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.
AbstractThe global ocean is Earth's largest biome, which extends into the sediments and igneous crust below the oceans. The abundance of microbial life beneath the sea floor is at least comparable to that in the oceans (1), but this biome remains poorly understood. The ramifications of a massive buried biosphere are important on a global scale, with sub–sea-floor microbes playing a crucial role in carbon sequestration, element cycles, and Earth's evolution, and likely encompassing staggering metabolic and genetic diversity. On page 420 of this issue, Inagaki et al. (2) report that even at almost 2.5 km beneath the sea floor, microbial life is not only present and compositionally distinct from that in shallower sediments, but also producing methane.
AbstractIn many habitats, microorganisms exhibit significant distance–decay patterns as determined by analysis of the 16S rRNA gene and various other genetic elements. However, there have been few studies that examine how the similarities of both taxonomic and functional genes co‐vary over geographic distance within a group of ecologically related microbes. Here, we determined the biogeographic patterns of the functional dissimilatory sulfite reductase gene (dsrA) and the 16S rRNA gene in sulfate‐reducing bacterial communities of US East Coast salt marsh sediments. Distance–decay, ordination and statistical analyses revealed that the distribution of 16S rRNA genes is strongly influenced by geographic distance and environmental factors, whereas the dsrA gene is not. Together, our results indicate that 16S rRNA genes are likely dispersal limited and under environmental selection, whereas dsrA genes appear randomly distributed and not selected for by any expected environmental variables. Selection, drift, dispersal and mutation are all factors that may help explain the decoupled biogeographic patterns for the two genes. These data suggest that both the taxonomic and functional elements of microbial communities should be considered in future studies of microbial biogeography to aid in our understanding of the diversity, distribution and function of microorganisms in the environment.
AbstractMost of the hydrothermal circulation through the ocean crust, in terms of mass, heat, and many solute fluxes, occurs on ridge-flanks. Far from the magmatic influence of mid-ocean ridges, fluid flow is driven by lithospheric heating from below and channeled through volcanic rock outcrops that serve as high-permeability conduits between the ocean and the underlying volcanic crust. Field data in this setting is sparse due to difficulties associated with accessing these remote locations, making geologically accurate modeling particularly valuable to assessing the nature of ridge-flank hydrothermal circulation. Each study in this thesis applies a combination of modeling and field observations to constrain the hydrogeologic properties and behaviors of ridge-flank hydrothermal systems, including: (1) deriving permeability estimates from flowing subsea boreholes, (2) investigating the sustainability of outcrop-to-outcrop hydrothermal flow, and (3) constraining the properties and behaviors on a well-studied outcrop-to-outcrop system. In the first study, thermal records from flowing boreholes in young oceanic crust are used to assess borehole and formation properties, including permeability, using analytic equations and a Markov chain Monte Carlo analysis to quantify uncertainty. We find the median bulk permeability at all sites to be between 0.4 to 1.5 x 10^-11 m2, with a standard deviation of 0.2 to 0.3 log-cycles at each borehole. These results are remarkably homogenous, given the much larger variability in permeability measurements in the oceanic crust. Results from the second study illuminate the controls on hydrogeologic sustainability, flow rate, and preferred flow direction in outcrop-to-outcrop hydrothermal systems. We find that sustained flow between outcrops over tens of kilometers depends on a contrast in transmittance (the product of outcrop permeability and the area of outcrop exposure) between recharging and discharging sites, and that discharge is favored through less transmissive outcrops. These systems require aquifer permeability values ranging from 10^-12 to 10^-11 m2, consistent with field measurements and values inferred from the first chapter. In the third study, a suite of three-dimensional numerical simulations are used to characterize and constrain the permeability and thickness of the upper crustal aquifer, the permeability of outcrops, and the potential for multiple discharging outcrops and azimuthal permeability anisotropy to influence hydrothermal processes at a field site on the eastern flank of the Juan de Fuca Ridge.
AbstractWhen exposed at Earth’s surface, rocks are out of thermodynamic equilibrium with respect to their environment. This disequilibrium drives the chemical transformation, or weathering, of these rocks into soils and governs the chemical composition of natural waters and the atmosphere. Over geologic timescales, complex feedbacks associated with weathering processes are presumed to regulate the concentrations of CO₂ and O₂ in the atmosphere with profound implications for the habitability of the planet. However, a mechanistic understanding of how biologic, tectonic, and climatic conditions interact to control weathering fluxes has remained elusive. In part, our understanding of weathering processes is hindered by the fact that they operate continuously over an enormous range of spatial (atomic to global) and temporal (microseconds to millions of years) scales, but we can only make measurements over discrete ranges of these values. While each scale of observation available offers unique insights, it is often difficult to link observations made at different scales. For my Ph.D., I focused on three distinct projects that span the range of observable scales in order to better understand the links between chemical weathering and long-term biogeochemical cycles. ❧ Chapter 2: Laboratory insights into microbial mineral dissolution. Rocks and minerals represent a major reservoir of bio-essential nutrients. While abundant, some of these lithogenic nutrients, like iron, are not readily bio-available. As a result, many organisms produce metal-binding ligands to scavenge these trace nutrients from the environment. Using targeted laboratory experiments with live microbial cultures and purified microbial ligands, I explored efficacy by which microbes can access trace nutrients from common silicate minerals (Torres et al., in prep). In addition to providing insight into biological nutrient scavenging strategies, this work also provides the basic research necessary to develop microbe-based CO₂ sequestration techniques since the dissolution of silicate minerals for nutrient acquisition also sequesters CO₂. ❧ Chapters 3 & 4: Geomorphic control on the hydrology and carbon budget of weathering. Erosional processes and hydrology are known to influence chemical weathering rates by controlling the timescales over which minerals react. Accurately describing the complex linkages between weathering, erosion, and hydrology observed in natural environments remains a major research challenge. To help address this problem, a major part of my Ph.D. was focused on characterizing how chemical weathering and hydrology are coupled in distinct erosional environments. This work combines hydrologic monitoring, solute chemistry, and water isotope analyses in order to robustly document how water is stored in catchments and link this to measured solute fluxes from chemical weathering (Clark et al., 2014; Torres et al., 2015). The results of this study are intriguing in that the hydrological control of weathering was found to vary predictably with the erosional regime, which has important implications for how changes in tectonic activity affect global weathering fluxes. ❧ By affecting the timescales over which weathering reactions occur, erosional processes also influence which minerals react due to the intrinsic variability in the reaction rates of different minerals. Rapid erosion rates favor the oxidation of sulfide minerals relative to the dissolution of silicate minerals, which leads to the release of CO₂ into the ocean-atmosphere system. To trace sulfide oxidation and its effect on the carbon budget, I combined multiple isotopic systems (e.g., S, C, and Sr) with major and trace element analyses (Torres et al., in prep). By making observations in catchments with diverse erosional regimes, it was possible to interrogate how sulfide oxidation fluxes relate to erosional processes. My results showed that sulfide oxidation dominates in rapidly eroding environments and leads to the significant release of CO₂. This is in contrast to more slowly eroding environments, where CO₂ consumption during silicate weathering dominates. ❧ Chapter 5: The evolution of the Cenozoic carbon cycle. My research on sulfide oxidation in modern systems suggested a link between tectonic uplift and the carbon budget of weathering processes with important implications for the long-term carbon cycle. To test this hypothesis, I incorporated the effects of sulfide-oxidation driven CO₂ release into a model of the Cenozoic carbon cycle. The Cenozoic carbon cycle has long plagued geochemists as isotopic records suggest changes in weathering fluxes that appear to be inconsistent with the requirement of mass balance in the long-term carbon cycle. By incorporating sulfide oxidation as a CO₂ source, I was able to provide a novel solution to the "Cenozoic isotope-weathering paradox" (Torres et al., 2014).
AbstractWhere Wild Microbes Grow is a children’s picture eBook about the search for life under the seafloor. Kids explore how scientists are discovering amazing creatures that may help us find life on other planets. Written in rhyming verse by Kevin Kurtz and illustrated by Alice Feagan, this eBook also includes interactive videos, photos and other media about the astonishing world of seafloor microbes.
AbstractPrimary productivity in at least a third of the sunlit open ocean is thought to be iron-limited. Primary sources of dissolved iron (dFe) to the ocean are hydrothermal venting, flux from the sediments along continental margins, and airborne dust. This article provides a general review of sources of hydrothermal and sedimentary iron to the ocean, and speculates upon the role that iron-cycling microbes play in controlling iron dynamics from these sources. Special attention is paid to iron-oxidizing bacteria (FeOB) that live by oxidizing iron and producing biogenic iron oxides as waste products. The presence and ubiquity of FeOB both at hydrothermal systems and in sediments is only beginning to be appreciated. The biogenic oxides they produce have unique properties that could contribute significantly to the dynamics of dFe in the ocean. Changes in the physical and chemical characteristics of the ocean due to climate change and ocean acidification will undoubtedly impact the microbial iron cycle. A better understanding of the contemporary role of microbes in the iron cycle will help in predicting how these changes could ultimately influence marine primary productivity.
AbstractThe oceanic crust forms two thirds of the Earth’s surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō’ihi Seamount, Hawai’i, and the East Pacific Rise (EPR; 9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō’ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy.
AbstractNitrogen (N) is a key component of fundamental biomolecules. Hence, its cycling and availability are central factors governing the extent of ecosystems across the Earth. In the organic-lean sediment porewaters underlying the oligotrophic ocean, where low levels of microbial activity persist despite limited organic matter delivery from overlying water, the extent and modes of nitrogen transformations have not been widely investigated. Here we use the N and oxygen (O) isotopic composition of porewater nitrate (NO3−) from a site in the oligotrophic North Atlantic (Integrated Ocean Drilling Program – IODP) to determine the extent and magnitude of microbial nitrate production (via nitrification) and consumption (via denitrification). We find that NO3- accumulates far above bottom seawater concentrations (~ 21 μM) throughout the sediment column (up to ~ 50 μM) down to the oceanic basement as deep as 90 m b.s.f. (below sea floor), reflecting the predominance of aerobic nitrification/remineralization within the deep marine sediments. Large changes in the δ15N and δ18O of nitrate, however, reveal variable influence of nitrate respiration across the three sites. We use an inverse porewater diffusion–reaction model, constrained by the N and O isotope systematics of nitrification and denitrification and the porewater NO3- isotopic composition, to estimate rates of nitrification and denitrification throughout the sediment column. Results indicate variability of reaction rates across and within the three boreholes that are generally consistent with the differential distribution of dissolved oxygen at this site, though not necessarily with the canonical view of how redox thresholds separate nitrate regeneration from dissimilative consumption spatially. That is, we provide stable isotopic evidence for expanded zones of co-occurring nitrification and denitrification. The isotope biogeochemical modeling also yielded estimates for the δ15N and δ18O of newly produced nitrate (δ15NNTR (NTR, referring to nitrification) and δ18ONTR), as well as the isotope effect for denitrification (15ϵDNF) (DNF, referring to denitrification), parameters with high relevance to global ocean models of N cycling. Estimated values of δ15NNTR were generally lower than previously reported δ15N values for sinking particulate organic nitrogen in this region. We suggest that these values may be, in part, related to sedimentary N2 fixation and remineralization of the newly fixed organic N. Values of δ18ONTR generally ranged between −2.8 and 0.0 ‰, consistent with recent estimates based on lab cultures of nitrifying bacteria. Notably, some δ18ONTR values were elevated, suggesting incorporation of 18O-enriched dissolved oxygen during nitrification, and possibly indicating a tight coupling of NH4+ and NO2− oxidation in this metabolically sluggish environment. Our findings indicate that the production of organic matter by in situ autotrophy (e.g., nitrification, nitrogen fixation) supplies a large fraction of the biomass and organic substrate for heterotrophy in these sediments, supplementing the small organic-matter pool derived from the overlying euphotic zone. This work sheds new light on an active nitrogen cycle operating, despite exceedingly low carbon inputs, in the deep sedimentary biosphere.
AbstractChemical input to the deep sea from hydrothermal systems is a globally distributed phenomenon. Hydrothermal discharge is one of the primary mechanisms by which the Earth’s interior processes manifest themselves at the Earth’s surface, and it provides a source of energy for autotrophic processes by microbes that are too deep to capitalize on sunlight. Much is known about the water-column signature of this discharge from high-temperature mid-ocean Ridge (MOR) environments and their neighboring low-temperature counterparts. Hydrothermal discharge farther away from the ridge, however, has garnered less attention, owing in part to the difficulty in finding this style of venting, which eludes methods of detection that work well for high-temperature ‘black smoker’-type venting. Here we present a case study of the plume from one such ‘invisible’ off-axis environment, The Lost City, with an emphasis on the dissolved volatile content of the hydrothermal plume. Serpentinization and abiotic organic synthesis generate significant concentrations of H2 and CH4 in vent fluid, but these species are unevenly transported to the overlying plume, which itself appears to be a composite of two different sources. A concentrated vent cluster on the talus slope channels fluid through at least eight chimneys, producing a water-column plume with the highest observed concentrations of CH4 in the field. In contrast, a saddle in the topography leading up to a carbonate cap hosts broadly distributed, nearly invisible venting apparent only in its water-column signals of redox potential and dissolved gas content, including the highest observed plume H2. After normalizing H2 and CH4 to the 3He background-corrected anomaly (3HeΔ) to account for mixing and relative amount of mantle input, it appears that, while a minimum of 60% of CH4 is transported out of the system, greater than 90% of the H2 is consumed in the subsurface prior to venting. The exception to this pattern occurs in the plume originating from the area dubbed Chaff Beach, in which somewhat more than 10% of the original H2 remains, indicating that this otherwise unremarkable plume, and others like it, may represent a significant source of H2 to the deep sea.
AbstractExtreme thermal gradients and compressed metabolic zones limit the depth range of microbial colonization in hydrothermally active sediments at Guaymas Basin. We investigated the physicochemical characteristics of this ecosystem and their influence on microbial community structure. Temperature‐related trends of δ13C values of methane and dissolved inorganic carbon from 36 sediment cores suggest in situ thermal limits for microbial anaerobic methane oxidation and organic carbon re‐mineralization near 80°C and 100°C respectively. Temperature logging probes deposited in hydrothermal sediments for 8 days demonstrate substantial thermal fluctuations of up to 25°C. Putative anaerobic methanotroph (ANME) populations dominate the archaeal community, transitioning from ANME‐1 archaea in warm surficial sediments towards ANME‐1 Guaymas archaea as temperatures increase downcore. Since ANME archaea performing anaerobic oxidation of methane double on longer time scales (months) compared with relatively rapid in situ temperature fluctuations (hours to days), we conclude that ANME archaea possess a high tolerance for short‐term shifts in the thermal regime.
A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30–70 °C (optimum 60 °C), 0–50 g NaCl l− 1 (optimum 15–20 g l− 1) and pH 5.5–8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( − )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T).