Sievert Stefan M.

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Sievert

First Name

Stefan M.

ORCID

0000-0002-9541-2707

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Now showing 1 - 20 of 47

Unexpected diversity of bacteria capable of carbon monoxide oxidation in a coastal marine environment, and contribution of the Roseobacter-cssociated clade to total CO oxidation

(American Society for Microbiology, 2006-03) Tolli, John D. ; Sievert, Stefan M. ; Taylor, Craig D.

The species diversity, phylogenetic affiliations, and physiological activity rates of carbon monoxide-oxidizing microorganisms were investigated, using new isolates from surface waters collected from the coast of New England and type strains from established collections. A direct isolation method allowed the simultaneous recovery of organisms with different growth rates and nutritional requirements and the identification of marine microorganisms that oxidize CO at an environmentally relevant concentration (42 nM CO). Isolates that oxidized CO at environmentally relevant rates (>4.5 x 10–11 nmol CO oxidized cell–1 h–1) were taxonomically diverse, with representatives in the alpha and gamma subclasses of the Proteobacteria and the phylum Bacteroidetes, and represent a hitherto unreported metabolic function for several diverse microbial types. Isolates and type strains having the greatest specific rates of CO metabolism (1.1 x 10–10 to 2.3 x 10–10 nmol CO oxidized cell–1 h–1) belonged to the Roseobacter-associated clade (RAC) of the alpha subclass of the Proteobacteria. By using triple-labeled slide preparations, differential counts of active CO-oxidizing RAC cells, total RAC cells, and total bacterial cell counts in environmental samples were obtained. RAC organisms were a major component of total cell numbers (36%). Based on the density of active CO-oxidizing RAC cells in natural samples and RAC-specific metabolic activities determined for pure cultures, active CO-oxidizing RAC cells may contribute up to 15% of the total CO oxidation occurring in coastal waters.
Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the ε subdivision of proteobacteria

(American Society for Microbiology, 2005-05) Hugler, Michael ; Wirsen, Carl O. ; Fuchs, Georg ; Taylor, Craig D. ; Sievert, Stefan M.

Based on 16S rRNA gene surveys, bacteria of the ε subdivision of proteobacteria have been identified to be important members of microbial communities in a variety of environments, and quite a few have been demonstrated to grow autotrophically. However, no information exists on what pathway of autotrophic carbon fixation these bacteria might use. In this study, Thiomicrospira denitrificans and Candidatus Arcobacter sulfidicus, two chemolithoautotrophic sulfur oxidizers of the ε subdivision of proteobacteria, were examined for activities of the key enzymes of the known autotrophic CO2 fixation pathways. Both organisms contained activities of the key enzymes of the reductive tricarboxylic acid cycle, ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase. Furthermore, no activities of key enzymes of other CO2 fixation pathways, such as the Calvin cycle, the reductive acetyl coenzyme A pathway, and the 3-hydroxypropionate cycle, could be detected. In addition to the key enzymes, the activities of the other enzymes involved in the reductive tricarboxylic acid cycle could be measured. Sections of the genes encoding the {alpha}- and ß-subunits of ATP citrate lyase could be amplified from both organisms. These findings represent the first direct evidence for the operation of the reductive tricarboxylic acid cycle for autotrophic CO2 fixation in {varepsilon}-proteobacteria. Since {varepsilon}-proteobacteria closely related to these two organisms are important in many habitats, such as hydrothermal vents, oxic-sulfidic interfaces, or oilfields, these results suggest that autotrophic CO2 fixation via the reductive tricarboxylic acid cycle might be more important than previously considered.
Spatiotemporal distribution of marine magnetotactic bacteria in a aeasonally stratified coastal salt pond

(American Society for Microbiology, 2004-10) Simmons, Sheri L. ; Sievert, Stefan M. ; Frankel, R. B. ; Bazylinski, D. A. ; Edwards, Katrina J.

The occurrence and distribution of magnetotactic bacteria (MB) were studied as a function of the physical and chemical conditions in meromictic Salt Pond, Falmouth, Mass., throughout summer 2002. Three dominant MB morphotypes were observed to occur within the chemocline. Small microaerophilic magnetite-producing cocci were present at the top of the chemocline, while a greigite-producing packet-forming bacterium occurred at the base of the chemocline. The distributions of these groups displayed sharp changes in abundance over small length scales within the water column as well as strong seasonal fluctuations in population abundance. We identified a novel, greigite-producing rod in the sulfidic hypolimnion that was present in relatively constant abundance over the course of the season. This rod is the first MB that appears to belong to the {gamma}-Proteobacteria, which may suggest an iron- rather than sulfur-based respiratory metabolism. Its distribution and phylogenetic identity suggest that an alternative model for the ecological and physiological role of magnetotaxis is needed for greigite-producing MB.
Bacterial diversity and successional patterns during biofilm formation on freshly exposed basalt surfaces at diffuse-flow deep-sea vents

(Frontiers Media, 2015-09-10) Gulmann, Lara K. ; Beaulieu, Stace E. ; Shank, Timothy M. ; Ding, Kang ; Seyfried, William E. ; Sievert, Stefan M.

Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4–293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9°50′ N vent field on the East Pacific Rise. Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern.
Submarine shallow-water fluid emissions and their geomicrobiological imprint: a global overview

(Frontiers Media, 2021-10-25) Caramanna, Giorgio ; Sievert, Stefan M. ; Bühring, Solveig I.

Submarine fluids emissions in the form of geothermal vents are widespread in a variety of geological settings ranging from volcanic to tectonically active areas. This overview aims to describe representative examples of submarine vents in shallow-water areas around the globe. The areas described include: Iceland, Azores, Mediterranean Sea (Italy and Greece), Caribbean, Baja California, Japan, Papua, New Zealand, Taiwan. Common and divergent characteristics in terms of origin and geochemistry of the emitted fluids and their impact on the indigenous organisms and the surrounding environment have been identified. In the hottest vents seawater concentration is common as well as some water vapor phase separation. Carbon dioxide is the most common gas often associated with compounds of sulfur and methane. In several vents precipitation of minerals can be identified in the surrounding sediments. The analyses of the microbial communities often revealed putative chemoautotrophs, with Campylobacteria abundantly present at many vents where reduced sulfur compounds are available. The techniques that can be used for the detection and quantification of underwater vents are also described, including geophysical and geochemical tools. Finally, the main geobiological effects due to the presence of the hydrothermal activity and the induced changes in water chemistry are assessed.
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans

(American Society for Microbiology, 2007-12-07) Sievert, Stefan M. ; Scott, Kathleen M. ; Klotz, Martin G. ; Chain, Patrick S. G. ; Hauser, Loren J. ; Hemp, James ; Hugler, Michael ; Land, Miriam L. ; Lapidus, Alla ; Larimer, Frank W. ; Lucas, Susan ; Malfatti, Stephanie A. ; Meyer, Folker ; Paulsen, Ian T. ; Ren, Qinghu ; Simon, Jörg ; USF Genomics Class

Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.
Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila

( 2006-11-14) Markert, Stephanie ; Arndt, Cordelia ; Felbeck, Horst ; Becher, Dorte ; Sievert, Stefan M. ; Hugler, Michael ; Albrecht, Dirk ; Robidart, Julie ; Bench, Shellie ; Feldman, Robert A. ; Hecker, Michael ; Schweder, Thomas

The bacterial endosymbiont of the deep-sea tube worm Riftia pachyptila has never been successfully cultivated outside its host. In the absence of cultivation data we have taken a proteomic approach based on the metagenome sequence to study the metabolism of this peculiar microorganism in detail. As one result, we found that three major sulfide oxidation proteins constitute ~12% of the total cytosolic proteome, highlighting the essential role of these enzymes for the symbiont’s energy metabolism. Unexpectedly, the symbiont uses the reductive tricarboxylic acid (TCA) cycle in addition to the previously identified Calvin cycle for CO2 fixation.
Relative importance of chemoautotrophy for primary production in a light exposed marine shallow hydrothermal system

(Frontiers Media, 2017-04-21) Gomez-Saez, Gonzalo V. ; Pop Ristova, Petra ; Sievert, Stefan M. ; Elvert, Marcus ; Hinrichs, Kai-Uwe ; Bühring, Solveig I.

The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.
The influence of near-surface sediment hydrothermalism on the TEX86 tetraether-lipid-based proxy and a new correction for ocean bottom lipid overprinting

(European Geosciences Union, 2022-09-15) Bentley, Jeremy N. ; Ventura, Gregory T. ; Walters, Clifford C. ; Sievert, Stefan M. ; Seewald, Jeffrey S.

The diversity and relative abundances of tetraether lipids produced by archaea and bacteria in soils and sediments are increasingly used to assess environmental change. For instance, the TetraEther indeX of 86 carbon atoms (TEX86), based on archaeal isoprenoidal glycerol dialkyl glycerol tetraether (iGDGT) lipids, is frequently applied to reconstruct past sea-surface temperatures (SSTs). Yet, it is unknown how the ratio fully responds to environmental and/or geochemical variations and if the produced signals are largely the adaptive response by Thaumarchaeota to oceanographic effects associated with climate or seasonal temperature changes in the upper water column. We present the results of a four push-core transect study of surface sediments collected along an environmental gradient at the Cathedral Hill hydrothermal-vent system in Guaymas Basin, Gulf of California. The transect crosses a region where advecting hydrothermal fluids reach 155 ∘C within the upper 21 cm below the seafloor (cm b.s.f.) close to the vent center to near-ambient conditions at the vent periphery. The recovered iGDGTs closest to the vent center experienced high rates of turnover with up to 94 % of the lipid pool being lost within the upper 21 cm b.s.f. Here, we show that the turnover is non-selective across TEX86 GDGT lipids and does not affect the ratio independently. However, as evident by TEX86 ratios being highly correlated to the Cathedral Hill vent sediment porewater temperatures (R2=0.84), the ratio can be strongly impacted by the combination of severe lipid loss coupled with the addition of in situ iGDGT production from archaeal communities living in the vent sediments. The resulting overprint produces absolute temperature offsets of up to 4 ∘C based on the TEX calibration relative to modern climate records of the region. The overprint is also striking given the flux of iGDGTs from the upper water column is estimated to be ∼ 93 % of the combined intact polar lipid (IPL) and core GDGT lipid pool initially deposited on the seafloor. A model to correct the overprint signal using IPLs is therefore presented that can similarly be applied to all near-surface marine sediment systems where calibration models or climate reconstructions are made based on the TEX86 measure.
In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device

(American Geophysical Union, 2011-06-21) Smith, Amy ; Popa, Radu ; Fisk, Martin ; Nielsen, Mark ; Wheat, C. Geoffrey ; Jannasch, Hans W. ; Fisher, Andrew T. ; Becker, Keir ; Sievert, Stefan M. ; Flores, Gilberto

The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge was used in the first long-term deployment of microbial enrichment flow cells using osmotically driven pumps in a subseafloor borehole. Three novel osmotically driven colonization systems with unidirectional flow were deployed in the borehole and incubated for 4 years to determine the microbial colonization preferences for 12 minerals and glasses present in igneous rocks. Following recovery of the colonization systems, we measured cell density on the minerals and glasses by fluorescent staining and direct counting and found some significant differences between mineral samples. We also determined the abundance of mesophilic and thermophilic culturable organotrophs grown on marine R2A medium and identified isolates by partial 16S or 18S rDNA sequencing. We found that nine distinct phylotypes of culturable mesophilic oligotrophs were present on the minerals and glasses and that eight of the nine can reduce nitrate and oxidize iron. Fe(II)-rich olivine minerals had the highest density of total countable cells and culturable organotrophic mesophiles, as well as the only culturable organotrophic thermophiles. These results suggest that olivine (a common igneous mineral) in seawater-recharged ocean crust is capable of supporting microbial communities, that iron oxidation and nitrate reduction may be important physiological characteristics of ocean crust microbes, and that heterogeneously distributed minerals in marine igneous rocks likely influence the distribution of microbial communities in the ocean crust.
The sulfur cycle

(Oceanography Society, 2007-06) Sievert, Stefan M. ; Kiene, Ronald P. ; Schultz-Vogt, Heide N.

The ocean represents a major reservoir of sulfur on Earth, with large quantities in the form of dissolved sulfate and sedimentary minerals (e.g., gypsum and pyrite). Sulfur occurs in a variety of valence states, ranging from –2 (as in sulfide and reduced organic sulfur) to +6 (as in sulfate). Sulfate is the most stable form of sulfur on today’s oxic Earth; weathering and leaching of rocks and sediments are its main sources to the ocean. In addition, the reduced inorganic forms of sulfur, with oxidation states of –2 and 0 (as in elemental sulfur) are quite common in anoxic environments, with sulfur compounds of mixed valence states (e.g., thiosulfate and polythionates) produced transiently. The natural release of volatile organic sulfur compounds from the ocean, mainly as dimethyl sulfide (DMS), transports sulfur from the ocean to terrestrial regions, and it also affects atmospheric chemistry and the climate system. While they remain very important, natural sulfur emissions have currently been overtaken by anthropogenic emissions, primarily from the burning of fossil fuels.
Pathways of carbon and energy metabolism of the epibiotic community associated with the deep-sea hydrothermal vent shrimp Rimicaris exoculata

(Public Library of Science, 2011-01-07) Hugler, Michael ; Petersen, Jillian M. ; Dubilier, Nicole ; Imhoff, Johannes F. ; Sievert, Stefan M.

The shrimp Rimicaris exoculata dominates the faunal biomass at many deep-sea hydrothermal vent sites at the Mid-Atlantic Ridge. In its enlarged gill chamber it harbors a specialized epibiotic bacterial community for which a nutritional role has been proposed. We analyzed specimens from the Snake Pit hydrothermal vent field on the Mid-Atlantic Ridge by complementing a 16S rRNA gene survey with the analysis of genes involved in carbon, sulfur and hydrogen metabolism. In addition to Epsilon- and Gammaproteobacteria, the epibiotic community unexpectedly also consists of Deltaproteobacteria of a single phylotype, closely related to the genus Desulfocapsa. The association of these phylogenetic groups with the shrimp was confirmed by fluorescence in situ hybridization. Based on functional gene analyses, we hypothesize that the Gamma- and Epsilonproteobacteria are capable of autotrophic growth by oxidizing reduced sulfur compounds, and that the Deltaproteobacteria are also involved in sulfur metabolism. In addition, the detection of proteobacterial hydrogenases indicates the potential for hydrogen oxidation in these communities. Interestingly, the frequency of these phylotypes in 16S rRNA gene clone libraries from the mouthparts differ from that of the inner lining of the gill chamber, indicating potential functional compartmentalization. Our data show the specific association of autotrophic bacteria with Rimicaris exoculata from the Snake Pit hydrothermal vent field, and suggest that autotrophic carbon fixation is contributing to the productivity of the epibiotic community with the reductive tricarboxylic acid cycle as one important carbon fixation pathway. This has not been considered in previous studies of carbon fixation and stable carbon isotope composition of the shrimp and its epibionts. Furthermore, the co-occurrence of sulfur-oxidizing and sulfur-reducing epibionts raises the possibility that both may be involved in the syntrophic exchange of sulfur compounds, which could increase the overall efficiency of this epibiotic community.
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2

(Public Library of Science (PLoS), 2006-11-14) Scott, Kathleen M. ; Sievert, Stefan M. ; Abril, Fereniki N. ; Ball, Lois A. ; Barrett, Chantell J. ; Blake, Rodrigo A. ; Boller, Amanda J. ; Chain, Patrick S. G. ; Clark, Justine A. ; Davis, Carisa R. ; Detter, Chris ; Do, Kimberly F. ; Dobrinski, Kimberly P. ; Faza, Brandon I. ; Fitzpatrick, Kelly A. ; Freyermuth, Sharyn K. ; Harmer, Tara L. ; Hauser, Loren J. ; Hugler, Michael ; Kerfeld, Cheryl A. ; Klotz, Martin G. ; Kong, William W. ; Land, Miriam L. ; Lapidus, Alla ; Larimer, Frank W. ; Longo, Dana L. ; Lucas, Susan ; Malfatti, Stephanie A. ; Massey, Steven E. ; Martin, Darlene D. ; McCuddin, Zoe ; Meyer, Folker ; Moore, Jessica L. ; Ocampo, Luis H. ; Paul, John H. ; Paulsen, Ian T. ; Reep, Douglas K. ; Ren, Qinghu ; Ross, Rachel L. ; Sato, Priscila Y. ; Thomas, Phaedra ; Tinkham, Lance E. ; Zeruth, Gary T.

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system

(Frontiers Media, 2019-06-12) Labonté, Jessica M. ; Pachiadaki, Maria G. ; Fergusson, Elizabeth ; McNichol, Jesse C. ; Grosche, Ashley ; Gulmann, Lara K. ; Vetriani, Costantino ; Sievert, Stefan M. ; Stepanauskas, Ramunas

Phage–host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage–host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host’s protection against toxic metals and antibacterial compounds.
Ancestral absence of electron transport chains in Patescibacteria and DPANN

(Frontiers Media, 2020-08-17) Beam, Jacob P. ; Becraft, Eric D. ; Brown, Julia M. ; Schulz, Frederik ; Jarett, Jessica K. ; Bezuidt, Oliver ; Poulton, Nicole J. ; Clark, Kayla ; Dunfield, Peter F. ; Ravin, Nikolai V. ; Spear, John R. ; Hedlund, Brian P. ; Kormas, Konstantinos Ar. ; Sievert, Stefan M. ; Elshahed, Mostafa S. ; Barton, Hazel A. ; Stott, Matthew B. ; Eisen, Jonathan A. ; Moser, Duane P. ; Onstott, Tullis C. ; Woyke, Tanja ; Stepanauskas, Ramunas

Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments

(Nature Research, 2022-04-22) Sievert, Stefan M. ; Bühring, Solveig I. ; Gulmann, Lara K. ; Hinrichs, Kai-Uwe ; Pop Ristova, Petra ; Gomez-Saez, Gonzalo V.

Hydrothermalism in coastal sediments strongly impacts biogeochemical processes and supports chemoautotrophy. Yet, the effect of fluid flow on microbial community composition and rates of chemoautotrophic production is unknown because rate measurements under natural conditions are difficult, impeding an assessment of the importance of these systems. Here, in situ incubations controlling fluid flow along a transect of three geochemically distinct locations at a shallow-water hydrothermal system off Milos (Greece) show that Campylobacteria dominated chemoautotrophy in the presence of fluid flow. Based on injected 13C-labelled dissolved inorganic carbon and its incorporation into fatty acids, we constrained carbon fixation to be as high as 12 µmol C cm−3 d−1, corresponding to areal rates up to 10-times higher than previously reported for coastal sediments, and showed the importance of fluid flow for supplying the necessary substrates to support chemoautotrophy. Without flow, rates were substantially lower and microbial community composition markedly shifted. Our results highlight the importance of fluid flow in shaping the composition and activity of microbial communities of shallow-water hydrothermal vents, identifying them as hotspots of microbial productivity.
Prolonged recovery time after eruptive disturbance of a deep-sea hydrothermal vent community

(The Royal Society, 2020-12-23) Mullineaux, Lauren S. ; Mills, Susan W. ; Le Bris, Nadine ; Beaulieu, Stace E. ; Sievert, Stefan M. ; Dykman, Lauren

Deep-sea hydrothermal vents are associated with seafloor tectonic and magmatic activity, and the communities living there are subject to disturbance. Eruptions can be frequent and catastrophic, raising questions about how these communities persist and maintain regional biodiversity. Prior studies of frequently disturbed vents have led to suggestions that faunal recovery can occur within 2–4 years. We use an unprecedented long-term (11-year) series of colonization data following a catastrophic 2006 seafloor eruption on the East Pacific Rise to show that faunal successional changes continue beyond a decade following the disturbance. Species composition at nine months post-eruption was conspicuously different than the pre-eruption ‘baseline' state, which had been characterized in 1998 (85 months after disturbance by the previous 1991 eruption). By 96 months post-eruption, species composition was approaching the pre-eruption state, but continued to change up through to the end of our measurements at 135 months, indicating that the ‘baseline' state was not a climax community. The strong variation observed in species composition across environmental gradients and successional stages highlights the importance of long-term, distributed sampling in order to understand the consequences of disturbance for maintenance of a diverse regional species pool. This perspective is critical for characterizing the resilience of vent species to both natural disturbance and human impacts such as deep-sea mining.
Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist

(Society for Applied Microbiology, 2022-03-07) Chen, Song-Can ; Ji, Jiaheng ; Popp, Denny ; Jaekel, Ulrike ; Richnow, Hans-Hermann ; Sievert, Stefan M. ; Musat, Florin

The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO2 via beta oxidation and the oxidative Wood–Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps.
Dissolved organic carbon compounds in deep-sea hydrothermal vent fluids from the East Pacific Rise at 9°50′N

( 2018-08) Longnecker, Krista ; Sievert, Stefan M. ; Sylva, Sean P. ; Seewald, Jeffrey S. ; Kujawinski, Elizabeth B.

Deep-sea hydrothermal vents are unique ecosystems that may release chemically distinct dissolved organic matter to the deep ocean. Here, we describe the composition and concentrations of polar dissolved organic compounds observed in low and high temperature hydrothermal vent fluids at 9°50’N on the East Pacific Rise. The concentration of dissolved organic carbon was 46 μM in the low temperature hydrothermal fluids and 14 μM in the high temperature hydrothermal fluids. In the low temperature vent fluids, quantifiable dissolved organic compounds were dominated by water-soluble vitamins and amino acids. Derivatives of benzoic acid and the organic sulfur compound 2,3-dihydroxypropane-1-sulfonate (DHPS) were also present in low and high temperature hydrothermal fluids. The low temperature vent fluids contain organic compounds that are central to biological processes, suggesting that they are a by-product of biological activity in the subseafloor. These compounds may fuel heterotrophic and other metabolic processes at deep-sea hydrothermal vents and beyond.
Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont

(BioMed Central, 2017-09-02) Ponnudurai, Ruby ; Sayavedra, Lizbeth ; Kleiner, Manuel ; Heiden, Stefan E. ; Thürmer, Andrea ; Felbeck, Horst ; Schlüter, Rabea ; Sievert, Stefan M. ; Daniel, Rolf ; Schweder, Thomas ; Markert, Stephanie

Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics. In this study, we report the first draft genome sequence of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045 protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation. Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates oxaloacetate and succinate were absent, suggesting that these intermediates may be substituted by metabolites from external sources. We also detected a repertoire of genes associated with cell surface adhesion, bacteriotoxicity and phage immunity, which may perform symbiosis-specific roles in the B. thermophilus symbiosis.

Sievert Stefan M.

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