, the SPG. Our results demonstrate that bacterial and archaeal tag-sequence assemblages of the DCM are strikingly similar throughout the SPG, in terms of the presence and abundance of the most dominant bacterial taxa. Comparison of our SPG bacterial results to samples from the NPG and the relatively nutrient- and chlorophyll-rich EQP shows that DCM assemblages of the SPG, NPG and EQP are statistically distinct from each other, although they have many abundant tags in common. This distinctness is influenced by environmental conditions, as the communities of the two gyres (SPG and NPG) resemble each other more closely than either resembles the EQP community (which lives geographically between them). My second manuscript, “Vertical changes in bacterial diversity and community composition from seasurface to subseafloor”, investigates the degree of connectivity between bacterial communities that reside in deep-sea sediment to those that reside throughout the water column at three Pacific Ocean (EQP and NPG) stations. In this study, my collaborators and I investigate a series of ecological gradients through examination into the vertical structure and richness of marine microbes and the how they are influenced by geographic location, light, oxygen concentration and depth. We provide the first pyrosequencing results to (i) address a possible mechanism by which deeply buried sedimentary communities develop deep beneath the seafloor and (ii) assess the degree to which the organisms in those communities are related to communities in the overlying ocean. My third manuscript, “Bacterial diversity, sediment age and organic respiration in the marine sedimentary environment”, investigates the drivers of microbial diversity and taxonomic richness in deep subseafloor sediment of four geographically distant sites in the Pacific and Indian oceans (U1343, NGHP-1-14, EQP1 and EQP8). To accomplish this goal, my collaborators and I took samples for molecular analysis and interstitial water from a wide range of sediment depths (up to 404 meters below seafloor) and sediment age (up to 5.5 Ma). Our study of these samples demonstrates that abundance-weighted bacterial community composition shifts in response to availability of dissolved metabolic reactants (e.g. oxygen, sulfate, methane). Our study also demonstrates taxonomic richness declines exponentially with sediment age and generally matches the canonical expectation for changing rates of organic oxidation in subseafloor sediment over time (Jorgensen, 1978; Middelburg, 1989; Westrich & Berner, 1984).
AbstractMicrobial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~104 cells cm−3. Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.
AbstractWithin hydrothermal plumes, chemosynthetic processes and microbe–mineral interactions drive primary productivity in deep-ocean food webs and may influence transport of elements such as iron. However, the source of microorganisms in plumes and the factors governing how these communities assemble are poorly understood, in part due to lack of data from early stages of plume formation. In this study, we examined microbial community composition of rising hydrothermal plumes from five vent fields along the Eastern Lau Spreading Center. Seafloor and plume microbial communities were significantly dissimilar and shared few phylotypes. Plume communities were highly similar to each other with significant differences in community membership only between Kilo Moana and Mariner, two vents that are separated by extremes in depth, latitude and geochemistry. Systematic sampling of waters surrounding the vents revealed that species richness and phylogenetic diversity was typically highest near the vent orifice, implying mixing of microbial communities from the surrounding habitats. Above-plume background communities were primarily dominated by SAR11, SAR324 and MG-I Archaea, while SUP05, Sulfurovum, Sulfurimonas, SAR324 and Alteromonas were abundant in plume and near-bottom background communities. These results show that the ubiquitous water-column microorganisms populate plume communities, and that the composition of background seawater exerts primary influence on plume community composition, with secondary influence from geochemical and/or physical properties of vents. Many of these pervasive deep-ocean organisms are capable of lithotrophy, suggesting that they are poised to use inorganic electron donors encountered in hydrothermal plumes.
BackgroundThe Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms.
MethodsAverage nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneusgenomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms.
ResultsThe three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene ofC. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases.
ConclusionsGenomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential.
AbstractThe continuous rise of atmospheric nitrous oxide (N2O) is an environmental issue of global concern. In biogeochemical studies, N2O production is commonly assumed to arise solely from enzymatic reactions in microbes and fungi. However, iron, manganese and organic compounds readily undergo redox reactions with intermediates in the nitrogen cycle that produce N2O abiotically under relevant environmental conditions at circumneutral pH. Although these abiotic N2O production pathways have been known to occur for close to a century, they are often neglected in modern ecological studies. In this Synthesis and Emerging Ideas paper, we highlight the defining characteristics, environmental controls, and isotopic signatures of abiotic reactions between nitrogen cycle intermediates (hydroxylamine, nitric oxide, and nitrite), redox-active metals (iron and manganese) and organic matter (humic and fulvic acids) that can lead to N2O production. We also discuss the emerging idea that abiotic reactions coupled to biotic processes have widespread ecological relevance and encourage consideration of abiotic production mechanisms in future biogeochemical investigations of N2O cycling.
AbstractThis paper presents data on the numbers of female and male professors at the 106 top US earth science PhD-ranting graduate programs during the 2010–2011 academic year. Overall, 20% of earth science faculty at PhD-granting research universities were women (470 female faculty members out of 2,324 total). By rank, 36% of assistant professors, 24% of associate professors, and 13% of full professors were women. Large ranges in percentages (0%–40%) of female professors were observed between departments. No geographic trends were observed, nor was there any correlation between the national ranking of department and the percentage of women faculty. A small positive correlation between the size of the department and the percentage of female faculty was present as department sizes increased from 5 to 30 faculty members, and a small decline occurred between 30 to 50 faculty. Percentages of tenured female faculty were generally lower than the total percentage of female faculty members in each department. The top 5 departments in terms of percentages of female faculty were SUNY Buffalo Department of Geology (40%), Louisiana State University–Baton Rouge Department of Geology and Geophysics (40%), University of New Hampshire Department of Earth Sciences (37%), University of Massachusetts–Amherst Department of Geosciences (36%), and University of Nevada–Las Vegas Department of Geoscience (35%).
- Environmental conditions and microbial lifestyles both influence which metal micronutrients particular microorganisms use.
- Variations in geochemical conditions over eons influenced what metals microorganisms use along with the metabolic apparatus needed to use those metals.
- Global cycles involving oxygen, carbon dioxide, nitrogen, and phosphorus depend on metalloenzymes that incorporate one or more metals and, in at least one case, a rare-earth element.
- Mass spectrometry is giving way to newer analytic methods that allow imaging of metals at parts-per-billion concentrations and that pinpoint metals in microbial cells, aggregates, and biofilms.
- Amid progress, efforts to characterize microbial metalloenzymes are still in their infancy.