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Kubik BC, Holden JF. Non-thermodynamic factors affect competition between thermophilic chemolithoautotrophs from deep-sea hydrothermal vents. Appl Environ Microbiol 2024:e0029224. [PMID: 39012100 DOI: 10.1128/aem.00292-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
Various environmental factors, including H2 availability, metabolic tradeoffs, optimal growth temperature, stochasticity, and hydrology, were examined to determine if they affect microbial competition between three autotrophic thermophiles. The thiosulfate reducer Desulfurobacterium thermolithotrophum (Topt72°C) was grown in mono- and coculture separately with the methanogens Methanocaldococcus jannaschii (Topt82°C) at 72°C and Methanothermococcus thermolithotrophicus (Topt65°C) at 65°C at high and low H2 concentrations. Both methanogens showed a metabolic tradeoff shifting from high growth rate-low cell yield at high H2 concentrations to low growth rate-high cell yield at low H2 concentrations and when grown in coculture with the thiosulfate reducer. In 1:1 initial ratios, D. thermolithotrophum outcompeted both methanogens at high and low H2, no H2S was detected on low H2, and it grew with only CO2 as the electron acceptor indicating a similar metabolic tradeoff with low H2. When the initial methanogen-to-thiosulfate reducer ratio varied from 1:1 to 104:1 with high H2, D. thermolithotrophum always outcompeted M. jannaschii at 72°C. However, M. thermolithotrophicus outcompeted D. thermolithotrophum at 65°C when the ratio was 103:1. A reactive transport model that mixed pure hydrothermal fluid with cold seawater showed that hyperthermophilic methanogens dominated in systems where the residence time of the mixed fluid above 72°C was sufficiently high. With shorter residence times, thermophilic thiosulfate reducers dominated. If residence times increased with decreasing fluid temperature along the flow path, then thermophilic methanogens could dominate. Thermophilic methanogen dominance spread to previously thiosulfate-reducer-dominated conditions if the initial ratio of thermophilic methanogen-to-thiosulfate reducer increased. IMPORTANCE The deep subsurface is the largest reservoir of microbial biomass on Earth and serves as an analog for life on the early Earth and extraterrestrial environments. Methanogenesis and sulfur reduction are among the more common chemolithoautotrophic metabolisms found in hot anoxic hydrothermal vent environments. Competition between H2-oxidizing sulfur reducers and methanogens is primarily driven by the thermodynamic favorability of redox reactions with the former outcompeting methanogens. This study demonstrated that competition between the hydrothermal vent chemolithoautotrophs Methanocaldococcus jannaschii, Methanothermococcus thermolithotrophicus, and Desulfurobacterium thermolithotrophum is also influenced by other overlapping factors such as staggered optimal growth temperatures, stochasticity, and hydrology. By modeling all aspects of microbial competition coupled with field data, a better understanding is gained on how methanogens can outcompete thiosulfate reducers in hot anoxic environments and how the deep subsurface contributes to biogeochemical cycling.
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Affiliation(s)
- Briana C Kubik
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - James F Holden
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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Bendia AG, Moreira JCF, Ferreira JCN, Romano RG, Ferreira IGC, Franco DC, Evangelista H, Montone RC, Pellizari VH. Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats. AN ACAD BRAS CIENC 2023; 95:e20211442. [PMID: 37820122 DOI: 10.1590/0001-3765202320211442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/27/2022] [Indexed: 10/13/2023] Open
Abstract
Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.
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Affiliation(s)
- Amanda G Bendia
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Julio Cezar F Moreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Juliana C N Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Renato G Romano
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Ivan G C Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Diego C Franco
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Heitor Evangelista
- Universidade do Estado do Rio de Janeiro (UERJ), Instituto de Biologia Roberto Alcantara Gomes, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Rosalinda C Montone
- Universidade de São Paulo (USP), Departamento de Oceanografia Física, Química e Geológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Vivian Helena Pellizari
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
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Sanz-Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME COMMUNICATIONS 2023; 3:92. [PMID: 37660234 PMCID: PMC10475052 DOI: 10.1038/s43705-023-00290-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/04/2023]
Abstract
Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
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Affiliation(s)
- Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering; The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016, Paris, France
- Directors' Research European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Susana Agustí
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
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Nagarajan V, Tsai HC, Chen JS, Hussain B, Fan CW, Asif A, Hsu BM. The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan. Microorganisms 2022; 10:microorganisms10030500. [PMID: 35336075 PMCID: PMC8949176 DOI: 10.3390/microorganisms10030500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
The Tatun Volcanic Group (TVG), located in northern Taiwan, is characterized by acidic hot springs where the outflow of the hot springs may affect the properties of the associated lotic water bodies. We investigated the bacterial diversity and functional profiles of the Peihuang (PHC), HuangGang (HGC), and Nanhuang Creeks (NHC) located in the TVG basin using 16S rRNA gene sequencing coupled with statistical analyses. Water samples were collected from various streams of the creeks for two months of the year. The NHC showed the highest diversity, richness, and a unique number of phyla, which was followed by the HGC. A reduced number of phyla and a lower diversity was noticed in the PHC. The NHC was found to be abundant in the genera Armatimonas, Prosthecobacter, Pirellula, and Bdellovibrio, whereas the HGC was rich in Thiomonas, Acidiphilium, Prevotella, Acidocella, Acidithiobacillus, and Metallibacterium. The PHC was abundant in Thiomonsa, Legionella, Acidocella, and Sulfuriferula. The samples did not show any strong seasonal variations with the bacterial diversity and abundance; however, the relative abundance of each sampling site varied within the sampling months. The iron transport protein- and the sulfur metabolism-related pathways were predicted to be the key functions in all the creeks, whereas the heavy metal-related functions, such as the cobalt/nickel transport protein and the cobalt–zinc–cadmium efflux system were found to be abundant in the HGC and PHC, respectively. The abundance of Bdellovibrio in the NHC, Diplorickettsia in the HGC, and Legionella in the PHC samples indicated a higher anthropogenic impact over the creek water quality. This study provides the data to understand the distinct bacterial community structure, as well as the functional potentials of the three major watersheds, and helps the knowledge of the impact of the physicochemical properties of the TVG hot springs upon the watersheds.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien 970, Taiwan;
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung 824, Taiwan;
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 621, Taiwan
| | - Cheng-Wei Fan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Doctoral Program in Science, Technology, Environment and Mathematics (STEM), National Chung Cheng University, Chiayi 621, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Correspondence: ; Tel.: +886-52-720-411 (ext. 66218)
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5
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François DX, Godfroy A, Mathien C, Aubé J, Cathalot C, Lesongeur F, L'Haridon S, Philippon X, Roussel EG. Persephonella atlantica sp. nov.: How to adapt to physico-chemical gradients in high temperature hydrothermal habitats. Syst Appl Microbiol 2020; 44:126176. [PMID: 33422731 DOI: 10.1016/j.syapm.2020.126176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
A novel thermophilic, microaerophilic and anaerobic, hydrogen- sulphur- and thiosulphate-oxidising bacterium, designated MO1340T, was isolated from a deep-sea hydrothermal chimney collected from the Lucky Strike hydrothermal vent field on the Mid-Atlantic Ridge. Cells were short, motile rods of 1.4-2.2μm length and 0.5-0.8μm width. Optimal growth was observed for a NaCl concentration of 2.5 % (w/v) at pH 6.5. As for other members of the genus Persephonella, strain MO1340T was strictly chemolithoautotrophic and could oxidise hydrogen, elemental sulphur or thiosulphate using oxygen as electron acceptor. Anaerobic nitrate reduction using hydrogen could also be performed. Each catabolic reaction had a different optimal growth temperature (65 to 75°C) and an optimal dissolved oxygen concentration (11.4 to 119.7 μM at 70°C for aerobic reactions) that varied according to the electron donors utilised. These experimental results are consistent with the distribution of these catabolic substrates along the temperature gradient observed in active hydrothermal systems. They strongly suggest that this adaptive strategy could confer a selective advantage for strain MO1340T in the dynamic part of the ecosystem where hot, reduced hydrothermal fluid mixes with cold, oxygenated seawater. Phylogenetic analysis indicated that strain MO1340T was a member of the genus Persephonella within the order Hydrogenothermales as it shared a 16S rRNA gene sequence similarity <95.5 % and ANI respectively 75.66 % with closest described Persephonella (P. hydrogeniphila 29WT). On the basis of the physiological and genomic properties of the new isolate, the name Persephonella atlantica sp. nov. is proposed. The type strain is MO1340T (=UBOCC-M-3359T =JCM 34026T).
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Affiliation(s)
- David X François
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Anne Godfroy
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Clémentine Mathien
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Johanne Aubé
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Cécile Cathalot
- Ifremer, Laboratoire Cycle Géochimique et Ressources (LCG/GM/REM), F-29280, Plouzané, France
| | - Françoise Lesongeur
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Stéphane L'Haridon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Xavier Philippon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France
| | - Erwan G Roussel
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes UMR6197, F-29280, Plouzané, France.
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6
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Sanz-Sáez I, Salazar G, Sánchez P, Lara E, Royo-Llonch M, Sà EL, Lucena T, Pujalte MJ, Vaqué D, Duarte CM, Gasol JM, Pedrós-Alió C, Sánchez O, Acinas SG. Diversity and distribution of marine heterotrophic bacteria from a large culture collection. BMC Microbiol 2020; 20:207. [PMID: 32660423 PMCID: PMC7359222 DOI: 10.1186/s12866-020-01884-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/26/2020] [Indexed: 01/09/2023] Open
Abstract
Background Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. Results The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. Conclusions Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.
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Affiliation(s)
- Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain.,Institute of Marine Sciences (CNR-ISMAR), National Research Council, Castello 2737/F Arsenale-Tesa 104, 30122, Venezia, Italy
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Elisabet L Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Teresa Lucena
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - María J Pujalte
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain.
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7
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Adam N, Perner M. Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents. Front Microbiol 2018; 9:2873. [PMID: 30532749 PMCID: PMC6265342 DOI: 10.3389/fmicb.2018.02873] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/08/2018] [Indexed: 11/13/2022] Open
Abstract
Deep-sea hydrothermal vents may provide one of the largest reservoirs on Earth for hydrogen-oxidizing microorganisms. Depending on the type of geological setting, hydrothermal environments can be considerably enriched in hydrogen (up to millimolar concentrations). As hot, reduced hydrothermal fluids ascend to the seafloor they mix with entrained cold, oxygenated seawater, forming thermal and chemical gradients along their fluid pathways. Consequently, in these thermally and chemically dynamic habitats biochemically distinct hydrogenases (adapted to various temperature regimes, oxygen and hydrogen concentrations) from physiologically and phylogenetically diverse Bacteria and Archaea can be expected. Hydrogen oxidation is one of the important inorganic energy sources in these habitats, capable of providing relatively large amounts of energy (237 kJ/mol H2) for driving ATP synthesis and autotrophic CO2 fixation. Therefore, hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production. So far, the specific role of hydrogen-utilizing microorganisms in deep-sea hydrothermal ecosystems has been investigated by isolating hydrogen-oxidizers, measuring hydrogen consumption (ex situ), studying hydrogenase gene distribution and more recently by analyzing metatranscriptomic and metaproteomic data. Here we summarize this available knowledge and discuss the advent of new techniques for the identification of novel hydrogen-uptake and -evolving enzymes from hydrothermal vent microorganisms.
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Affiliation(s)
| | - Mirjam Perner
- Geomicrobiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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8
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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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Ferrera I, Arístegui J, González JM, Montero MF, Fraile-Nuez E, Gasol JM. Transient changes in bacterioplankton communities induced by the submarine volcanic eruption of El Hierro (Canary Islands). PLoS One 2015; 10:e0118136. [PMID: 25671714 PMCID: PMC4324844 DOI: 10.1371/journal.pone.0118136] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/08/2015] [Indexed: 11/24/2022] Open
Abstract
The submarine volcanic eruption occurring near El Hierro (Canary Islands) in October 2011 provided a unique opportunity to determine the effects of such events on the microbial populations of the surrounding waters. The birth of a new underwater volcano produced a large plume of vent material detectable from space that led to abrupt changes in the physical-chemical properties of the water column. We combined flow cytometry and 454-pyrosequencing of 16S rRNA gene amplicons (V1–V3 regions for Bacteria and V3–V5 for Archaea) to monitor the area around the volcano through the eruptive and post-eruptive phases (November 2011 to April 2012). Flow cytometric analyses revealed higher abundance and relative activity (expressed as a percentage of high-nucleic acid content cells) of heterotrophic prokaryotes during the eruptive process as compared to post-eruptive stages. Changes observed in populations detectable by flow cytometry were more evident at depths closer to the volcano (~70–200 m), coinciding also with oxygen depletion. Alpha-diversity analyses revealed that species richness (Chao1 index) decreased during the eruptive phase; however, no dramatic changes in community composition were observed. The most abundant taxa during the eruptive phase were similar to those in the post-eruptive stages and to those typically prevalent in oceanic bacterioplankton communities (i.e. the alphaproteobacterial SAR11 group, the Flavobacteriia class of the Bacteroidetes and certain groups of Gammaproteobacteria). Yet, although at low abundance, we also detected the presence of taxa not typically found in bacterioplankton communities such as the Epsilonproteobacteria and members of the candidate division ZB3, particularly during the eruptive stage. These groups are often associated with deep-sea hydrothermal vents or sulfur-rich springs. Both cytometric and sequence analyses showed that once the eruption ceased, evidences of the volcano-induced changes were no longer observed.
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Affiliation(s)
- Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
- * E-mail:
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - José M. González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - María F. Montero
- Instituto de Oceanografía y Cambio Global, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Eugenio Fraile-Nuez
- Instituto Español de Oceanografía, Centro Oceanográfico de Canarias, Santa Cruz de Tenerife, Spain
| | - Josep M. Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
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