Pan-Genome Analyses Identify Lineage- and Niche-Specific Markers of Evolution and Adaptation in \u3cem\u3eEpsilonproteobacteria\u3c/em\u3e

The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is imposed by the potential existence of taxonomic boundaries. The analyses of pan-genomes has also defined a set of universally conserved core genes, based on which a phylogenetic tree was constructed to confirm that thermophilic species from deep-sea hydrothermal vents represent the most ancient lineages of Epsilonproteobacteria. Moreover, by comparing the flexible genome of a chemoautotrophic deep-sea vent species to (1) genomes of species belonging to the same genus, but inhabiting different environments, and (2) genomes of other vent species, but belonging to different genera, we were able to delineate the relative importance of lineage-specific versus niche-specific genes. This result not only emphasizes the overall importance of phylogenetic proximity in shaping the variable part of the genome, but also highlights the adaptive functions of niche-specific genes. Overall, by modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria

Chemoautotrophy at deep-sea vents : past, present, and future

Author Posting. © The Oceanography Society, 2012. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 25, no. 1 (2012): 218–233, doi:10.5670/oceanog.2012.21.Chemolithoautotrophic microorganisms are at the nexus of hydrothermal systems by effectively transferring the energy from the geothermal source to the higher trophic levels. While the validity of this conceptual framework is well established at this point, there are still significant gaps in our understanding of the microbiology and biogeochemistry of deep-sea hydrothermal systems. Important questions in this regard are: (1) How much, at what rates, and where in the system is organic carbon being produced? (2) What are the dominant autotrophs, where do they reside, and what is the relative importance of free-swimming, biofilm-forming, and symbiotic microbes? (3) Which metabolic pathways are they using to conserve energy and to fix carbon? (4) How does community-wide gene expression in fluid and biofilm communities compare? and (5) How efficiently is the energy being utilized, transformed into biomass, and transferred to higher trophic levels? In particular, there is currently a notable lack of process-oriented studies that would allow an assessment of the larger role of these ecosystems in global biogeochemical cycles. By combining the presently available powerful "omic" and single-cell tools with thermodynamic modeling, experimental approaches, and new in situ instrumentation to measure rates and concentrations, it is now possible to bring our understanding of these truly fascinating ecosystems to a new level and to place them in a quantitative framework and thus a larger global context.This review was written with support from NSF grants OCE-1136727, OCE-1038131, and OCE-1131095 (SMS) and OCE-1136451 (CV). Research mentioned in the review that was carried out in the labs of CV and SMS was supported by NSF grants MCB-0843678 (CV) and OCE-0452333 (SMS)

The sulfur cycle

Author Posting. © Oceanography Society, 2007. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 20, 2 (2007): 117-123.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.Preparation of this manuscript was partially supported by National Science Foundation grant OCE-0452333 and a fellowship from the Hanse- Wissenschaftskolleg (http://www. h-w-k.de) to SMS, National Science Foundation grants OPP-0230497 and OPP-0083078 to RPK, as well as the Research Center Ocean Margins (RCOM) of the University of Bremen (Germany) to HNSV (RCOM-Nr. 0476)

Genus-specific carbon fixation activity measurements reveal distinct responses to oxygen among hydrothermal vent campylobacteria

Author Posting. © American Society for Microbiology, 2022. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 88(2),(2022): e02083-21, https://doi.org/10.1128/AEM.02083-21.Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (previously Epsilonproteobacteria) often dominate the microbial community and that three genera, Arcobacter, Sulfurimonas, and Sulfurovum, frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances.This research was funded by the U.S. National Science Foundation grants OCE-1131095 (S.M.S.) and OCE-1136727 (S.M.S., J.S.S.). Further support was provided by the WHOI Investment in Science Fund (S.M.S.). Funding for J.M. was further provided by doctoral fellowships from the Natural Sciences and Engineering Research Council of Canada (PGSD3-430487-2013, PGSM-405117-2011) and the National Aeronautics and Space Administration Earth Systems Science Fellowship (PLANET14F-0075), an award from the Canadian Meteorological and Oceanographic Society, and the WHOI Academic Programs Office

Dissolved organic carbon compounds in deep-sea hydrothermal vent fluids from the East Pacific Rise at 9°50′N

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Organic Geochemistry 125 (2018): 41-49, doi:10.1016/j.orggeochem.2018.08.004.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.This project was funded by a grant from WHOI’s Deep Ocean Exploration Institute and WHOI’s Ocean Ridge Initiative (to EBK and SMS) and by NSF OCE-1154320 (to EBK and KL), OCE- 1136727 (to SMS and JSS), and OCE 1131095 (to SMS)

Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 647, doi:10.3389/fmicb.2014.00647.The Southern Ocean is currently subject to intense investigations, mainly related to its importance for global biogeochemical cycles and its alarming rate of warming in response to climate change. Microbes play an essential role in the functioning of this ecosystem and are the main drivers of the biogeochemical cycling of elements. Yet, the diversity and abundance of microorganisms in this system remain poorly studied, in particular with regards to changes along environmental gradients. Here, we used amplicon sequencing of 16S rRNA gene tags using primers covering both Bacteria and Archaea to assess the composition and diversity of the microbial communities from four sampling depths (surface, the maximum and minimum of the oxygen concentration, and near the seafloor) at 10 oceanographic stations located in Bransfield Strait [northwest of the Antarctic Peninsula (AP)] and near the sea ice edge (north of the AP). Samples collected near the seafloor and at the oxygen minimum exhibited a higher diversity than those from the surface and oxygen maximum for both bacterial and archaeal communities. The main taxonomic groups identified below 100 m were Thaumarchaeota, Euryarchaeota and Proteobacteria (Gamma-, Delta-, Beta-, and Alphaproteobacteria), whereas in the mixed layer above 100 m Bacteroidetes and Proteobacteria (mainly Alpha- and Gammaproteobacteria) were found to be dominant. A combination of environmental factors seems to influence the microbial community composition. Our results help to understand how the dynamic seascape of the Southern Ocean shapes the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes.This work was supported by the Brazilian National Counsel of Technological and Scientific Development (Polar Canion CNPq 556848/2009-8, ProOasis CNPq 565040/2010-3, Interbiota CNPq 407889/2013-2 and INCT-MAR-COI). Alex Enrich-Prast received a CNPq Productivity fellowship. Camila N. Signori was supported by a WHOI Mary Sears Visitor Award (for the microbial community analyses) and by the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) for the “Doctorate Sandwich” scholarship (n. 18835/12-0)

Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chen, S.-C., Ji, J., Popp, D., Jaekel, U., Richnow, H.-H., Sievert, S. M., & Musat, F. Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist. Environmental Microbiology, 24, (2022): 1964-1976, https://doi.org/10.1111/1462-2920.15956.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.This study was financed by the Max Planck Society and by the Helmholtz Association of German Research Centres. The draft genome was sequenced as part of the U.S. Department of Energy Joint Genome Institute (DOE-JGI) Community Science Program project 1078203 awarded to S. M. Sievert and F. Musat. The work conducted by the DOE-JGI, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Lynne Goodwin (Los Alamos National Laboratory) is acknowledged for project management support of the draft genome sequencing. Further support was provided by the U.S. National Science Foundation grant MCB-0702677 (to SMS), and by the Helmholtz Association grant ERC-RA-0020 (to FM). We acknowledge the Centre for Chemical Microscopy (ProVIS) platform at the Helmholtz Centre for Environmental Research – UFZ, for using their analytical facilities. ProVIS is supported by European Regional Development Funds (EFRE – Europe funds Saxony). We acknowledge the Bundesministerium für Bildung und Forschung (BMBF)-funded German Network for Bioinformatics Infrastructure de.NBI (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B) for providing computational resources

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hou, J., Sievert, S. M., Wang, Y., Seewald, J. S., Natarajan, V. P., Wang, F., & Xiao, X. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. Microbiome, 8(1), (2020): 102, doi:10.1186/s40168-020-00851-8.Background Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys. Results Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9–10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased. Conclusions This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a “fluid-shaped” microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a “mineral-shaped” community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years.This work was supported by the China Ocean Mineral Resources R&D Association (grant No. DY135-B2-12), the Natural Science Foundation of China (grant No. 41530967, 41921006, 91751205), the Senior User Project of RV KEXUE (KEXUE2019GZ06), and by the US National Science Foundation grant OCE-1136727 and the WHOI Investment in Science Fund to S.M.S

Primary productivity below the seafloor at deep-sea hot springs

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 6756–6761, doi:10.1073/pnas.1804351115.The existence of a chemosynthetic subseafloor biosphere was immediately recognized when deep-sea hot springs were discovered in 1977. However, quantifying how much new carbon is fixed in this environment has remained elusive. In this study, we incubated natural subseafloor communities under in situ pressure/temperature and measured their chemosynthetic growth efficiency and metabolic rates. Combining these data with fluid flux and in situ chemical measurements, we derived empirical constraints on chemosynthetic activity in the natural environment. Our study shows subseafloor microorganisms are highly productive (up to 1.4 Tg C produced yearly), fast-growing (turning over every 17–41 hours), and physiologically diverse. These estimates place deep-sea hot springs in a quantitative framework and allow us to assess their importance for global biogeochemical cycles.This research was funded by a grant of the Dimensions of Biodiversity program of the US National Science Foundation (NSF-OCE-1136727 to S.M.S. and J.S.S.). Funding for J.M. was further provided by doctoral fellowships from the Natural Sciences and Engineering Research Council of Canada (PGSD3-430487-2013, PGSM-405117-2011) and the National Aeronautics and Space Administration Earth Systems Science Fellowship (PLANET14F-0075), an award from the Canadian Meteorological and Oceanographic Society, and the WHOI Academic Programs Office

Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sievert, S. M., Buehring, S., Gulmann, L. K., Hinrichs, K.-U., Ristova, P. P., & Gomez-Saez, G. Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments. Communications Earth & Environment, 3(1), (2022): 96, https://doi.org/10.1038/s43247-022-00426-5.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.Open Access funding enabled and organized by Projekt DEAL