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Dixit S, Kumar S, Sharma R, Banakar PS, Singh M, Keshri A, Tyagi AK. Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review. Anim Biotechnol 2023; 34:3187-3205. [PMID: 35713100 DOI: 10.1080/10495398.2022.2078979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Manvendra Singh
- Krishi Vigyan Kendra, Banda University of Agriculture and Technology, Banda, India
| | - Anchal Keshri
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - A K Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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2
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Arcadi E, Buschi E, Rastelli E, Tangherlini M, De Luca P, Esposito V, Calogero R, Andaloro F, Romeo T, Danovaro R. Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field. Microorganisms 2023; 11:2464. [PMID: 37894122 PMCID: PMC10608945 DOI: 10.3390/microorganisms11102464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/18/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.
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Affiliation(s)
- Erika Arcadi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Valentina Esposito
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale—OGS Borgo Grotta Gigante 42/C, 34010 Sgonico, Italy;
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Via dei Mille 46, 98057 Milazzo, Italy
- National Institute for Environmental Protection and Research, Via dei Mille 46, 98057 Milazzo, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
- National Biodiversity Future Centre (NBFC), 90133 Palermo, Italy
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3
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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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4
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Barosa B, Ferrillo A, Selci M, Giardina M, Bastianoni A, Correggia M, di Iorio L, Bernardi G, Cascone M, Capuozzo R, Intoccia M, Price R, Vetriani C, Cordone A, Giovannelli D. Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy. Front Microbiol 2023; 14:1134114. [PMID: 37637107 PMCID: PMC10452888 DOI: 10.3389/fmicb.2023.1134114] [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: 12/29/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.
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Affiliation(s)
- Bernardo Barosa
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Marco Giardina
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Alessia Bastianoni
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Monica Correggia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Luciano di Iorio
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Rosaria Capuozzo
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Michele Intoccia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Roy Price
- School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Costantino Vetriani
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale Delle Ricerche, CNR-IRBIM, Ancona, Italy
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan
- Marine Chemistry and Geochemistry Department–Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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5
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Patwardhan S, Phan J, Smedile F, Vetriani C. The Genome of Varunaivibrio sulfuroxidans Strain TC8 T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea. Microorganisms 2023; 11:1366. [PMID: 37374867 DOI: 10.3390/microorganisms11061366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
Varunaivibrio sulfuroxidans type strain TC8T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin-Benson-Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism's metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jonathan Phan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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6
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Sciutteri V, Smedile F, Vizzini S, Mazzola A, Vetriani C. Microbial Biofilms Along a Geochemical Gradient at the Shallow-Water Hydrothermal System of Vulcano Island, Mediterranean Sea. Front Microbiol 2022; 13:840205. [PMID: 35283854 PMCID: PMC8905295 DOI: 10.3389/fmicb.2022.840205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
Shallow water hydrothermal vents represent highly dynamic environments where strong geochemical gradients can shape microbial communities. Recently, these systems are being widely used for investigating the effects of ocean acidification on biota as vent emissions can release high CO2 concentrations causing local pH reduction. However, other gas species, as well as trace elements and metals, are often released in association with CO2 and can potentially act as confounding factors. In this study, we evaluated the composition, diversity and inferred functional profiles of microbial biofilms in Levante Bay (Vulcano Island, Italy, Mediterranean Sea), a well-studied shallow-water hydrothermal vent system. We analyzed 16S rRNA transcripts from biofilms exposed to different intensity of hydrothermal activity, following a redox and pH gradient across the bay. We found that elevated CO2 concentrations causing low pH can affect the response of bacterial groups and taxa by either increasing or decreasing their relative abundance. H2S proved to be a highly selective factor shaping the composition and affecting the diversity of the community by selecting for sulfide-dependent, chemolithoautotrophic bacteria. The analysis of the 16S rRNA transcripts, along with the inferred functional profile of the communities, revealed a strong influence of H2S in the southern portion of the study area, and temporal succession affected the inferred abundance of genes for key metabolic pathways. Our results revealed that the composition of the microbial assemblages vary at very small spatial scales, mirroring the highly variable geochemical signature of vent emissions and cautioning for the use of these environments as models to investigate the effects of ocean acidification on microbial diversity.
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Affiliation(s)
- Valentina Sciutteri
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Department of Earth and Marine Sciences, University of Palermo, Palermo, Italy
| | - Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Salvatrice Vizzini
- Department of Earth and Marine Sciences, University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare, Rome, Italy
| | - Antonio Mazzola
- Department of Earth and Marine Sciences, University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare, Rome, Italy
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
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7
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Ecological and Biotechnological Relevance of Mediterranean Hydrothermal Vent Systems. MINERALS 2022. [DOI: 10.3390/min12020251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Marine hydrothermal systems are a special kind of extreme environments associated with submarine volcanic activity and characterized by harsh chemo-physical conditions, in terms of hot temperature, high concentrations of CO2 and H2S, and low pH. Such conditions strongly impact the living organisms, which have to develop adaptation strategies to survive. Hydrothermal systems have attracted the interest of researchers due to their enormous ecological and biotechnological relevance. From ecological perspective, these acidified habitats are useful natural laboratories to predict the effects of global environmental changes, such as ocean acidification at ecosystem level, through the observation of the marine organism responses to environmental extremes. In addition, hydrothermal vents are known as optimal sources for isolation of thermophilic and hyperthermophilic microbes, with biotechnological potential. This double aspect is the focus of this review, which aims at providing a picture of the ecological features of the main Mediterranean hydrothermal vents. The physiological responses, abundance, and distribution of biotic components are elucidated, by focusing on the necto-benthic fauna and prokaryotic communities recognized to possess pivotal role in the marine ecosystem dynamics and as indicator species. The scientific interest in hydrothermal vents will be also reviewed by pointing out their relevance as source of bioactive molecules.
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8
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Rodríguez-Valdez G, Romero-Geraldo R, Medina-Basulto G, Reyes-Becerril M, Angulo C. Immunostimulant Activity of Bacteria Isolated from Extreme Environments in Baja California Sur, Mexico: A Bioprospecting Approach. Indian J Microbiol 2022; 62:234-241. [DOI: 10.1007/s12088-022-01002-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022] Open
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9
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Wang Z, Wang L, Liu R, Li Z, Wu J, Wei X, Wei W, Fang J, Cao J, Wei Y, Xie Z. Community structure and activity potentials of archaeal communities in hadal sediments of the Mariana and Mussau trenches. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:150-161. [PMID: 37073355 PMCID: PMC10077302 DOI: 10.1007/s42995-021-00105-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/16/2021] [Indexed: 05/03/2023]
Abstract
Hadal trenches are the least explored marine habitat on earth. Archaea has been shown to be the dominant group in trench sediments. However, the activity potentials and detailed diversity of these communities as well as their inter-trench variations are still not known. In this study, we combined datasets from two pairs of primers to investigate at high resolution the structure and activity potentials of the archaeal communities in vertically sectioned sediment cores taken from the deepest points of the Mariana (10,853 m) and Mussau (7011 m) trenches. The compositions of the potentially active communities revealed, via 16S ribosomal RNA gene (rDNA) and RNA (rRNA), significant differences between samples. Marine Group I (MGI), with nine identified subgroups, was the most dominant class in the active archaeal communities of the two trenches. Significantly different species composition and vertical variations were observed between the two trenches. Vertical transitions from aerobic MGI α to anaerobic MGI η and υ subgroups were observed in MST but not in MT sediments, which might be related to the faster microbial oxygen consumption in MST. These results provide a better understanding on archaeal activity and diversity in trench sediments. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00105-y.
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Affiliation(s)
- Zixuan Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Zhenzhen Li
- State Key Laboratory of Geological Process and Mineral Resources, Department of Earth Sciences, China University of Geosciences, Wuhan, 430074 China
| | - JiaXin Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Xing Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Wenxia Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813 USA
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 China
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10
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Lin YS, Lin HT, Wang BS, Huang WJ, Lin LH, Tsai AY. Intense but variable autotrophic activity in a rapidly flushed shallow-water hydrothermal plume (Kueishantao Islet, Taiwan). GEOBIOLOGY 2021; 19:87-101. [PMID: 33043601 DOI: 10.1111/gbi.12418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/11/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
Shallow-water hydrothermal plumes concomitantly host both photosynthetic and chemoautotrophic organisms in a single biotope. Yet, rate measurements to quantify the contributions of different autotrophic activity types are scarce. Herein, we measured the light and dark dissolved inorganic carbon (DIC) uptake rates in the plume water of the Kueishantao hydrothermal field using the 13 C-labeling approach. Seventy percent of the plume-water samples had chemoautotrophy as the dominant mode of carbon fixation, with the dark DIC uptake rates (up to 18.6 mg C/m3 /h) within the range of the primary production in productive inner-shelf waters. When considered alongside the geochemical and microbiological observations, the rate data reveal the distribution of different trophic activities in the hydrothermal plume. The autotrophic activity at the initial phase of plume dispersal is low. This is explained by the short response time the chemoautotrophs have to the stimulation from vent-fluid discharge, and the harmful effects of hydrothermal substances on phytoplankton. As plume dispersal and mixing continue, chemoautotrophic activities begin to rise and peak in waters that have low-to-moderate Si(OH)4 content. Toward the plume margin, chemoautotrophy declines to background levels, whereas photosynthesis by phytoplankton regains importance. Our results also provide preliminary indication to the loci of enhanced heterotrophy in the plume. Results of artificial mixing experiments suggest that previously formed plume water is the primary source of microbial inoculum for new plume water. This self-inoculation mechanism, in combination with the intense DIC uptake, helps to sustain a distinct planktonic autotrophic community in this rapidly flushed hydrothermal plume.
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Affiliation(s)
- Yu-Shih Lin
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Huei-Ting Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Bo-Shian Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan
- National Academy of Marine Research, Kaohsiung, Taiwan
| | - Wei-Jen Huang
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - An-Yi Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
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11
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Bellec L, Cambon-Bonavita MA, Durand L, Aube J, Gayet N, Sandulli R, Brandily C, Zeppilli D. Microbial Communities of the Shallow-Water Hydrothermal Vent Near Naples, Italy, and Chemosynthetic Symbionts Associated With a Free-Living Marine Nematode. Front Microbiol 2020; 11:2023. [PMID: 32973733 PMCID: PMC7469538 DOI: 10.3389/fmicb.2020.02023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/30/2020] [Indexed: 11/17/2022] Open
Abstract
Shallow-water hydrothermal vents are widespread, especially in the Mediterranean Sea, owing to the active volcanism of the area. Apart free microbial communities’ investigations, few biological studies have been leaded yet. Investigations of microbial communities associated with Nematoda, an ecologically important group in sediments, can help to improve our overall understanding of these ecosystems. We used a multidisciplinary-approach, based on microscopic observations (scanning electron microscopy: SEM and Fluorescence In Situ Hybridization: FISH) coupled with a molecular diversity analysis using metabarcoding, based on the 16S rRNA gene (V3-V4 region), to characterize the bacterial community of a free-living marine nematode and its environment, the shallow hydrothermal vent near Naples (Italy). Observations of living bacteria in the intestine (FISH), molecular and phylogenetic analyses showed that this species of nematode harbors its own bacterial community, distinct from the surrounding sediment and water. Metabarcoding results revealed the specific microbiomes of the sediment from three sites of this hydrothermal area to be composed mainly of sulfur oxidizing and reducing related bacteria.
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Affiliation(s)
- Laure Bellec
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, Plouzané, France.,EPOC, UMR 5805, University of Bordeaux, Arcachon, France
| | | | - Lucile Durand
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, Plouzané, France
| | - Johanne Aube
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, Plouzané, France
| | - Nicolas Gayet
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France
| | - Roberto Sandulli
- Laboratory of Marine Ecology, Department of Science and Technology, University of Naples "Parthenope," Naples, Italy
| | - Christophe Brandily
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France
| | - Daniela Zeppilli
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France
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12
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Marine bacteria associated with shallow hydrothermal systems in the Gulf of California with the capacity to produce biofilm inhibiting compounds. Arch Microbiol 2020; 202:1477-1488. [DOI: 10.1007/s00203-020-01851-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/09/2019] [Accepted: 03/01/2020] [Indexed: 12/28/2022]
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13
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Phylogenetic Diversity of Archaea in Shallow Hydrothermal Vents of Eolian Islands, Italy. DIVERSITY 2019. [DOI: 10.3390/d11090156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant to the extreme conditions than prokaryotes. Archaea and bacteria are the key elements for the functioning of these ecosystems, as they are involved in the transformation of inorganic compounds released from the vent emissions and are at the basis of the hydrothermal system food web. New extremophilic archaea (thermophilic, hyperthermophilic, acidophilic, alkalophilic, etc.) have been isolated from vents of Vulcano Island, exhibiting interesting features potentially valuable in biotechnology. Metagenomic analyses, which mainly involved molecular studies of the 16S rRNA gene, provided different insights into microbial composition associated with Eolian SHS. Archaeal community composition at Eolian vent sites results greatly affected by the geochemistry of the studied vents, principally by hypersaline conditions and declining temperatures. Archaeal community in sediments was mostly composed by hyperthermophilic members of Crenarchaeota (class Thermoprotei) and Euryarchaeota (Thermococci and Methanococci) at the highest temperature condition. Mesophilic Euryarchaeota (Halobacteria, Methanomicrobia, and Methanobacteria) increased with decreasing temperatures. Eolian SHS harbor a high diversity of largely unknown archaea, and the studied vents may be an important source of new isolates potentially useful for biotechnological purposes.
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14
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Pohlner M, Dlugosch L, Wemheuer B, Mills H, Engelen B, Reese BK. The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions. Front Microbiol 2019; 10:659. [PMID: 31001232 PMCID: PMC6454203 DOI: 10.3389/fmicb.2019.00659] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/15/2019] [Indexed: 12/21/2022] Open
Abstract
General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the Rhodobacteraceae are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range. Thus, knowledge on these community members is limited, even though their absolute numbers might exceed those from the pelagic zone by orders of magnitudes. To unravel the distribution and diversity of benthic, metabolically active Rhodobacteraceae, we have now analyzed an already existing library of bacterial 16S rRNA transcripts. The dataset originated from 154 individual sediment samples comprising seven oceanic regions and a broad variety of environmental conditions. Across all samples, a total of 0.7% of all 16S rRNA transcripts was annotated as Rhodobacteraceae. Among those, Sulfitobacter, Paracoccus, and Phaeomarinomonas were the most abundant cultured representatives, but the majority (78%) was affiliated to uncultured family members. To define them, the 45 most abundant Rhodobacteraceae-OTUs assigned as "uncultured" were phylogenetically assembled in new clusters. Their next relatives particularly belonged to different subgroups other than the Roseobacter group, reflecting a large part of the hidden diversity within the benthic Rhodobacteraceae with unknown functions. The general composition of active Rhodobacteraceae communities was found to be specific for the geographical location, exhibiting a decreasing richness with sediment depth. One-third of the Rhodobacteraceae-OTUs significantly responded to the prevailing redox regime, suggesting an adaption to anoxic conditions. A possible approach to predict their physiological properties is to identify the metabolic capabilities of their nearest relatives. Those need to be proven by physiological experiments, as soon an isolate is available. Because many uncultured members of these subgroups likely thrive under anoxic conditions, in future research, a molecular-guided cultivation strategy can be pursued to isolate novel Rhodobacteraceae from sediments.
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Affiliation(s)
- Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Group “Biology of Geological Processes”, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - Heath Mills
- Rhodium Scientific LLC, San Antonio, TX, United States
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States
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15
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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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16
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Zammuto V, Fuchs FM, Fiebrandt M, Stapelmann K, Ulrich NJ, Maugeri TL, Pukall R, Gugliandolo C, Moeller R. Comparing Spore Resistance of Bacillus Strains Isolated from Hydrothermal Vents and Spacecraft Assembly Facilities to Environmental Stressors and Decontamination Treatments. ASTROBIOLOGY 2018; 18:1425-1434. [PMID: 30289268 DOI: 10.1089/ast.2017.1715] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Submarine hydrothermal vents are inhabited by a variety of microorganisms capable of tolerating environmental extremes, making them ideal candidates to further expand our knowledge of the limitations for terrestrial life, including their ability to survive the exposure of spaceflight-relevant conditions. The spore resistance of two Bacillus spp. strains, APA and SBP3, isolated from two shallow vents off Panarea Island (Aeolian Islands, Italy), to artificial and environmental stressors (i.e., UVC radiation, X-rays, heat, space vacuum, hydrogen peroxide [H2O2], and low-pressure plasma), was compared with that of two close phylogenetic relatives (Bacillus horneckiae and Bacillus oceanisediminis). Additional comparisons were made with Bacillus sp. isolated from spacecraft assembly facilities (B. horneckiae, Bacillus pumilus SAFR-032, and Bacillus nealsonii) and the biodosimetry strain and space microbiology model organism Bacillus subtilis. Overall, a high degree of spore resistance to stressors was observed for the strains isolated from spacecraft assembly facilities, with an exceptional level of resistance seen by B. pumilus SAFR-032. The environmental isolate SBP3 showed a more robust spore resistance to UVC, X-rays, H2O2, dry heat, and space vacuum than the closely related B. horneckiae. Both strains (SBP3 and APA) were more thermotolerant than their relatives, B. horneckiae and B. oceanisediminis, respectively. SBP3 may have a novel use as a bacterial model organism for future interrogations into the potential of forward contamination in extraterrestrial environments (e.g., icy moons of Jupiter or Saturn), spacecraft sterilization and, broadly, microbial responses to spaceflight-relevant environmental stressors.
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Affiliation(s)
- Vincenzo Zammuto
- 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Center for Extreme Environments and Extremophiles, University of Messina , Messina, Italy
| | - Felix M Fuchs
- 2 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Marcel Fiebrandt
- 3 Biomedical Applications of Plasma Technology, Institute for Electrical Engineering and Plasma Technology, Faculty of Electrical Engineering and Information Technology, Ruhr University Bochum , Bochum, Germany
| | - Katharina Stapelmann
- 3 Biomedical Applications of Plasma Technology, Institute for Electrical Engineering and Plasma Technology, Faculty of Electrical Engineering and Information Technology, Ruhr University Bochum , Bochum, Germany
| | - Nikea J Ulrich
- 2 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Teresa L Maugeri
- 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Center for Extreme Environments and Extremophiles, University of Messina , Messina, Italy
| | - Rüdiger Pukall
- 4 Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig, Germany
| | - Concetta Gugliandolo
- 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Center for Extreme Environments and Extremophiles, University of Messina , Messina, Italy
| | - Ralf Moeller
- 2 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR e.V.), Cologne, Germany
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17
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Bendia AG, Signori CN, Franco DC, Duarte RTD, Bohannan BJM, Pellizari VH. A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica. Front Microbiol 2018; 9:899. [PMID: 29867810 PMCID: PMC5949364 DOI: 10.3389/fmicb.2018.00899] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
Active volcanoes in Antarctica contrast with their predominantly cold surroundings, resulting in environmental conditions capable of selecting for versatile and extremely diverse microbial communities. This is especially true on Deception Island, where geothermal, marine, and polar environments combine to create an extraordinary range of environmental conditions. Our main goal in this study was to understand how microbial community structure is shaped by gradients of temperature, salinity, and geochemistry in polar marine volcanoes. Thereby, we collected surface sediment samples associated with fumaroles and glaciers at two sites on Deception, with temperatures ranging from 0 to 98°C. Sequencing of the 16S rRNA gene was performed to assess the composition and diversity of Bacteria and Archaea. Our results revealed that Deception harbors a combination of taxonomic groups commonly found both in cold and geothermal environments of continental Antarctica, and also groups normally identified at deep and shallow-sea hydrothermal vents, such as hyperthermophilic archaea. We observed a clear separation in microbial community structure across environmental gradients, suggesting that microbial community structure is strongly niche driven on Deception. Bacterial community structure was significantly associated with temperature, pH, salinity, and chemical composition; in contrast, archaeal community structure was strongly associated only with temperature. Our work suggests that Deception represents a peculiar "open-air" laboratory to elucidate central questions regarding molecular adaptability, microbial evolution, and biogeography of extremophiles in polar regions.
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Affiliation(s)
- Amanda G Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Camila N Signori
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Diego C Franco
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Rubens T D Duarte
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
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18
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Pop Ristova P, Pichler T, Friedrich MW, Bühring SI. Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles). Front Microbiol 2017; 8:2400. [PMID: 29255454 PMCID: PMC5722836 DOI: 10.3389/fmicb.2017.02400] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022] Open
Abstract
Shallow-water hydrothermal systems represent extreme environments with unique biogeochemistry and high biological productivity, at which autotrophic microorganisms use both light and chemical energy for the production of biomass. Microbial communities of these ecosystems are metabolically diverse and possess the capacity to transform a large range of chemical compounds. Yet, little is known about their diversity or factors shaping their structure or how they compare to coastal sediments not impacted by hydrothermalism. To this end, we have used automated ribosomal intergenic spacer analysis (ARISA) and high-throughput Illumina sequencing combined with porewater geochemical analysis to investigate microbial communities along geochemical gradients in two shallow-water hydrothermal systems off the island of Dominica (Lesser Antilles). At both sites, venting of hydrothermal fluids substantially altered the porewater geochemistry by enriching it with silica, iron and dissolved inorganic carbon, resulting in island-like habitats with distinct biogeochemistry. The magnitude of fluid flow and difference in sediment grain size, which impedes mixing of the fluids with seawater, were correlated with the observed differences in the porewater geochemistry between the two sites. Concomitantly, individual sites harbored microbial communities with a significantly different community structure. These differences could be statistically linked to variations in the porewater geochemistry and the hydrothermal fluids. The two shallow-water hydrothermal systems of Dominica harbored bacterial communities with high taxonomical and metabolic diversity, predominated by heterotrophic microorganisms associated with the Gammaproteobacterial genera Pseudomonas and Pseudoalteromonas, indicating the importance of heterotrophic processes. Overall, this study shows that shallow-water hydrothermal systems contribute substantially to the biogeochemical heterogeneity and bacterial diversity of coastal sediments.
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Affiliation(s)
- Petra Pop Ristova
- Hydrothermal Geomicrobiology Group, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Pichler
- Geochemistry and Hydrogeology, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Solveig I. Bühring
- Hydrothermal Geomicrobiology Group, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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19
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Wang L, Cheung MK, Liu R, Wong CK, Kwan HS, Hwang JS. Diversity of Total Bacterial Communities and Chemoautotrophic Populations in Sulfur-Rich Sediments of Shallow-Water Hydrothermal Vents off Kueishan Island, Taiwan. MICROBIAL ECOLOGY 2017; 73:571-582. [PMID: 27909749 DOI: 10.1007/s00248-016-0898-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/10/2016] [Indexed: 06/06/2023]
Abstract
Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM). In the vent area, Sulfurovum and Sulfurimonas of Epsilonproteobacteria appeared to dominate the benthic bacterial community. Results of aclB gene analysis also suggested involvement of these bacteria in carbon fixation using the reductive tricarboxylic acid (rTCA) cycle. Analysis of the cbbM gene showed that Alphaproteobacterial members such as the purple non-sulfur bacteria were the major chemoautotrophic bacteria involving in carbon fixation via the Calvin-Benson-Bassham (CBB) cycle. However, they only accounted for <2% of the total bacterial community in the vent area. These findings suggest that the rTCA cycle is the major chemoautotrophic carbon fixation pathway in sediments of the shallow-water HTVs off Kueishan Island.
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Affiliation(s)
- Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Chong Kim Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
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20
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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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21
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Shen LD, Wu HS, Gao ZQ, Liu X, Li J. Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats. Sci Rep 2016; 6:25647. [PMID: 27157928 PMCID: PMC4860643 DOI: 10.1038/srep25647] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/20/2016] [Indexed: 12/26/2022] Open
Abstract
Methane oxidation coupled to nitrite reduction is mediated by 'Candidatus Methylomirabilis oxyfera' (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4-2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 10(6) and 3.2 × 10(7) copies g(-1) sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.,Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Hong-Sheng Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.,Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhi-Qiu Gao
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Science, Beijing, China.,College of Geophysics and Remote Sensing, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xu Liu
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Ji Li
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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22
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Shen LD, Wu HS, Gao ZQ, Li J, Liu X. Presence of diverse Candidatus Methylomirabilis oxyfera
-like bacteria of NC10 phylum in agricultural soils. J Appl Microbiol 2016; 120:1552-60. [DOI: 10.1111/jam.13119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/02/2016] [Accepted: 02/23/2016] [Indexed: 12/26/2022]
Affiliation(s)
- L.-d. Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - H.-s. Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - Z.-q. Gao
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry; Institute of Atmospheric Physics; Chinese Academy of Science; Beijing China
- College of Geophysics and Remote Sensing; Nanjing University of Information Science and Technology; Nanjing China
| | - J. Li
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - X. Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; College of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
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23
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Lau E, Iv EJN, Dillard ZW, Dague RD, Semple AL, Wentzell WL. High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA. Microorganisms 2015; 3:113-36. [PMID: 27682082 PMCID: PMC5023241 DOI: 10.3390/microorganisms3020113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 02/23/2015] [Accepted: 03/26/2015] [Indexed: 01/08/2023] Open
Abstract
Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region) gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units), 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. Methylacidiphilum-like methanotrophs were not detected. Proteobacterial methanotrophic bacteria constitute <2% of microbiota in these environments, with the Methylocystaceae one to two orders of magnitude more abundant than the Methylococcaceae in all environments sampled. The Methylococcaceae are also less diverse in forest soil compared to the other two habitats. Nonmetric multidimensional scaling analyses indicated that the majority of methanotrophs from the Methylococcaceae and Methylocystaceae tend to occur in one habitat only (peat or Sphagnum moss) or co-occurred in both Sphagnum moss and peat. This study provides insights into the structure of methanotrophic communities in relationship to habitat type, and suggests that peat and Sphagnum moss can influence methanotroph community structure and biogeography.
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Affiliation(s)
- Evan Lau
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Edward J Nolan Iv
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA
| | - Zachary W Dillard
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Ryan D Dague
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Amanda L Semple
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Wendi L Wentzell
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
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Gugliandolo C, Lentini V, Bunk B, Overmann J, Italiano F, Maugeri TL. Changes in prokaryotic community composition accompanying a pronounced temperature shift of a shallow marine thermal brine pool (Panarea Island, Italy). Extremophiles 2015; 19:547-59. [PMID: 25716144 DOI: 10.1007/s00792-015-0737-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/27/2015] [Indexed: 01/07/2023]
Abstract
Hot Lake is a recently described thermal brine pool off Panarea Island (Eolian Islands, Italy) where emitted fluids are highly saline and rich in CO2 and H2S. The prokaryotic community composition in surface sediment samples was analyzed by high-throughput Illumina sequencing targeting the V3 region of the 16S rRNA at two time points that differed mainly with respect to temperature conditions, high-temperature (94 °C, HT09) and low-temperature (28.5 °C, LT10). Bacterial richness and diversity were greater than those of Archaea under both temperature conditions. In contrast to Bacteria, diversity and evenness of Archaea greatly increased at LT10. While the phylogenetic analysis indicated the presence of members mostly affiliated with the same taxonomic groups, their relative abundances differed from HT09 to LT10, resulting in different bacterial and archaeal assemblages. Both HT09 and LT10 were dominated by members of the Epsilonproteobacteria. Within this subphylum, bacteria of the genus Sulfurimonas were most frequently detected at HT09, while Arcobacter prevailed at LT10. The abundance of other dominant taxonomic groups (≥1 % of Illumina reads) also correlated with temperature conditions. Members assigned to hyperthermophilic Euryarchaeota (Thermococci) or to thermophilic (Caldiserica) and thermoresistant (Firmicutes) bacterial taxa were dominant at HT09, while those related to non-thermophilic Bacteroidetes, Fusobacteria and Actinobacteria were dominant at LT10. Several, probably photosynthetic, members of the Alphaproteobacteria, Chlorobi, Cyanobacteria and Chloroflexi were recovered under both temperature conditions. The co-occurrence of photosynthetic and chemolithotrophic microorganisms represents a unique feature of shallow vents such as Hot Lake.
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Affiliation(s)
- Concetta Gugliandolo
- Department of Biological and Environmental Sciences, Research Centre for Extreme Environments and Extremophiles, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy,
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Zhang J, Yang Y, Zhao L, Li Y, Xie S, Liu Y. Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes. Appl Microbiol Biotechnol 2014; 99:3291-302. [PMID: 25432677 DOI: 10.1007/s00253-014-6262-x] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 11/30/2022]
Abstract
Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.
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Affiliation(s)
- Jingxu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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