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Boyd BM, James I, Johnson KP, Weiss RB, Bush SE, Clayton DH, Dale C. Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria. Nat Commun 2024; 15:4571. [PMID: 38811551 PMCID: PMC11137140 DOI: 10.1038/s41467-024-48784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Evolution results from the interaction of stochastic and deterministic processes that create a web of historical contingency, shaping gene content and organismal function. To understand the scope of this interaction, we examine the relative contributions of stochasticity, determinism, and contingency in shaping gene inactivation in 34 lineages of endosymbiotic bacteria, Sodalis, found in parasitic lice, Columbicola, that are independently undergoing genome degeneration. Here we show that the process of genome degeneration in this system is largely deterministic: genes involved in amino acid biosynthesis are lost while those involved in providing B-vitamins to the host are retained. In contrast, many genes encoding redundant functions, including components of the respiratory chain and DNA repair pathways, are subject to stochastic loss, yielding historical contingencies that constrain subsequent losses. Thus, while selection results in functional convergence between symbiont lineages, stochastic mutations initiate distinct evolutionary trajectories, generating diverse gene inventories that lack the functional redundancy typically found in free-living relatives.
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Affiliation(s)
- Bret M Boyd
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, US.
| | - Ian James
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, US
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT, US
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Colin Dale
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
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Diaz-Recio Lorenzo C, Tran Lu Y A, Brunner O, Arbizu PM, Jollivet D, Laurent S, Gollner S. Highly structured populations of copepods at risk to deep-sea mining: Integration of genomic data with demogenetic and biophysical modelling. Mol Ecol 2024; 33:e17340. [PMID: 38605683 DOI: 10.1111/mec.17340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024]
Abstract
Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where hard substrate is available. Despite the increasing interest in seafloor massive sulphides exploitation, there have been no population genomic studies conducted on vent meiofauna, which are known to contribute over 50% to metazoan biodiversity at vents. To bridge this knowledge gap, restriction-site-associated DNA sequencing, specifically 2b-RADseq, was used to retrieve thousands of genome-wide single-nucleotide polymorphisms (SNPs) from abundant populations of the vent-obligate copepod Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate population structure, demographic histories and genotype-environment associations at a basin scale. Genetic analyses also helped to evaluate the suitability of tailored larval dispersal models and the parameterization of life-history traits that better fit the population patterns observed in the genomic dataset for the target organism. Highly structured populations were observed on both spatial and temporal scales, with divergence of populations between the north, mid, and south of the basin estimated to have occurred after the creation of the major transform fault dividing the Australian and the Niuafo'ou tectonic plate (350 kya), with relatively recent secondary contact events (<20 kya). Larval dispersal models were able to predict the high levels of structure and the highly asymmetric northward low-level gene flow observed in the genomic data. These results differ from most studies conducted on megafauna in the region, elucidating the need to incorporate smaller size when considering site prospecting for deep-sea exploitation of seafloor massive sulphides, and the creation of area-based management tools to protect areas at risk of local extinction, should mining occur.
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Affiliation(s)
- Coral Diaz-Recio Lorenzo
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Adrien Tran Lu Y
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Otis Brunner
- Okinawa Institute for Science and Technology, Kunigami-gun, Okinawa, Japan
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Wilhelmshaven, Germany
| | - Didier Jollivet
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Sabine Gollner
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, 't Horntje (Texel), The Netherlands
- Utrecht University, Utrecht, The Netherlands
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Methou P, Cueff‐Gauchard V, Michel LN, Gayet N, Pradillon F, Cambon‐Bonavita M. Symbioses of alvinocaridid shrimps from the South West Pacific: No chemosymbiotic diets but conserved gut microbiomes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:614-630. [PMID: 37752716 PMCID: PMC10667644 DOI: 10.1111/1758-2229.13201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Rimicaris exoculata shrimps from hydrothermal vent ecosystems are known to host dense epibiotic communities inside their enlarged heads and digestive systems. Conversely, other shrimps from the family, described as opportunistic feeders have received less attention. We examined the nutrition and bacterial communities colonising 'head' chambers and digestive systems of three other alvinocaridids-Rimicaris variabilis, Nautilocaris saintlaurentae and Manuscaris sp.-using a combination of electron microscopy, stable isotopes and sequencing approaches. Our observations inside 'head' cavities and on mouthparts showed only a really low coverage of bacterial epibionts. In addition, no clear correlation between isotopic ratios and relative abundance of epibionts on mouthparts could be established among shrimp individuals. Altogether, these results suggest that none of these alvinocaridids rely on chemosynthetic epibionts as their main source of nutrition. Our analyses also revealed a substantial presence of several Firmicutes and Deferribacterota lineages within the foreguts and midguts of these shrimps, which closest known lineages were systematically digestive symbionts associated with alvinocaridids, and more broadly for Firmicutes from digestive systems of other crustaceans from marine and terrestrial ecosystems. Overall, our study opens new perspectives not only about chemosynthetic symbioses of vent shrimps but more largely about digestive microbiomes with potential ancient and evolutionarily conserved bacterial partnerships among crustaceans.
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Affiliation(s)
- Pierre Methou
- X‐STARJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Valérie Cueff‐Gauchard
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
| | - Loïc N. Michel
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
- Laboratory of Oceanology, Freshwater, and Oceanic Sciences Unit of reSearch (FOCUS)University of LiègeLiègeBelgium
| | - Nicolas Gayet
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
| | - Florence Pradillon
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
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Sun Y, Wang M, Cao L, Seim I, Zhou L, Chen J, Wang H, Zhong Z, Chen H, Fu L, Li M, Li C, Sun S. Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont. MICROBIOME 2023; 11:253. [PMID: 37974296 PMCID: PMC10652631 DOI: 10.1186/s40168-023-01695-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 10/11/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear. RESULTS Here, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes. CONCLUSIONS The current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses. Video Abstract.
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Affiliation(s)
- Yan Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Lei Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Li Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Jianwei Chen
- BGI Research-Qingdao, BGI, Qingdao, 266555, China
| | - Hao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Zhaoshan Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Hao Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Lulu Fu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Mengna Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
| | - Chaolun Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Song Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Breusing C, Xiao Y, Russell SL, Corbett-Detig RB, Li S, Sun J, Chen C, Lan Y, Qian PY, Beinart RA. Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation. mSystems 2023; 8:e0028423. [PMID: 37493648 PMCID: PMC10469979 DOI: 10.1128/msystems.00284-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/13/2023] [Indexed: 07/27/2023] Open
Abstract
The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental, and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with little exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria gastropod symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that occupy contrasting ecological niches. IMPORTANCE Beneficial relationships between animals and microbial organisms (symbionts) are ubiquitous in nature. In the ocean, microbial symbionts are typically acquired from the environment and their composition across geographic locations is often shaped by adaptation to local habitat conditions. However, it is currently unknown how generalizable these patterns are across symbiotic systems that have contrasting ecological characteristics. To address this question, we compared symbiont population structure between deep-sea hydrothermal vent mussels and co-occurring but ecologically distinct snail species. Our analyses show that mussel symbiont populations are less partitioned by geography and do not demonstrate evidence for environmental adaptation. We posit that the mussel's mixotrophic feeding mode may lower its need to affiliate with locally adapted symbiont strains, while microhabitat stability and symbiont genomic mixing likely favors persistence of symbiont strains across geographic locations. Altogether, these findings further our understanding of the mechanisms shaping symbiont population structure in marine environmentally transmitted symbioses.
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Affiliation(s)
- Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Yao Xiao
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
| | - Shelbi L. Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Sixuan Li
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yi Lan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
| | - Roxanne A. Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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Hauer MA, Breusing C, Trembath-Reichert E, Huber JA, Beinart RA. Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts. MICROBIOME 2023; 11:106. [PMID: 37189129 DOI: 10.1186/s40168-023-01493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 02/11/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Marine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to their host-associated counterparts are sparse. Here, we assembled the first genomes of the chemoautotrophic gammaproteobacterial symbionts affiliated with the deep-sea snail Alviniconcha hessleri from two separate hydrothermal vent fields of the Mariana Back-Arc Basin. We used phylogenomic and population genomic methods to assess sequence and gene content variation between free-living and host-associated symbionts. RESULTS Our phylogenomic analyses show that the free-living and host-associated symbionts of A. hessleri from both vent fields are populations of monophyletic strains from a single species. Furthermore, genetic structure and gene content analyses indicate that these symbiont populations are differentiated by vent field rather than by lifestyle. CONCLUSION Together, this work suggests that, despite the potential influence of host-mediated acquisition and release processes on horizontally transmitted symbionts, geographic isolation and/or adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition. Video Abstract.
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Affiliation(s)
- Michelle A Hauer
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | | | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, USA
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA.
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Bojar AV, Lécuyer C, Maher W, Bojar HP, Fourel F, Vasile Ş. Multi-element stable isotope geochemistry and arsenic speciation of hydrothermal vent fauna (Alviniconcha sp., Ifremeria nautilei and Eochionelasmus ohtai manusensis), Manus Basin, Papua New Guinea. CHEMOSPHERE 2023; 324:138258. [PMID: 36898438 DOI: 10.1016/j.chemosphere.2023.138258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Deep-sea hydrothermal vent communities, revealing patterns of niche partitioning, live in a limited area characterised by sharp physico-chemical gradients. In this study, we investigated carbon, sulfur, nitrogen stable isotopes as well as arsenic (As) speciations and concentrations for two snails (Alviniconcha sp. and Ifremeria nautilei) and a crustacean, (Eochionelasmus ohtai manusensis), occupying distinct niches in the hydrothermal vent field of the Vienna Woods, Manus Basin, Western Pacific. δ13C values of Alviniconcha sp. (foot), I. nautilei (foot and chitin) and E. o. manusensis (soft tissue) are similar, from -28 to -33‰ (V-PDB). The δ15N values of Alviniconcha sp. (foot and chitin), I. nautilei (foot and chitin) and E. o. manusensis (soft tissue) range from 8.4 to 10.6‰. The δ34S values of Alviniconcha sp. (foot and chitin), I. nautilei (foot) and E. o. manusensis (soft tissue) range from 5.9 to 11.1‰. Using stable isotopes, for the first time, we inferred a Calvin-Benson (RuBisCo) metabolic pathway for Alviniconcha sp. along with the presence of γ-Proteobacteria symbionts for the Vienna Woods communities. For I. nautilei, a feeding pattern is proposed with γ-Proteobacteria symbiosis and a Calvin-Benson-Bassham diet with mixotrophic feeding. E. ohtai manusensis is filtering bacteria with a CBB feeding strategy, with δ15N values indicating possible higher position in the trophic chain. Arsenic concentrations in the dry tissue of Alviniconcha (foot), I. nautilei (foot) and E. o. manusensis (soft tissue) are high, from 4134 to 8478 μg/g, with inorganic As concentrations of 607, 492 and 104 μg/g, respectively and dimethyl arsenic (DMA) concentrations of 11.12, 0.25 and 11.2 μg/g, respectively. Snails occurring in a vent proximal position have higher As concentration than barnacles, a pattern not observed for S concentrations. Arsenosugars were not put in evidence indicating that the available organic material for the vent organisms are not surface derived.
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Affiliation(s)
- Ana-Voica Bojar
- Department of Environment and Biodiversity, Salzburg University, Hellbrunnerstrasse 34, A-5020, Salzburg, Austria; Department of Mineralogy, Universalmuseum Joanneum, Weinzöttlstrasse 16, A-8045, Graz, Austria; Faculty of Physics, University of Bucharest, 405 Atomiștilor Street, Măgurele 077125, Romania.
| | - Christophe Lécuyer
- Laboratoire de Géologie de Lyon, CNRS UMR 5276, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France; Institut Universitaire de France, 103 Boulevard, Saint-Michel, 75005 Paris, France
| | - William Maher
- Research School of Earth Sciences, Australian National University, Canberra 2000 Australia
| | - Hans-Peter Bojar
- Department of Mineralogy, Universalmuseum Joanneum, Weinzöttlstrasse 16, A-8045, Graz, Austria
| | - François Fourel
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, LEHNA UMR CNRS 5023, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
| | - Ştefan Vasile
- Department of Geology, Mineralogy, and Paleontology, Faculty of Geology and Geophysics, University of Bucharest, 1 Nicolae Bălcescu Avenue, 010041 Bucharest, Romania
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Lo Giudice A, Rizzo C. Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules. Mar Drugs 2022; 20:617. [PMID: 36286440 PMCID: PMC9605250 DOI: 10.3390/md20100617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 09/07/2024] Open
Abstract
Microbe-invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate-bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.
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Affiliation(s)
- Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy
- Stazione Zoologica Anton Dohrn, National Institute of Biology, Sicily Marine Centre, Department Ecosustainable Marine Biotechnology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
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Lan Y, Sun J, Chen C, Wang H, Xiao Y, Perez M, Yang Y, Kwan YH, Sun Y, Zhou Y, Han X, Miyazaki J, Watsuji TO, Bissessur D, Qiu JW, Takai K, Qian PY. Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont. THE ISME JOURNAL 2022; 16:2132-2143. [PMID: 35715703 PMCID: PMC9381778 DOI: 10.1038/s41396-022-01261-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022]
Abstract
The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host’s cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.
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Affiliation(s)
- Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Prefecture, Japan
| | - Hao Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yao Xiao
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Maeva Perez
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Yi Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yick Hang Kwan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanan Sun
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Xiqiu Han
- Key Laboratory of Submarine Geosciences & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Junichi Miyazaki
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Prefecture, Japan
| | - Tomo-O Watsuji
- Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kitakyusyu, 803-0846, Japan
| | - Dass Bissessur
- Department for Continental Shelf, Maritime Zones Administration & Exploration, Prime Minister's Office, 2nd Floor, Belmont House, 12 Intendance Street, Port Louis, 11328, Mauritius
| | - Jian-Wen Qiu
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ken Takai
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Kanagawa Prefecture, Japan
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China. .,Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
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10
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Castel J, Hourdez S, Pradillon F, Daguin-Thiébaut C, Ballenghien M, Ruault S, Corre E, Tran Lu Y A, Mary J, Gagnaire PA, Bonhomme F, Breusing C, Broquet T, Jollivet D. Inter-Specific Genetic Exchange Despite Strong Divergence in Deep-Sea Hydrothermal Vent Gastropods of the Genus Alviniconcha. Genes (Basel) 2022; 13:985. [PMID: 35741747 PMCID: PMC9223106 DOI: 10.3390/genes13060985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/29/2022] [Accepted: 05/17/2022] [Indexed: 02/05/2023] Open
Abstract
Deep hydrothermal vents are highly fragmented and unstable habitats at all temporal and spatial scales. Such environmental dynamics likely play a non-negligible role in speciation. Little is, however, known about the evolutionary processes that drive population-level differentiation and vent species isolation and, more specifically, how geography and habitat specialisation interplay in the species history of divergence. In this study, the species range and divergence of Alviniconcha snails that occupy active Western Pacific vent fields was assessed by using sequence variation data of the mitochondrial Cox1 gene, RNAseq, and ddRAD-seq. Combining morphological description and sequence datasets of the three species across five basins, we confirmed that A. kojimai, A. boucheti, and A. strummeri, while partially overlapping over their range, display high levels of divergence in the three genomic compartments analysed that usually encompass values retrieved for reproductively isolated species with divergences rang from 9% to 12.5% (mtDNA) and from 2% to 3.1% (nuDNA). Moreover, the three species can be distinguished on the basis of their external morphology by observing the distribution of bristles and the shape of the columella. According to this sampling, A. boucheti and A. kojimai form an east-to-west species abundance gradient, whereas A. strummeri is restricted to the Futuna Arc/Lau and North Fiji Basins. Surprisingly, population models with both gene flow and population size heterogeneities among genomes indicated that these three species are still able to exchange genes due to secondary contacts at some localities after a long period of isolation.
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Affiliation(s)
- Jade Castel
- ‘Dynamique de la Diversité Marine’ (DyDiv) Lab, Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 7144, Place G. Teissier, 29680 Roscoff, France; (C.D.-T.); (M.B.); (S.R.); (J.M.); (T.B.); (D.J.)
| | - Stéphane Hourdez
- Laboratoire d’Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Sorbonne Université, CNRS, UMR 8222, Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France;
| | - Florence Pradillon
- Unité Biologie et Ecologie des Ecosystèmes Marins Profonds, Université de Brest, Ifremer, CNRS, 29280 Plouzané, France;
| | - Claire Daguin-Thiébaut
- ‘Dynamique de la Diversité Marine’ (DyDiv) Lab, Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 7144, Place G. Teissier, 29680 Roscoff, France; (C.D.-T.); (M.B.); (S.R.); (J.M.); (T.B.); (D.J.)
| | - Marion Ballenghien
- ‘Dynamique de la Diversité Marine’ (DyDiv) Lab, Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 7144, Place G. Teissier, 29680 Roscoff, France; (C.D.-T.); (M.B.); (S.R.); (J.M.); (T.B.); (D.J.)
| | - Stéphanie Ruault
- ‘Dynamique de la Diversité Marine’ (DyDiv) Lab, Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 7144, Place G. Teissier, 29680 Roscoff, France; (C.D.-T.); (M.B.); (S.R.); (J.M.); (T.B.); (D.J.)
| | - Erwan Corre
- ABiMS Bioinformatics Facility, Station biologique de Roscoff, Sorbonne Université, CNRS, FR2424, Place G. Teissier, 29680 Roscoff, France;
| | - Adrien Tran Lu Y
- Team MBE, Department Genφ, ISEM, Université de Montpellier, CNRS, EPHE, IRD, 34110 Montpellier, France; (A.T.L.Y.); (P.-A.G.); (F.B.)
| | - Jean Mary
- ‘Dynamique de la Diversité Marine’ (DyDiv) Lab, Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 7144, Place G. Teissier, 29680 Roscoff, France; (C.D.-T.); (M.B.); (S.R.); (J.M.); (T.B.); (D.J.)
| | - Pierre-Alexandre Gagnaire
- Team MBE, Department Genφ, ISEM, Université de Montpellier, CNRS, EPHE, IRD, 34110 Montpellier, France; (A.T.L.Y.); (P.-A.G.); (F.B.)
| | - François Bonhomme
- Team MBE, Department Genφ, ISEM, Université de Montpellier, CNRS, EPHE, IRD, 34110 Montpellier, France; (A.T.L.Y.); (P.-A.G.); (F.B.)
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, 215 South Ferry Rd, Narragansett, RI 02882, USA;
| | - Thomas Broquet
- ‘Dynamique de la Diversité Marine’ (DyDiv) Lab, Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 7144, Place G. Teissier, 29680 Roscoff, France; (C.D.-T.); (M.B.); (S.R.); (J.M.); (T.B.); (D.J.)
| | - Didier Jollivet
- ‘Dynamique de la Diversité Marine’ (DyDiv) Lab, Station Biologique de Roscoff, Sorbonne Université, CNRS, UMR 7144, Place G. Teissier, 29680 Roscoff, France; (C.D.-T.); (M.B.); (S.R.); (J.M.); (T.B.); (D.J.)
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11
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Breusing C, Genetti M, Russell SL, Corbett-Detig RB, Beinart RA. Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses. Proc Natl Acad Sci U S A 2022; 119:e2115608119. [PMID: 35349333 PMCID: PMC9168483 DOI: 10.1073/pnas.2115608119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
SignificanceIn marine ecosystems, transmission of microbial symbionts between host generations occurs predominantly through the environment. Yet, it remains largely unknown how host genetics, symbiont competition, environmental conditions, and geography shape the composition of symbionts acquired by individual hosts. To address this question, we applied population genomic approaches to four species of deep-sea hydrothermal vent snails that live in association with chemosynthetic bacteria. Our analyses show that environment is more important to strain-level symbiont composition than host genetics and that symbiont strains show genetic variation indicative of adaptation to the distinct geochemical conditions at each vent site. This corroborates a long-standing hypothesis that hydrothermal vent invertebrates affiliate with locally adapted symbiont strains to cope with the variable conditions characterizing their habitats.
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Affiliation(s)
- Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882
| | - Maximilian Genetti
- Jack Baskin School of Engineering, University of California, Santa Cruz, CA 95064
| | - Shelbi L. Russell
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064
| | | | - Roxanne A. Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882
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12
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Breusing C, Castel J, Yang Y, Broquet T, Sun J, Jollivet D, Qian P, Beinart RA. Global 16S rRNA diversity of provannid snail endosymbionts from Indo-Pacific deep-sea hydrothermal vents. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:299-307. [PMID: 35170217 PMCID: PMC9303550 DOI: 10.1111/1758-2229.13051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Symbioses between invertebrate animals and chemosynthetic bacteria build the foundation of deep-sea hydrothermal ecosystems worldwide. Despite the importance of these symbioses for ecosystem functioning, the diversity of symbionts within and between host organisms and geographic regions is still poorly understood. In this study we used 16S rRNA amplicon sequencing to determine the diversity of gill endosymbionts in provannid snails of the genera Alviniconcha and Ifremeria, which are key species at deep-sea hydrothermal vents in the Indo-Pacific Ocean. Our analysis of 761 snail samples across the distributional range of these species confirms previous findings that symbiont lineages are strongly partitioned by host species and broad-scale geography. Less structuring was observed within geographic regions, probably due to insufficient strain resolution of the 16S rRNA gene. Symbiont richness in individual hosts appeared to be unrelated to host size, suggesting that provannid snails might acquire their symbionts only during a permissive time window in early developmental stages in contrast to other vent molluscs that obtain their symbionts throughout their lifetime. Despite the extent of our dataset, symbiont accumulation curves did not reach saturation, highlighting the need for increased sampling efforts to uncover the full diversity of symbionts within these and other hydrothermal vent species.
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Affiliation(s)
- Corinna Breusing
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRIUSA
| | - Jade Castel
- CNRS UMR 7144 ‘Adaptation et Diversité en Milieux Marins’ (AD2M)Team ‘Dynamique de la Diversité Marine’ (DyDiv), Station Biologique de RoscoffRoscoffFrance
| | - Yi Yang
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)The Hong Kong University of Science and TechnologyHong KongChina
| | - Thomas Broquet
- CNRS UMR 7144 ‘Adaptation et Diversité en Milieux Marins’ (AD2M)Team ‘Dynamique de la Diversité Marine’ (DyDiv), Station Biologique de RoscoffRoscoffFrance
| | - Jin Sun
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Didier Jollivet
- CNRS UMR 7144 ‘Adaptation et Diversité en Milieux Marins’ (AD2M)Team ‘Dynamique de la Diversité Marine’ (DyDiv), Station Biologique de RoscoffRoscoffFrance
| | - Pei‐Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)The Hong Kong University of Science and TechnologyHong KongChina
| | - Roxanne A. Beinart
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRIUSA
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13
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Breusing C, Johnson SB, Mitarai S, Beinart RA, Tunnicliffe V. Differential patterns of connectivity in Western Pacific hydrothermal vent metapopulations: A comparison of biophysical and genetic models. Evol Appl 2021; 16:22-35. [PMID: 36699127 PMCID: PMC9850011 DOI: 10.1111/eva.13326] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/18/2021] [Accepted: 11/21/2021] [Indexed: 01/28/2023] Open
Abstract
Hydrothermal ecosystems face threats from planned deep-seabed mining activities, despite the fact that patterns of realized connectivity among vent-associated populations and communities are still poorly understood. Since populations of vent endemic species depend on larval dispersal to maintain connectivity and resilience to habitat changes, effective conservation strategies for hydrothermal ecosystems should include assessments of metapopulation dynamics. In this study, we combined population genetic methods with biophysical models to assess strength and direction of gene flow within four species of the genus Alviniconcha (A. boucheti, A. kojimai, A. strummeri and A. hessleri) that are ecologically dominant taxa at Western Pacific hydrothermal vents. In contrast to predictions from dispersal models, among-basin migration in A. boucheti occurred predominantly in an eastward direction, while populations within the North Fiji Basin were clearly structured despite the absence of oceanographic barriers. Dispersal models and genetic data were largely in agreement for the other Alviniconcha species, suggesting limited between-basin migration for A. kojimai, lack of genetic structure in A. strummeri within the Lau Basin and restricted gene flow between northern and southern A. hessleri populations in the Mariana back-arc as a result of oceanic current conditions. Our findings show that gene flow patterns in ecologically similar congeneric species can be remarkably different and surprisingly limited depending on environmental and evolutionary contexts. These results are relevant to regional conservation planning and to considerations of similar integrated analyses for any vent metapopulations under threat from seabed mining.
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Affiliation(s)
- Corinna Breusing
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode IslandUSA
| | | | - Satoshi Mitarai
- Okinawa Institute of Science and Technology Graduate UniversityKunigami‐gunJapan
| | - Roxanne A. Beinart
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode IslandUSA
| | - Verena Tunnicliffe
- Department of BiologySchool of Earth and Ocean SciencesUniversity of VictoriaVictoriaBritish ColumbiaCanada
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14
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Abstract
Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Eslam O Osman
- Biology Department, Eberly College, Pennsylvania State University, State College, Pennsylvania, USA; .,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Biology Lab, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Alexis M Weinnig
- Biology Department, Temple University, Philadelphia, Pennsylvania, USA
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15
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Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses. Annu Rev Microbiol 2021; 75:695-718. [PMID: 34351792 DOI: 10.1146/annurev-micro-051021-123130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; ,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
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16
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Ma L, Wang WX. Zinc source differentiation in hydrothermal vent mollusks: Insight from Zn isotope ratios. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145653. [PMID: 33582336 DOI: 10.1016/j.scitotenv.2021.145653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/08/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Hydrothermal vent represents an extreme environment where metal-enriched fluids are in contact with chemosymbiotic animals. In the present study, Zn isotopic compositions were determined in multiple tissues of three dominant hydrothermal vent mollusks (the mussel Bathymodiolus marisindicus and two gastropods Chrysomallon squamiferum and Gigantopelta aegis) collected from a hydrothermal vent field (Southwest Indian Ridge in the Indian Ocean). We found approximately 1.78‰ differences in the δ66Zn values among the three vent mollusks despite of their similar range of Zn concentrations. The significant variation in the δ66Zn values was considered to be indicative of different Zn uptake sources among the three species as a result of their morphological adaptations. Zinc uptake associated with symbiotic activities may be more relevant in the vent gastropods, whereas Zn uptake from hydrothermal fluids during filter-feeding may also play a role in the vent mussels. However, no significant difference in δ66Zn values was observed among tissues of any of the mollusks, showing the absence of Zn isotope fractionation during internal Zn transport. Our results demonstrated that variable Zn uptake pathways existed among different hydrothermal vent mollusks and could be differentiated by determining the Zn isotopic compositions in their tissues. We also highlight that Zn isotope ratios can be used to track Zn sources to the vent mollusks.
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Affiliation(s)
- Lan Ma
- School of Energy and Environment, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China.
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17
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Breusing C, Johnson SB, Tunnicliffe V, Clague DA, Vrijenhoek RC, Beinart RA. Allopatric and Sympatric Drivers of Speciation in Alviniconcha Hydrothermal Vent Snails. Mol Biol Evol 2020; 37:3469-3484. [PMID: 32658967 PMCID: PMC7743903 DOI: 10.1093/molbev/msaa177] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Despite significant advances in our understanding of speciation in the marine environment, the mechanisms underlying evolutionary diversification in deep-sea habitats remain poorly investigated. Here, we used multigene molecular clocks and population genetic inferences to examine processes that led to the emergence of the six extant lineages of Alviniconcha snails, a key taxon inhabiting deep-sea hydrothermal vents in the Indo-Pacific Ocean. We show that both allopatric divergence through historical vicariance and ecological isolation due to niche segregation contributed to speciation in this genus. The split between the two major Alviniconcha clades (separating A. boucheti and A. marisindica from A. kojimai, A. hessleri, and A. strummeri) probably resulted from tectonic processes leading to geographic separation, whereas the splits between co-occurring species might have been influenced by ecological factors, such as the availability of specific chemosynthetic symbionts. Phylogenetic origin of the sixth species, Alviniconcha adamantis, remains uncertain, although its sister position to other extant Alviniconcha lineages indicates a possible ancestral relationship. This study lays a foundation for future genomic studies aimed at deciphering the roles of local adaptation, reproductive biology, and host–symbiont compatibility in speciation of these vent-restricted snails.
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Affiliation(s)
- Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI
| | | | - Verena Tunnicliffe
- Department of Biology and School of Earth and Ocean Sciences, University of Victoria, Victoria, BC, Canada
| | - David A Clague
- Monterey Bay Aquarium Research Institute, Moss Landing, CA
| | | | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI
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18
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Endosymbionts of Metazoans Dwelling in the PACManus Hydrothermal Vent: Diversity and Potential Adaptive Features Revealed by Genome Analysis. Appl Environ Microbiol 2020; 86:AEM.00815-20. [PMID: 32859597 PMCID: PMC7580541 DOI: 10.1128/aem.00815-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/22/2020] [Indexed: 12/04/2022] Open
Abstract
Deep-sea hydrothermal vents are dominated by several invertebrate species. The establishment of symbiosis has long been thought to be the key to successful colonization by these sedentary species in such harsh environments. However, the relationships between symbiotic bacteria and their hosts and their role in environmental adaptations generally remain unclear. In this paper, we show that the distribution of three host species showed characteristic niche partitioning in the Manus Basin, giving us the opportunity to understand how they adapt to their particular habitats. This study also revealed three novel genomes of symbionts from the snails of A. boucheti. Combined with a data set on other ectosymbiont and free-living bacteria, genome comparisons for the snail endosymbionts pointed to several genetic traits that may have contributed to the lifestyle shift of Epsilonproteobacteria into the epithelial cells. These findings could increase our understanding of invertebrate-endosymbiont relationships in deep-sea ecosystems. Deep-sea hydrothermal vent communities are dominated by invertebrates, namely, bathymodiolin mussels, siboglinid tubeworms, and provannid snails. Symbiosis is considered key to successful colonization by these sedentary species in such extreme environments. In the PACManus vent fields, snails, tubeworms, and mussels each colonized a niche with distinct geochemical characteristics. To better understand the metabolic potentials and genomic features contributing to host-environment adaptation, we compared the genomes of the symbionts of Bathymodiolus manusensis, Arcovestia ivanovi, and Alviniconcha boucheti sampled at PACManus, and we discuss their environmentally adaptive features. We found that B. manusensis and A. ivanovi are colonized by Gammaproteobacteria from distinct clades, whereas endosymbionts of B. manusensis feature high intraspecific heterogeneity with differing metabolic potentials. A. boucheti harbored three novel Epsilonproteobacteria symbionts, suggesting potential species-level diversity of snail symbionts. Genome comparisons revealed that the relative abundance of gene families related to low-pH homeostasis, metal resistance, oxidative stress resistance, environmental sensing/responses, and chemotaxis and motility was the highest in A. ivanovi’s symbiont, followed by symbionts of the vent-mouth-dwelling snail A. boucheti, and was relatively low in the symbiont of the vent-periphery-dwelling mussel B. manusensis, which is consistent with their environmental adaptations and host-symbiont interactions. Gene families classified as encoding host interaction/attachment, virulence factors/toxins, and eukaryotic-like proteins were most abundant in symbionts of mussels and least abundant in those of snails, indicating that these symbionts may differ in their host colonization strategies. Comparison of Epsilonproteobacteria symbionts to nonsymbionts demonstrated that the expanded gene families in symbionts were related to vitamin B12 synthesis, toxin-antitoxin systems, methylation, and lipopolysaccharide biosynthesis, suggesting that these are vital to symbiont establishment and development in Epsilonproteobacteria. IMPORTANCE Deep-sea hydrothermal vents are dominated by several invertebrate species. The establishment of symbiosis has long been thought to be the key to successful colonization by these sedentary species in such harsh environments. However, the relationships between symbiotic bacteria and their hosts and their role in environmental adaptations generally remain unclear. In this paper, we show that the distribution of three host species showed characteristic niche partitioning in the Manus Basin, giving us the opportunity to understand how they adapt to their particular habitats. This study also revealed three novel genomes of symbionts from the snails of A. boucheti. Combined with a data set on other ectosymbiont and free-living bacteria, genome comparisons for the snail endosymbionts pointed to several genetic traits that may have contributed to the lifestyle shift of Epsilonproteobacteria into the epithelial cells. These findings could increase our understanding of invertebrate-endosymbiont relationships in deep-sea ecosystems.
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19
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20
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Breusing C, Mitchell J, Delaney J, Sylva SP, Seewald JS, Girguis PR, Beinart RA. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. ISME JOURNAL 2020; 14:2568-2579. [PMID: 32616905 PMCID: PMC7490688 DOI: 10.1038/s41396-020-0707-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022]
Abstract
Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host-symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.
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Affiliation(s)
- Corinna Breusing
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, USA.
| | - Jessica Mitchell
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, USA
| | - Jennifer Delaney
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, USA
| | - Sean P Sylva
- Woods Hole Oceanographic Institution, Department of Marine Chemistry and Geochemistry, Woods Hole, MA, USA
| | - Jeffrey S Seewald
- Woods Hole Oceanographic Institution, Department of Marine Chemistry and Geochemistry, Woods Hole, MA, USA
| | - Peter R Girguis
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, USA
| | - Roxanne A Beinart
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, USA
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21
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Freeman CJ, Easson CG, Matterson KO, Thacker RW, Baker DM, Paul VJ. Microbial symbionts and ecological divergence of Caribbean sponges: A new perspective on an ancient association. THE ISME JOURNAL 2020; 14:1571-1583. [PMID: 32203120 PMCID: PMC7242429 DOI: 10.1038/s41396-020-0625-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 12/26/2022]
Abstract
Marine sponges host diverse communities of microbial symbionts that expand the metabolic capabilities of their host, but the abundance and structure of these communities is highly variable across sponge species. Specificity in these interactions may fuel host niche partitioning on crowded coral reefs by allowing individual sponge species to exploit unique sources of carbon and nitrogen, but this hypothesis is yet to be tested. Given the presence of high sponge biomass and the coexistence of diverse sponge species, the Caribbean Sea provides a unique system in which to investigate this hypothesis. To test for ecological divergence among sympatric Caribbean sponges and investigate whether these trends are mediated by microbial symbionts, we measured stable isotope (δ13C and δ15N) ratios and characterized the microbial community structure of sponge species at sites within four regions spanning a 1700 km latitudinal gradient. There was a low (median of 8.2 %) overlap in the isotopic niches of sympatric species; in addition, host identity accounted for over 75% of the dissimilarity in both δ13C and δ15N values and microbiome community structure among individual samples within a site. There was also a strong phylogenetic signal in both δ15N values and microbial community diversity across host phylogeny, as well as a correlation between microbial community structure and variation in δ13C and δ15N values across samples. Together, this evidence supports a hypothesis of strong evolutionary selection for ecological divergence across sponge lineages and suggests that this divergence is at least partially mediated by associations with microbial symbionts.
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Affiliation(s)
- Christopher J Freeman
- Smithsonian Marine Station, Fort Pierce, FL, USA.
- Department of Biology, College of Charleston, Charleston, SC, USA.
| | - Cole G Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, USA
- Biology Department, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Kenan O Matterson
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - David M Baker
- The Swire Institute of Marine Science, School of Biological Sciences, University of Hong Kong, Hong Kong, PR China
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22
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Laming SR, Hourdez S, Cambon-Bonavita MA, Pradillon F. Classical and computed tomographic anatomical analyses in a not-so-cryptic Alviniconcha species complex from hydrothermal vents in the SW Pacific. Front Zool 2020; 17:12. [PMID: 32391066 PMCID: PMC7203863 DOI: 10.1186/s12983-020-00357-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/16/2020] [Indexed: 01/21/2023] Open
Abstract
The chemosymbiotic gastropod Alviniconcha (Provannidae), first described in 1988, is one of the most emblematic hydrothermal-vent taxa described from the Central Indian Ridge and the Southwest (SW) Pacific. Symbiotic bacteria found in the gill of Alviniconcha are thought to be their principal source of nutrition. In the SW Pacific, species distributions for A. kojimai, A. boucheti - and to a lesser extent A. strummeri - overlap. While Alviniconcha species do not appear to truly co-exist in these highly energetic but spatially limited habitats, certain species regularly co-occur within a single vent field and in rare instances, the same edifice. Past research suggests that SW-Pacific Alviniconcha species might aggregate around fluids with distinct geothermal profiles. These small-scale distribution patterns have been attributed to differences in their symbiont assemblages or host physiologies. However, little is known about the anatomy of most Alviniconcha species, beyond that detailed for the type species Alviniconcha hessleri, whose geographic range does not overlap with other congeners. In fact, species within this genus are currently described as cryptic, despite the absence of any comparative morphological studies to assess this. To test whether the genus is genuinely cryptic and identify any functional differences in host anatomy that might also mediate habitat partitioning in SW Pacific species, the current study examined the morphoanatomy of A. kojimai, A. boucheti and A. strummeri from the Fatu Kapa vent field, an area of hydrothermal activity recently discovered north of the Lau Basin near the Wallis and Futuna Islands and the only known example where all three species occur within adjacent vent fields. A combination of detailed dissections, histology and X-ray computed tomography demonstrate that A. kojimai, A. strummeri and A. boucheti are readily identifiable based on shell morphology and ornamentation alone, and therefore not truly cryptic. These traits provide a rapid and reliable means for species identification. However, aside from some subtle differences in radular morphology, these species of Alviniconcha exhibit conserved anatomical features, providing no evidence that functional host anatomy is implicated in habitat partitioning. This provides support for the current belief that host-species distributions are probably governed by symbiont-mediated physiological factors.
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Affiliation(s)
- Sven R Laming
- 1Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France.,2Ifremer, Univ Brest, CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), Plouzané, France.,3Current address: LEME, CESAM - Centre for Environmental and Marine Studies, Department of Biology, Universidade de Aveiro, Santiago Campus, 3810-193 Aveiro, Portugal
| | - Stéphane Hourdez
- 4UMR 8222 CNRS-Sorbonne Université, Laboratoire d'écogéochimie des environnements benthiques (LECOB), Banyuls-sur-Mer, France
| | - Marie-Anne Cambon-Bonavita
- 2Ifremer, Univ Brest, CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), Plouzané, France
| | - Florence Pradillon
- 1Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
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23
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Miyazaki J, Ikuta T, Watsuji TO, Abe M, Yamamoto M, Nakagawa S, Takaki Y, Nakamura K, Takai K. Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica. ISME JOURNAL 2020; 14:1273-1289. [PMID: 32051527 PMCID: PMC7174374 DOI: 10.1038/s41396-020-0605-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastropod Alviniconcha marisindica in the Kairei and Edmond fields (kAlv and eAlv populations, respectively) of the Indian Ocean, utilize H2 in response to their physical and environmental H2 conditions, although the 16S rRNA gene sequence of both the endosymbionts shared 99.6% identity. A thermodynamic calculation using in situ H2 and hydrogen sulfide (H2S) concentrations indicated that chemosynthetic symbiosis could be supported by metabolic energy via H2 oxidation, particularly for the kAlv holobiont. Metabolic activity measurements showed that both the living individuals and the gill tissues consumed H2 and H2S at similar levels. Moreover, a combination of fluorescence in situ hybridization, quantitative transcript analyses, and enzymatic activity measurements showed that the kAlv endosymbiont expressed the genes and enzymes for both H2- and sulfur-oxidations. These results suggest that both H2 and H2S could serve as the primary energy sources for the kAlv holobiont. The eAlv holobiont had the ability to utilize H2, but the gene expression and enzyme activity for hydrogenases were much lower than for sulfur-oxidation enzymes. These results suggest that the energy acquisitions of A. marisindica holobionts are dependent on H2- and sulfur-oxidation in the H2-enriched Kairei field and that the mechanism of dual metabolism is controlled by the in situ H2 concentration.
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Affiliation(s)
- Junichi Miyazaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Tetsuro Ikuta
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Tomo-O Watsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kitakyusyu, 803-0846, Japan
| | - Mariko Abe
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Satoshi Nakagawa
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Kentaro Nakamura
- Department of Systems Innovation, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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24
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Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol 2020; 17:271-283. [PMID: 30867583 DOI: 10.1038/s41579-019-0160-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of chemosynthetic ecosystems at deep-sea hydrothermal vents in 1977 changed our view of biology. Chemosynthetic bacteria and archaea form the foundation of vent ecosystems by exploiting the chemical disequilibrium between reducing hydrothermal fluids and oxidizing seawater, harnessing this energy to fix inorganic carbon into biomass. Recent research has uncovered fundamental aspects of these microbial communities, including their relationships with underlying geology and hydrothermal geochemistry, interactions with animals via symbiosis and distribution both locally in various habitats within vent fields and globally across hydrothermal systems in diverse settings. Although 'black smokers' and symbioses between microorganisms and macrofauna attract much attention owing to their novelty and the insights they provide into life under extreme conditions, habitats such as regions of diffuse flow, subseafloor aquifers and hydrothermal plumes have important roles in the global cycling of elements through hydrothermal systems. Owing to sharp contrasts in physical and chemical conditions between these various habitats and their dynamic, extreme and geographically isolated nature, hydrothermal vents provide a valuable window into the environmental and ecological forces that shape microbial communities and insights into the limits, origins and evolution of microbial life.
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Affiliation(s)
- Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA.
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25
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Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria). ISME JOURNAL 2019; 14:104-122. [PMID: 31562384 PMCID: PMC6908604 DOI: 10.1038/s41396-019-0508-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 11/30/2022]
Abstract
Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.
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Beinart RA, Luo C, Konstantinidis KT, Stewart FJ, Girguis PR. The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content. Front Microbiol 2019; 10:1818. [PMID: 31474946 PMCID: PMC6702916 DOI: 10.3389/fmicb.2019.01818] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/23/2019] [Indexed: 12/29/2022] Open
Abstract
Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic bacterial lineages. At the broadest level, these symbioses share primary function: the bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals to power the fixation of inorganic carbon and/or other nutrients, providing the bulk of host nutrition. However, it is unclear to what extent the ecological niche of the host species is influenced by differences in symbiont traits, particularly those involved in chemoautotrophic function and interaction with the geochemical environment. Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine whether differences in chemoautotrophic capacity exist among these symbionts that could explain the observed distribution of these snail species into distinct geochemical habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four distinct lineages in the classes γ-proteobacteria or Campylobacteria. The genomes differed with respect to genes related to motility, adhesion, secretion, and amino acid uptake or excretion, though were quite similar in chemoautotrophic function, with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, and oxygen and nitrate respiration. This indicates that differences in the presence or absence of symbiont chemoautotrophic functions does not likely explain the observed geochemical habitat partitioning. Rather, differences in gene expression and regulation, biochemical differences among these chemoautotrophic pathways, and/or differences in host physiology could all influence the observed patterns of habitat partitioning.
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Affiliation(s)
- Roxanne A. Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States
| | - Chengwei Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
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27
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Seah BKB, Antony CP, Huettel B, Zarzycki J, Schada von Borzyskowski L, Erb TJ, Kouris A, Kleiner M, Liebeke M, Dubilier N, Gruber-Vodicka HR. Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO 2 Fixation. mBio 2019; 10:e01112-19. [PMID: 31239380 PMCID: PMC6593406 DOI: 10.1128/mbio.01112-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 01/25/2023] Open
Abstract
Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO2 by the symbionts drives these nutritional associations. In this study, we investigated "Candidatus Kentron," the clade of symbionts hosted by Kentrophoros, a diverse genus of ciliates which are found in marine coastal sediments around the world. Despite being the main food source for their hosts, Kentron bacteria lack the key canonical genes for any of the known pathways for autotrophic carbon fixation and have a carbon stable isotope fingerprint that is unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic analyses instead found metabolic features consistent with growth on organic carbon, especially organic and amino acids, for which they have abundant uptake transporters. All known thiotrophic symbionts have converged on using reduced sulfur to gain energy lithotrophically, but they are diverse in their carbon sources. Some clades are obligate autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with heterotrophic capabilities similar to those in Kentron. Here we show that Kentron bacteria are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or the reverse tricarboxylic acid cycle for autotrophy.IMPORTANCE Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, "Candidatus Kentron," associated with marine ciliates. They lack genes for known autotrophic pathways and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead, they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.
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Affiliation(s)
| | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Angela Kouris
- Energy Bioengineering and Geomicrobiology Group, University of Calgary, Calgary, Alberta, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa. ISME JOURNAL 2019; 13:2264-2279. [PMID: 31073213 PMCID: PMC6775965 DOI: 10.1038/s41396-019-0431-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 01/21/2023]
Abstract
There are many unknowns regarding the distribution, activity, community composition, and metabolic repertoire of microbial communities in the subseafloor of deep-sea hydrothermal vents. Here we provide the first characterization of subseafloor microbial communities from venting fluids along the central Mariana back-arc basin (15.5–18°N), where the slow-spreading rate, depth, and variable geochemistry along the back-arc distinguish it from other spreading centers. Results indicated that diverse Epsilonbacteraeota were abundant across all sites, with a population of high temperature Aquificae restricted to the northern segment. This suggests that differences in subseafloor populations along the back-arc are associated with local geologic setting and resultant geochemistry. Metatranscriptomics coupled to stable isotope probing revealed bacterial carbon fixation linked to hydrogen oxidation, denitrification, and sulfide or thiosulfate oxidation at all sites, regardless of community composition. NanoSIMS (nanoscale secondary ion mass spectrometry) incubations at 80 °C show only a small portion of the microbial community took up bicarbonate, but those autotrophs had the highest overall rates of activity detected across all experiments. By comparison, acetate was more universally utilized to sustain growth, but within a smaller range of activity. Together, results indicate that microbial communities in venting fluids from the Mariana back-arc contain active subseafloor communities reflective of their local conditions with metabolisms commonly shared across geologically disparate spreading centers throughout the ocean.
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29
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Lee WK, Kim SJ, Hou BK, Van Dover CL, Ju SJ. Population genetic differentiation of the hydrothermal vent crab Austinograea alayseae (Crustacea: Bythograeidae) in the Southwest Pacific Ocean. PLoS One 2019; 14:e0215829. [PMID: 31017948 PMCID: PMC6481846 DOI: 10.1371/journal.pone.0215829] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/09/2019] [Indexed: 12/03/2022] Open
Abstract
To understand the origin, migration, and distribution of organisms across disjunct deep-sea vent habitats, previous studies have documented the population genetic structures of widely distributed fauna, such as gastropods, bivalves, barnacles, and squat lobsters. However, a limited number of investigations has been conducted in the Southwest Pacific Ocean, and many questions remain. In this study, we determined the population structure of the bythograeid crab Austinograea alayseae from three adjacent vent systems (Manus Basin, North Fiji Basin, and Tonga Arc) in the Southwest Pacific Ocean using the sequences of two mitochondrial genes (COI and 16S rDNA) and one nuclear gene (28S rDNA). Populations were divided into a Manus clade and a North Fiji-Tonga clade, with sequence divergence values in the middle of the barcoding gap for bythograeids. We inferred that hydrographic and/or physical barriers act on the gene flow of A. alayseae between the Manus and North Fiji basins. Austinograea alayseae individuals interact freely between the North Fiji Basin and the Lau Basin (Tonga Arc). Although further studies of genetic differentiation over a geological time scale, life-history attributes, and genome-based population genetics are needed to improve our understanding of the evolutionary history of A. alayseae, our results contribute to elucidating the phylogeny, evolution, and biogeography of bythograeids.
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Affiliation(s)
- Won-Kyung Lee
- Global Ocean Resources Research Center, Korea Institute of Ocean Science & Technology, Busan Metropolitan City, Republic of Korea
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Se-Joo Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Bo Kyeng Hou
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Cindy Lee Van Dover
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, United States of America
| | - Se-Jong Ju
- Global Ocean Resources Research Center, Korea Institute of Ocean Science & Technology, Busan Metropolitan City, Republic of Korea
- Marine Biology Major, University of Science & Technology, Daejeon, Republic of Korea
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30
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Johnson G. High throughput DNA extraction of legume root nodules for rhizobial metagenomics. AMB Express 2019; 9:47. [PMID: 30969386 PMCID: PMC6458200 DOI: 10.1186/s13568-019-0771-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022] Open
Abstract
A novel combination of tissue homogenization, cell lysis, and DNA purification techniques was developed for isolating total DNA from whole legume root nodules on an automated robotic system. Silica dehydrated root nodules from soy bean, Glycine max cv. Tara, and mung bean, Vigna radiata cv. Crystal, were homogenized in 96-well plates and were enzymatically and chemically lysed before being loaded into the AutoGenprep 965 for automated phenol–chloroform based DNA isolation. The resulting DNAs were of relatively high concentration, low fragmentation, and free of phenolic and polysaccharide contaminants. In contrast to manual methods, this adaptation of the Autogen Prep automated DNA extraction instrument allows for 100’s to 1000’s of samples to be prepared in a fraction of the time and cost.
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Hakim JA, Schram JB, Galloway AWE, Morrow CD, Crowley MR, Watts SA, Bej AK. The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence. Microorganisms 2019; 7:E35. [PMID: 30691133 PMCID: PMC6406795 DOI: 10.3390/microorganisms7020035] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/13/2019] [Accepted: 01/21/2019] [Indexed: 12/13/2022] Open
Abstract
The sea urchin Strongylocentrotus purpuratus (order Camarodonta, family Strongylocentrotidae) can be found dominating low intertidal pool biomass on the southern coast of Oregon, USA. In this case study, three adult sea urchins were collected from their shared intertidal pool, and the bacteriome of their pharynx, gut tissue, and gut digesta, including their tide pool water and algae, was determined using targeted high-throughput sequencing (HTS) of the 16S rRNA genes and bioinformatics tools. Overall, the gut tissue demonstrated Arcobacter and Sulfurimonas (Epsilonproteobacteria) to be abundant, whereas the gut digesta was dominated by Psychromonas (Gammaproteobacteria), Propionigenium (Fusobacteria), and Flavobacteriales (Bacteroidetes). Alpha and beta diversity analyses indicated low species richness and distinct microbial communities comprising the gut tissue and digesta, while the pharynx tissue had higher richness, more closely resembling the water microbiota. Predicted functional profiles showed Kyoto Encyclopedia of Genes and Genomes (KEGG) Level-2 categories of energy metabolism, membrane transport, cell motility, and signal transduction in the gut tissue, and the gut digesta represented amino acid, carbohydrate, vitamin and cofactor metabolisms, and replication and repair. Co-occurrence network analysis showed the potential relationships and key taxa, such as the highly abundant Arcobacter and Propionigenium, influencing population patterns and taxonomic organization between the gut tissue and digesta. These results demonstrate a trend of microbial community integration, allocation, predicted metabolic roles, and taxonomic co-occurrence patterns in the S. purpuratus gut ecosystem.
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Affiliation(s)
- Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
| | - Julie B Schram
- Oregon Institute of Marine Biology, University of Oregon, 63466 Boat Basin Rd, Charleston, OR 97420, USA.
| | - Aaron W E Galloway
- Oregon Institute of Marine Biology, University of Oregon, 63466 Boat Basin Rd, Charleston, OR 97420, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA.
| | - Michael R Crowley
- Department of Genetics, Heflin Center Genomics Core, School of Medicine, University of Alabama at Birmingham, 705 South 20th Street, Birmingham, AL 35294, USA.
| | - Stephen A Watts
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
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Sen A, Duperron S, Hourdez S, Piquet B, Léger N, Gebruk A, Le Port AS, Svenning MM, Andersen AC. Cryptic frenulates are the dominant chemosymbiotrophic fauna at Arctic and high latitude Atlantic cold seeps. PLoS One 2018; 13:e0209273. [PMID: 30592732 PMCID: PMC6310283 DOI: 10.1371/journal.pone.0209273] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/03/2018] [Indexed: 12/02/2022] Open
Abstract
We provide the first detailed identification of Barents Sea cold seep frenulate hosts and their symbionts. Mitochondrial COI sequence analysis, in combination with detailed morphological investigations through both light and electron microscopy was used for identifying frenulate hosts, and comparing them to Oligobrachia haakonmosbiensis and Oligobrachia webbi, two morphologically similar species known from the Norwegian Sea. Specimens from sites previously assumed to host O. haakonmosbiensis were included in our molecular analysis, which allowed us to provide new insight on the debate regarding species identity of these Oligobrachia worms. Our results indicate that high Arctic seeps are inhabited by a species that though closely related to Oligobrachia haakonmosbiensis, is nonetheless distinct. We refer to this group as the Oligobrachia sp. CPL-clade, based on the colloquial names of the sites they are currently known to inhabit. Since members of the Oligobrachia sp. CPL-clade cannot be distinguished from O. haakonmosbiensis or O. webbi based on morphology, we suggest that a complex of cryptic Oligobrachia species inhabit seeps in the Norwegian Sea and the Arctic. The symbionts of the Oligobrachia sp. CPL-clade were also found to be closely related to O. haakonmosbiensis symbionts, but genetically distinct. Fluorescent in situ hybridization and transmission electron micrographs revealed extremely dense populations of bacteria within the trophosome of members of the Oligobrachia sp. CPL-clade, which is unusual for frenulates. Bacterial genes for sulfur oxidation were detected and small rod shaped bacteria (round in cross section), typical of siboglinid-associated sulfur-oxidizing bacteria, were seen on electron micrographs of trophosome bacteriocytes, suggesting that sulfide constitutes the main energy source. We hypothesize that specific, local geochemical conditions, in particular, high sulfide fluxes and concentrations could account for the unusually high symbiont densities in members of the Oligrobrachia sp. CPL-clade.
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Affiliation(s)
- Arunima Sen
- Centre for Arctic Gas Hydrate, Environment and Climate (CAGE), UiT The Arctic University of Norway, Tromsø, Norway
| | - Sébastien Duperron
- Sorbonne Université, UMR7208 (MNHN, CNRS, IRD, UCN, UA) Biologie des organismes et écosystèmes aquatiques (BOREA), Paris, France.,Muséum National d'Histoire Naturelle-UMR7245 (MNHN CNRS) Mécanismes de Communication et Adaptation des Micro-organismes (MCAM), Paris, France
| | - Stéphane Hourdez
- UMR7144 Sorbonne Université, CNRS-Equipe Adaptation et Biologie des Invertébrés Marins en Conditions Extrêmes (ABICE)-Station Biologique de Roscoff, Roscoff, France
| | - Bérénice Piquet
- Sorbonne Université, UMR7208 (MNHN, CNRS, IRD, UCN, UA) Biologie des organismes et écosystèmes aquatiques (BOREA), Paris, France.,UMR7144 Sorbonne Université, CNRS-Equipe Adaptation et Biologie des Invertébrés Marins en Conditions Extrêmes (ABICE)-Station Biologique de Roscoff, Roscoff, France
| | - Nelly Léger
- Sorbonne Université, UMR7208 (MNHN, CNRS, IRD, UCN, UA) Biologie des organismes et écosystèmes aquatiques (BOREA), Paris, France
| | | | - Anne-Sophie Le Port
- UMR7144 Sorbonne Université, CNRS-Equipe Adaptation et Biologie des Invertébrés Marins en Conditions Extrêmes (ABICE)-Station Biologique de Roscoff, Roscoff, France
| | - Mette Marianne Svenning
- Centre for Arctic Gas Hydrate, Environment and Climate (CAGE), UiT The Arctic University of Norway, Tromsø, Norway.,Department of Arctic Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ann C Andersen
- UMR7144 Sorbonne Université, CNRS-Equipe Adaptation et Biologie des Invertébrés Marins en Conditions Extrêmes (ABICE)-Station Biologique de Roscoff, Roscoff, France
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33
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Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, Strous M. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A 2018; 115:E5576-E5584. [PMID: 29844191 PMCID: PMC6004456 DOI: 10.1073/pnas.1722325115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present "direct protein-SIF" and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts' metabolism. This confirms the usefulness of this approach to accurately determine δ13C values for different species in microbial community samples.
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Affiliation(s)
- Manuel Kleiner
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Tjorven Hinzke
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Juliane Wippler
- Symbiosis Department, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Erin Thorson
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
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Thaler AD, Saleu W, Carlsson J, Schultz TF, Van Dover CL. Population structure of Bathymodiolus manusensis, a deep-sea hydrothermal vent-dependent mussel from Manus Basin, Papua New Guinea. PeerJ 2017; 5:e3655. [PMID: 28852590 PMCID: PMC5572536 DOI: 10.7717/peerj.3655] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/14/2017] [Indexed: 11/20/2022] Open
Abstract
Deep-sea hydrothermal vents in the western Pacific are increasingly being assessed for their potential mineral wealth. To anticipate the potential impacts on biodiversity and connectivity among populations at these vents, environmental baselines need to be established. Bathymodiolus manusensis is a deep-sea mussel found in close association with hydrothermal vents in Manus Basin, Papua New Guinea. Using multiple genetic markers (cytochrome C-oxidase subunit-1 sequencing and eight microsatellite markers), we examined population structure at two sites in Manus Basin separated by 40 km and near a potential mining prospect, where the species has not been observed. No population structure was detected in mussels sampled from these two sites. We also compared a subset of samples with B. manusensis from previous studies to infer broader population trends. The genetic diversity observed can be used as a baseline against which changes in genetic diversity within the population may be assessed following the proposed mining event.
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Affiliation(s)
- Andrew D. Thaler
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
- Blackbeard Biologic: Science and Environmental Advisors, St. Michaels, MD, USA
| | - William Saleu
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
- BETA Scientific, Port Moresby, Papua New Guinea
| | - Jens Carlsson
- Area52 Research Group, School of Biology and Environmental Science, Earth Institute, University College Dublin, Dublin, Ireland
| | - Thomas F. Schultz
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
| | - Cindy L. Van Dover
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
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35
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Ho PT, Park E, Hong SG, Kim EH, Kim K, Jang SJ, Vrijenhoek RC, Won YJ. Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents. BMC Evol Biol 2017; 17:121. [PMID: 28558648 PMCID: PMC5450337 DOI: 10.1186/s12862-017-0966-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each generation via infection by free-living forms. This study examined geographical subdivision of the thiotrophic endosymbionts hosted by Bathymodiolus mussels living along the eastern Pacific hydrothermal vents. High-throughput sequencing data of 16S ribosomal RNA encoding gene and fragments of six protein-coding genes of symbionts were examined in the samples collected from nine vent localities at the East Pacific Rise, Galápagos Rift, and Pacific-Antarctic Ridge. RESULTS Both of the parapatric sister-species, B. thermophilus and B. antarcticus, hosted the same numerically dominant phylotype of thiotrophic Gammaproteobacteria. However, sequences from six protein-coding genes revealed highly divergent symbiont lineages living north and south of the Easter Microplate and hosted by these two Bathymodiolus mussel species. High heterogeneity of symbiont haplotypes among host individuals sampled from the same location suggested that stochasticity associated with initial infections was amplified as symbionts proliferated within the host individuals. The mussel species presently contact one another and hybridize along the Easter Microplate, but the northern and southern symbionts appear to be completely isolated. Vicariance associated with orogeny of the Easter Microplate region, 2.5-5.3 million years ago, may have initiated isolation of the symbiont and host populations. Estimates of synonymous substitution rates for the protein-coding bacterial genes examined in this study were 0.77-1.62%/nucleotide/million years. CONCLUSIONS Our present study reports the most comprehensive population genetic analyses of the chemosynthetic endosymbiotic bacteria based on high-throughput genetic data and extensive geographical sampling to date, and demonstrates the role of the geographical features, the Easter Microplate and geographical distance, in the intraspecific divergence of this bacterial species along the mid-ocean ridge axes in the eastern Pacific. Altogether, our results provide insights into extrinsic and intrinsic factors affecting the dispersal and evolution of chemosynthetic symbiotic partners in the hydrothermal vents along the eastern Pacific Ocean.
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Affiliation(s)
- Phuong-Thao Ho
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea
| | - Eunji Park
- Division of EcoScience, Ewha Womans University, Seoul, 03760, Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Eun-Hye Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Kangchon Kim
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea
| | - Sook-Jin Jang
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea
| | | | - Yong-Jin Won
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea. .,Division of EcoScience, Ewha Womans University, Seoul, 03760, Korea.
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36
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Breusing C, Vrijenhoek RC, Reusch TBH. Widespread introgression in deep-sea hydrothermal vent mussels. BMC Evol Biol 2017; 17:13. [PMID: 28086786 PMCID: PMC5237248 DOI: 10.1186/s12862-016-0862-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/21/2016] [Indexed: 11/29/2022] Open
Abstract
Background The analysis of hybrid zones is crucial for gaining a mechanistic understanding of the process of speciation and the maintenance of species boundaries. Hybrid zones have been studied intensively in terrestrial and shallow-water ecosystems, but very little is known about their occurrence in deep-sea environments. Here we used diagnostic, single nucleotide polymorphisms in combination with one mitochondrial gene to re-examine prior hypotheses about a contact zone involving deep-sea hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis, living along the Mid-Atlantic Ridge. Results Admixture was found to be asymmetric with respect to the parental species, while introgression was more widespread geographically than previously recognized. Admixed individuals with a majority of alleles from one of the parental species were most frequent in habitats corresponding to that species. Mussels found at a geographically intermediate vent field constituted a genetically mixed population that showed no evidence for hybrid incompatibilities, a finding that does not support a previously inferred tension zone model. Conclusions Our analyses indicate that B. azoricus and B. puteoserpentis hybridize introgressively across a large geographic area without evidence for general hybrid incompatibilities. While these findings shed new light onto the genetic structure of this hybrid zone, many aspects about its nature still remain obscure. Our study sets a baseline for further research that should primarily focus on the acquisition of additional mussel samples and environmental data, a detailed exploration of vent areas and hidden populations as well as genomic analyses in both mussel hosts and their bacterial symbionts. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0862-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Corinna Breusing
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany. .,Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA.
| | - Robert C Vrijenhoek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA, 95039, USA
| | - Thorsten B H Reusch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany
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37
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Tobler M, Passow CN, Greenway R, Kelley JL, Shaw JH. The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032418] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydrogen sulfide (H2S) is a respiratory toxicant that creates extreme environments tolerated by few organisms. H2S is also produced endogenously by metazoans and plays a role in cell signaling. The mechanisms of H2S toxicity and its physiological functions serve as a basis to discuss the multifarious strategies that allow animals to survive in H2S-rich environments. Despite their toxicity, H2S-rich environments also provide ecological opportunities, and complex selective regimes of covarying abiotic and biotic factors drive trait evolution in organisms inhabiting H2S-rich environments. Furthermore, adaptation to H2S-rich environments can drive speciation, giving rise to biodiversity hot spots with high levels of endemism in deep-sea hydrothermal vents, cold seeps, and freshwater sulfide springs. The diversity of H2S-rich environments and their inhabitants provides ideal systems for comparative studies of the effects of a clear-cut source of selection across vast geographic and phylogenetic scales, ultimately informing our understanding of how environmental stressors affect ecological and evolutionary processes.
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Affiliation(s)
- Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | | | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Jennifer H. Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078
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38
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39
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Lindgren AR, Buckley BA, Eppley SM, Reysenbach AL, Stedman KM, Wagner JT. Life on the Edge-the Biology of Organisms Inhabiting Extreme Environments: An Introduction to the Symposium. Integr Comp Biol 2016; 56:493-9. [PMID: 27471225 DOI: 10.1093/icb/icw094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Life persists, even under extremely harsh conditions. While the existence of extremophiles is well known, the mechanisms by which these organisms evolve, perform basic metabolic functions, reproduce, and survive under extreme physical stress are often entirely unknown. Recent technological advances in terms of both sampling and studying extremophiles have yielded new insight into their evolution, physiology and behavior, from microbes and viruses to plants to eukaryotes. The goal of the "Life on the Edge-the Biology of Organisms Inhabiting Extreme Environments" symposium was to unite researchers from taxonomically and methodologically diverse backgrounds to highlight new advances in extremophile biology. Common themes and new insight that emerged from the symposium included the important role of symbiotic associations, the continued challenges associated with sampling and studying extremophiles and the important role these organisms play in terms of studying climate change. As we continue to explore our planet, especially in difficult to reach areas from the poles to the deep sea, we expect to continue to discover new and extreme circumstances under which life can persist.
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Affiliation(s)
- Annie R Lindgren
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Bradley A Buckley
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Sarah M Eppley
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Anna-Louise Reysenbach
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Kenneth M Stedman
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Josiah T Wagner
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
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40
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Beinart RA, Gartman A, Sanders JG, Luther GW, Girguis PR. The uptake and excretion of partially oxidized sulfur expands the repertoire of energy resources metabolized by hydrothermal vent symbioses. Proc Biol Sci 2016; 282:20142811. [PMID: 25876848 PMCID: PMC4426611 DOI: 10.1098/rspb.2014.2811] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Symbiotic associations between animals and chemoautotrophic bacteria crowd around hydrothermal vents. In these associations, symbiotic bacteria use chemical reductants from venting fluid for the energy to support autotrophy, providing primary nutrition for the host. At vents along the Eastern Lau Spreading Center, the partially oxidized sulfur compounds (POSCs) thiosulfate and polysulfide have been detected in and around animal communities but away from venting fluid. The use of POSCs for autotrophy, as an alternative to the chemical substrates in venting fluid, could mitigate competition in these communities. To determine whether ESLC symbioses could use thiosulfate to support carbon fixation or produce POSCs during sulfide oxidation, we used high-pressure, flow-through incubations to assess the productivity of three symbiotic mollusc genera—the snails Alviniconcha spp. and Ifremeria nautilei, and the mussel Bathymodiolus brevior—when oxidizing sulfide and thiosulfate. Via the incorporation of isotopically labelled inorganic carbon, we found that the symbionts of all three genera supported autotrophy while oxidizing both sulfide and thiosulfate, though at different rates. Additionally, by concurrently measuring their effect on sulfur compounds in the aquaria with voltammetric microelectrodes, we showed that these symbioses excreted POSCs under highly sulfidic conditions, illustrating that these symbioses could represent a source for POSCs in their habitat. Furthermore, we revealed spatial disparity in the rates of carbon fixation among the animals in our incubations, which might have implications for the variability of productivity in situ. Together, these results re-shape our thinking about sulfur cycling and productivity by vent symbioses, demonstrating that thiosulfate may be an ecologically important energy source for vent symbioses and that they also likely impact the local geochemical regime through the excretion of POSCs.
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Affiliation(s)
- R A Beinart
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02136, USA
| | - A Gartman
- School of Marine Science and Policy, College of Earth, Ocean and Environment, University of Delaware, Lewes, MD, USA
| | - J G Sanders
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02136, USA
| | - G W Luther
- School of Marine Science and Policy, College of Earth, Ocean and Environment, University of Delaware, Lewes, MD, USA
| | - P R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02136, USA
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41
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Ikuta T, Takaki Y, Nagai Y, Shimamura S, Tsuda M, Kawagucci S, Aoki Y, Inoue K, Teruya M, Satou K, Teruya K, Shimoji M, Tamotsu H, Hirano T, Maruyama T, Yoshida T. Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. ISME JOURNAL 2015; 10:990-1001. [PMID: 26418631 PMCID: PMC4796938 DOI: 10.1038/ismej.2015.176] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022]
Abstract
Chemosynthetic symbiosis is one of the successful systems for adapting to a wide range of habitats including extreme environments, and the metabolic capabilities of symbionts enable host organisms to expand their habitat ranges. However, our understanding of the adaptive strategies that enable symbiotic organisms to expand their habitats is still fragmentary. Here, we report that a single-ribotype endosymbiont population in an individual of the host vent mussel, Bathymodiolus septemdierum has heterogeneous genomes with regard to the composition of key metabolic gene clusters for hydrogen oxidation and nitrate reduction. The host individual harbours heterogeneous symbiont subpopulations that either possess or lack the gene clusters encoding hydrogenase or nitrate reductase. The proportions of the different symbiont subpopulations in a host appeared to vary with the environment or with the host's development. Furthermore, the symbiont subpopulations were distributed in patches to form a mosaic pattern in the gill. Genomic heterogeneity in an endosymbiont population may enable differential utilization of diverse substrates and confer metabolic flexibility. Our findings open a new chapter in our understanding of how symbiotic organisms alter their metabolic capabilities and expand their range of habitats.
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Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Miwako Tsuda
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Koji Inoue
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Morimi Teruya
- Okinawa Industrial Technology Center, 12-2 Suzaki, Uruma, Okinawa, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Hinako Tamotsu
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan.,Okinawa Science and Technology Promotion Center (OSTC), 112-18 Asahimachi, Naha, Okinawa, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
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Chen C, Copley JT, Linse K, Rogers AD, Sigwart JD. The heart of a dragon: 3D anatomical reconstruction of the 'scaly-foot gastropod' (Mollusca: Gastropoda: Neomphalina) reveals its extraordinary circulatory system. Front Zool 2015; 12:13. [PMID: 26085836 PMCID: PMC4470333 DOI: 10.1186/s12983-015-0105-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/15/2015] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The 'scaly-foot gastropod' (Chrysomallon squamiferum Chen et al., 2015) from deep-sea hydrothermal vent ecosystems of the Indian Ocean is an active mobile gastropod occurring in locally high densities, and it is distinctive for the dermal scales covering the exterior surface of its foot. These iron-sulfide coated sclerites, and its nutritional dependence on endosymbiotic bacteria, are both noted as adaptations to the extreme environment in the flow of hydrogen sulfide. We present evidence for other adaptations of the 'scaly-foot gastropod' to life in an extreme environment, investigated through dissection and 3D tomographic reconstruction of the internal anatomy. RESULTS Our anatomical investigations of juvenile and adult specimens reveal a large unganglionated nervous system, a simple and reduced digestive system, and that the animal is a simultaneous hermaphrodite. We show that Chrysomallon squamiferum relies on endosymbiotic bacteria throughout post-larval life. Of particular interest is the circulatory system: Chrysomallon has a very large ctenidium supported by extensive blood sinuses filled with haemocoel. The ctenidium provides oxygen for the host but the circulatory system is enlarged beyond the scope of other similar vent gastropods. At the posterior of the ctenidium is a remarkably large and well-developed heart. Based on the volume of the auricle and ventricle, the heart complex represents approximately 4 % of the body volume. This proportionally giant heart primarily sucks blood through the ctenidium and supplies the highly vascularised oesophageal gland. Thus we infer the elaborate cardiovascular system most likely evolved to oxygenate the endosymbionts in an oxygen poor environment and/or to supply hydrogen sulfide to the endosymbionts. CONCLUSIONS This study exemplifies how understanding the autecology of an organism can be enhanced by detailed investigation of internal anatomy. This gastropod is a large and active species that is abundant in its hydrothermal vent field ecosystem. Yet all of its remarkable features-protective dermal sclerites, circulatory system, high fecundity-can be viewed as adaptations beneficial to its endosymbiont microbes. We interpret these results to show that, as a result of specialisation to resolve energetic needs in an extreme chemosynthetic environment, this dramatic dragon-like species has become a carrying vessel for its bacteria.
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Affiliation(s)
- Chong Chen
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS UK
| | - Jonathan T Copley
- Ocean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH UK
| | - Katrin Linse
- British Antarctic Survey, High Cross, Cambridge, CB3 0ET UK
| | - Alex D Rogers
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS UK
| | - Julia D Sigwart
- Queen's University Belfast, Marine Laboratory, Portaferry, BT22 1PF Northern Ireland
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Lee S, Kim SJ, Ju SJ, Pak SJ, Son SK, Yang J, Han S. Mercury accumulation in hydrothermal vent mollusks from the southern Tonga Arc, southwestern Pacific Ocean. CHEMOSPHERE 2015; 127:246-253. [PMID: 25748345 DOI: 10.1016/j.chemosphere.2015.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/31/2014] [Accepted: 01/03/2015] [Indexed: 06/04/2023]
Abstract
We provide the mercury (Hg) and monomethylmercury (MMHg) levels of the plume water, sulfide ore, sediment, and mollusks located at the hydrothermal vent fields of the southern Tonga Arc, where active volcanism and intense seismic activity occur frequently. Our objectives were: (1) to address the potential release of Hg from hydrothermal fluids and (2) to examine the distribution of Hg and MMHg levels in hydrothermal mollusks (mussels and snails) harboring chemotrophic bacteria. While high concentrations of Hg in the sediment and Hg, As, and Sb in the sulfide ore indicates that their source is likely hydrothermal fluids, the MMHg concentration in the sediment was orders of magnitude lower than the Hg (<0.001%). It suggests that Hg methylation may have not been favorable in the vent field sediment. In addition, Hg concentrations in the mollusks were much higher (10-100 times) than in other hydrothermal vent environments, indicating that organisms located at the Tonga Arc are exposed to exceedingly high Hg levels. While Hg concentration was higher in the gills and digestive glands than in the mantles and residues of snails and mussels, the MMHg concentrations in the gills and digestive glands were orders of magnitude lower (0.004-0.04%) than Hg concentrations. In summary, our results suggest that the release of Hg from the hydrothermal vent fields of the Tonga Arc and subsequent bioaccumulation are substantial, but not for MMHg.
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Affiliation(s)
- Seyong Lee
- School of Environmental Science & Engineering, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, Republic of Korea
| | - Se-Joo Kim
- Korean Bioinformation Center, Korea Institute of Bioscience & Biotechnology, Daejeon 305-806, Republic of Korea
| | - Se-Jong Ju
- Deep-Sea and Seabed Resources Research Center, Korea Institute of Ocean Science & Technology, Gyeonggi-do 426-744, Republic of Korea; Marine Biology Major, University of Science & Technology, Daejeon 305-350, Republic of Korea
| | - Sang-Joon Pak
- Deep-Sea and Seabed Resources Research Center, Korea Institute of Ocean Science & Technology, Gyeonggi-do 426-744, Republic of Korea
| | - Seung-Kyu Son
- Deep-Sea and Seabed Resources Research Center, Korea Institute of Ocean Science & Technology, Gyeonggi-do 426-744, Republic of Korea
| | - Jisook Yang
- School of Environmental Science & Engineering, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, Republic of Korea
| | - Seunghee Han
- School of Environmental Science & Engineering, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, Republic of Korea.
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Zwirglmaier K, Reid WDK, Heywood J, Sweeting CJ, Wigham BD, Polunin NVC, Hawkes JA, Connelly DP, Pearce D, Linse K. Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents. Microbiologyopen 2014; 4:136-50. [PMID: 25515351 PMCID: PMC4335981 DOI: 10.1002/mbo3.227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/16/2014] [Accepted: 10/27/2014] [Indexed: 11/12/2022] Open
Abstract
We analyzed the diversity of bacterial epibionts and trophic ecology of a new species of Kiwa yeti crab discovered at two hydrothermal vent fields (E2 and E9) on the East Scotia Ridge (ESR) in the Southern Ocean using a combination of 454 pyrosequencing, Sanger sequencing, and stable isotope analysis. The Kiwa epibiont communities were dominated by Epsilon- and Gammaproteobacteria. About 454 sequencing of the epibionts on 15 individual Kiwa specimen revealed large regional differences between the two hydrothermal vent fields: at E2, the bacterial community on the Kiwa ventral setae was dominated (up to 75%) by Gammaproteobacteria, whereas at E9 Epsilonproteobacteria dominated (up to 98%). Carbon stable isotope analysis of both Kiwa and the bacterial epibionts also showed distinct differences between E2 and E9 in mean and variability. Both stable isotope and sequence data suggest a dominance of different carbon fixation pathways of the epibiont communities at the two vent fields. At E2, epibionts were putatively fixing carbon via the Calvin-Benson-Bassham and reverse tricarboxylic acid cycle, while at E9 the reverse tricarboxylic acid cycle dominated. Co-varying epibiont diversity and isotope values at E2 and E9 also present further support for the hypothesis that epibionts serve as a food source for Kiwa.
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Affiliation(s)
- Katrin Zwirglmaier
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, United Kingdom
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Freeman CJ, Easson CG, Baker DM. Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras. PeerJ 2014; 2:e695. [PMID: 25548731 PMCID: PMC4273936 DOI: 10.7717/peerj.695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/21/2014] [Indexed: 11/20/2022] Open
Abstract
Hosting symbionts provides many eukaryotes with access to the products of microbial metabolism that are crucial for host performance. On tropical coral reefs, many (High Microbial Abundance [HMA]) but not all (Low Microbial Abundance [LMA]) marine sponges host abundant symbiont communities. Although recent research has revealed substantial variation in these sponge-microbe associations (termed holobionts), little is known about the ecological implications of this diversity. We investigated the expansion of diverse sponge species across isotopic niche space by calculating niche size (as standard ellipse area [SEAc]) and assessing the relative placement of common sponge species in bivariate (δ13C and δ15N) plots. Sponges for this study were collected from the relatively isolated reefs within the Miskito Cays of Honduras. These reefs support diverse communities of HMA and LMA species that together span a gradient of photosymbiont abundance, as revealed by chlorophyll a analysis. HMA sponges occupied unique niche space compared to LMA species, but the placement of some HMA sponges was driven by photosymbiont abundance. In addition, photosymbiont abundance explained a significant portion of the variation in isotope values, suggesting that access to autotrophic metabolism provided by photosymbionts is an important predictor in the location of species within isotopic space. Host identity accounted for over 70% of the variation in isotope values within the Miskito Cays and there was substantial variation in the placement of individual species within isotopic niche space, suggesting that holobiont metabolic diversity may allow taxonomically diverse sponge species to utilize unique sources of nutrients within a reef system. This study provides initial evidence that microbial symbionts allow sponges to expand into novel physiochemical niche space. This expansion may reduce competitive interactions within coral reefs and promote diversification of these communities.
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Affiliation(s)
| | - Cole G Easson
- Department of Biology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - David M Baker
- School of Biological Sciences and Swire Institute of Marine Science, University of Hong Kong , Hong Kong , PRC
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Johnson SB, Warén A, Tunnicliffe V, Dover CV, Wheat CG, Schultz TF, Vrijenhoek RC. Molecular taxonomy and naming of five cryptic species ofAlviniconchasnails (Gastropoda: Abyssochrysoidea) from hydrothermal vents. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.970673] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Van Dover CL. Impacts of anthropogenic disturbances at deep-sea hydrothermal vent ecosystems: a review. MARINE ENVIRONMENTAL RESEARCH 2014; 102:59-72. [PMID: 24725508 DOI: 10.1016/j.marenvres.2014.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/25/2014] [Accepted: 03/11/2014] [Indexed: 06/03/2023]
Abstract
Deep-sea hydrothermal-vent ecosystems have stimulated decades of scientific research and hold promise of mineral and genetic resources that also serve societal needs. Some endemic taxa thrive only in vent environments, and vent-associated organisms are adapted to a variety of natural disturbances, from tidal variations to earthquakes and volcanic eruptions. In this paper, physicochemical and biological impacts of a range of human activities at vents are considered. Mining is currently the only anthropogenic activity projected to have a major impact on vent ecosystems, albeit at a local scale, based on our current understanding of ecological responses to disturbance. Natural recovery from a single mining event depends on immigration and larval recruitment and colonization; understanding processes and dynamics influencing life-history stages may be a key to effective minimization and mitigation of mining impacts. Cumulative impacts on benthic communities of several mining projects in a single region, without proper management, include possible species extinctions and shifts in community structure and function.
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Affiliation(s)
- Cindy Lee Van Dover
- Marine Laboratory, Nicholas School of the Environment, Duke University, 135 Marine Lab Rd, Beaufort, NC 28516, USA.
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Beinart RA, Nyholm SV, Dubilier N, Girguis PR. Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, γ-Proteobacterial symbionts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:656-664. [PMID: 25756119 DOI: 10.1111/1758-2229.12183] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Associations between bacteria from the γ-Proteobacterial order Oceanospirillales and marine invertebrates are quite common. Members of the Oceanospirillales exhibit a diversity of interactions with their various hosts, ranging from the catabolism of complex compounds that benefit host growth to attacking and bursting host nuclei. Here, we describe the association between a novel Oceanospirillales phylotype and the hydrothermal vent snail Alviniconcha. Alviniconcha typically harbour chemoautotrophic γ- or ε-Proteobacterial symbionts inside their gill cells. Via fluorescence in situ hybridization and transmission electron microscopy, we observed an Oceanospirillales phylotype (named AOP for ‘Alviniconcha Oceanospirillales phylotype’) in membrane-bound vacuoles that were separate from the known γ- or ε-Proteobacterial symbionts. Using quantitative polymerase chain reaction, we surveyed 181 Alviniconcha hosting γ-Proteobacterial symbionts and 102 hosting ε-Proteobacterial symbionts, and found that the population size of AOP was always minor relative to the canonical symbionts (median 0.53% of the total quantified 16S rRNA genes). Additionally, we detected AOP more frequently in Alviniconcha hosting γ-Proteobacterial symbionts than in those hosting ε-Proteobacterial symbionts (96% and 5% of individuals respectively). The high incidence of AOP in γ-Proteobacteria hosting Alviniconcha implies that it could play a significant ecological role either as a host parasite or as an additional symbiont with unknown physiological capacities.
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Ferrera I, Banta AB, Reysenbach AL. Spatial patterns of Aquificales in deep-sea vents along the Eastern Lau Spreading Center (SW Pacific). Syst Appl Microbiol 2014; 37:442-8. [DOI: 10.1016/j.syapm.2014.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 11/28/2022]
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50
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Thaler AD, Plouviez S, Saleu W, Alei F, Jacobson A, Boyle EA, Schultz TF, Carlsson J, Van Dover CL. Comparative population structure of two deep-sea hydrothermal-vent-associated decapods (Chorocaris sp. 2 and Munidopsis lauensis) from southwestern Pacific back-arc basins. PLoS One 2014; 9:e101345. [PMID: 24983244 PMCID: PMC4077841 DOI: 10.1371/journal.pone.0101345] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 06/05/2014] [Indexed: 12/03/2022] Open
Abstract
Studies of genetic connectivity and population structure in deep-sea chemosynthetic ecosystems often focus on endosymbiont-hosting species that are directly dependent on chemical energy extracted from vent effluent for survival. Relatively little attention has been paid to vent-associated species that are not exclusively dependent on chemosynthetic ecosystems. Here we assess connectivity and population structure of two vent-associated invertebrates—the shrimp Chorocaris sp. 2 and the squat lobster Munidopsis lauensis—that are common at deep-sea hydrothermal vents in the western Pacific. While Chorocaris sp. 2 has only been observed at hydrothermal vent sites, M. lauensis can be found throughout the deep sea but occurs in higher abundance around the periphery of active vents We sequenced mitochondrial COI genes and deployed nuclear microsatellite markers for both species at three sites in Manus Basin and either North Fiji Basin (Chorocaris sp. 2) or Lau Basin (Munidopsis lauensis). We assessed genetic differentiation across a range of spatial scales, from approximately 2.5 km to more than 3000 km. Population structure for Chorocaris sp. 2 was comparable to that of the vent-associated snail Ifremeria nautilei, with a single seemingly well-mixed population within Manus Basin that is genetically differentiated from conspecifics in North Fiji Basin. Population structure for Munidopsis lauensis was more complex, with two genetically differentiated populations in Manus Basin and a third well-differentiated population in Lau Basin. The unexpectedly high level of genetic differentiation between M. lauensis populations in Manus Basin deserves further study since it has implications for conservation and management of diversity in deep-sea hydrothermal vent ecosystems.
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Affiliation(s)
- Andrew David Thaler
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
- * E-mail:
| | - Sophie Plouviez
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - William Saleu
- Nautilus Minerals, Port Moresby, NCD, Papua New Guinea
| | - Freddie Alei
- Environmental Science and Geography Division, School of Natural and Physical Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Alixandra Jacobson
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - Emily A. Boyle
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - Thomas F. Schultz
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - Jens Carlsson
- School of Biology & Environmental Science, University College Dublin, Dublin, Ireland
| | - Cindy Lee Van Dover
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
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