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Publications > Journal Article

Earth and Planetary Science Letters

Three-dimensional models of hydrothermal circulation through a seamount network on fast-spreading crust

Authors: Rachel M. Lauer, Andrew T. Fisher, Dustin M. Winslow

Published: November 1, 2018

C-DEBI Contribution Number: 439

Abstract

We present results from three-dimensional, transient, fully coupled simulations of fluid and heat transport on a ridge flank in fast-spread ocean crust. The simulations quantify relationships between rates of fluid flow, the extent of advective heat extraction, the geometry of crustal aquifers and outcrops, and crustal hydrologic parameters, with the goal of simulating conditions similar to those seen on 18–24 M.y. old seafloor of the Cocos plate, offshore Costa Rica. Extensive surveys of this region documented a ∼14,500 km² area of the seafloor with heat flux values that are 10–35% of those predicted from conductive cooling models, and identified basement outcrops that serve as pathways for hydrothermal circulation via recharge of bottom water and discharge of cool hydrothermal fluid. Simulations suggest that in order for rapid hydrothermal circulation to achieve observed seafloor heat flux values, upper crustal permeability is likely to be ~10^-10 to 10^-9m², with more simulations matching observations at the upper end of this range. These permeabilities are at the upper end of values measured in boreholes elsewhere in the volcanic ocean crust, and higher than inferred from three-dimensional modeling of another ridge-flank field site where there is less fluid flow and lower advective power output. The simulations also show that, in a region with high crustal permeability and variable sized outcrops, hydrothermal outcrop-to-outcrop circulation is likely to constitute a small fraction of total fluid circulation, with most of fluid flow occurring locally through individual outcrops that both recharge and discharge hydrothermal fluid.

Source: http://dx.doi.org/10.1016/j.epsl.2018.08.025

Publications > Journal Article

Environmental Microbiology

Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments

Authors: Bonita R. Lam, Annette R. Rowe, Kenneth H. Nealson

Published: June 1, 2018

C-DEBI Contribution Number: 433

Abstract

Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favourable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods. Working electrodes buried in sediment microcosms were poised at seven redox potentials between −300 and −750 mV versus Ag/AgCl using a three‐electrode system. In electrode biofilms recovered after 2‐month incubations, overall community diversity increased with more negative redox potentials. Abundances of known EET‐capable groups (e.g., Alteromonadales and Desulfuromonadales) varied with redox potential. Motility and chemotaxis genes were found in greater abundance in electrode communities, suggesting a possible selective advantage of these pathways for colonization and utilization of the electrode. Our enrichments demonstrated the validity of this approach in capturing groups known, as well as novel groups (e.g., Campylobacterales) that perform EET. The diverse nature of the enriched cathode communities suggest that insoluble substrate oxidation may be a critical, although poorly described microbial metabolic process in marine sediment.

Source: http://dx.doi.org/10.1111/1462-2920.14275

Publications > Journal Article

Environmental Microbiology

Elemental sulfur reduction in the deep-sea vent thermophile, Thermovibrio ammonificans

Authors: Benjamin I. Jelen, Donato Giovannelli, Paul G. Falkowski, Costantino Vetriani

Published: June 1, 2018

C-DEBI Contribution Number: 434

Abstract

The reduction of elemental sulfur is an important energy‐conserving pathway in prokaryotes inhabiting geothermal environments, where sulfur respiration contributes to sulfur biogeochemical cycling. Despite this, the pathways through which elemental sulfur is reduced to hydrogen sulfide remain unclear in most microorganisms. We integrated growth experiments using Thermovibrio ammonificans, a deep‐sea vent thermophile that conserves energy from the oxidation of hydrogen and reduction of both nitrate and elemental sulfur, with comparative transcriptomic and proteomic approaches, coupled with scanning electron microscopy. Our results revealed that two members of the FAD‐dependent pyridine nucleotide disulfide reductase family, similar to sulfide‐quinone reductase and to NADH‐dependent sulfur reductase (NSR), respectively, are over‐expressed during sulfur respiration. Scanning electron micrographs and sulfur sequestration experiments indicated that direct access of T. ammonificans to sulfur particles strongly promoted growth. The sulfur metabolism of T. ammonificans appears to require abiotic transition from bulk elemental sulfur to polysulfide to nanoparticulate sulfur at an acidic pH, coupled to biological hydrogen oxidation. A coupled biotic‐abiotic mechanism for sulfur respiration is put forward, mediated by an NSR‐like protein as the terminal reductase.

Source: http://dx.doi.org/10.1111/1462-2920.14280

Publications > Journal Article

Proceedings of the International Ocean Discovery Program

Data report: IODP Expedition 366 pore water trace element (V, Mo, Rb, Cs, U, Ba, and Li) compositions

Authors: Charles Geoffrey Wheat, Trevor Fournier, Claudia Paul, Catriona Menzies, Roy E. Price, Jeffrey Ryan, Oliver Sissman

Published: August 13, 2018

C-DEBI Contribution Number: 429

Abstract

International Ocean Discovery Program (IODP) Expedition 366 focused, in part, on the study of geochemical cycling, matrix alteration and transport, and deep biosphere processes in the Mariana subduction zone. This research was accomplished by sampling the summit and flank regions of three active serpentinite mud volcanoes in the Mariana forearc: Yinazao (Blue Moon), Fantangisña (Celestial), and Asùt Tesoro (Big Blue) Seamounts. These mud volcanoes represent a transect with increasing distance from the trench. Because these mud volcanoes discharge fluids and materials from the subduction channel, they provide a means to characterize thermal, geochemical, and pressure conditions within the seismogenic zone. Previous coring on Ocean Drilling Program (ODP) Legs 125 and 195 at two other serpentinite mud volcanoes (Conical and South Chamorro Seamounts, respectively) and piston, gravity, and push cores from several other Mariana serpentinite mud volcanoes add to this transect of deep-sourced material that is discharged at the seafloor.

Pore waters were squeezed from cored serpentinite materials to determine the composition of deep-sourced fluid from the subduction channel and to assess the character, extent, and effect of diagenetic reactions and mixing with seawater on the flanks of three serpentinite seamounts (Yinazao, Fantangisña, and Asùt Tesoro). In addition, two water-sampling temperature probe (WSTP) fluid samples were collected in two of the cased boreholes, each with at least 30 m of screened casing that allowed formation fluids to discharge into the borehole. Here we report shore-based Li, Rb, Cs, Ba, V, Mo, and U measurements of pore waters and one of the WSTP samples. The alkali metals were analyzed to constrain the temperature of reaction in the subduction channel. The other elements were analyzed to assess potential biogenic and diagenetic reactions as the serpentinite material weathers and exchanges with bottom seawater via diffusion. Results were generally consistent with earlier coring and drilling operations, resulting in systematic changes in the composition of the deep-sourced fluid with distance from the trench.

Source: https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lom3.10264

Publications > Journal Article

Limnology and Oceanography: Methods

Influence of commercial DNA extraction kit choice on prokaryotic community metrics in marine sediment

Authors: Gustavo A. Ramírez, Dennis Graham, Steven L. D’Hondt

Published: August 7, 2018

C-DEBI Contribution Number: 432

Abstract

Commercial DNA extraction kits are widely used for cultivation‐free surveys of marine sediment. However, the consequences of popular extraction‐kit choices for sequence‐based biological inferences about marine sedimentary communities have not previously been exhaustively assessed. To address this issue, we extracted DNA from multiple paired subsamples of marine sediment using two popular commercial extraction kits (MO BIO Laboratories PowerSoil^® DNA isolation kit and MP Biomedicals FastDNA^TM Spin Kit for Soil). We report comparisons of (1) total DNA yield, (2) extract purity, (3) gene‐targeted quantification, and (4) post‐sequencing ecological inferences in near‐seafloor (< 1 meter below seafloor [mbsf]) and subsurface (> 1 mbsf) marine sediment. In near‐seafloor sediment, the MP Biomedicals FastDNA^TM Spin Kit for Soil exhibits higher extraction yields, higher 16S rRNA gene loads, higher taxonomic diversity, and lower contaminant loads. In subseafloor sediment, both kits yield similar values for all of these parameters. The MO BIO Laboratories PowerSoil^® DNA isolation kit generally co‐extracts less protein with the DNA in both near‐seafloor and subseafloor sediment. For samples from all depths, both kits exhibit similar depth‐dependent community richness patterns, taxonomic composition, and ordination‐based similarity trends. We conclude that, despite kit‐specific differences in extract yields, purity and reagent contaminant loads, ecological inferences based on next‐generation sequencing of DNA extracted using these popular commercial kits are robustly comparable, particularly for subseafloor sediment samples.

Source: http://dx.doi.org/10.1002/lom3.10264

Publications > Journal Article

Frontiers in Microbiology

Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration

Authors: Laura A. Zinke, Brandi Kiel Reese, James McManus, Charles Geoffrey Wheat, Beth N. Orcutt, Jan P. Amend

Published: June 13, 2018

C-DEBI Contribution Number: 430

Abstract

Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15^∘C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I), Alphaproteobacteria (Rhodospirillales), Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.

Source: http://dx.doi.org/10.3389/fmicb.2018.01249

Publications > Journal Article

Organic Geochemistry

Assessment of apolar lipids in subseafloor rocks and potential contaminants from the Atlantis Massif (IODP Expedition 357)

Authors: Katherine A. Hickok, Tran B. Nguyen, Susan Q. Lang

Published: May 1, 2018

C-DEBI Contribution Number: 428

Abstract

International Ocean Discovery Program Expedition 357 drilled 17 boreholes across the Atlantis Massif with the goals of investigating carbon cycling and the presence of life in a zone of active serpentinization. The expedition recovered multiple lithologies including gabbros, basalts, carbonate sands, and serpentinites. A subset of contrasting lithologies were analyzed for apolar lipid content to determine if non-volatile organic molecules can be detected in the oceanic subsurface. The definitive detection and identification of abiotic and biological lipids in the subsurface of an actively serpentinizing system would be a significant step towards understanding a variety of scientific processes, including the evolution of pre-biotic chemistry, microbial habitability, and the global carbon cycle. Given the high potential for contamination during drilling, a suite of materials used in sample collection and processing were also analyzed to characterize their signatures. An n-alkane series ranging from C₁₈ to C₃₀with δ¹³C isotopic values of –30.9‰ to –28.8‰ was present in lithologically diverse samples. Multiple lines of evidence point to the rock saw used to remove core exteriors during sample processing as the source of these compounds. Many of the other sample-handling procedures designed to reduce surface contamination were determined to be effective and could be implemented in future projects. This result highlights the value of careful prevention and characterization of contamination to allow for more accurate interpretations of complex and dynamic subsurface processes, and the importance that future reports of these compounds occurs in conjunction with thorough contamination assessments.

Source: http://dx.doi.org/10.1016/j.orggeochem.2018.05.003

Publications > Journal Article

PeerJ

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

Authors: Angus Angermeyer, Sarah C. Crosby, Julie A. Huber

Published: May 1, 2018

C-DEBI Contribution Number: 426

Abstract

Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature.

Source: http://dx.doi.org/10.7717/peerj.4735

Publications > Journal Article

Frontiers in Microbiology

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

Authors: Michael F. Graw, Grace D’Angelo, Matthew Borchers, Andrew R. Thurber, Joel. E. Johnson, Chuanlun Zhang, Haodong Liu, Frederick S. Colwell

Published: April 11, 2018

C-DEBI Contribution Number: 423

Abstract

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

Source: http://dx.doi.org/10.3389/fmicb.2018.00729

Publications > Journal Article

Deep Sea Research Part I: Oceanographic Research Papers

Clusters of deep-sea egg-brooding octopods associated with warm fluid discharge: an ill-fated fragment of a larger, discrete population?

Authors: Anne. M. Hartwell, Janet. R. Voight, Charles Geoffrey Wheat

Published: March 28, 2018

C-DEBI Contribution Number: 419

Abstract

Benthic octopods cluster on bare rock on Dorado Outcrop, a ~3000 m deep basalt exposure. The outcrop hosts intermittent discharge of relatively cool (up to 12.3 °C) hydrothermal fluid that carries about half as much oxygen as bottom seawater (~54 μM vs. 108 μM). We analyzed 231 hours of video footage and still images taken by sub-sea vehicles in 2013 and 2014 that documented the clustered octopods, members of the poorly-known genus Muusoctopus. The largest cluster (102 octopods) occurred in a 19 m² area of fluid discharge, where the basalt was sediment-free; individual octopods were also seen across the outcrop. The clustered octopods appeared to be brooding eggs and a total of 11 egg clutches were confirmed. None of the 186 eggs closely examined showed embryonic development. The intermittent fluid discharge may clear the basalt of sediment and attract gravid octopods which then spawn. However, the increased temperature and limited oxygen of the discharging fluids may threaten the octopods’ survival. Octopods in/near areas of discharging fluid had significantly higher estimated respiration rates (3.1–9.8 contractions/minute) than did octopods away from discharging fluid (0.8–6.0 contractions/minute). Warm fluids likely increase the octopods’ metabolic rate and thus their oxygen demand but provide only limited oxygen. The resultant physiological stress is hypothesized to eventually kill eggs near fluid discharge. We hypothesize, because these eggs do not survive, the population is sustained by a larger pool of undetectable females that brood their eggs inside cool conduits of this and perhaps other, unstudied basalt outcrops.

Source: http://dx.doi.org/10.1016/j.dsr.2018.03.011

Publications > Journal Article

International Journal of Systematic and Evolutionary Microbiology

Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments

Authors: Rachel Chang, Lina. J. Bird, Casey Barr, Magdalena R. Osburn, Elizabeth Wilbanks, Kenneth H. Nealson, Annette R. Rowe

Published: March 23, 2018

C-DEBI Contribution Number: 420

Abstract

A taxonomic and physiologic characterization was carried out on Thioclava strain ElOx9T, which was isolated from a bacterial consortium enriched on electrodes poised at electron donating potentials. The isolate is Gram-negative, catalase-positive and oxidase-positive; the cells are motile short rods. The bacterium is facultatively anaerobic with the ability to utilize nitrate as an electron acceptor. Autotrophic growth with H₂ and S0 (oxidized to sulfate) was observed. The isolate also grows heterotrophically with organic acids and sugars. Growth was observed at salinities from 0 to 10% NaCl and at temperatures from 15 to 41 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs in the genus Thioclava ; it had the highest sequence similarity of 98.8 % to Thioclava atlantica 13D2W-2T, followed by Thioclava dalianensis DLFJ1-1T with 98.5 % similarity, Thioclava pacifica TL 2T with 97.7 % similarity, and then Thioclava indica DT23-4T with 96.9 %. All other sequence similarities were below 97 % to characterized strains. The digital DNA–DNA hybridization estimated when compared to T. atlantica 13D2W-2T, T. dalianensis DLFJ1-1T, T. pacifica TL 2T and T. indica DT23-4T were 15.8±2.1, 16.7+2.1, 14.3±1.9 and 18.3±2.1 %. The corresponding average nucleotide identity values between these strains were determined to be 65.1, 67.8, 68.4 and 64.4 %, respectively. The G+C content of the chromosomal DNA is 63.4 mol%. Based on these results, a novel species Thioclava electrotropha sp. nov. is proposed, with the type strain ElOx9T (=DSM 103712T=ATCC TSD-100T).

Source: http://dx.doi.org/10.1099/ijsem.0.002723

Publications > Journal Article

mBio

Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors

Authors: Annette R. Rowe, Pournami Rajeev, Abhiney Jain, Sahand Pirbadian, Akihiro Okamoto, Jeffrey A. Gralnick, Mohamed. Y. El-Naggar, Kenneth H. Nealson

Editors: Markus. W. Ribbe

Published: February 27, 2018

C-DEBI Contribution Number: 417

Abstract

While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes, Shewanella oneidensis MR-1 can also facilitate electron flow from a cathode to terminal electron acceptors, such as fumarate or oxygen, thereby providing a model system for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of S. oneidensis when oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells than in controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH₂) pool determined with a bioluminescence assay, a proton uncoupler, and a mutant of proton-pumping NADH oxidase complex I. This work suggested that the generation of NADH/FMNH₂ under cathodic conditions was linked to reverse electron flow mediated by complex I. A decrease in cathodic electron uptake was observed in various mutant strains, including those lacking the extracellular electron transfer components necessary for anodic-current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy acquisition, resulting in a quantifiable reduction in the cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence on cathodes, which might extend to environments where growth and division are severely limited.

Source: http://dx.doi.org/10.1128/mbio.02203-17

Publications > Journal Article

Frontiers in Microbiology

Bioenergetic Controls on Microbial Ecophysiology in Marine Sediments

Authors: James A. Bradley, Jan P. Amend, Douglas E. LaRowe

Published: February 13, 2018

C-DEBI Contribution Number: 415

Abstract

Marine sediments constitute one of the most energy-limited habitats on Earth, in which microorganisms persist over extraordinarily long timescales with very slow metabolisms. This habitat provides an ideal environment in which to study the energetic limits of life. However, the bioenergetic factors that can determine whether microorganisms will grow, lie dormant, or die, as well as the selective environmental pressures that determine energetic trade-offs between growth and maintenance activities, are not well understood. Numerical models will be pivotal in addressing these knowledge gaps. However, models rarely account for the variable physiological states of microorganisms and their demand for energy. Here, we review established modeling constructs for microbial growth rate, yield, maintenance, and physiological state, and then provide a new model that incorporates all of these factors. We discuss this new model in context with its future application to the marine subsurface. Understanding the factors that regulate cell death, physiological state changes, and the provenance of maintenance energy (i.e., endogenous versus exogenous metabolism), is crucial to the design of this model. Further, measurements of growth rate, growth yield, and basal metabolic activity will enable bioenergetic parameters to be better constrained. Last, biomass and biogeochemical rate measurements will enable model simulations to be validated. The insight provided from the development and application of new microbial modeling tools for marine sediments will undoubtedly advance the understanding of the minimum power required to support life, and the ecophysiological strategies that organisms utilize to cope under extreme energy limitation for extended periods of time.

Source: http://dx.doi.org/10.3389/fmicb.2018.00180

Publications > Journal Article

Geobiology

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles

Authors: Benjamin Kimball Harrison, A. Myrbo, B. E. Flood, Jake V. Bailey

Published: January 19, 2018

C-DEBI Contribution Number: 408

Abstract

The emplacement of subaqueous gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro-organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the buried La Jolla Canyon sediment–water interface reflect turbidite-induced changes to the geochemical environment. Species-level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1-cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low-energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.

Source: http://dx.doi.org/10.1111/gbi.12271

Publications > Journal Article

mBio

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

Authors: Holly L. Sewell, Anne-Kristen Kaster, Alfred M. Spormann

Editors: Colleen M. Cavanaugh, ,

Published: December 19, 2017

C-DEBI Contribution Number: 410

Abstract

The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi.

Source: http://dx.doi.org/10.1128/mbio.02022-17

Publications > Journal Article

npj Biofilms and Microbiomes

Carbonate-rich dendrolitic cones: insights into a modern analog for incipient microbialite formation, Little Hot Creek, Long Valley Caldera, California

Authors: James A. Bradley, Leslie. K. Daille, Christopher. B. Trivedi, Caitlin. L. Bojanowski, Blake. W. Stamps, Bradley. S. Stevenson, Heather. S. Nunn, Hope. A. Johnson, Sean. J. Loyd, William. M. Berelson, Frank. A. Corsetti, John R. Spear

Published: November 21, 2017

C-DEBI Contribution Number: 392

Abstract

Ancient putative microbial structures that appear in the rock record commonly serve as evidence of early life on Earth, but the details of their formation remain unclear. The study of modern microbial mat structures can help inform the properties of their ancient counterparts, but modern mineralizing mat systems with morphological similarity to ancient structures are rare. Here, we characterize partially lithified microbial mats containing cm-scale dendrolitic coniform structures from a geothermal pool (“Cone Pool”) at Little Hot Creek, California, that if fully lithified, would resemble ancient dendrolitic structures known from the rock record. Light and electron microscopy revealed that the cm-scale ‘dendrolitic cones’ were comprised of intertwined microbial filaments and grains of calcium carbonate. The degree of mineralization (carbonate content) increased with depth in the dendrolitic cones. Sequencing of 16S rRNA gene libraries revealed that the dendrolitic cone tips were enriched in OTUs most closely related to the genera Phormidium, Leptolyngbya, and Leptospira, whereas mats at the base and adjacent to the dendrolitic cones were enriched in Synechococcus. We hypothesize that the consumption of nutrients during autotrophic and heterotrophic growth may promote movement of microbes along diffusive nutrient gradients, and thus microbialite growth. Hour-glass shaped filamentous structures present in the dendrolitic cones may have formed around photosynthetically-produced oxygen bubbles—suggesting that mineralization occurs rapidly and on timescales of the lifetime of a bubble. The dendrolitic-conical structures in Cone Pool constitute a modern analog of incipient microbialite formation by filamentous microbiota that are morphologically distinct from any structure described previously. Thus, we provide a new model system to address how microbial mats may be preserved over geological timescales.

Source: http://dx.doi.org/10.1038/s41522-017-0041-2

Publications > Report

International Ocean Discovery Program Preliminary Report

International Ocean Discovery Program Expedition 370 Preliminary Report: Temperature Limit of the Deep Biosphere off Muroto

Authors: Victoria B. Heuer, Fumio Inagaki, Yuki Morono, Yusuke Kubo, Lena Maeda, Expedition 370 Scientists

Published: January 30, 2017

C-DEBI Contribution Number: 406

Abstract

International Ocean Discovery Program (IODP) Expedition 370 aimed to explore the limits of life in the deep subseafloor biosphere at a location where temperature increases with depth at an intermediate rate and exceeds the known temperature maximum of microbial life (~120°C) at the sediment/basement interface ~1.2 km below the seafloor. Drilling Site C0023 is located in the vicinity of Ocean Drilling Program (ODP) Sites 808 and 1174 at the protothrust zone in the Nankai Trough off Cape Muroto at a water depth of 4776 m. ODP Leg 190 in 2000, revealed the presence of microbial cells at Site 1174 to a depth of ~600 meters below seafloor (mbsf), which corresponds to an estimated temperature of ~70°C, and reliably identified a single zone of higher cell concentrations just above the décollement at around 800 mbsf, where temperature presumably reached 90°C; no cell count data was reported for other sediment layers in the 70°–120°C range, because the limit of manual cell count for low-biomass samples was not high enough. With the establishment of Site C0023, we aimed to detect and investigate the presence or absence of life and biological processes at the biotic–abiotic transition with unprecedented analytical sensitivity and precision. Expedition 370 was the first expedition dedicated to subseafloor microbiology that achieved time-critical processing and analyses of deep biosphere samples by simultaneous shipboard and shore-based investigations. Our primary objectives during Expedition 370 were to study the relationship between the deep subseafloor biosphere and temperature. We aimed to comprehensively study the factors that control biomass, activity, and diversity of microbial communities in a subseafloor environment where temperatures increase from ~2°C at the seafloor to ~120°C at the sediment/basement interface and thus likely encompasses the biotic–abiotic transition zone. We also aimed to determine geochemical, geophysical, and hydrogeological characteristics in sediment and the underlying basaltic basement and elucidate if the supply of fluids containing thermogenic and/or geogenic nutrient and energy substrates may support subseafloor microbial communities in the Nankai accretionary complex. To address these primary scientific objectives and questions, we penetrated 1180 m and recovered 112 cores across the sediment/basalt interface. More than 13,000 samples were collected, and selected samples were transferred to the Kochi Core Center by helicopter for simultaneous microbiological sampling and analysis in laboratories with a super-clean environment. Following the coring operations, a temperature observatory with 13 thermistor sensors was installed in the borehole to 863 mbsf.

Source: http://dx.doi.org/10.14379/iodp.pr.370.2017

Publications > Thesis

Ph.D. Thesis

Water radiolysis and chemical production rates near solid-water boundaries

Authors: Mary E. Dzaugis

Published: January 1, 2016

C-DEBI Contribution Number: 405

Abstract

Water radiolysis is the dissociation of water molecules by ionizing radiation from the decay of radionuclides. Primary products of water radiolysis include reactive chemicals, such as H₂ and H₂O₂. For this reason, radiolysis is studied in many domains, including nuclear waste, microbiology and planetary evolution. In order to understand the importance of radiolysis in many of these environments, accurate quantification of radiolytic production rates is vital. In this dissertation, I present a new quantitative model calculating radiolytic production rates at solid-water interfaces and apply it to understand the role that radiolysis plays in various environments. ^ This radiolytic model is the first to explicitly calculate radiolytic production due to α-, β- and γ-radiation near solid-water interfaces. We use this model to investigate the effects of radiolytic compounds on the dissolution rate of spent nuclear fuel. The production of rate of H₂ and H₂O₂, which control the dissolution rate of the fuel, depends on the amount and type of radiation surrounding breached nuclear spent fuel rods. Understanding the distribution of radiolytic products is important in assessing different hazards associated with spent fuel storage and the potential release of radionuclides into the environment. We find that in old (1000-year-old) spent fuel α-radiation dominates radiolysis, while β- and γ-radiation control the production rates near young (20-year-old) spent fuel.^ Radiolysis also is an important process in understanding the extent of life on Earth, as well as possibly providing a means for life on Mars. We investigate the significance of water radiolysis in sustaining microbial communities in Earth’s oceanic crust and the potential extent of radiolysis in wet martian environments (such as the ancient martian surface and the present martian subsurface). These two studies focus specifically on the production of radiolytic H₂ as an electron donor. H₂ is an important source of energy in these two environments where there other resources for microbes are limited. In the oceanic basaltic aquifer of the South Pacific Gyre, we find that radiolytic H₂ production yields depend largely on the width of fractures in basalt and on radionuclide concentrations. We show that in old seafloor (>10 Ma), where there are no other readily available electron donors, radiolytic H₂ may dominate and is able to support up to 10³ cells in the water adjacent to a square cm of basaltic fracture.^ The extent of water radiolysis on Mars can be determined for water-saturated martian environments, such as the ancient martian surface or the present martian subsurface. Using the fractured rock radiolytic model as well as a previously developed sediment radiolytic model, we calculate potential H₂ production rates for eleven martian lithologies assuming contact with water. The highest rates on Mars are for water-saturated material with the radionuclide concentrations of Acidalia Planitia, a region with surface materials that are enriched in uranium and thorium. We also calculate production rates for the eight proposed Mars 2020 landing sites, assuming water-saturated porosity. Radiolytic H₂ production rates calculated for wet martian sediment and water-filled microfractured rock are comparable to the range of rates calculated for Earth’s South Pacific basement basalt which is known to harbor low concentrations of microbial life.

Source: http://digitalcommons.uri.edu/dissertations/AAI10240698/

Publications > Journal Article

Elem Sci Anth

Microbial response to oil enrichment in Gulf of Mexico sediment measured using a novel long-term benthic lander system

Authors: Beth N. Orcutt, Laura L. Lapham, Jennifer Delaney, Neha Sarode, Kathleen. S. Marshall, Kelly. J. Whaley-Martin, Greg F. Slater, Charles Geoffrey Wheat, Peter R. Girguis

Published: April 19, 2017

C-DEBI Contribution Number: 404

Abstract

Weathered crude oil sank to the seafloor following the Deepwater Horizon disaster in 2010, removing this oil from further physical and photo-chemical degradation processes and leaving benthic processes as the mechanisms for altering and remediating this hydrocarbon source. To quantify potential microbial oil degradation rates at the seafloor, and associated changes in sediment microbial community structure and pore fluid composition, we used a benthic lander system to deploy novel sediment flow-through chambers at a natural hydrocarbon seep in the Gulf of Mexico (at a depth of 1226 m in lease block GC600) roughly 265 km southwest of the Deepwater Horizon wellhead (at 1500 m depth). Sediment amended with 20% unweathered crude oil had elevated rates of sulfate reduction over the course of the 5-month-long experiment as compared to an unamended control, yielding potential rates of sulfate reduction (600–800 mmol m^–2d^–1) among the highest measured in hydrocarbon-influenced seafloor sediment. Oil amendment also stimulated methane production towards the end of the experiment, and led to slightly higher cell densities without significant changes in microbial community structure, based on 16S rRNA gene sequence libraries and fatty acid profiles. Assuming a link between sulfate reduction and hydrocarbon degradation, these results suggest that electron acceptor availability may become limiting in heavily oiled deep-sea environments, resulting in minimal degradation of deposited oil. This study provides unique data on seafloor sediment responses to oil deposition, and reveals the value of using observatories to fill the gap in understanding deep-sea microbial processes, especially for ephemeral and stochastic events such as oil spills.

Source: http://dx.doi.org/10.1525/elementa.129

Publications > Journal Article

The ISME Journal

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

Authors: Benjamin J. Tully, Charles Geoffrey Wheat, Brian T. Glazer, Julie A. Huber

Published: November 3, 2017

C-DEBI Contribution Number: 395

Abstract

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb₃- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Source: http://dx.doi.org/10.1038/ismej.2017.187

Publications > Journal Article

Geochimica et Cosmochimica Acta

Influences of the Tonga Subduction Zone on seafloor massive sulfide deposits along the Eastern Lau Spreading Center and Valu Fa Ridge

Authors: Guy. N. Evans, Margaret K. Tivey, Jeffrey S. Seewald, Charles Geoffrey Wheat

Published: October 1, 2017

C-DEBI Contribution Number: 403

Abstract

This study investigates the morphology, mineralogy, and geochemistry of seafloor massive sulfide (SMS) deposits from six back-arc hydrothermal vent fields along the Eastern Lau Spreading Center (ELSC) and Valu Fa Ridge (VFR) in the context of endmember vent fluid chemistry and proximity to the Tonga Subduction Zone. To complement deposit geochemistry, vent fluid analyses of Cu, Zn, Ba, Pb and H_2,(aq)were completed to supplement existing data and enable thermodynamic calculations of mineral saturation states at in situ conditions. Results document southward increases in the abundance of mantle-incompatible elements in hydrothermal fluids (Ba and Pb) and SMS deposits (Ba, Pb, As, and Sb), which is also expressed in the abundance of barite (BaSO₄) and galena (PbS) in SMS deposits. These increases correspond to a decrease in distance between the ELSC/VFR and the Tonga Subduction Zone that correlates with a change in crustal lithology from back-arc basin basalt in the north to mixed andesite, rhyolite, and dacite in the south. Barite influences deposit morphology, contributing to the formation of horizontal flanges and squat terraces. Results are also consistent with a regional-scale lowering of hydrothermal reaction zone temperatures from north to south (except at the southernmost Mariner vent field) that leads to lower-temperature, higher-pH vent fluids relative to mid-ocean ridges of similar spreading rates (Mottl et al., 2011). These fluids are Cu- and Zn-poor and the deposits formed from these fluids are Cu-poor but Zn-rich. In contrast, at the Mariner vent field, higher-temperature and lower pH vent fluids are hypothesized to result from higher reaction zone temperatures and the localized addition of acidic magmatic volatiles (Mottl et al., 2011). The Mariner fluids are Cu- and Zn-rich and vent from SMS deposits that are rich in Cu but poor in Zn with moderate amounts of Pb. Thermodynamic calculations indicate that the contrasting metal contents of vent fluids and SMS deposits can be accounted for by vent fluid pH. Wurtzite/sphalerite ((Zn, Fe)S) and galena (PbS) are saturated at higher temperatures in higher-pH, Zn-, Cu-, and Pb-poor ELSC/VFR vent fluids, but are undersaturated at similar temperatures in low-pH, Zn-, Cu-, and Pb-rich vent fluids from the Mariner vent field.

Indicators of pH in the ELSC and VFR SMS deposits include the presence of co-precipitated wurtzite and chalcopyrite along conduit linings in deposits formed from higher pH fluids, and different correlations between concentrations of Zn and Ag in bulk geochemical analyses. Significant positive bulk geochemical Zn:Ag correlations occur for deposits at vent fields where hydrothermal fluids have a minimum pH (at 25 °C) < 3.3, while correlations of Zn:Ag are weak or negative for deposits at vent fields where the minimum vent fluid pH (at 25 °C) > 3.6. Data show that the compositions of the mineral linings of open conduit chimneys (minerals present, mol% FeS in (Zn,Fe)S) that precipitate directly from hydrothermal fluids closely reflect the temperature and sulfur fugacity of sampled hydrothermal fluids. These mineral lining compositions thus can be used as indicators of hydrothermal fluid temperature and composition (pH, metal content, sulfur fugacity).

Source: http://dx.doi.org/10.1016/j.gca.2017.08.010

Publications > Journal Article

Applied and Environmental Microbiology

Estimating population turnover rates from relative quantification methods reveals microbial dynamics in marine sediment

Authors: Richard T. Kevorkian, Jordan T. Bird, Alexander K. Shumaker, Karen G. Lloyd

Published: October 20, 2017

C-DEBI Contribution Number: 400

Abstract

Difficulty quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentration consistent with predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, for fraction of read abundance times cells), to estimate population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply-branching uncultured groups and ∼ 98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from quantitative PCR (qPCR) at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate reducing bacteria, Desulfovibrio sp., Desulfobacter sp., and Desulfobacterium sp. increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions only stimulates growth in a few clades directly involved in methanogenesis, rather than the whole microbial community.

Source: http://dx.doi.org/10.1128/aem.01443-17

Publications > Journal Article

Proceedings of the National Academy of Sciences

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

Authors: Elizabeth Trembath-Reichert, Yuki Morono, Akira Ijiri, Tatsuhiko Hoshino, Katherine. S. Dawson, Fumio Inagaki, Victoria J. Orphan

Published: October 3, 2017

C-DEBI Contribution Number: 389

Abstract

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of ¹³C- or ¹⁵N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.

Source: http://dx.doi.org/10.1073/pnas.1707525114

Publications > Journal Article

Geology

Alkaline vents and steep Na+ gradients from ridge-flank basalts—Implications for the origin and evolution of life

Authors: Roy E. Price, Eric Boyd, Tori M. Hoehler, Laura. M. Wehrmann, Erlendur Bogason, Hreiðar. Þór. Valtýsson, Jóhann Örlygsson, Bjarni Gautason, Jan P. Amend

Published: October 19, 2017

C-DEBI Contribution Number: 393

Abstract

Life may have emerged on early Earth in serpentinizing systems, where ultramafic rocks react with aqueous solutions to generate high levels of dissolved H₂ and CH₄ and, on meeting seawater, steep redox, ionic, and pH gradients. Most extant life harnesses energy as ion (e.g., H⁺, Na⁺) gradients across membranes, and it seems reasonable to suggest that environments with steep ion gradients would have also been important for early life forms. The Strytan Hydrothermal Field (SHF) is a mid-ocean ridge–flank submarine hydrothermal (~70 °C) vent in Iceland that produces steep Na⁺ (<3–468 mM) and pH (8.1–10.2) gradients, concomitant with enrichments in methane (0.5–1.4 μM) and hydrogen (0.1–5.2 μM), relative to seawater. Large (up to 55 m) saponite towers create ideal "incubators" similar to other proposed origin-of-life analogs (e.g., Lost City hydrothermal field in the mid-Atlantic). However, the SHF is basalt hosted. We suggest that the observed conditions are generated by (1) plagioclase hydrolysis, coupled with calcite precipitation, and (2) hydration of Mg in pyroxene and olivine in basalt. Along with microbial activity, aqueous reactions of Fe in olivine and pyroxene are possible sources of the observed H₂. Although the δ¹³C-CH₄ values were highly variable (–53‰ to –8‰), isotopically heavy CH₄ suggests possible abiotic formation or the imprint of methane oxidation. If environments similar to SHF occurred on the early Earth, they should be considered as potential origin-of-life environments.

Source: http://dx.doi.org/10.1130/g39474.1

Publications > Journal Article

The ISME Journal

Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov.

Authors: Jiro. F. Mori, Jarrod. J. Scott, Kevin W. Hager, Craig L. Moyer, Kirsten Küsel, David Emerson

Published: August 18, 2017

C-DEBI Contribution Number: 379

Abstract

Chemosynthetic Fe-oxidizing communities are common at diffuse-flow hydrothermal vents throughout the world’s oceans. The foundational members of these communities are the Zetaproteobacteria, a class of Proteobacteria that is primarily associated with ecosystems fueled by ferrous iron, Fe(II). We report here the discovery of two new isolates of Zetaproteobacteria isolated from the Mid-Atlantic Ridge (TAG-1), and the Mariana back-arc (SV-108), that are unique in that they can utilize either Fe(II) or molecular hydrogen (H2) as sole electron donor and oxygen as terminal electron acceptor for growth. Both strains precipitated Fe-oxyhydroxides as amorphous particulates. The cell doubling time on H2 vs Fe(II) for TAG-1 was 14.1 vs 21.8 h, and for SV-108 it was 16.3 vs 20 h, and it appeared both strains could use either H2 or Fe(II) simultaneously. The strains were close relatives, based on genomic analysis, and both possessed genes for the uptake NiFe-hydrogenase required for growth on H2. These two strains belong to Zetaproteobacteria operational taxonomic unit 9 (ZetaOTU9). A meta-analysis of public databases found ZetaOTU9 was only associated with Fe(II)-rich habitats, and not in other environments where known H2-oxidizers exist. These results expand the metabolic repertoire of the Zetaproteobacteria, yet confirm that Fe(II) metabolism is the primary driver of their physiology and ecology.

Source: http://dx.doi.org/10.1038/ismej.2017.132

Publications > Journal Article

International Journal of Systematic and Evolutionary Microbiology

Sulfurovum riftiae sp. nov., a mesophilic, thiosulfate-oxidizing, nitrate-reducing chemolithoautotrophic epsilonproteobacterium isolated from the tube of the deep-sea hydrothermal vent polychaete Riftia pachyptila

Authors: Donato Giovannelli, Matthew Chung, Justin Staley, Costantino Vetriani, Valentin Starovoytov, Nadine Le Bris

Published: July 1, 2016

C-DEBI Contribution Number: 382

Abstract

An anaerobic, nitrate-reducing, sulfur- and thiosulfate-oxidizing bacterium, designated strain 1812ET, was isolated from the vent polychaete Riftia pachyptila, which was collected from a deep-sea hydrothermal vent on the East Pacific Rise. Cells were Gram-stain-negative rods, measuring approximately 1.05±0.11 µm by 0.40±0.05 µm. Strain 1812ET grew at 25 – –45 °C (optimum 35 °C), with 1.5–4.0 % (w/v) NaCl (optimum 3.0 %) and at pH 5.0–8.0 (optimum pH 6.0). The generation time under optimal conditions was 3 h. Strain 1812ET was an anaerobic chemolithotroph that grew with either sulfur or thiosulfate as the energy source and carbon dioxide as the sole carbon source. Nitrate was used as a sole terminal electron acceptor. The predominant fatty acids were C_16 : 1 ω7c, C_18 : 1 ω7c and C_16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 47.4 mol%. Phylogenetic analysis of the 16S rRNA gene of strain 1812ET showed that the isolate belonged to the Epsilonproteobacteria , and its closest relatives were Sulfurovum lithotrophicum 42BKTT and Sulfurovum aggregans Monchim 33T (98.3 and 95.7 % sequence similarity, respectively). DNA–DNA relatedness between strain 1812ET and the type strain of S. lithotrophicum was 29.7 %, demonstrating that the two strains are not members of the same species. Based on the phylogenetic, molecular, chemotaxonomic and physiological evidence, strain 1812ET represents a novel species within the genus Sulfurovum , for which the name Sulfurovum riftiae sp. nov. is proposed. The type strain is 1812ET (=DSM 101780T=JCM 30810T).

Source: http://dx.doi.org/10.1099/ijsem.0.001106

Publications > Journal Article

Deep Sea Research Part II: Topical Studies in Oceanography

Microbial biofilms associated with fluid chemistry and megafaunal colonization at post-eruptive deep-sea hydrothermal vents

Authors: Charles. E. O’Brien, Donato Giovannelli, Breea Govenar, George. W. Luther, Richard A. Lutz, Timothy. M. Shank, Costantino Vetriani

Published: November 1, 2015

C-DEBI Contribution Number: 386

Abstract

At deep-sea hydrothermal vents, reduced, super-heated hydrothermal fluids mix with cold, oxygenated seawater. This creates temperature and chemical gradients that support chemosynthetic primary production and a biomass-rich community of invertebrates. In late 2005/early 2006 an eruption occurred on the East Pacific Rise at 9°50′N, 104°17′W. Direct observations of the post-eruptive diffuse-flow vents indicated that the earliest colonizers were microbial biofilms. Two cruises in 2006 and 2007 allowed us to monitor and sample the early steps of ecosystem recovery. The main objective of this work was to characterize the composition of microbial biofilms in relation to the temperature and chemistry of the hydrothermal fluids and the observed patterns of megafaunal colonization. The area selected for this study had local seafloor habitats of active diffuse flow (in-flow) interrupted by adjacent habitats with no apparent expulsion of hydrothermal fluids (no-flow). The in-flow habitats were characterized by higher temperatures (1.6–25.2 °C) and H₂S concentrations (up to 67.3 µM) than the no-flow habitats, and the microbial biofilms were dominated by chemosynthetic Epsilonproteobacteria. The no-flow habitats had much lower temperatures (1.2–5.2 °C) and H₂S concentrations (0.3–2.9 µM), and Gammaproteobacteria dominated the biofilms. Siboglinid tubeworms colonized only in-flow habitats, while they were absent at the no-flow areas, suggesting a correlation between siboglinid tubeworm colonization, active hydrothermal flow, and the composition of chemosynthetic microbial biofilms.

Source: http://dx.doi.org/10.1016/j.dsr2.2015.07.020

Publications > Journal Article

Frontiers in Marine Science

Exploring the Relationship between Macrofaunal Biodiversity and Ecosystem Functioning in the Deep Sea

Authors: Elisa Baldrighi, Donato Giovannelli, Giuseppe D’Errico, Marc Lavaleye, Elena Manini

Published: June 28, 2017

C-DEBI Contribution Number: 381

Abstract

The global scale of the biodiversity crisis has stimulated research into the relationship between biodiversity and ecosystem functioning (BEF). Even though the deep sea is the largest biome on Earth, BEF studies in deep-sea benthic ecosystems are scant. Moreover, the small number of recent studies, which mostly focus on meiobenthic nematodes, report conflicting results that range from a very clear positive relationship to none at all. In this BEF study, the deep-sea macrofauna were used as a model to investigate the structural and functional diversity of macrofauna assemblages at three depths (1,200, 1,900, and 3,000 m) in seven open-slope systems from the North-Eastern Atlantic Ocean to the Central-Eastern Mediterranean Sea. The presence and nature of BEF relationships were studied considering two spatial scales, the large and the basin scale, in different environmental settings. Total benthic biomass and macrofaunal predator biomass were used as proxies to assess ecosystem functioning. Ecosystem efficiency was expressed as macrofaunal biomass to biopolymeric carbon content ratio, macrofaunal biomass to prokaryotic biomass ratio, macrofaunal biomass to meiofaunal biomass ratio, and meiofaunal biomass to prokaryotic biomass ratio. On both large and basin spatial scales, some significant relationships between macrofaunal diversity and ecosystem functioning and efficiency were reported. When significant, the nature of BEF relations was positive and exponential or linear supporting the general idea that a higher diversity can enhance ecosystem functioning. Other BEF relationships were explained by the effect of environmental variables. More data from different deep-sea systems are needed, to better elucidate the consequences of biodiversity loss on the ocean floor.

Source: http://dx.doi.org/10.3389/fmars.2017.00198

Publications > Journal Article

Frontiers in Microbiology

Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

Authors: Jessica. M. Labonté, Mark A. Lever, Katrina J. Edwards, Beth N. Orcutt

Published: August 2, 2017

C-DEBI Contribution Number: 370

Abstract

Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.

Source: http://dx.doi.org/10.3389/fmicb.2017.01434

Publications > Journal Article

Scientific Reports

Climate oscillations reflected within the microbiome of Arabian Sea sediments

Authors: William D. Orsi, Marco J. L. Coolen, Cornelia Wuchter, Lijun He, Kuldeep. D. More, Xabier Irigoien, Guillem Chust, Carl Johnson, Jordon. D. Hemingway, Mitchell Lee, Valier Galy, Liviu Giosan

Published: July 20, 2017

C-DEBI Contribution Number: 358

Abstract

Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.

Source: http://dx.doi.org/10.1038/s41598-017-05590-9

Publications > Journal Article

Geochimica et Cosmochimica Acta

Biogeochemical N signatures from rate-yield trade-offs during in vitro chemosynthetic NO 3 - reduction by deep-sea vent ε-Proteobacteria and Aquificae growing at different temperatures

Authors: Ileana Pérez-Rodríguez, Stefan M. Sievert, Marilyn. L. Fogel, Dionysis I. Foustoukos

Published: May 1, 2017

C-DEBI Contribution Number: 238

Abstract

NO₃^- reduction is a metabolism that is widespread among ε-Proteobacteria and Aquificae, two abundant classes of microorganisms found at deep-sea vents. In this study, we used Sulfurovum lithotrophicum, Caminibacter mediatlanticus and Thermovibrio ammonificans as representatives of these groups to study ecophysiological, metabolic and biogeochemical parameters associated with chemolithoautotrophic NO₃^- reduction under different temperature regimes. We observed that while S. lithotrophicum and C. mediatlanticus achieved higher cell densities than T. ammonificans, the overall NO₃^- consumption by the latter was on average ∼ 9 and ∼ 5 times faster on a per cell basis, respectively. Comparison with previously published data from other cultured vent ε-Proteobacteria and Aquificae suggests that the rate-yield trade-offs observed in our experiments are generally conserved between these two groups in line with their ecophysiologies. Kinetic isotope effects of N from NO₃^- reduction were 9.6 ± 2.7 ‰ for S. lithotrophicum, 6.4 ± 0.7 ‰ for C. mediatlanticus and 8.8 ± 0.6 ‰ for T. ammonificans. Our results help evaluate how metabolic partitioning between growth efficiency and reaction kinetics during chemolithoautotrophic NO₃^- reduction affect the concentration and isotope composition of N compounds at deep-sea hydrothermal vents.

Source: http://dx.doi.org/10.1016/j.gca.2017.05.014

Publications >

eLife

Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans

Authors: Donato Giovannelli, Stefan M. Sievert, Michael Hügler, Stephanie Markert, Dörte Becher, Thomas Schweder, Costantino Vetriani

Published: April 24, 2017

C-DEBI Contribution Number: 368

Abstract

Anaerobic thermophiles inhabit relic environments that resemble the early Earth. However, the lineage of these modern organisms co-evolved with our planet. Hence, these organisms carry both ancestral and acquired genes and serve as models to reconstruct early metabolism. Based on comparative genomic and proteomic analyses, we identified two distinct groups of genes in Thermovibrio ammonificans: the first codes for enzymes that do not require oxygen and use substrates of geothermal origin; the second appears to be a more recent acquisition, and may reflect adaptations to cope with the rise of oxygen on Earth. We propose that the ancestor of the Aquificae was originally a hydrogen oxidizing, sulfur reducing bacterium that used a hybrid carbon fixation pathway for CO₂fixation. With the gradual rise of oxygen in the atmosphere, more efficient terminal electron acceptors became available and this lineage acquired genes that increased its metabolic flexibility while retaining ancestral metabolic traits.

Source: http://dx.doi.org/10.7554/elife.18990

Publications > Journal Article

Geobiology

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations

Authors: M. S. Bray, J. Wu, B. C. Reed, Cecilia Batmalle Kretz, K. M. Belli, R. L. Simister, C. Henny, Frank J. Stewart, T. J. DiChristina, J. A. Brandes, D. A. Fowle, Sean A. Crowe, Jennifer B. Glass

Published: April 17, 2017

C-DEBI Contribution Number: 365

Abstract

Reactive Fe(III) minerals can influence methane (CH₄) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH₄ oxidation. The balance between Fe(III) reduction, methanogenesis, and CH₄oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH₄ fluxes to the atmosphere, thereby regulating the capacity for CH₄ to warm the early Earth under the Faint Young Sun. We studied CH₄ and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH₄ oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH₄ production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH₄ oxidation, although some incubations displayed CH₄-stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH₄ as a greenhouse gas throughout the first half of Earth history.

Source: http://dx.doi.org/10.1111/gbi.12239

Publications > Journal Article

Environmental Microbiology

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria

Authors: Nagissa Mahmoudi, Steven. R. Beaupré, Andrew D. Steen, Ann Pearson

Published: March 1, 2017

C-DEBI Contribution Number: 366

Abstract

Aquatic sediments harbor diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic-rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO₂ production rates, as well as sequential sampling of isotopic signatures (δ¹³C, Δ¹⁴C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton-derived compounds were degraded first, followed by petroleum-derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations. This article is protected by copyright. All rights reserved.

Source: http://dx.doi.org/10.1111/1462-2920.13745

Publications > Journal Article

Frontiers in Earth Science

Microbial and Biogeochemical Dynamics in Glacier Forefields Are Sensitive to Century-Scale Climate and Anthropogenic Change

Authors: James A. Bradley, Alexandre. M. Anesio, Sandra Arndt

Published: April 3, 2017

C-DEBI Contribution Number: 363

Abstract

The recent retreat of glaciers and ice sheets as a result of global warming exposes forefield soils that are rapidly colonized by microbes. These ecosystems are dominant in high-latitude carbon and nutrient cycles as microbial activity drives biogeochemical transformations within these newly exposed soils. Despite this, little is known about the response of these emerging ecosystems and associated biogeochemical cycles to projected changes in environmental factors due to human impacts. Here, we applied the model SHIMMER to quantitatively explore the sensitivity of biogeochemical dynamics in the forefield of Midtre Lovénbreen, Svalbard, to future changes in climate and anthropogenic forcings including soil temperature, snow cover, and nutrient and organic substrate deposition. Model results indicated that the rapid warming of the Arctic, as well as an increased deposition of organic carbon and nutrients, may impact primary microbial colonizers in Arctic soils. Warming and increased snow-free conditions resulted in enhanced bacterial production and an accumulation of biomass that was sustained throughout 200 years of soil development. Nitrogen deposition stimulated growth during the first 50 years of soil development following exposure. Increased deposition of organic carbon sustained higher rates of bacterial production and heterotrophic respiration leading to decreases in net ecosystem production and thus net CO₂ efflux from soils. Pioneer microbial communities were particularly susceptible to future changes. All future climate simulations encouraged a switch from allochthonously-dominated young soils (<40 years) to microbially-dominated older soils, due to enhanced heterotrophic degradation of organic matter. Critically, this drove remineralisation and increased nutrient availability. Overall, we show that human activity, especially the burning of fossil fuels and the enhanced deposition of nitrogen and organic carbon, has the potential to considerably affect the biogeochemical development of recently exposed Arctic soils in the present day and for centuries into the future. These effects must be acknowledged when attempting to make accurate predictions of the future fate of Arctic soils that are exposed over large expanses of presently ice-covered regions.

Source: http://journal.frontiersin.org/article/10.3389/feart.2017.00026/full

Publications > Journal Article

Environmental Microbiology

In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring

Authors: Annette R. Rowe, Miho Yoshimura, Douglas E. LaRowe, Lina. J. Bird, Jan P. Amend, Kazuhito Hashimoto, Kenneth H. Nealson, Akihiro Okamoto

Published: March 1, 2017

C-DEBI Contribution Number: 364

Abstract

Serpentinization is a geologic process that produces highly reduced, hydrogen-rich fluids that support microbial communities under high pH conditions. We investigated the activity of microbes capable of extracellular electron transfer in a terrestrial serpentinizing system known as “The Cedars”. Measuring current generation with an on-site two-electrode system, we observed daily oscillations in current with the current maxima and minima occurring during daylight hours. Distinct members of the microbial community were enriched. Current generation in lab-scale electrochemical reactors did not oscillate, but was correlated with carbohydrate amendment in Cedars-specific minimal media. Gammaproteobacteria and Firmicutes were consistently enriched from lab electrochemical systems on δ-MnO₂ and amorphous Fe(OH)₃ at pH 11. However, isolation of an electrogenic strain proved difficult as transfer cultures failed to grow after multiple rounds of media transfer. Lowering the bulk pH in the media allowed us to isolate a Firmicutes strain (Paenibacillus sp.). This strain was capable of electrode and mineral reduction (including magnetite) at pH 9. This report provides evidence of the in situ activity of microbes using extracellular substrates as sinks for electrons at The Cedars, but also highlights the potential importance of community dynamics for supporting microbial life through either carbon fixation and/or moderating pH stress.

Source: http://dx.doi.org/10.1111/1462-2920.13723

Publications > Journal Article

Nature Microbiology

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea

Authors: Blair Paul, David Burstein, Cindy. J. Castelle, Sumit Handa, Diego Arambula, Elizabeth Czornyj, Brian. C. Thomas, Partho Ghosh, Jeff. F. Miller, Jillian. F. Banfield, David Valentine

Published: April 3, 2017

C-DEBI Contribution Number: 361

Abstract

Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.

Source: http://dx.doi.org/10.1038/nmicrobiol.2017.45

Publications > Monograph

Ph.D. Thesis

Geochemical controls on the distribution and composition of biogenic and sedimentary carbon

Authors: Emily R. Estes

Published: February 1, 2017

C-DEBI Contribution Number: 359

Abstract

Organic carbon (OC) preserved in marine sediments acts as a reduced carbon sink that balances the global carbon cycle. Understanding the biogeochemical mechanisms underpinning the balance between OC preservation and degradation is thus critical both to quantifying this carbon reservoir and to estimating the extent of life in the deep subsurface biosphere. This work utilizes bulk and spatially-resolved X-ray absorption spectroscopy to characterize the OC content and composition of various environmental systems in order to identify the role of minerals and surrounding geochemistry in organic carbon preservation in sediments. Biogenic manganese (Mn) oxides formed either in pure cultures of Mn-oxidizing microorganisms, in incubations of brackish estuarine waters, or as ferromanganese deposits in karstic cave systems rapidly associate with OC following precipitation. This association is stable despite Mn oxide structural ripening, suggesting that mineral-associated OC could persist during early diagenetic reactions. OC associated with bacteriogenic Mn oxides is primarily proteinaceous, including intact proteins involved in Mn oxidation and likely oxide nucleation and aggregation. Pelagic sediments from 16 sites underlying the South Pacific and North Atlantic gyres and spanning a gradient of sediment age and redox state were analyzed in order to contrast the roles of oxygen exposure, OC recalcitrance, and mineral-based protection of OC as preservation mechanisms. OC and nitrogen concentrations measured at these sites are among the lowest globally (<0.1%) and, to a first order, scale with sediment oxygenation. In the deep subsurface, however, molecular recalcitrance becomes more important than oxygen exposure time in protecting OC against remineralization. Deep OC consists of primarily amide and carboxylic carbon in a scaffolding of aliphatic and O-alkyl moieties, corroborating the extremely low C/N values observed. These findings suggest that microbes in oxic pelagic sediments are carbon-limited and may preferentially remove carbon relative to nitrogen from the organic matter pool. As a whole, this work documents how interactions with mineral surfaces and exposure to oxygen generate a reservoir of OC stabilized in sediments on at least 25-million year time scales.

Source: http://dx.doi.org/10.1575/1912/8762

Publications > Journal Article

Limnology and Oceanography: Methods

A new solution 31P NMR sample preparation scheme for marine sediments

Authors: Delphine Defforey, Barbara J. Cade-Menun, Adina Paytan

Published: February 1, 2017

C-DEBI Contribution Number: 353

Abstract

A new approach for the preparation of marine sediment samples for solution ³¹P nuclear magnetic resonance spectroscopy (³¹P NMR) has been developed and tested. This approach addresses important aspects associated with sample pretreatments for marine sediments, including the effects of sample pretreatment on sedimentary P composition. The method increases the signals of low abundance P species in ³¹P NMR spectra by quantitatively and precisely removing up to 80% of inorganic P (orthophosphate) from sediment samples while causing minimal alteration of the chemical structure of organic P compounds. This method uses a reductive step to solubilize P bound to iron oxyhydroxides, followed by a low pH digestion to extract P from authigenic and biogenic apatite, as well as P bound to calcium carbonate. These P forms combined represent the most abundant inorganic P reservoir in marine sediments. The sample residue is then extracted in an alkaline solvent, 0.25 M NaOH with 0.05 M Na₂EDTA, and processed for ³¹P NMR spectroscopy. The method was tested on natural marine sediment samples from different localities with high inorganic P content (>85% molybdate reactive P), and allowed for the detection of orthophosphate monoesters and pyrophosphate in samples for which only an orthophosphate signal could be resolved with an NaOH-EDTA extraction alone. This new approach will allow the use of ³¹P NMR on samples for which low organic P concentrations previously hindered the use of this tool, and will help answer longstanding question regarding the fate of organic P in marine sediments.

Source: http://dx.doi.org/10.1002/lom3.10166

Publications > Journal Article

mBio

Viruses in the Oceanic Basement

Authors: Olivia Nigro, Sean P. Jungbluth, Huei-Ting Lin, Chih-Chiang Hsieh, Jaclyn. A. Miranda, Christopher. R. Schvarcz, Michael S. Rappé, Grieg Steward

Editors: Stephen J. Giovannoni

Published: March 7, 2017

C-DEBI Contribution Number: 354

Abstract

Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 10⁵ to 2 × 10⁵ ml⁻¹ (n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome.

IMPORTANCE The hydrothermally active ocean basement is voluminous and likely provided conditions critical to the origins of life, but the microbiology of this vast habitat is not well understood. Viruses in particular, although integral to the origins, evolution, and ecology of all life on earth, have never been documented in basement fluids. This report provides the first estimate of free virus particles (virions) within fluids circulating through the extrusive basalt of the seafloor and describes the morphological and genetic signatures of basement viruses. These data push the known geographical limits of the virosphere deep into the ocean basement and point to a wealth of novel viral diversity, exploration of which could shed light on the early evolution of viruses.

This paper is dedicated to the late James P. Cowen, whose collegiality, infectious enthusiasm for science, and pioneering studies of the ocean basement microbiome inspired the work.

Source: http://dx.doi.org/10.1128/mbio.02129-16

Publications > Journal Article

Geochimica et Cosmochimica Acta

The relative abundances of resolved ^l2CH₂D₂ and ^13CH₃D and mechanisms controlling isotopic bond ordering in abiotic and biotic methane gases

Published: April 1, 2017

C-DEBI Contribution Number: 362

Abstract

We report measurements of resolved ¹²CH₂D₂ and ¹³CH₃D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve ¹²CH₂D₂ from ¹³CH₃D provides unprecedented insights into the origin and evolution of CH₄. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ¹²CH₂D₂ and Δ¹³CH₃D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH₄/H₂ D/H exchange, underscoring the importance of reliable thermometry based on the CH₄ molecules themselves. Where Δ¹²CH₂D₂ and Δ¹³CH₃D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide novel information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis vs. biological processes. Deficits in ¹²CH₂D₂ compared with equilibrium values in CH₄ gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in ¹³CH₃D that accompany the low ¹²CH₂D₂ abundances produced by abiotic reactions. The tunneling signature may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ¹²CH₂D₂ values are a key tracer of microbial recycling.

Source: http://dx.doi.org/10.1016/j.gca.2016.12.041

Publications > Journal Article

Frontiers in Earth Science

Improved Measurement of Extracellular Enzymatic Activities in Subsurface Sediments Using Competitive Desorption Treatment

Authors: Adrienne Hoarfrost, Rachel Snider, Carol Arnosti

Published: February 16, 2017

C-DEBI Contribution Number: 355

Abstract

Extracellular enzymatic activities initiate microbially-driven heterotrophic carbon cycling in subsurface sediments. While measurement of hydrolytic activities in sediments is fundamental to our understanding of carbon cycling, these measurements are often technically difficult due to sorption of organic substrates to the sediment matrix. Most methods that measure hydrolysis of organic substrates in sediments rely on recovery of a fluorophore or fluorescently-labeled target substrate from a sediment incubation. The tendency for substrates to sorb to sediments results in lower recovery of an added substrate, and can result in data that are unusable or difficult to interpret. We developed a treatment using competitive desorption of a fluorescently-labeled, high molecular weight organic substrate that improves recovery of the labeled substrate from sediment subsamples. Competitive desorption treatment improved recovery of the fluorescent substrate by a median of 66%, expanded the range of sediments for which activity measurements could be made, and was effective in sediments from a broad range of geochemical contexts. More reliable measurements of hydrolytic activities in sediments will yield usable and more easily interpretable data from a wider range of sedimentary environments, enabling better understanding of microbially-catalyzed carbon cycling in subsurface environments.

Source: http://dx.doi.org/10.3389/feart.2017.00013

Publications > Journal Article

FEMS Microbiology Ecology

Inter-laboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347)

Authors: Joy Buongiorno, Stephanie Turner, Gordon Webster, Masanori Asai, Alexander K. Shumaker, Taylor Roy, Andrew Weightman, Axel Schippers, Karen G. Lloyd

Published: January 18, 2017

C-DEBI Contribution Number: 341

Abstract

Two common quantification methods for subseafloor microorganisms are catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and quantitative PCR (qPCR). Using these methods, we quantified Bacteria and Archaea in Baltic Sea basin sediments (IODP Exp. 347) down to 90 mbsf, testing the following hypotheses in an inter-laboratory comparison: 1) proteinase K permeabilization of Archaeal cell walls increases CARD-FISH accuracy, and 2) qPCR varies by more than an order of magnitude between laboratories using similar protocols. CARD-FISH counts did not differ between permeabilization treatments, demonstrating that proteinase K did not increase accuracy of CARD-FISH counts. However, 91% of these counts were below the quantification limit of 1.3 × 10⁷ cells cm⁻³. For qPCR, data varied between laboratories, but were largely within the same order of magnitude if the same primers were used, with 88% of samples being above the quantification limit. Copy number values were elevated by preparing a sediment slurry before DNA extraction: 3.88 ×10⁶ to 2.34 ×10⁹ 16S rRNA gene copies cm⁻³ vs. 1.39 × 10⁷ to 1.87 × 10⁹ total cells cm⁻³. By qPCR, Bacteria were more abundant than Archaea, although they usually were within the same order of magnitude. Overall, qPCR is more sensitive than CARD-FISH, but both require optimization to consistently achieve both precision and accuracy.

Source: http://dx.doi.org/10.1093/femsec/fix007

Publications > Proceedings

Proceedings of the IODP

Data report: quantification of potential drilling contamination using perfluorocarbon tracer at IODP Expedition 329 sites

Authors: Justine Sauvage, Leah Lewis, Dennis Graham, Arthur J. Spivack, Steven L. D’Hondt

Published: January 30, 2017

C-DEBI Contribution Number: 335

Abstract

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 ng_PFT/g_sediment or 1.78 × 10^–3 µL_DF/g_sediment on average). We observed higher contamination values (i.e., 7.28 × 10^–3 ng_PFT/g_sediment or 6.98 × 10^–2 µL_DF/g_sediment 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 ng_PFT/g_sediment or 6.60 × 10^–1µL_DF/g_sediment on average). We observe no apparent correlation of sample PFT content to sediment lithology, degree of sediment disturbance, core section number, or porosity.

Source: http://dx.doi.org/10.2204/iodp.proc.329.204.2017

Publications > Journal Article

Archaea

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments

Authors: Leah D. Brandt, Christopher H. House

Published: October 23, 2016

C-DEBI Contribution Number: 352

Abstract

Sediments 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.

Source: http://dx.doi.org/10.1155/2016/2690329

Publications > Journal Article

Proceedings of the National Academy of Sciences

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

Published: November 21, 2016

C-DEBI Contribution Number: 340

Abstract

Subsurface 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.

Source: http://dx.doi.org/10.1073/pnas.1612244113

Publications > Journal Article

Frontiers in Microbiology

Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin

Authors: Frederick Dowell, Zena Cardman, Srishti Dasarathy, Matthias Y. Kellermann, Julius S. Lipp, S. Emil Ruff, Jennifer F. Biddle, Luke J. McKay, Barbara J. MacGregor, Karen G. Lloyd, Daniel B. Albert, Howard P. Mendlovitz, Kai-Uwe Hinrichs, Andreas P. Teske

Published: January 29, 2016

C-DEBI Contribution Number: 349

Abstract

The 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.

Source: http://dx.doi.org/10.3389/fmicb.2016.00017

Publications > Thesis

Ph.D. Thesis

Carbonate-Associated Microbial Ecology at Methane Seeps: Assemblage Composition, Response to Changing Environmental Conditions, and Implications for Biomarker Longevity

Authors: David Hamilton Case

Published: May 31, 2016

C-DEBI Contribution Number: 348

Abstract

Methane 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.

Source: http://thesis.library.caltech.edu/9776/

Publications > Journal Article

PeerJ

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

Authors: Elizabeth Trembath-Reichert, David Hamilton Case, Victoria J. Orphan

Published: April 18, 2016

C-DEBI Contribution Number: 345

Abstract

Methane 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.

Source: http://dx.doi.org/10.7717/peerj.1913

Publications > Thesis

Ph.D. Thesis

Molecular and geochemical insights into microbial life centimeters to kilometers below the seafloor

Authors: Elizabeth Trembath-Reichert

Published: May 26, 2016

C-DEBI Contribution Number: 344

Abstract

At 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.

Source: http://thesis.library.caltech.edu/9768/

Publications > Journal Article

The ISME Journal

Evolutionary tradeoffs in cellular composition across diverse bacteria

Authors: Christopher P. Kempes, Lawrence Wang, Jan P. Amend, John Doyle, Tori M. Hoehler

Published: April 5, 2016

C-DEBI Contribution Number: 342

Abstract

One 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.

Source: http://www.nature.com/ismej/journal/v10/n9/full/ismej201621a.html

Publications > Journal Article

Frontiers in Microbiology

Physiological Ecology of Microorganisms in Subglacial Lake Whillans

Authors: Trista J. Vick-Majors, Andrew C. Mitchell, Amanda M. Achberger, Brent C. Christner, John E. Dore, Alexander B. Michaud, Jill A. Mikucki, Alicia M. Purcell, Mark L. Skidmore, John C. Priscu

Published: October 27, 2016

C-DEBI Contribution Number: 337

Abstract

Subglacial 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.

Source: http://dx.doi.org/10.3389/fmicb.2016.01705

Publications > Journal Article

Frontiers in Microbiology

Assessing Marine Microbial Induced Corrosion at Santa Catalina Island, California

Authors: Gustavo A. Ramírez, Colleen L. Hoffman, Michael D. Lee, Ryan A. Lesniewski, Roman A. Barco, Arkadiy Garber, Brandy M. Toner, Charles Geoffrey Wheat, Katrina J. Edwards, Beth N. Orcutt

Published: October 25, 2016

C-DEBI Contribution Number: 336

Abstract

High 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.

Source: http://dx.doi.org/10.3389/fmicb.2016.01679

Publications > Journal Article

Marine Chemistry

Amorphous As-sulfide precipitates from the shallow-water hydrothermal vents off Milos Island (Greece)

Authors: A. Godelitsas, Roy E. Price, Thomas Pichler, Jan P. Amend, P. Gamaletsos, J. Göttlicher

Published: December 1, 2015

C-DEBI Contribution Number: 313

Abstract

Amorphous 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.

Source: http://dx.doi.org/10.1016/j.marchem.2015.09.004

Publications > Journal Article

Geochimica et Cosmochimica Acta

Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii

Authors: Jason B. Sylvan, Scott D. Wankel, Douglas E. LaRowe, Chawalit N. Charoenpong, Julie A. Huber, Craig L. Moyer, Katrina J. Edwards

Published: November 1, 2016

C-DEBI Contribution Number: 338

Abstract

The 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.

Source: http://dx.doi.org/10.1016/j.gca.2016.10.029

Publications > Journal Article

Lithos

Sulfur and carbon geochemistry of the Santa Elena peridotites: Comparing oceanic and continental processes during peridotite alteration

Authors: Esther M. Schwarzenbach, Benjamin C. Gill, Esteban Gazel, Pilar Madrigal

Published: May 1, 2016

C-DEBI Contribution Number: 334

Abstract

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 δ³⁴S_sulfide (up to + 23.1‰) and δ³⁴S_sulfatevalues (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.

Source: http://dx.doi.org/10.1016/j.lithos.2016.02.017

Publications > Journal Article

Frontiers in Microbiology

Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales

Authors: Jordan T. Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd

Published: August 5, 2016

C-DEBI Contribution Number: 332

Abstract

The 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.

Source: http://dx.doi.org/10.3389/fmicb.2016.01221

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