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Astorch-Cardona A, Odin GP, Chavagnac V, Dolla A, Gaussier H, Rommevaux C. Linking Zetaproteobacterial diversity and substratum type in iron-rich microbial mats from the Lucky Strike hydrothermal field (EMSO-Azores observatory). Appl Environ Microbiol 2024; 90:e0204123. [PMID: 38193671 PMCID: PMC10880625 DOI: 10.1128/aem.02041-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named "corals." Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity.IMPORTANCEUp until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria.
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Affiliation(s)
- Aina Astorch-Cardona
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Giliane P. Odin
- Laboratoire Géomatériaux et Environnement, Université Gustave Eiffel, Marne-la-Vallée, France
| | - Valérie Chavagnac
- Géosciences Environnement Toulouse, CNRS UMR 5563 (CNRS/UPS/IRD/CNES), Université de Toulouse, Observatoire Midi-Pyrénées, Toulouse, France
| | - Alain Dolla
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Gaussier
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Céline Rommevaux
- Aix-Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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Hribovšek P, Olesin Denny E, Dahle H, Mall A, Øfstegaard Viflot T, Boonnawa C, Reeves EP, Steen IH, Stokke R. Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 2023; 8:e0054323. [PMID: 37921472 PMCID: PMC10734525 DOI: 10.1128/msystems.00543-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
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Affiliation(s)
- Petra Hribovšek
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Emily Olesin Denny
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Achim Mall
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Thomas Øfstegaard Viflot
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Chanakan Boonnawa
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Eoghan P. Reeves
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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Skoog EJ, Fournier GP, Bosak T. Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia. Genes (Basel) 2023; 14:2168. [PMID: 38136990 PMCID: PMC10742547 DOI: 10.3390/genes14122168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.
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Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Gregory P. Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
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Mara P, Zhou YL, Teske A, Morono Y, Beaudoin D, Edgcomb V. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation. THE ISME JOURNAL 2023; 17:1907-1919. [PMID: 37658181 PMCID: PMC10579382 DOI: 10.1038/s41396-023-01492-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Ying-Li Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - David Beaudoin
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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Arcadi E, Rizzo C, Calogero R, Sciutteri V, Fabiano F, Consoli P, Andaloro F, Romeo T. Microbial communities inhabiting shallow hydrothermal vents as sentinels of acidification processes. Front Microbiol 2023; 14:1233893. [PMID: 37727286 PMCID: PMC10505797 DOI: 10.3389/fmicb.2023.1233893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023] Open
Abstract
Introduction Shallow hydrothermal vents are considered natural laboratories to study the effects of acidification on biota, due to the consistent CO2 emissions with a consequent decrease in the local pH. Methods Here the microbial communities of water and sediment samples from Levante Bay (Vulcano Island) with different pH and redox conditions were explored by Next Generation Sequencing techniques. The taxonomic structure was elucidated and compared with previous studies from the same area in the last decades. Results and discussion The results revealed substantial shifts in the taxonomic structure of both bacterial and archaeal communities, with special relevance in the sediment samples, where the effects of external parameters probably act for a long time. The study demonstrates that microbial communities could be used as indicators of acidification processes, by shaping the entire biogeochemical balance of the ecosystem in response to stress factors. The study contributes to understanding how much these communities can tell us about future changes in marine ecosystems.
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Affiliation(s)
- Erika Arcadi
- Department of Biology and Evolution of Marine Organism, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Carmen Rizzo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Valentina Sciutteri
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Francesco Fabiano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
| | - Pierpaolo Consoli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
- National Institute for Environmental Protection and Research, Milazzo, Italy
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:ijms24076491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
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Le Moine Bauer S, Lu GS, Goulaouic S, Puzenat V, Schouw A, Barreyre T, Pawlowsky-Glahn V, Egozcue JJ, Martelat JE, Escartin J, Amend JP, Nomikou P, Vlasopoulos O, Polymenakou P, Jørgensen SL. Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece. Front Microbiol 2023; 13:1060168. [PMID: 36687571 PMCID: PMC9852839 DOI: 10.3389/fmicb.2022.1060168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/01/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing. Methods We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities. Results We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community. Discussion Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling.
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Affiliation(s)
- Sven Le Moine Bauer
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway,*Correspondence: Sven Le Moine Bauer,
| | - Guang-Sin Lu
- Cooperative Institute for Climate, Ocean and Ecosystem Studies, University of Washington, Seattle, WA, United States,NOAA Pacific Marine Environmental Laboratory, Seattle, WA, United States
| | - Steven Goulaouic
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Valentine Puzenat
- Institut de Physique du Globe de Paris, CNRS, Université Paris Cité, Paris, France
| | - Anders Schouw
- Center for Deep Sea Research, Department of Biology, University of Bergen, Bergen, Norway
| | - Thibaut Barreyre
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Vera Pawlowsky-Glahn
- Department of Computer Science, Applied Mathematics and Statistics, University of Girona, Girona, Spain
| | - Juan José Egozcue
- Department of Civil and Environmental Engineering, University Politécnica de Cataluña, Barcelona, Spain
| | - Jean-Emmanuel Martelat
- Université de Lyon, UCBL, ENSL, CNRS, Laboratoire de Géologie LGL-TPE, Villeurbanne, France
| | - Javier Escartin
- Laboratoire de Géologie (CNRS UMR8538), Ecole Normale Supérieure de Paris, PSL University, Paris, France
| | - Jan P. Amend
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Othonas Vlasopoulos
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Paraskevi Polymenakou
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Steffen Leth Jørgensen
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
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Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps. mSystems 2022; 7:e0032022. [PMID: 35938718 PMCID: PMC9426478 DOI: 10.1128/msystems.00320-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.
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Abstract
Microbes rely on signal transduction systems to sense and respond to environmental changes for survival and reproduction. It is generally known that niche adaptation plays an important role in shaping the signaling repertoire. However, the evolution of bacterial signaling capacity lacks systematic studies with a temporal direction. In particular, it is unclear how complexity evolved from simplicity or vice versa for signaling networks. Here, we examine the evolutionary processes of major signal transduction systems in Campylobacterota (formerly Epsilonproteobacteria), a phylum with sufficient evolutionary depth and ecological diversity. We discovered that chemosensory system increases complexity by horizontal gene transfer (HGT) of entire chemosensory classes, and different chemosensory classes rarely mix their components. Two-component system gains complexity by atypical histidine kinases fused with receiver domain to achieve multistep or branched signal transduction process. The presence and complexity of c-di-GMP-mediated system is related to the size of signaling network, and c-di-GMP pathways are easy to rewire, since enzymes and effectors can be linked without direct protein-protein interaction. Overall, signaling capacity and complexity rise and drop together in Campylobacterota, determined by sensory demand, genetic resources, and coevolution within the genomic context. These findings reflect plausible evolutionary principles for other cellular networks and genome evolution of the Bacteria domain.
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Symbiont Community Composition in Rimicaris kairei Shrimps from Indian Ocean Vents with Notes on Mineralogy. Appl Environ Microbiol 2022; 88:e0018522. [PMID: 35404070 PMCID: PMC9040608 DOI: 10.1128/aem.00185-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Hydrothermal vent ecosystems are home to a wide array of symbioses between animals and chemosynthetic microbes, among which shrimps in the genus Rimicaris is one of the most iconic. So far, studies of Rimicaris symbioses have been restricted to Atlantic species, including Rimicaris exoculata, which is totally reliant on the symbionts for nutrition, and the mixotrophic species Rimicaris chacei. Here, we expand this by investigating and characterizing the symbiosis of the Indian Ocean species Rimicaris kairei using specimens from two vent fields, Kairei and Edmond. We also aimed to evaluate the differences in mineralogy and microbial communities between two cephalothorax color morphs, black and brown, through a combination of 16S metabarcoding, scanning electron microscopy, fluorescent in situ hybridization, energy-dispersive X-ray spectroscopy, and synchrotron near-edge X-ray absorption structure analyses. Overall, our results highlight that R. kairei exhibits similar symbiont lineages to those of its Atlantic congeners, although with a few differences, such as the lack of Zetaproteobacteria. We found distinct mineralization processes behind the two color morphs that were linked to differences in the vent fluid composition, but the symbiotic community composition was surprisingly similar. In R. exoculata, such mineralogical differences have been shown to stem from disparity in the microbial communities, but our results indicate that in R. kairei this is instead due to the shift of dominant metabolisms by the same symbiotic partners. We suggest that a combination of local environmental factors and biogeographic barriers likely contribute to the differences between Atlantic and Indian Ocean Rimicaris symbioses. IMPORTANCE Hydrothermal vent shrimps in the genus Rimicaris are among the most charismatic deep-sea animals of Atlantic and Indian Oceans, often occurring on towering black smokers in dense aggregates of thousands of individuals. Although this dominance is only possible because of symbiosis, no study on the symbiosis of Indian Ocean Rimicaris species has been conducted. Here, we characterize the Rimicaris kairei symbiosis by combining molecular, microscopic, and elemental analyses, making comparisons with those of the Atlantic species possible for the first time. Although most symbiotic partners remained consistent across the two oceans, some differences were recognized in symbiont lineages, as well as in the mechanisms behind the formation of two color morphs with distinct mineralogies. Our results shed new light on relationships among mineralogy, environmental factors, and microbial communities that are useful for understanding other deep-sea symbioses in the future.
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11
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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Leng H, Zhao W, Xiao X. Cultivation and metabolic insights of an uncultured clade, Bacteroidetes VC2.1 Bac22 (Candidatus Sulfidibacteriales ord. nov.), from deep-sea hydrothermal vents. Environ Microbiol 2022; 24:2484-2501. [PMID: 35165999 DOI: 10.1111/1462-2920.15931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 01/05/2022] [Accepted: 01/31/2022] [Indexed: 01/28/2023]
Abstract
Bacteroidetes VC2.1 Bac22 (referred to as VC2.1) is an uncultured clade that is widely distributed in marine ecosystems, including hydrothermal vents, oxygen-minimum zones and other anoxic, sulfide-rich environments. However, the lack of cultured representatives and sequenced genomes of VC2.1 limit our understanding of its physiology, metabolism and ecological functions. Here, we obtained a stable co-culture of VC2.1 with autotrophic microbes by establishing an autotrophy-based enrichment from a hydrothermal vent chimney sample. We recovered a high-quality metagenome-assembled genome (MAG) that belonged to VC2.1. Phylogenetic analyses of both 16S rRNA genes and conserved protein markers suggested that VC2.1 belongs to a novel order in the Bacteroidetes phylum, which we named Candidatus Sulfidibacteriales. The metabolic reconstruction of this MAG indicated that VC2.1 could utilize polysaccharides, protein polymers and fatty acids as well as flexibly obtain energy via NO/N2 O reduction and polysulfide reduction. Our results reveal the ecological potential of this novel Bacteroidetes for complex organic carbons mineralization and N2 O sinks in deep-sea hydrothermal vents. Furthermore, guided by the genome information, we designed a new culture medium in which starch, ammonium and polysulfide were used as the carbon source, nitrogen source and electron acceptor respectively, to isolate VC2.1 successfully.
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Affiliation(s)
- Hao Leng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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13
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Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
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Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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14
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Genus-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen Among Hydrothermal Vent Campylobacteria. Appl Environ Microbiol 2021; 88:e0208321. [PMID: 34788061 DOI: 10.1128/aem.02083-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. 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. Importance: Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria. Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria. In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ. These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.
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15
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Three-dimensional morphology of bacterial community developed on the index-matched materials. Sci Rep 2021; 11:19508. [PMID: 34593946 PMCID: PMC8484612 DOI: 10.1038/s41598-021-98943-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/17/2021] [Indexed: 11/08/2022] Open
Abstract
Herein, we demonstrate that the use of index-matching materials (IMMs) allows direct visualization of microbial cells maintained at a solid-liquid interface through confocal reflection microscopy (CRM). The refractive index mismatch induces a background reflection at the solid-liquid interface that dwarfs the reflection signals from the cells and results in low-contrast images. We found that the IMMs sufficiently suppressed the background reflection at the solid-liquid interface, facilitating the imaging of microbes at the solid surface using CRM. The use of IMMs allowed quantitative analysis of the morphology of the mesh-like structure of Pseudomonas aeruginosa biofilms formed under denitrifying conditions, which led us to propose a novel structural model of the highly porous biofilm structure. These results indicate that the use of CRM coupled with an IMM offers a unique and promising tool for probing the dynamics of biofilm formation, along with visualization of environmental organisms and newly isolated bacteria, for which transformation methods are difficult to establish.
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16
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Murdock SA, Tunnicliffe V, Boschen-Rose RE, Juniper SK. Emergent "core communities" of microbes, meiofauna and macrofauna at hydrothermal vents. ISME COMMUNICATIONS 2021; 1:27. [PMID: 36739470 PMCID: PMC9723782 DOI: 10.1038/s43705-021-00031-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Assessment of ecosystem health entails consideration of species interactions within and between size classes to determine their contributions to ecosystem function. Elucidating microbial involvement in these interactions requires tools to distil diverse microbial information down to relevant, manageable elements. We used covariance ratios (proportionality) between pairs of species and patterns of enrichment to identify "core communities" of likely interacting microbial (<64 µm), meiofaunal (64 µm to 1 mm) and macrofaunal (>1 mm) taxa within assemblages hosted by a foundation species, the hydrothermal vent tubeworm Ridgeia piscesae. Compared with samples from co-located hydrothermal fluids, microbial communities within R. piscesae assemblages are hotspots of taxonomic richness and are high in novelty (unclassified OTUs) and in relative abundance of Bacteroidetes. We also observed a robust temperature-driven distinction in assemblage composition above and below ~25 °C that spanned micro to macro size classes. The core high-temperature community included eight macro- and meiofaunal taxa and members of the Bacteroidetes and Epsilonbacteraeota, particularly the genera Carboxylicivirga, Nitratifractor and Arcobacter. The core low-temperature community included more meiofaunal species in addition to Alpha- and Gammaproteobacteria, and Actinobacteria. Inferred associations among high-temperature core community taxa suggest increased reliance on species interactions under more severe hydrothermal conditions. We propose refinement of species diversity to "core communities" as a tool to simplify investigations of relationships between taxonomic and functional diversity across domains and scales by narrowing the taxonomic scope.
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Affiliation(s)
- S A Murdock
- School of Earth & Ocean Sciences, University of Victoria, Victoria, Canada.
| | - V Tunnicliffe
- School of Earth & Ocean Sciences, University of Victoria, Victoria, Canada
- Department of Biology, University of Victoria, Victoria, Canada
| | - R E Boschen-Rose
- Department of Biology, University of Victoria, Victoria, Canada
- Ocean & Earth Science, University of Southampton, Southampton, UK
| | - S K Juniper
- School of Earth & Ocean Sciences, University of Victoria, Victoria, Canada
- Ocean Networks Canada, University of Victoria, Victoria, Canada
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17
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Lee W, Juniper SK, Perez M, Ju S, Kim S. Diversity and characterization of bacterial communities of five co-occurring species at a hydrothermal vent on the Tonga Arc. Ecol Evol 2021; 11:4481-4493. [PMID: 33976824 PMCID: PMC8093707 DOI: 10.1002/ece3.7343] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/06/2022] Open
Abstract
Host-symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co-occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill-associated symbiotic bacteria (gill symbionts) of five co-occurring hosts, three mollusks ("Bathymodiolus" manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ-proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co-occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.
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Affiliation(s)
- Won‐Kyung Lee
- Genome Editing Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
| | - S. Kim Juniper
- Department of BiologySchool of Earth and Ocean SciencesUniversity of VictoriaVictoriaBCCanada
| | - Maëva Perez
- Département des Sciences BiologiquesUniversité de MontréalMontrealQCCanada
| | - Se‐Jong Ju
- Korea Institute of Ocean Science & TechnologyBusanKorea
| | - Se‐Joo Kim
- Genome Editing Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
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18
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Qiang W, Xuan H, Yu S, Hailun P, Yueli Z, Zhiguo P, Lei S. Impact of the gut microbiota on heat stroke rat mediated by Xuebijing metabolism. Microb Pathog 2021; 155:104861. [PMID: 33864878 DOI: 10.1016/j.micpath.2021.104861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/17/2022]
Abstract
The goal of the present study was to evaluate the fecal microbiome and serum metabolites in Xuebijing (XBJ)-injected rats after heat stroke using 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics. Eighteen rats were divided into the control group (CON), heat stroke group (HS), and XBJ group. The 16S rRNA gene sequencing results revealed that the abundance of Bacteroidetes was overrepresented in the XBJ group compared to the HS group, while Actinobacteria was underrepresented. Metabolomic profiling showed that the pyrimidine metabolism pathway, pentose phosphate pathway, and glycerophospholipid metabolism pathway were upregulated in the XBJ group compared to the HS group. Taken together, these results demonstrated that heat stroke not only altered the gut microbiome community structure of rats but also greatly affected metabolic functions, leading to gut microbiome toxicity.
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Affiliation(s)
- Wen Qiang
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - He Xuan
- Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Shao Yu
- Second Department of Internal Medicine for Cadres, General Hospital of Guangzhou Military Command, China
| | - Peng Hailun
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Zhao Yueli
- Graduate School, Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Pan Zhiguo
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China.
| | - Su Lei
- The First Clinical Medical College, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China.
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19
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Brandt MI, Pradillon F, Trouche B, Henry N, Liautard-Haag C, Cambon-Bonavita MA, Cueff-Gauchard V, Wincker P, Belser C, Poulain J, Arnaud-Haond S, Zeppilli D. Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA. Sci Rep 2021; 11:7856. [PMID: 33846371 PMCID: PMC8041860 DOI: 10.1038/s41598-021-86396-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1-V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.
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Affiliation(s)
- Miriam I. Brandt
- grid.121334.60000 0001 2097 0141MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
| | - Florence Pradillon
- grid.4825.b0000 0004 0641 9240Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), IFREMER, CS10070, 29280 Plouzané, France
| | - Blandine Trouche
- grid.4825.b0000 0004 0641 9240IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
| | - Nicolas Henry
- grid.462844.80000 0001 2308 1657CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Sorbonne University, 29680 Roscoff, France
| | - Cathy Liautard-Haag
- grid.121334.60000 0001 2097 0141MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
| | - Marie-Anne Cambon-Bonavita
- grid.4825.b0000 0004 0641 9240IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
| | - Valérie Cueff-Gauchard
- grid.4825.b0000 0004 0641 9240IFREMER, CNRS, Laboratoire de Microbiologie Des Environnements Extrêmes (LM2E), Univ Brest, Plouzané, France
| | - Patrick Wincker
- grid.434728.e0000 0004 0641 2997Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057 Evry, France
| | - Caroline Belser
- grid.434728.e0000 0004 0641 2997Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057 Evry, France
| | - Julie Poulain
- grid.434728.e0000 0004 0641 2997Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ of Évry, Paris-Saclay University, 91057 Evry, France
| | - Sophie Arnaud-Haond
- grid.121334.60000 0001 2097 0141MARBEC, IFREMER, IRD, CNRS, Univ Montpellier, Sète, France
| | - Daniela Zeppilli
- grid.4825.b0000 0004 0641 9240Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), IFREMER, CS10070, 29280 Plouzané, France
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20
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Wang CH, Gulmann LK, Zhang T, Farfan GA, Hansel CM, Sievert SM. Microbial colonization of metal sulfide minerals at a diffuse-flow deep-sea hydrothermal vent at 9°50'N on the East Pacific Rise. GEOBIOLOGY 2020; 18:594-605. [PMID: 32336020 DOI: 10.1111/gbi.12396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/24/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Metal sulfide minerals, including mercury sulfides (HgS), are widespread in hydrothermal vent systems where sulfur-oxidizing microbes are prevalent. Questions remain as to the impact of mineral composition and structure on sulfur-oxidizing microbial populations at deep-sea hydrothermal vents, including the possible role of microbial activity in remobilizing elemental Hg from HgS. In the present study, metal sulfides varying in metal composition, structure, and surface area were incubated for 13 days on and near a diffuse-flow hydrothermal vent at 9°50'N on the East Pacific Rise. Upon retrieval, incubated minerals were examined by scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS), X-ray diffraction (XRD), and epifluorescence microscopy (EFM). DNA was extracted from mineral samples, and the 16S ribosomal RNA gene sequenced to characterize colonizing microbes. Sulfur-oxidizing genera common to newly exposed surfaces (Sulfurimonas, Sulfurovum, and Arcobacter) were present on all samples. Differences in their relative abundance between and within incubation sites point to constraining effects of the immediate environment and the minerals themselves. Greater variability in colonizing community composition on off-vent samples suggests that the bioavailability of mineral-derived sulfide (as influenced by surface area, crystal structure, and reactivity) exerted greater control on microbial colonization in the ambient environment than in the vent environment, where dissolved sulfide is more abundant. The availability of mineral-derived sulfide as an electron donor may thus be a key control on the activity and proliferation of deep-sea chemosynthetic communities, and this interpretation supports the potential for microbial dissolution of HgS at hydrothermal vents.
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Affiliation(s)
- Chloe H Wang
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Chemistry, Haverford College, Haverford, PA, USA
| | - Lara K Gulmann
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Tong Zhang
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin, China
| | - Gabriela A Farfan
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Mineral Sciences, Smithsonian Institution, Washington, DC, USA
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Stefan M Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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21
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Methou P, Michel LN, Segonzac M, Cambon-Bonavita MA, Pradillon F. Integrative taxonomy revisits the ontogeny and trophic niches of Rimicaris vent shrimps. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200837. [PMID: 32874664 PMCID: PMC7428246 DOI: 10.1098/rsos.200837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Among hydrothermal vent species, Rimicaris exoculata is one of the most emblematic, hosting abundant and diverse ectosymbioses that provide most of its nutrition. Rimicaris exoculata co-occurs in dense aggregates with the much less abundant Rimicaris chacei in many Mid-Atlantic Ridge vent fields. This second shrimp also houses ectosymbiotic microorganisms but has a mixotrophic diet. Recent observations have suggested potential misidentifications between these species at their juvenile stages, which could have led to misinterpretations of their early-life ecology. Here, we confirm erroneous identification of the earliest stages and propose a new set of morphological characters unambiguously identifying juveniles of each species. On the basis of this reassessment, combined use of C, N and S stable isotope ratios reveals distinct ontogenic trophic niche shifts in both species, from photosynthesis-based nutrition before settlement, towards a chemosynthetic diet afterwards. Furthermore, isotopic compositions in the earliest juvenile stages suggest differences in larval histories. Each species thus exhibits specific early-life strategies that would, without our re-examination, have been interpreted as ontogenetic variations. Overall, our results provide a good illustration of the identification issues persisting in deep-sea ecosystems and the importance of integrative taxonomy in providing an accurate view of fundamental aspects of the biology and ecology of species inhabiting these environments.
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Affiliation(s)
- Pierre Methou
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, F-29280 Plouzané, France
- Ifremer, Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), ZI de la pointe du Diable, F-29280 Plouzané, France
| | - Loïc N. Michel
- Ifremer, Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), ZI de la pointe du Diable, F-29280 Plouzané, France
| | - Michel Segonzac
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, case postale 53, 57 rue Cuvier, F-75231 Paris cedex 05, France
| | - Marie-Anne Cambon-Bonavita
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, F-29280 Plouzané, France
| | - Florence Pradillon
- Ifremer, Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), ZI de la pointe du Diable, F-29280 Plouzané, France
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22
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Hou J, Sievert SM, Wang Y, Seewald JS, Natarajan VP, Wang F, Xiao X. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. MICROBIOME 2020; 8:102. [PMID: 32605604 PMCID: PMC7329443 DOI: 10.1186/s40168-020-00851-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 05/19/2023]
Abstract
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. Video Abstract.
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Affiliation(s)
- Jialin Hou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jeffrey S Seewald
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Vengadesh Perumal Natarajan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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23
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Stokke R, Reeves EP, Dahle H, Fedøy AE, Viflot T, Lie Onstad S, Vulcano F, Pedersen RB, Eijsink VGH, Steen IH. Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy. Front Microbiol 2020; 11:249. [PMID: 32153535 PMCID: PMC7046548 DOI: 10.3389/fmicb.2020.00249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/03/2020] [Indexed: 11/13/2022] Open
Abstract
Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.
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Affiliation(s)
- Runar Stokke
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Eoghan P Reeves
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Thomas Viflot
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Solveig Lie Onstad
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Francesca Vulcano
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Rolf B Pedersen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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24
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Stepnov AA, Fredriksen L, Steen IH, Stokke R, Eijsink VGH. Identification and characterization of a hyperthermophilic GH9 cellulase from the Arctic Mid-Ocean Ridge vent field. PLoS One 2019; 14:e0222216. [PMID: 31491027 PMCID: PMC6731012 DOI: 10.1371/journal.pone.0222216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/23/2019] [Indexed: 11/29/2022] Open
Abstract
A novel GH9 cellulase (AMOR_GH9A) was discovered by sequence-based mining of a unique metagenomic dataset collected at the Jan Mayen hydrothermal vent field. AMOR_GH9A comprises a signal peptide, a catalytic domain and a CBM3 cellulose-binding module. AMOR_GH9A is an exceptionally stable enzyme with a temperature optimum around 100°C and an apparent melting temperature of 105°C. The novel cellulase retains 64% of its activity after 4 hours of incubation at 95°C. The closest characterized homolog of AMOR_GH9A is TfCel9A, a processive endocellulase from the model thermophilic bacterium Thermobifida fusca (64.2% sequence identity). Direct comparison of AMOR_GH9A and TfCel9A revealed that AMOR_GH9A possesses higher activity on soluble and amorphous substrates (phosphoric acid swollen cellulose, konjac glucomannan) and has an ability to hydrolyse xylan that is lacking in TfCel9A.
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Affiliation(s)
- Anton A. Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU—Norwegian University of Life Sciences, Ås, Norway
| | - Lasse Fredriksen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU—Norwegian University of Life Sciences, Ås, Norway
| | - Ida H. Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU—Norwegian University of Life Sciences, Ås, Norway
- * E-mail:
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25
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Ziko L, Adel M, Malash MN, Siam R. Insights into Red Sea Brine Pool Specialized Metabolism Gene Clusters Encoding Potential Metabolites for Biotechnological Applications and Extremophile Survival. Mar Drugs 2019; 17:md17050273. [PMID: 31071993 PMCID: PMC6562949 DOI: 10.3390/md17050273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/12/2019] [Accepted: 04/19/2019] [Indexed: 12/21/2022] Open
Abstract
The recent rise in antibiotic and chemotherapeutic resistance necessitates the search for novel drugs. Potential therapeutics can be produced by specialized metabolism gene clusters (SMGCs). We mined for SMGCs in metagenomic samples from Atlantis II Deep, Discovery Deep and Kebrit Deep Red Sea brine pools. Shotgun sequence assembly and secondary metabolite analysis shell (antiSMASH) screening unraveled 2751 Red Sea brine SMGCs, pertaining to 28 classes. Predicted categorization of the SMGC products included those (1) commonly abundant in microbes (saccharides, fatty acids, aryl polyenes, acyl-homoserine lactones), (2) with antibacterial and/or anticancer effects (terpenes, ribosomal peptides, non-ribosomal peptides, polyketides, phosphonates) and (3) with miscellaneous roles conferring adaptation to the environment/special structure/unknown function (polyunsaturated fatty acids, ectoine, ladderane, others). Saccharide (80.49%) and putative (7.46%) SMGCs were the most abundant. Selected Red Sea brine pool sites had distinct SMGC profiles, e.g., for bacteriocins and ectoine. Top promising candidates, SMs with pharmaceutical applications, were addressed. Prolific SM-producing phyla (Proteobacteria, Actinobacteria, Cyanobacteria), were ubiquitously detected. Sites harboring the largest numbers of bacterial and archaeal phyla, had the most SMGCs. Our results suggest that the Red Sea brine niche constitutes a rich biological mine, with the predicted SMs aiding extremophile survival and adaptation.
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Affiliation(s)
- Laila Ziko
- Graduate Program of Biotechnology, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
| | - Mustafa Adel
- Graduate Program of Biotechnology, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
| | - Mohamed N Malash
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
- Microbiology and Immunology Department, Faculty of Pharmacy, Ahram Canadian University, Giza 12581, Egypt.
| | - Rania Siam
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
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26
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Methou P, Hernández-Ávila I, Aube J, Cueff-Gauchard V, Gayet N, Amand L, Shillito B, Pradillon F, Cambon-Bonavita MA. Is It First the Egg or the Shrimp? - Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development. Front Microbiol 2019; 10:808. [PMID: 31057515 PMCID: PMC6478704 DOI: 10.3389/fmicb.2019.00808] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/29/2019] [Indexed: 12/26/2022] Open
Abstract
Rimicaris exoculata is one of the most well-known and emblematic species of endemic vent fauna. Like many other species from these ecosystems, Rimicaris shrimps host important communities of chemosynthetic bacteria living in symbiosis with their host inside the cephalothorax and gut. For many of these symbiotic partners, the mode of transmission remains to be elucidated and the starting point of the symbiotic relationship is not yet defined, but could begin with the egg. In this study, we explored the proliferation of microbial communities on R. exoculata broods through embryonic development using a combination of NGS sequencing and microscopy approaches. Variations in abundance and diversity of egg microbial communities were analyzed in broods at different developmental stages and collected from mothers at two distinct vent fields on the Mid-Atlantic Ridge (TAG and Snake Pit). We also assessed the specificity of the egg microbiome by comparing communities developing on egg surfaces with those developing on the cuticle of pleopods, which are thought to be exposed to similar environmental conditions because the brood is held under the female's abdomen. In terms of abundance, bacterial colonization clearly increases with both egg developmental stage and the position of the egg within the brood: those closest to the exterior having a higher bacterial coverage. Bacterial biomass increase also accompanies an increase of mineral precipitations and thus clearly relates to the degree of exposure to vent fluids. In terms of diversity, most bacterial lineages were found in all samples and were also those found in the cephalothorax of adults. However, significant variation occurs in the relative abundance of these lineages, most of this variation being explained by body surface (egg vs. pleopod), vent field, and developmental stage. The occurrence of symbiont-related lineages of Epsilonbacteraeota, Gammaproteobacteria, Zetaproteobacteria, and Mollicutes provide a basis for discussion on both the acquisition of symbionts and the potential roles of these bacterial communities during egg development.
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Affiliation(s)
- Pierre Methou
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Ivan Hernández-Ávila
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Johanne Aube
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Valérie Cueff-Gauchard
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Nicolas Gayet
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Louis Amand
- Unité Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d’Histoire Naturelle, Eq. Adaptations aux Milieux Extrêmes (BOREA), CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Paris, France
| | - Bruce Shillito
- Unité Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d’Histoire Naturelle, Eq. Adaptations aux Milieux Extrêmes (BOREA), CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Paris, France
| | - Florence Pradillon
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
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27
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Meier DV, Pjevac P, Bach W, Markert S, Schweder T, Jamieson J, Petersen S, Amann R, Meyerdierks A. Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. Environ Microbiol 2019; 21:682-701. [PMID: 30585382 PMCID: PMC6850669 DOI: 10.1111/1462-2920.14514] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 01/02/2023]
Abstract
Metal‐sulfides are wide‐spread in marine benthic habitats. At deep‐sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene‐based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate‐reducing Nitrospirae and sulfide‐oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr‐clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide‐oxidizers potentially facilitating metal‐sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.
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Affiliation(s)
- Dimitri V Meier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Petra Pjevac
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Wolfgang Bach
- MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group, University of Bremen, Leobener Str., 28359, Bremen, Germany
| | - Stephanie Markert
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße 17, 17489, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Straße 17, 17489, Greifswald, Germany
| | - John Jamieson
- Department of Earth Sciences, Memorial University of Newfoundland, 40 Arctic Ave, Saint John's, NL, A1B 3X7, Canada
| | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Anke Meyerdierks
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
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28
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Patwardhan S, Foustoukos DI, Giovannelli D, Yücel M, Vetriani C. Ecological Succession of Sulfur-Oxidizing Epsilon- and Gammaproteobacteria During Colonization of a Shallow-Water Gas Vent. Front Microbiol 2018; 9:2970. [PMID: 30574130 PMCID: PMC6291522 DOI: 10.3389/fmicb.2018.02970] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/18/2018] [Indexed: 02/01/2023] Open
Abstract
In this study, we integrated geochemical measurements, microbial diversity surveys and physiological characterization of laboratory strains to investigate substrate-attached filamentous microbial biofilms at Tor Caldara, a shallow-water gas vent in the Tyrrhenian Sea. At this site, the venting gases are mainly composed of CO2 and H2S and the temperature at the emissions is the same as that of the surrounding water. To investigate the composition of the total and active fraction of the Tor Caldara biofilm communities, we collected established and newly formed filaments and we sequenced the 16S rRNA genes (DNA) and the 16S rRNA transcripts (cDNA). Chemoautotrophic sulfur-oxidizing members of the Gammaproteobacteria (predominantly Thiotrichales) dominate the active fraction of the established microbial filaments, while Epsilonproteobacteria (predominantly Sulfurovum spp.) are more prevalent in the young filaments. This indicates a succession of the two communities, possibly in response to age, sulfide and oxygen concentrations. Growth experiments with representative laboratory strains in sulfide gradient medium revealed that Sulfurovum riftiae (Epsilonproteobacteria) grew closer to the sulfide source than Thiomicrospira sp. (Gammaproteobacteria, Thiotrichales). Overall, our findings show that sulfur-oxidizing Epsilonproteobacteria are the dominant pioneer colonizers of the Tor Caldara biofilm communities and that Gammaproteobacteria become prevalent once the community is established. This succession pattern appears to be driven - among other factors - by the adaptation of Epsilon- and Gammaproteobacteria to different sulfide concentrations.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Dionysis I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, United States
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.,Institute of Marine Science, National Research Council, Ancona, Italy.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Mustafa Yücel
- Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
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29
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Dahle H, Le Moine Bauer S, Baumberger T, Stokke R, Pedersen RB, Thorseth IH, Steen IH. Energy Landscapes in Hydrothermal Chimneys Shape Distributions of Primary Producers. Front Microbiol 2018; 9:1570. [PMID: 30061874 PMCID: PMC6055050 DOI: 10.3389/fmicb.2018.01570] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022] Open
Abstract
Hydrothermal systems are excellent natural laboratories for the study of how chemical energy landscapes shape microbial communities. Yet, only a few attempts have been made to quantify relationships between energy availability and microbial community structure in these systems. Here, we have investigated how microbial communities and chemical energy availabilities vary along cross-sections of two hydrothermal chimneys from the Soria Moria Vent Field and the Bruse Vent Field. Both vent fields are located on the Arctic Mid-Ocean Ridge, north of the Jan Mayen Island and the investigated chimneys were venting fluids with markedly different H2S:CH4 ratios. Energy landscapes were inferred from a stepwise in silico mixing of hydrothermal fluids (HFs) with seawater, where Gibbs energies of relevant redox-reactions were calculated at each step. These calculations formed the basis for simulations of relative abundances of primary producers in microbial communities. The simulations were compared with an analysis of 24 samples from chimney wall transects by sequencing of 16S rRNA gene amplicons using 454 sequencing. Patterns in relative abundances of sulfide oxidizing Epsilonproteobacteria and methane oxidizing Methylococcales and ANME-1, were consistent with simulations. However, even though H2 was present in HFs from both chimneys, the observed abundances of putative hydrogen oxidizing anaerobic sulfate reducers (Archaeoglobales) and methanogens (Methanococcales) in the inner parts of the Soria Moria Chimney were considerably higher than predicted by simulations. This indicates biogenic production of H2 in the chimney wall by fermentation, and suggests that biological activity inside the chimneys may modulate energy landscapes significantly. Our results are consistent with the notion that energy landscapes largely shape the distribution of primary producers in hydrothermal systems. Our study demonstrates how a combination of modeling and field observations can be useful in deciphering connections between chemical energy landscapes and metabolic networks within microbial communities.
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Affiliation(s)
- Håkon Dahle
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Tamara Baumberger
- Pacific Marine Environmental Laboratory (NOAA), Newport, OR, United States
| | - Runar Stokke
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Rolf B. Pedersen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ingunn H. Thorseth
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida H. Steen
- K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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30
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Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018; 6:E63. [PMID: 29973550 PMCID: PMC6163223 DOI: 10.3390/microorganisms6030063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.
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Affiliation(s)
- Anders Schouw
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Francesca Vulcano
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Irene Roalkvam
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - William Peter Hocking
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Eoghan Reeves
- Department of Earth Science and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Gunhild Bødtker
- Centre for Integrated Petroleum Research (CIPR), Uni Research AS, Nygårdsgaten 112, N-5008 Bergen, Norway.
| | - Ida Helene Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
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31
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Pjevac P, Meier DV, Markert S, Hentschker C, Schweder T, Becher D, Gruber-Vodicka HR, Richter M, Bach W, Amann R, Meyerdierks A. Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys. Front Microbiol 2018; 9:680. [PMID: 29696004 PMCID: PMC5904459 DOI: 10.3389/fmicb.2018.00680] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/22/2018] [Indexed: 11/15/2022] Open
Abstract
At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys.
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Affiliation(s)
- Petra Pjevac
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dimitri V Meier
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | | | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Harald R Gruber-Vodicka
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Symbiosis, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Michael Richter
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Ribocon GmbH, Bremen, Germany
| | - Wolfgang Bach
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Anke Meyerdierks
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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32
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Götz F, Longnecker K, Kido Soule MC, Becker KW, McNichol J, Kujawinski EB, Sievert SM. Targeted metabolomics reveals proline as a major osmolyte in the chemolithoautotroph Sulfurimonas denitrificans. Microbiologyopen 2018; 7:e00586. [PMID: 29423975 PMCID: PMC6079173 DOI: 10.1002/mbo3.586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/08/2017] [Accepted: 12/28/2017] [Indexed: 01/15/2023] Open
Abstract
Chemoautotrophic bacteria belonging to the genus Sulfurimonas in the class Campylobacteria are widespread in many marine environments characterized by redox interfaces, yet little is known about their physiological adaptations to different environmental conditions. Here, we used liquid chromatography coupled with tandem mass spectrometry (LC‐MS/MS) in a targeted metabolomics approach to study the adaptations of Sulfurimonas denitrificans to varying salt concentrations that are found in its natural habitat of tidal mudflats. Proline was identified as one of the most abundant internal metabolites and its concentration showed a strong positive correlation with ionic strength, suggesting that it acts as an important osmolyte in S. denitrificans. 2,3‐dihydroxypropane‐1‐sulfonate was also positively correlated with ionic strength, indicating it might play a previously unrecognized role in osmoregulation. Furthermore, the detection of metabolites from the reductive tricarboxylic acid cycle at high internal concentrations reinforces the importance of this pathway for carbon fixation in Campylobacteria and as a hub for biosynthesis. As the first report of metabolomic data for an campylobacterial chemolithoautotroph, this study provides data that will be useful to understand the adaptations of Campylobacteria to their natural habitat at redox interfaces.
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Affiliation(s)
- Florian Götz
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMAUSA
| | - Krista Longnecker
- Department of Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMAUSA
| | - Melissa C. Kido Soule
- Department of Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMAUSA
| | - Kevin W. Becker
- Department of Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMAUSA
| | - Jesse McNichol
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMAUSA
- Present address:
Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Elizabeth B. Kujawinski
- Department of Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMAUSA
| | - Stefan M. Sievert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMAUSA
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33
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Muto H, Takaki Y, Hirai M, Mino S, Sawayama S, Takai K, Nakagawa S. A Simple and Efficient RNA Extraction Method from Deep-Sea Hydrothermal Vent Chimney Structures. Microbes Environ 2017; 32:330-335. [PMID: 29187693 PMCID: PMC5745017 DOI: 10.1264/jsme2.me17048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals. This decrease in RNA was prevented by the addition of sodium tripolyphosphate (STPP), deoxynucleotide triphosphates (dNTPs), salmon sperm DNA, and NaOH. The addition of STPP was also effective for RNA extraction from the mixture of E. coli cells and mock chimney minerals when TRIzol reagent and the RNeasy column were used, but not when the RNeasy PowerSoil total RNA kit was used. A combination of STPP, TRIzol reagent, the RNeasy column, and sonication resulted in the highest RNA yield from a natural chimney. This indirect extraction procedure is simple, rapid, inexpensive, and may be used for large-scale RNA extraction.
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Affiliation(s)
- Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development (R&D) Center for Marine Biosciences, Marine Functional Biology Group (MFbio), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University.,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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34
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Gomez-Saez GV, Pop Ristova P, Sievert SM, Elvert M, Hinrichs KU, Bühring SI. Relative Importance of Chemoautotrophy for Primary Production in a Light Exposed Marine Shallow Hydrothermal System. Front Microbiol 2017; 8:702. [PMID: 28484442 PMCID: PMC5399606 DOI: 10.3389/fmicb.2017.00702] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/05/2017] [Indexed: 01/09/2023] Open
Abstract
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.
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Affiliation(s)
- Gonzalo V Gomez-Saez
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Petra Pop Ristova
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
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35
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Meier DV, Pjevac P, Bach W, Hourdez S, Girguis PR, Vidoudez C, Amann R, Meyerdierks A. Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. ISME JOURNAL 2017; 11:1545-1558. [PMID: 28375213 DOI: 10.1038/ismej.2017.37] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/30/2017] [Accepted: 02/02/2017] [Indexed: 11/09/2022]
Abstract
At deep-sea hydrothermal vents, primary production is carried out by chemolithoautotrophic microorganisms, with the oxidation of reduced sulfur compounds being a major driver for microbial carbon fixation. Dense and highly diverse assemblies of sulfur-oxidizing bacteria (SOB) are observed, yet the principles of niche differentiation between the different SOB across geochemical gradients remain poorly understood. In this study niche differentiation of the key SOB was addressed by extensive sampling of active sulfidic vents at six different hydrothermal venting sites in the Manus Basin, off Papua New Guinea. We subjected 33 diffuse fluid and water column samples and 23 samples from surfaces of chimneys, rocks and fauna to a combined analysis of 16S rRNA gene sequences, metagenomes and real-time in situ measured geochemical parameters. We found Sulfurovum Epsilonproteobacteria mainly attached to surfaces exposed to diffuse venting, while the SUP05-clade dominated the bacterioplankton in highly diluted mixtures of vent fluids and seawater. We propose that the high diversity within Sulfurimonas- and Sulfurovum-related Epsilonproteobacteria observed in this study derives from the high variation of environmental parameters such as oxygen and sulfide concentrations across small spatial and temporal scales.
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Affiliation(s)
- Dimitri V Meier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Petra Pjevac
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wolfgang Bach
- Department of Geosciences and MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Stephane Hourdez
- CNRS, Genetics of Adaptation to Extreme Environments Group, Roscoff, France.,Université Pierre et Marie Curie, Genetics of Adaptation to Extreme Environments Group, Roscoff, France
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Charles Vidoudez
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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36
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Wissuwa J, Bauer SLM, Steen IH, Stokke R. Complete genome sequence of Lutibacter profundi LP1 T isolated from an Arctic deep-sea hydrothermal vent system. Stand Genomic Sci 2017; 12:5. [PMID: 28078050 PMCID: PMC5219744 DOI: 10.1186/s40793-016-0219-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/07/2016] [Indexed: 11/10/2022] Open
Abstract
Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki's Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways. However, genes for the oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon sources. In accordance, the genome harbours 130 proteases and 104 carbohydrate-active enzymes, indicating a specialization in degrading organic matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization cluster was identified. Furthermore, a variety of enzymes may be secreted via T9SS and contribute to the hydrolytic variety of the microorganism. Genes for gliding motility are present, which may enable the bacteria to move within the biofilm. A substantial number of genes encoding for extracellular polysaccharide synthesis pathways, curli fibres and attachment to surfaces could mediate adhesion in the biofilm and may contribute to the biofilm formation. In addition to aerobic respiration, the complete denitrification pathway and genes for sulphide oxidation e.g. sulphide:quinone reductase are present in the genome. sulphide:quinone reductase and denitrification may serve as detoxification systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched environment. The information gained from the genome gives a greater insight in the functional role of L. profundi LP1T in the biofilm and its adaption strategy in an extreme environment.
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Affiliation(s)
- Juliane Wissuwa
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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37
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Scott JJ, Glazer BT, Emerson D. Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō'ihi Seamount. Environ Microbiol 2016; 19:301-316. [PMID: 27871143 DOI: 10.1111/1462-2920.13607] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 01/22/2023]
Abstract
Thirty kilometers south of the island of Hawai'i lies the Lō'ihi Seamount, an active submarine volcano that hosts a network of low-temperature hydrothermal vents enriched in ferrous iron that supports extensive microbial mats. These mats, which can be a half a meter deep, are composed of ferric iron bound to organic polymers - the metabolic byproduct of iron-oxidizing Zetaproteobacteria. Though the role of Zetaproteobacteria in mat formation is well established, we have a limited understanding of how differences in diversity are related to mat morphology. We used Minimum Entropy Decomposition and ZetaOtu classification to demonstrate cryptic diversity between closely related Zetaproteobacteria while showing habitat and geographic specificity. Veiled mats, common structures at Lō'ihi, exhibit distinct community composition and contain diversity not detected in other mat types, including specific Zetaproteobacteria and an unclassified Gammaproteobacteria. Our analyses also indicate that diversity can change dramatically across small spatial transects from points of active venting, yet we found comparatively few differences between major sampling sites. This study provides a better picture of the microbiome responsible for iron mat production at Lō'ihi and has broad implications for our understanding of these globally distributed communities.
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Affiliation(s)
- Jarrod J Scott
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
| | - Brian T Glazer
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd. Honolulu, HI, 96822, USA
| | - David Emerson
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
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38
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Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge. Sci Rep 2016; 6:25982. [PMID: 27169490 PMCID: PMC4864381 DOI: 10.1038/srep25982] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/25/2016] [Indexed: 02/01/2023] Open
Abstract
Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.
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39
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Meier DV, Bach W, Girguis PR, Gruber-Vodicka HR, Reeves EP, Richter M, Vidoudez C, Amann R, Meyerdierks A. HeterotrophicProteobacteriain the vicinity of diffuse hydrothermal venting. Environ Microbiol 2016; 18:4348-4368. [DOI: 10.1111/1462-2920.13304] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/13/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Dimitri V. Meier
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Wolfgang Bach
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
| | - Peter R. Girguis
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | | | - Eoghan P. Reeves
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
- University of Bergen, Department of Earth Science and Centre for Geobiology; Postboks 7803 N-5020 Bergen Norway
| | - Michael Richter
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Charles Vidoudez
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Anke Meyerdierks
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
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40
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Steen IH, Dahle H, Stokke R, Roalkvam I, Daae FL, Rapp HT, Pedersen RB, Thorseth IH. Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems. Front Microbiol 2016; 6:1510. [PMID: 26779165 PMCID: PMC4703759 DOI: 10.3389/fmicb.2015.01510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 01/23/2023] Open
Abstract
In order to fully understand the cycling of elements in hydrothermal systems it is critical to understand intra-field variations in geochemical and microbiological processes in both focused, high-temperature and diffuse, low-temperature areas. To reveal important causes and effects of this variation, we performed an extensive chemical and microbiological characterization of a low-temperature venting area in the Loki's Castle Vent Field (LCVF). This area, located at the flank of the large sulfide mound, is characterized by numerous chimney-like barite (BaSO4) structures (≤ 1 m high) covered with white cotton-like microbial mats. Results from geochemical analyses, microscopy (FISH, SEM), 16S rRNA gene amplicon-sequencing and metatranscriptomics were compared to results from previous analyses of biofilms growing on black smoker chimneys at LCVF. Based on our results, we constructed a conceptual model involving the geochemistry and microbiology in the LCVF. The model suggests that CH4 and H2S are important electron donors for microorganisms in both high-temperature and low-temperature areas, whereas the utilization of H2 seems restricted to high-temperature areas. This further implies that sub-seafloor processes can affect energy-landscapes, elemental cycling, and the metabolic activity of primary producers on the seafloor. In the cotton-like microbial mats on top of the active barite chimneys, a unique network of single cells of Epsilonproteobacteria interconnected by threads of extracellular polymeric substances (EPS) was seen, differing significantly from the long filamentous Sulfurovum filaments observed in biofilms on the black smokers. This network also induced nucleation of barite crystals and is suggested to play an essential role in the formation of the microbial mats and the chimneys. Furthermore, it illustrates variations in how different genera of Epsilonproteobacteria colonize and position cells in different vent fluid mixing zones within a vent field. This may be related to niche-specific physical characteristics. Altogether, the model provides a reference for future studies and illustrates the importance of systematic comparative studies of spatially closely connected niches in order to fully understand the geomicrobiology of hydrothermal systems.
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Affiliation(s)
- Ida H Steen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Frida-Lise Daae
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Hans Tore Rapp
- Centre for Geobiology, University of BergenBergen, Norway; Department of Biology, University of BergenBergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology, University of BergenBergen, Norway; Department of Earth Science, University of BergenBergen, Norway
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41
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Keller AH, Schleinitz KM, Starke R, Bertilsson S, Vogt C, Kleinsteuber S. Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer. Front Microbiol 2015; 6:1396. [PMID: 26696999 PMCID: PMC4674564 DOI: 10.3389/fmicb.2015.01396] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/23/2015] [Indexed: 11/13/2022] Open
Abstract
The population genome of an uncultured bacterium assigned to the Campylobacterales (Epsilonproteobacteria) was reconstructed from a metagenome dataset obtained by whole-genome shotgun pyrosequencing. Genomic DNA was extracted from a sulfate-reducing, m-xylene-mineralizing enrichment culture isolated from groundwater of a benzene-contaminated sulfidic aquifer. The identical epsilonproteobacterial phylotype has previously been detected in toluene- or benzene-mineralizing, sulfate-reducing consortia enriched from the same site. Previous stable isotope probing (SIP) experiments with 13C6-labeled benzene suggested that this phylotype assimilates benzene-derived carbon in a syntrophic benzene-mineralizing consortium that uses sulfate as terminal electron acceptor. However, the type of energy metabolism and the ecophysiological function of this epsilonproteobacterium within aromatic hydrocarbon-degrading consortia and in the sulfidic aquifer are poorly understood. Annotation of the epsilonproteobacterial population genome suggests that the bacterium plays a key role in sulfur cycling as indicated by the presence of an sqr gene encoding a sulfide quinone oxidoreductase and psr genes encoding a polysulfide reductase. It may gain energy by using sulfide or hydrogen/formate as electron donors. Polysulfide, fumarate, as well as oxygen are potential electron acceptors. Auto- or mixotrophic carbon metabolism seems plausible since a complete reductive citric acid cycle was detected. Thus the bacterium can thrive in pristine groundwater as well as in hydrocarbon-contaminated aquifers. In hydrocarbon-contaminated sulfidic habitats, the epsilonproteobacterium may generate energy by coupling the oxidation of hydrogen or formate and highly abundant sulfide with the reduction of fumarate and/or polysulfide, accompanied by efficient assimilation of acetate produced during fermentation or incomplete oxidation of hydrocarbons. The highly efficient assimilation of acetate was recently demonstrated by a pulsed 13C2-acetate protein SIP experiment. The capability of nitrogen fixation as indicated by the presence of nif genes may provide a selective advantage in nitrogen-depleted habitats. Based on this metabolic reconstruction, we propose acetate capture and sulfur cycling as key functions of Epsilonproteobacteria within the intermediary ecosystem metabolism of hydrocarbon-rich sulfidic sediments.
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Affiliation(s)
- Andreas H Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany ; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Kathleen M Schleinitz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Robert Starke
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University Uppsala, Sweden
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
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