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Wang H, He K, Zhang H, Zhang Q, Cao L, Li J, Zhong Z, Chen H, Zhou L, Lian C, Wang M, Chen K, Qian PY, Li C. Deciphering deep-sea chemosynthetic symbiosis by single-nucleus RNA-sequencing. eLife 2024; 12:RP88294. [PMID: 39102287 PMCID: PMC11299980 DOI: 10.7554/elife.88294] [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] [Indexed: 08/06/2024] Open
Abstract
Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host-symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100 m depth) using single-nucleus RNA-sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gill's structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into the principles of host-symbiont interaction and the bivalves' environmental adaption mechanisms.
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Affiliation(s)
- Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan LaboratoryQingdaoChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Kai He
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou UniversityGuangzhouChina
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Lei Cao
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Jing Li
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Hao Chen
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Li Zhou
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Chao Lian
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
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Castel J, Pradillon F, Cueff V, Leger G, Daguin-Thiébaut C, Ruault S, Mary J, Hourdez S, Jollivet D, Broquet T. Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals. J Evol Biol 2024; 37:779-794. [PMID: 38699972 DOI: 10.1093/jeb/voae051] [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: 02/14/2024] [Revised: 03/27/2024] [Accepted: 05/02/2024] [Indexed: 05/05/2024]
Abstract
Molluscs have undergone many transitions between separate sexes and hermaphroditism, which is of interest in studying the evolution of sex determination and differentiation. Here, we combined multi-locus genotypes obtained from restriction site-associated DNA (RAD) sequencing with anatomical observations of the gonads of three deep-sea hydrothermal vent gastropods of the genus Alviniconcha living in the southwest Pacific. We found that all three species (Alviniconcha boucheti, Alviniconcha strummeri, and Alviniconcha kojimai) share the same male-heterogametic XY sex-determination system but that the gonads of XX A. kojimai individuals are invaded by a variable proportion of male reproductive tissue. The identification of Y-specific RAD loci (found only in A. boucheti) and the phylogenetic analysis of three sex-linked loci shared by all species suggested that X-Y recombination has evolved differently within each species. This situation of three species showing variation in gonadal development around a common sex-determination system provides new insights into the reproductive mode of poorly known deep-sea species and opens up an opportunity to study the evolution of recombination suppression on sex chromosomes and its association with mixed or transitory sexual systems.
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Affiliation(s)
- Jade Castel
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Florence Pradillon
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, Plouzané, France
| | - Valérie Cueff
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, Plouzané, France
| | - Guillaume Leger
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, Plouzané, France
| | | | - Stéphanie Ruault
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Jean Mary
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Stéphane Hourdez
- UMR 8222 LECOB CNRS-Sorbonne Université, Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Didier Jollivet
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Thomas Broquet
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
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Nakajima Y, Nakamura M, Watanabe HK, Ishibashi J, Yamamoto H, Mitarai S. Ocean circulation contributes to genetic connectivity of limpet populations at deep-sea hydrothermal vents in a back-arc basin. Evol Appl 2024; 17:e13727. [PMID: 38894981 PMCID: PMC11183178 DOI: 10.1111/eva.13727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/15/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
For endemic benthos inhabiting hydrothermal vent fields, larval recruitment is critical for population maintenance and colonization via migration among separated sites. The vent-endemic limpet, Lepetodrilus nux, is abundant at deep-sea hydrothermal vents in the Okinawa Trough, a back-arc basin in the northwestern Pacific; nonetheless, it is endangered due to deep-sea mining. This species is associated with many other vent species and is an important successor in these vent ecosystems. However, limpet genetic diversity and connectivity among local populations have not yet been examined. We conducted a population genetics study of L. nux at five hydrothermal vent fields (maximum geographic distance, ~545 km; depths ~700 m to ~1650 m) using 14 polymorphic microsatellite loci previously developed. Genetic diversity has been maintained among these populations. Meanwhile, fine population genetic structure was detected between distant populations, even within this back-arc basin, reflecting geographic distances between vent fields. There was a significant, positive correlation between genetic differentiation and geographic distance, but no correlation with depth. Contrary to dispersal patterns predicted by an ocean circulation model, genetic migration is not necessarily unidirectional, based on relative migration rates. While ocean circulation contributes to dispersal of L. nux among vent fields in the Okinawa Trough, genetic connectivity may be maintained by complex, bidirectional dispersal processes over multiple generations.
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Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
- Center for Climate Change AdaptationNational Institute for Environmental StudiesTsukubaIbarakiJapan
| | - Masako Nakamura
- School of Marine Science and TechnologyTokai UniversityShizuokaJapan
| | - Hiromi Kayama Watanabe
- Institute for Extra‐Cutting‐Edge Science and Technology Avant‐Garde Research (X‐Star)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawaJapan
| | | | - Hiroyuki Yamamoto
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawaJapan
| | - Satoshi Mitarai
- Marine Biophysics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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Alfaro-Lucas JM, Martin D, Michel LN, Laes A, Cathalot C, Fuchs S, Sarrazin J. Fluid chemistry alters faunal trophodynamics but not composition on the deep-sea Capelinhos hydrothermal edifice (Lucky Strike vent field, Mid-Atlantic Ridge). Sci Rep 2024; 14:1940. [PMID: 38253666 PMCID: PMC10803789 DOI: 10.1038/s41598-024-52186-1] [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: 05/17/2023] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The recently discovered deep-sea Capelinhos hydrothermal edifice, ~ 1.5 km of the main Lucky Strike (LS) vent field (northern Mid-Atlantic Ridge), contrasts with the other LS edifices in having poorly-altered end-member hydrothermal fluids with low pH and chlorine, and high metal concentrations. Capelinhos unique chemistry and location offer the opportunity to test the effects of local abiotic filters on faunal community structure while avoiding the often-correlated influence of dispersal limitation and depth. In this paper, we characterize for the first time the distribution patterns of the Capelinhos faunal communities, and analyze the benthic invertebrates (> 250 µm) inhabiting diffusive-flow areas and their trophic structures (δ13C, δ15N and δ34S). We hypothesized that faunal communities would differ from those of the nearest LS vent edifices, showing an impoverished species subset due to the potential toxicity of the chemical environment. Conversely, our results show that: (1) community distribution resembles that of other LS edifices, with assemblages visually dominated by shrimps (close to high-temperature focused-fluid areas) and mussels (at low-temperature diffuse flow areas); (2) most species from diffuse flow areas are well-known LS inhabitants, including the bed-forming and chemosymbiotic mussel Bathymodiolus azoricus and (3) communities are as diverse as those of the most diverse LS edifices. On the contrary, stable isotopes suggest different trophodynamics at Capelinhos. The high δ15N and, especially, δ13C and δ34S values suggest an important role of methane oxidation (i.e., methanotrophy), rather than the sulfide oxidation (i.e., thiotrophy) that predominates at most LS edifices. Our results indicate that Capelinhos shows unique environmental conditions, trophic structure and trophodynamics, yet similar fauna, compared to other LS edifices, which suggest a great environmental and trophic plasticity of the vent faunal communities at the LS.
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Affiliation(s)
- Joan M Alfaro-Lucas
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France.
- Department of Biology, University of Victoria, Victoria, BC, Canada.
| | - Daniel Martin
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Catalonia, Spain
| | - Loïc N Michel
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
- Université de Liège, Liège, Belgium
| | - Agathe Laes
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
| | - Cécile Cathalot
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
| | - Sandra Fuchs
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
| | - Jozée Sarrazin
- Univ Brest, Ifremer, CNRS, Unité BEEP, 29280, Plouzané, France
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Betters MJ, Cordes EE. New records of Provanna (Gastropoda, Provannidae) from the Costa Rica Margin and an identification key for the genus. Zookeys 2024; 1189:1-32. [PMID: 38314107 PMCID: PMC10836654 DOI: 10.3897/zookeys.1189.109734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/20/2023] [Indexed: 02/06/2024] Open
Abstract
Consistent species identification is foundational to biological research and requires coordination among a diversity of researchers and institutions. However, such consistency may be hindered for rare organisms where specimens, identification resources, and taxonomic experts are few. This is often the case for deep-sea taxonomic groups. For example, the deep-sea gastropod genus Provanna Dall, 1918 is common at chemosynthetic sites throughout the world's oceans, yet no formal guide to these species has yet been produced. Recent exploration has recovered new specimens of Provanna from hydrocarbon seeps off the Pacific Costa Rica Margin. The current work assesses the species identity of these specimens using shell morphology, radular morphology, and genetic barcoding (mitochondrial CO1 and nuclear H3). Records of occurrence for P.laevis Warén & Ponder, 1991, P.ios Warén & Bouchet, 1986, and P.pacifica Warén & Bouchet, 1986 are herein presented from the Costa Rica Margin. A critical taxonomic review of the 29 extant species within this genus was conducted and their genetic, morphological, and biogeographical distinction assessed. In this review, genetic and morphological support was found for nearly all current species delineations except for P.glabraOkutani et al., 1992, syn. nov. and P.laevis, syn. nov., which are herein synonymized to P.laevis, and for P.ios, syn. nov. and P.goniata Warén & Bouchet, 1986, syn. nov., which are synonymized to P.ios. Finally, the first species identification key for the extant species in this genus is presented. This work clarifies the taxonomy and systematics of this deep-sea gastropod genus and contributes a novel polytomous key for use in future research.
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Affiliation(s)
- Melissa J Betters
- Department of Biology, Temple University, Philadelphia, PA, USA Temple University Philadelphia United States of America
| | - Erik E Cordes
- Department of Biology, Temple University, Philadelphia, PA, USA Temple University Philadelphia United States of America
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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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Stewart ECD, Bribiesca‐Contreras G, Taboada S, Wiklund H, Ravara A, Pape E, De Smet B, Neal L, Cunha MR, Jones DOB, Smith CR, Glover AG, Dahlgren TG. Biodiversity, biogeography, and connectivity of polychaetes in the world's largest marine minerals exploration frontier. DIVERS DISTRIB 2023. [DOI: 10.1111/ddi.13690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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Wang M, Ruan L, Liu M, Liu Z, He J, Zhang L, Wang Y, Shi H, Chen M, Yang F, Zeng R, He J, Guo C, Chen J. The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment. BMC Genomics 2023; 24:72. [PMID: 36774470 PMCID: PMC9921365 DOI: 10.1186/s12864-023-09166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated. RESULT We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae. CONCLUSION Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.
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Affiliation(s)
- Muhua Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Lingwei Ruan
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Meng Liu
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Zixuan Liu
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Jian He
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Long Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Yuanyuan Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Hong Shi
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Mingliang Chen
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Feng Yang
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Runying Zeng
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Changjun Guo
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, China. .,Fujian Key Laboratory On Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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10
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Xi L, Sun Y, Xu T, Wang Z, Chiu MY, Plouviez S, Jollivet D, Qiu J. Phylogenetic divergence and population genetics of the hydrothermal vent annelid genus
Hesiolyra
along the East Pacific Rise: Reappraisal using multi‐locus data. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Leyi Xi
- Department of Biology Hong Kong Baptist University Hong Kong China
| | - Yanan Sun
- Department of Biology Hong Kong Baptist University Hong Kong China
- 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
| | - Ting Xu
- 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
| | - Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences Xiamen University Xiamen China
| | - Man Ying Chiu
- Department of Biology Hong Kong Baptist University Hong Kong China
| | - Sophie Plouviez
- Department of Biology University of Louisiana at Lafayette Lafayette Louisiana USA
| | - Didier Jollivet
- Sorbonne Université‐CNRS, UMR 7144 Adaptation et Diversité en Milieu Marin, Equipe DyDiv Station Biologique de Roscoff Roscoff France
| | - Jian‐Wen Qiu
- Department of Biology Hong Kong Baptist University Hong Kong China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China
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11
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Poitrimol C, Thiébaut É, Daguin-Thiébaut C, Le Port AS, Ballenghien M, Tran Lu Y A, Jollivet D, Hourdez S, Matabos M. Contrasted phylogeographic patterns of hydrothermal vent gastropods along South West Pacific: Woodlark Basin, a possible contact zone and/or stepping-stone. PLoS One 2022; 17:e0275638. [PMID: 36197893 PMCID: PMC9534440 DOI: 10.1371/journal.pone.0275638] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Understanding drivers of biodiversity patterns is essential to evaluate the potential impact of deep-sea mining on ecosystems resilience. While the South West Pacific forms an independent biogeographic province for hydrothermal vent fauna, different degrees of connectivity among basins were previously reported for a variety of species depending on their ability to disperse. In this study, we compared phylogeographic patterns of several vent gastropods across South West Pacific back-arc basins and the newly-discovered La Scala site on the Woodlark Ridge by analysing their genetic divergence using a barcoding approach. We focused on six genera of vent gastropods widely distributed in the region: Lepetodrilus, Symmetromphalus, Lamellomphalus, Shinkailepas, Desbruyeresia and Provanna. A wide-range sampling was conducted at different vent fields across the Futuna Volcanic Arc, the Manus, Woodlark, North Fiji, and Lau Basins, during the CHUBACARC cruise in 2019. The Cox1-based genetic structure of geographic populations was examined for each taxon to delineate putative cryptic species and assess potential barriers or contact zones between basins. Results showed contrasted phylogeographic patterns among species, even between closely related species. While some species are widely distributed across basins (i.e. Shinkailepas tollmanni, Desbruyeresia melanioides and Lamellomphalus) without evidence of strong barriers to gene flow, others are restricted to one (i.e. Shinkailepas tufari complex of cryptic species, Desbruyeresia cancellata and D. costata). Other species showed intermediate patterns of isolation with different lineages separating the Manus Basin from the Lau/North Fiji Basins (i.e. Lepetodrilus schrolli, Provanna and Symmetromphalus spp.). Individuals from the Woodlark Basin were either endemic to this area (though possibly representing intermediate OTUs between the Manus Basin and the other eastern basins populations) or, coming into contact from these basins, highlighting the stepping-stone role of the Woodlark Basin in the dispersal of the South West Pacific vent fauna. Results are discussed according to the dispersal ability of species and the geological history of the South West Pacific.
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Affiliation(s)
- Camille Poitrimol
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
- Biologie et Ecologie des Ecosystèmes marins Profonds, Ifremer, CNRS, UBO, Plouzané, France
- * E-mail:
| | - Éric Thiébaut
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Claire Daguin-Thiébaut
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Anne-Sophie Le Port
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Marion Ballenghien
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Adrien Tran Lu Y
- Institut des Sciences de l’Evolution de Montpellier, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Didier Jollivet
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Stéphane Hourdez
- Laboratoire d’Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Marjolaine Matabos
- Biologie et Ecologie des Ecosystèmes marins Profonds, Ifremer, CNRS, UBO, Plouzané, France
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12
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Pereira OS, Gonzalez J, Mendoza G, Le J, McNeill M, Ontiveros J, Lee RW, Rouse GW, Cortés J, Levin LA. Does substrate matter in the deep sea? A comparison of bone, wood, and carbonate rock colonizers. PLoS One 2022; 17:e0271635. [PMID: 35857748 PMCID: PMC9299329 DOI: 10.1371/journal.pone.0271635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022] Open
Abstract
Continental margins host methane seeps, animal falls and wood falls, with chemosynthetic communities that may share or exchange species. The goal of this study was to examine the existence and nature of linkages among chemosynthesis-based ecosystems by deploying organic fall mimics (bone and wood) alongside defaunated carbonate rocks within high and lesser levels of seepage activity for 7.4 years. We compared community composition, density, and trophic structure of invertebrates on these hard substrates at active methane seepage and transition (less seepage) sites at Mound 12 at ~1,000 m depth, a methane seep off the Pacific coast of Costa Rica. At transition sites, the community composition on wood and bone was characteristic of natural wood- and whale-fall community composition, which rely on decay of the organic substrates. However, at active sites, seepage activity modified the relationship between fauna and substrate, seepage activity had a stronger effect in defining and homogenizing these communities and they depend less on organic decay. In contrast to community structure, macrofaunal trophic niche overlap between substrates, based on standard ellipse areas, was greater at transition sites than at active sites, except between rock and wood. Our observations suggest that whale- and wood-fall substrates can function as stepping stones for seep fauna even at later successional stages, providing hard substrate for attachment and chemosynthetic food.
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Affiliation(s)
- Olívia S. Pereira
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
| | - Jennifer Gonzalez
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
| | - Guillermo Mendoza
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
| | - Jennifer Le
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
| | - Madison McNeill
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
- College of Health and Sciences, East Central University, Ada, Oklahoma, United States of America
| | - Jorge Ontiveros
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
- Instituto Tecnológico de Tijuana, Tijuana, Mexico
| | - Raymond W. Lee
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Greg W. Rouse
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
| | - Jorge Cortés
- Centro de Investigación en Ciencias del Mar y Limnología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Lisa A. Levin
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, United States of America
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13
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Tran Lu Y A, Ruault S, Daguin-Thiébaut C, Castel J, Bierne N, Broquet T, Wincker P, Perdereau A, Arnaud-Haond S, Gagnaire PA, Jollivet D, Hourdez S, Bonhomme F. Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei. Mol Ecol 2022; 31:2796-2813. [PMID: 35305041 DOI: 10.1111/mec.16430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022]
Abstract
Hydrothermal vents form archipelagos of ephemeral deep-sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction-recolonization processes. These metal-rich environments are coveted for the mineral resources they harbor, thus raising recent conservation concerns. The evolutionary fate and demographic resilience of hydrothermal species strongly depend on the degree of connectivity among and within their fragmented metapopulations. In the deep sea, however, assessing connectivity is difficult and usually requires indirect genetic approaches. Improved detection of fine-scale genetic connectivity is now possible based on genome-wide screening for genetic differentiation. Here, we explored population connectivity in the hydrothermal vent snail Ifremeria nautilei across its species range encompassing five distinct back-arc basins in the Southwest Pacific. The global analysis, based on 10 570 single nucleotide polymorphism (SNP) markers derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), depicted two semi-isolated and homogeneous genetic clusters. Demo-genetic modeling suggests that these two groups began to diverge about 70 000 generations ago, but continue to exhibit weak and slightly asymmetrical gene flow. Furthermore, a careful analysis of outlier loci showed subtle limitations to connectivity between neighboring basins within both groups. This finding indicates that migration is not strong enough to totally counterbalance drift or local selection, hence questioning the potential for demographic resilience at this latter geographical scale. These results illustrate the potential of large genomic datasets to understand fine-scale connectivity patterns in hydrothermal vents and the deep sea.
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Affiliation(s)
- Adrien Tran Lu Y
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stéphanie Ruault
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Jade Castel
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Nicolas Bierne
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thomas Broquet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Patrick Wincker
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Aude Perdereau
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sophie Arnaud-Haond
- MARBEC, Marine Biodiversity Exploitation and Conservation, Univ Montpellier, CNRS, IFREMER, IRD, Sète, France
| | | | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Stéphane Hourdez
- Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - François Bonhomme
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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14
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Perez M, Breusing C, Angers B, Beinart RA, Won YJ, Young CR. Divergent paths in the evolutionary history of maternally transmitted clam symbionts. Proc Biol Sci 2022; 289:20212137. [PMID: 35259985 PMCID: PMC8905170 DOI: 10.1098/rspb.2021.2137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.
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Affiliation(s)
- Maëva Perez
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
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15
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Balanced Polymorphism at the Pgm-1 Locus of the Pompeii Worm Alvinella pompejana and Its Variant Adaptability Is Only Governed by Two QE Mutations at Linked Sites. Genes (Basel) 2022; 13:genes13020206. [PMID: 35205251 PMCID: PMC8872362 DOI: 10.3390/genes13020206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 11/16/2022] Open
Abstract
The polychaete Alvinella pompejana lives exclusively on the walls of deep-sea hydrothermal chimneys along the East Pacific Rise (EPR), and displays specific adaptations to withstand the high temperatures and hypoxia associated with this highly variable habitat. Previous studies have revealed the existence of a balanced polymorphism on the enzyme phosphoglucomutase associated with thermal variations, where allozymes 90 and 100 exhibit different optimal activities and thermostabilities. Exploration of the mutational landscape of phosphoglucomutase 1 revealed the maintenance of four highly divergent allelic lineages encoding the three most frequent electromorphs over the geographic range of A. pompejana. This polymorphism is only governed by two linked amino acid replacements, located in exon 3 (E155Q and E190Q). A two-niche model of selection, including ‘cold’ and ‘hot’ conditions, represents the most likely scenario for the long-term persistence of these isoforms. Using directed mutagenesis and the expression of the three recombinant variants allowed us to test the additive effect of these two mutations on the biochemical properties of this enzyme. Our results are coherent with those previously obtained from native proteins, and reveal a thermodynamic trade-off between protein thermostability and catalysis, which is likely to have maintained these functional phenotypes prior to the geographic separation of populations across the Equator about 1.2 million years ago.
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16
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Zvi-Kedem T, Shemesh E, Tchernov D, Rubin-Blum M. The worm affair: fidelity and environmental adaptation in symbiont species that co-occur in vestimentiferan tubeworms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:744-752. [PMID: 34374209 DOI: 10.1111/1758-2229.12994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/20/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The symbioses between the vestimentiferan tubeworms and their chemosynthetic partners (Gammaproteobacteria, Chromatiales and Sedimenticolaceae) hallmark the success of these organisms in hydrothermal vent and hydrocarbon seep deep-sea habitats. The fidelity of these associations varies, as both the hosts and the symbionts can be loose in partner choice. Some tubeworms may host distinct symbiont phylotypes, which often co-occur in a single host individual. To better understand the genetic basis for the promiscuity of tubeworm symbioses, we assembled and investigated metagenome-assembled genomes of two symbiont phylotypes (species, based on the average nucleotide identity < 95%) in Lamellibrachia anaximandri, a vestimentiferan endemic to the Mediterranean Sea, in individuals collected from Palinuro hydrothermal vents (Italy) and hydrocarbon seeps (Eratosthenes seamount and Palmahim disturbance). Using comparative genomics, we show that mainly mobilome and genes involved in defence mechanisms distinguish the symbiont genotypes. While many central metabolic functions are conserved in the tubeworm symbionts, nitrate respiration (Nar, Nap and Nas proteins) is modular, yet this modularity is not linked to phylotype, but rather to geographic location, potentially implying adaptation to the local environment. Our results hint that variation in a single moonlighting protein may be responsible for the fidelity of these symbioses.
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Affiliation(s)
- Tal Zvi-Kedem
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Eli Shemesh
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, Haifa, 3108000, Israel
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17
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Xu T, Wang Y, Sun J, Chen C, Watanabe HK, Chen J, Qian PY, Qiu JW. Hidden historical habitat-linked population divergence and contemporary gene flow of a deep-sea patellogastropod limpet. Mol Biol Evol 2021; 38:5640-5654. [PMID: 34534352 PMCID: PMC8662656 DOI: 10.1093/molbev/msab278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hydrothermal vents and hydrocarbon seeps in the deep ocean are rare oases fueled by chemosynthesis. Biological communities inhabiting these ecosystems are often distributed in widely separated habitats, raising intriguing questions on how these organisms achieve connectivity and whether habitat types facilitate intraspecific divergence. The deep-sea patellogastropod limpet Bathyacmaea nipponica that colonizes both vents and seeps across ∼2,400 km in the Northwest Pacific is a feasible model to answer these questions. We analyzed 123 individuals from four vents and three seeps using a comprehensive method incorporating population genomics and physical ocean modeling. Genome survey sequencing and genotyping-by-sequencing resulted in 9,838 single-nucleotide polymorphisms for population genomic analyses. Genetic divergence and demographic analyses revealed four habitat-linked (i.e., three seep and one vent) genetic groups, with the vent genetic group established via the opportunistic invasion of a few limpet larvae from a nearby seep genetic group. TreeMix analysis uncovered three historical seep-to-vent migration events. ADMIXTURE and divMigrate analyses elucidated weak contemporary gene flow from a seep genetic group to the vent genetic group. Physical ocean modeling underlined the potential roles of seafloor topography and ocean currents in shaping the genetic connectivity, contemporary migration, and local hybridization of these deep-sea limpets. Our study highlighted the power of integrating genomic and oceanographic approaches in deciphering the demography and diversification of deep-sea organisms. Given the increasing anthropogenic activities (e.g., mining and gas hydrate extraction) affecting the deep ocean, our results have implications for the conservation of deep-sea biodiversity and establishment of marine protected areas.
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Affiliation(s)
- Ting Xu
- Department of Ocean 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.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong, China
| | - Yan Wang
- Department of Ocean 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.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Sun
- Institute of Evolution and 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, Kanagawa, 237-0061, Japan
| | - Hiromi Kayama Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Junlin Chen
- Department of Ocean 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.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Pei-Yuan Qian
- Department of Ocean 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.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong, China
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18
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Wang CQ, Zheng XT, Chen XF, Jiang H, Huang J, Jiang Y, Hu SS, Huang XR, Liu SY, Gong QH, Feng JH, Xiao X, Li XF, Xiao Z. The Optimal Adjuvant Strategy of Aidi Injection With Gemcitabine and Cisplatin in Advanced Non-small Cell Lung Cancer: A Meta-analysis of 70 Randomized Controlled Trials. Front Pharmacol 2021; 12:582447. [PMID: 34122057 PMCID: PMC8194277 DOI: 10.3389/fphar.2021.582447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 02/22/2021] [Indexed: 01/10/2023] Open
Abstract
Introduction: Aidi injection (Aidi) is composed of cantharidin, astragaloside, ginsenoside, and elentheroside E. As an important adjuvant therapy, Aidi in combination with gemcitabine and cisplatin (GP) is often used in the treatment of non-small cell lung cancer (NSCLC). Objectives: We performed a new evaluation to demonstrate the clinical efficacy and safety of the Aidi and GP combination and further explored an optimal strategy for achieving an ideal response and safety level in advanced NSCLC. Methodology: We collected all the related trials from Chinese and English-language databases, analyzed their methodological bias risk using the Cochrane evaluation Handbook for Systematic Reviews of Interventions Version 5.1.0, extracted all the data using a predefined data extraction form, pooled the data using a series of meta-analyses, and finally summarized the quality of evidence using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. Results: We included 70 trials with 5,509 patients. Compared with GP alone, the Aidi and GP combination showed a significant improvement in the objective response rate (ORR) [1.82 (1.62-2.04)], disease control rate (DCR) [2.29 (1.97-2.67)], and quality of life (QOL) [3.03 (2.55-3.60)] and a low incidence of hematotoxicity and gastrointestinal and hepatorenal toxicity. Aidi might be more suitable for patients who are first-treated, elderly, or patients with a Karnofsky Performance Status (KPS) score ≥ 60 or anticipated survival time (AST) ≥3 months. An Aidi (50 ml/day, 7-14 days/cycle for one to two cycles), gemcitabine (1000 mg/m2), and cisplatin (20-30 mg/m2, 40-50 mg/m2, or 60-80 mg/m2) might be an optimal regimen for realizing an ideal response and safety level. Most results were robust and of moderate quality. Conclusion: Current evidence indicates that Aidi's value in adjuvant chemotherapy may be broad-spectrum, not just for some regimens. The Aidi and GP combination may show a good short-term response, antitumor immunity, and safety level in patients with NSCLC. Aidi (50 ml/day, 7-14 days/cycle for one and two cycles) with GEM (1000 mg/m2) and DDP (20-30 mg/m2 or 40-50 mg/m2) may be an optimal regimen for realizing an ideal goal in patients who are first-treatment, elderly, or have a KPS score ≥ 60 or AST≥3 months.
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Affiliation(s)
- Cheng-Qiong Wang
- Department of General Practice, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Evidence-Based Medicine Center, MOE Virtual Research Center of Evidence-based Medicine at Zunyi Medical College, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiao-Tian Zheng
- Department of General Practice, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Evidence-Based Medicine Center, MOE Virtual Research Center of Evidence-based Medicine at Zunyi Medical College, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiao-Fan Chen
- Evidence-Based Medicine Research Centre, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Hong Jiang
- Department of General Practice, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Evidence-Based Medicine Center, MOE Virtual Research Center of Evidence-based Medicine at Zunyi Medical College, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jun Huang
- Department of Pharmacy, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yuan Jiang
- Evidence-Based Medicine Center, MOE Virtual Research Center of Evidence-based Medicine at Zunyi Medical College, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- School of Management, Zunyi Medical University, Zunyi, China
| | - Shan-Shan Hu
- GCP Center, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiao-Rong Huang
- GCP Center, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shi-Yu Liu
- Evidence-Based Medicine Center, MOE Virtual Research Center of Evidence-based Medicine at Zunyi Medical College, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Qi-Hai Gong
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Ji-Hong Feng
- Department of Oncology, Lishui People’s Hospital, Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Xue Xiao
- Department of General Practice, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Evidence-Based Medicine Center, MOE Virtual Research Center of Evidence-based Medicine at Zunyi Medical College, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xiao-Fei Li
- Special Key Laboratory of Special Antitumor Drugs of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Zheng Xiao
- Department of General Practice, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Evidence-Based Medicine Center, MOE Virtual Research Center of Evidence-based Medicine at Zunyi Medical College, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- School of Management, Zunyi Medical University, Zunyi, China
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19
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Lee W, Juniper SK, Perez M, Ju S, Kim S. Diversity and characterization of bacterial communities of five co-occurring species at a hydrothermal vent on the Tonga Arc. Ecol Evol 2021; 11:4481-4493. [PMID: 33976824 PMCID: PMC8093707 DOI: 10.1002/ece3.7343] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/06/2022] Open
Abstract
Host-symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co-occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill-associated symbiotic bacteria (gill symbionts) of five co-occurring hosts, three mollusks ("Bathymodiolus" manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ-proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co-occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.
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Affiliation(s)
- Won‐Kyung Lee
- Genome Editing Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
| | - S. Kim Juniper
- Department of BiologySchool of Earth and Ocean SciencesUniversity of VictoriaVictoriaBCCanada
| | - Maëva Perez
- Département des Sciences BiologiquesUniversité de MontréalMontrealQCCanada
| | - Se‐Jong Ju
- Korea Institute of Ocean Science & TechnologyBusanKorea
| | - Se‐Joo Kim
- Genome Editing Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
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20
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Wang H, Zhang H, Zhong Z, Sun Y, Wang M, Chen H, Zhou L, Cao L, Lian C, Li C. Molecular analyses of the gill symbiosis of the bathymodiolin mussel Gigantidas platifrons. iScience 2020; 24:101894. [PMID: 33364583 PMCID: PMC7750550 DOI: 10.1016/j.isci.2020.101894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/07/2020] [Accepted: 12/02/2020] [Indexed: 11/29/2022] Open
Abstract
Although the deep-sea bathymodiolin mussels have been intensively studied as a model of animal-bacteria symbiosis, it remains challenging to assess the host-symbiont interactions due to the complexity of the symbiotic tissue-the gill. Using cold-seep mussel Gigantidas platifrons as a model, we isolated the symbiont harboring bacteriocytes and profiled the transcriptomes of the three major parts of the symbiosis-the gill, the bacteriocyte, and the symbiont. This breakdown of the complex symbiotic tissue allowed us to characterize the host-symbiont interactions further. Our data showed that the gill's non-symbiotic parts play crucial roles in maintaining and protecting the symbiosis; the bacteriocytes supply the symbiont with metabolites, control symbiont population, and shelter the symbiont from phage infection; the symbiont dedicates to the methane oxidation and energy production. This study demonstrates that the bathymodiolin symbiosis interacts at the tissue, cellular, and molecular level, maintaining high efficiency and harmonic chemosynthetic micro niche.
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Affiliation(s)
- Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Sun
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Minxiao Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Hao Chen
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Li Zhou
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Lei Cao
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chao Lian
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
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21
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Population connectivity of the hydrothermal-vent limpet Shinkailepas tollmanni in the Southwest Pacific (Gastropoda: Neritimorpha: Phenacolepadidae). PLoS One 2020; 15:e0239784. [PMID: 32991635 PMCID: PMC7523946 DOI: 10.1371/journal.pone.0239784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/13/2020] [Indexed: 11/19/2022] Open
Abstract
The Southwest Pacific represents an independent biogeographic province for deep-sea hydrothermal vent fauna. Different degrees of genetic connectivity among vent fields in Manus, North Fiji and Lau Basins have been reported for various molluscan and crustacean species, presumably reflecting their different levels of dispersal ability as swimming larvae. The present study investigates the population connectivity of the hydrothermal vent limpet Shinkailepas tollmanni (family Phenacolepadidae) in the Southwest Pacific. Our analyses using mitochondrial COI-gene sequences and shell morphometric traits suggest a panmictic population structure throughout its geographic and bathymetric ranges, spanning 4,000 km from the westernmost Manus Basin (151ºE; 1,300 m deep) to the easternmost Lau Basin (176ºE; 2,720 m). The measurements of its embryonic and larval shells demonstrate that the species hatches as a planktotrophic veliger larva with an embryonic shell diameter of 170–180 μm and settles at the vent environment with the larval shell diameter of 750–770 μm. This substantial growth as a feeding larva, ca. 80 times in volume, is comparable or even greater than those of confamilial species in the hydrothermal-vent and methane-seep environments in the Northwest Pacific and Atlantic Oceans. Large pigmented eyes in newly settled juveniles are another common feature in this and other phenacolepadids inhabiting the chemosynthetic environments. These results put together suggest that the larvae of S. tollmanni migrate vertically from deep-sea vents to surface waters to take advantages of richer food supplies and faster currents and stay pelagic for an extended period of time (> 1 year), as previously indicated for the confamilial species.
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22
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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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23
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Moulana A, Anderson RE, Fortunato CS, Huber JA. Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents. mSystems 2020; 5:e00673-19. [PMID: 32291353 PMCID: PMC7159903 DOI: 10.1128/msystems.00673-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.IMPORTANCE Microbes can alter their gene content through the gain and loss of genes. However, there is some debate as to whether natural selection or neutral processes play a stronger role in molding the gene content of microbial genomes. In this study, we examined variation in gene content for the Epsilonbacteraeota genus Sulfurovum from deep-sea hydrothermal vents, which are dynamic habitats known for extensive horizontal gene transfer within microbial populations. Our results show that natural selection is a strong driver of Sulfurovum gene content and that nutrient limitation in particular has shaped the Sulfurovum genome, leading to differences in gene content between ocean basins. Our results also suggest that recently acquired genes undergo stronger selection than genes that were acquired in the more distant past. Overall, our results highlight the importance of natural selection in driving the evolution of microbial populations in these dynamic habitats.
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Affiliation(s)
- Alief Moulana
- Biology Department, Carleton College, Northfield, Minnesota, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, Minnesota, USA
| | | | - Julie A Huber
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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24
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Kersten O, Vetter EW, Jungbluth MJ, Smith CR, Goetze E. Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy. PeerJ 2019; 7:e7691. [PMID: 31579593 PMCID: PMC6766376 DOI: 10.7717/peerj.7691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/19/2019] [Indexed: 11/20/2022] Open
Abstract
Abyssal plains are among the most biodiverse yet least explored marine ecosystems on our planet, and they are increasingly threatened by human impacts, including future deep seafloor mining. Recovery of abyssal populations from the impacts of polymetallic nodule mining will be partially determined by the availability and dispersal of pelagic larvae leading to benthic recolonization of disturbed areas of the seafloor. Here we use a tree-of-life (TOL) metabarcoding approach to investigate the species richness, diversity, and spatial variability of the larval assemblage at mesoscales across the abyssal seafloor in two mining-claim areas in the eastern Clarion Clipperton Fracture Zone (CCZ; abyssal Pacific). Our approach revealed a previously unknown taxonomic richness within the meroplankton assemblage, detecting larvae from 12 phyla, 23 Classes, 46 Orders, and 65 Families, including a number of taxa not previously reported at abyssal depths or within the Pacific Ocean. A novel suite of parasitic copepods and worms were sampled, from families that are known to associate with other benthic invertebrates or demersal fishes as hosts. Larval assemblages were patchily distributed at the mesoscale, with little similarity in OTUs detected among deployments even within the same 30 × 30 km study area. Our results provide baseline observations on larval diversity prior to polymetallic nodule mining in this region, and emphasize our overwhelming lack of knowledge regarding larvae of the benthic boundary layer in abyssal plain ecosystems.
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Affiliation(s)
- Oliver Kersten
- Hawaii Pacific University, Kaneohe, HI, United States of America
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Eric W. Vetter
- Hawaii Pacific University, Kaneohe, HI, United States of America
| | - Michelle J. Jungbluth
- Hawaii Pacific University, Kaneohe, HI, United States of America
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Craig R. Smith
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States of America
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25
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Yang M, Gong L, Sui J, Li X. The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids. PLoS One 2019; 14:e0217952. [PMID: 31536521 PMCID: PMC6752807 DOI: 10.1371/journal.pone.0217952] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022] Open
Abstract
The deep-sea chemosynthetic environment is one of the most extreme environments on the Earth, with low oxygen, high hydrostatic pressure and high levels of toxic substances. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea chemosynthetic environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea chemosynthetic environment.
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Affiliation(s)
- Mei Yang
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Gong
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jixing Sui
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinzheng Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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26
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Thaler AD, Amon D. 262 Voyages Beneath the Sea: a global assessment of macro- and megafaunal biodiversity and research effort at deep-sea hydrothermal vents. PeerJ 2019; 7:e7397. [PMID: 31404427 PMCID: PMC6688594 DOI: 10.7717/peerj.7397] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
For over 40 years, hydrothermal vents and the communities that thrive on them have been a source of profound discovery for deep-sea ecologists. These ecosystems are found throughout the world on active plate margins as well as other geologically active features. In addition to their ecologic interest, hydrothermal vent fields are comprised of metallic ores, sparking a nascent industry that aims to mine these metal-rich deposits for their mineral wealth. Here, we provide the first systematic assessment of macrofaunal and megafaunal biodiversity at hydrothermal vents normalized against research effort. Cruise reports from scientific expeditions as well as other literature were used to characterize the extent of exploration, determine the relative biodiversity of different biogeographic provinces, identify knowledge gaps related to the distribution of research effort, and prioritize targets for additional sampling to establish biodiversity baselines ahead of potential commercial exploitation. The Northwest Pacific, Southwest Pacific, and Southern Ocean biogeographic provinces were identified as high biodiversity using rarefaction of family-level incidence data, whereas the North East Pacific Rise, Northern East Pacific, Mid-Atlantic Ridge, and Indian Ocean provinces had medium biodiversity, and the Mid-Cayman Spreading Center was identified as a province of relatively low biodiversity. A North/South divide in the extent of biological research and the targets of hydrothermal vent mining prospects was also identified. Finally, we provide an estimate of sampling completeness for each province to inform scientific and stewardship priorities.
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Affiliation(s)
- Andrew D Thaler
- Blackbeard Biologic: Science and Environmental Advisors, St. Michaels, MD, USA.,Center for Environmental Science, Horn Point Laboratory, University of Maryland, Cambridge, MD, USA
| | - Diva Amon
- Department of Life Sciences, Natural History Museum, London, UK
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27
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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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28
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Xu T, Sun J, Watanabe HK, Chen C, Nakamura M, Ji R, Feng D, Lv J, Wang S, Bao Z, Qian P, Qiu J. Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific. Evol Appl 2018; 11:1915-1930. [PMID: 30459838 PMCID: PMC6231483 DOI: 10.1111/eva.12696] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 01/09/2023] Open
Abstract
Studying population genetics of deep-sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis-based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6, cox1, and nad4) and 6,398 genomewide single nucleotide polymorphisms (SNPs) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea (SCS) and three individuals in Sagami Bay (SB) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co-occurrence of two cryptic semi-isolated lineages. When using 125 outlier SNPs identified focusing on individuals in the Okinawa Trough (OT) and SB, a minor genetic subdivision was detected between individuals in the southern OT (S-OT) and those in the middle OT (M-OT) and SB. This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S-OT and the M-OT. Introgression analyses based on these outlier SNPs revealed that Hatoma Knoll in the S-OT represents a possible contact zone for individuals in the OT-SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai-yon Yonaguni Knoll in the S-OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific.
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Affiliation(s)
- Ting Xu
- Department of BiologyHong Kong Baptist UniversityHong KongChina
| | - Jin Sun
- Department of Ocean ScienceHong Kong University of Science and TechnologyHong KongChina
| | - Hiromi K. Watanabe
- Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Chong Chen
- Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Masako Nakamura
- School of Marine Science and TechnologyTokai UniversityShizuokaJapan
| | - Rubao Ji
- Department of BiologyWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Dong Feng
- CAS Key Laboratory of Ocean and Marginal Sea GeologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Jia Lv
- Ministry of Education Key Laboratory of Marine Genetics and BreedingCollege of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and BreedingCollege of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and BreedingCollege of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Pei‐Yuan Qian
- Department of Ocean ScienceHong Kong University of Science and TechnologyHong KongChina
| | - Jian‐Wen Qiu
- Department of BiologyHong Kong Baptist UniversityHong KongChina
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29
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Taboada S, Riesgo A, Wiklund H, Paterson GLJ, Koutsouveli V, Santodomingo N, Dale AC, Smith CR, Jones DOB, Dahlgren TG, Glover AG. Implications of population connectivity studies for the design of marine protected areas in the deep sea: An example of a demosponge from the Clarion-Clipperton Zone. Mol Ecol 2018; 27:4657-4679. [PMID: 30378207 DOI: 10.1111/mec.14888] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 08/31/2018] [Accepted: 09/20/2018] [Indexed: 01/06/2023]
Abstract
The abyssal demosponge Plenaster craigi inhabits the Clarion-Clipperton Zone (CCZ) in the northeast Pacific, a region with abundant seafloor polymetallic nodules with potential mining interest. Since P. craigi is a very abundant encrusting sponge on nodules, understanding its genetic diversity and connectivity could provide important insights into extinction risks and design of marine protected areas. Our main aim was to assess the effectiveness of the Area of Particular Environmental Interest 6 (APEI-6) as a potential genetic reservoir for three adjacent mining exploration contract areas (UK-1A, UK-1B and OMS-1A). As in many other sponges, COI showed extremely low variability even for samples ~900 km apart. Conversely, the 168 individuals of P. craigi, genotyped for 11 microsatellite markers, provided strong genetic structure at large geographical scales not explained by isolation by distance (IBD). Interestingly, we detected molecular affinities between samples from APEI-6 and UK-1A, despite being separated ~800 km. Although our migration analysis inferred very little progeny dispersal of individuals between areas, the major differentiation of OMS-1A from the other areas might be explained by the occurrence of predominantly northeasterly transport predicted by the HYCOM hydrodynamic model. Our study suggests that although APEI-6 does serve a conservation role, with species connectivity to the exploration areas, it is on its own inadequate as a propagule source for P. craigi for the entire eastern portion of the CCZ. Our new data suggest that an APEI located to the east and/or the south of the UK-1, OMS-1, BGR, TOML and NORI areas would be highly valuable.
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Affiliation(s)
- Sergi Taboada
- Life Sciences Department, The Natural History Museum, London, UK.,Departamento de Ciencias de la Vida, Ecología y Ciencias Ambientales, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, London, UK
| | - Helena Wiklund
- Life Sciences Department, The Natural History Museum, London, UK
| | | | | | | | - Andrew C Dale
- The Scottish Association for Marine Science, Oban, UK
| | - Craig R Smith
- Department of Oceanography, University of Hawaii, Honolulu, Hawaii
| | - Daniel O B Jones
- National Oceanography Centre, University of Southampton Waterfront Campus, Southampton, UK
| | - Thomas G Dahlgren
- NORCE, Uni Research, Bergen, Norway.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Adrian G Glover
- Life Sciences Department, The Natural History Museum, London, UK
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30
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Ogura T, Watanabe HK, Chen C, Sasaki T, Kojima S, Ishibashi JI, Fujikura K. Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific. PeerJ 2018; 6:e5673. [PMID: 30280041 PMCID: PMC6163031 DOI: 10.7717/peerj.5673] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022] Open
Abstract
Background Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. Methods We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. Results We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata). Discussion Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.
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Affiliation(s)
- Tomomi Ogura
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Hiromi Kayama Watanabe
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Jun-Ichiro Ishibashi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Katsunori Fujikura
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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31
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Abstract
Seamounts are one of the major biomes of the global ocean. The last 25 years of research has seen considerable advances in the understanding of these ecosystems. The interactions between seamounts and steady and variable flows have now been characterised providing a better mechanistic understanding of processes influencing biology. Processes leading to upwelling, including Taylor column formation and tidal rectification, have now been defined as well as those leading to draw down of organic matter from the ocean surface to seamount summit and flanks. There is also an improved understanding of the interactions between seamounts, zooplankton and micronekton communities especially with respect to increased predation pressure in the vicinity of seamounts. Evidence has accumulated of the role of seamounts as hot spots for ocean predators including large pelagic fish, sharks, pinnipeds, cetaceans and seabirds. The complexity of benthic communities associated with seamounts is high and drivers of biodiversity are now being resolved. Claims of high endemism resulting from isolation of seamounts as islands of habitat and speciation have not been supported. However, for species characterised by low dispersal capability, such as some groups of benthic sessile or low-mobility invertebrates, low connectivity between seamount populations has been found with evidence of endemism at a local level. Threats to seamounts have increased in the last 25 years and include overfishing, destructive fishing, marine litter, direct and indirect impacts of climate change and potentially marine mining in the near future. Issues around these threats and their management are discussed.
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Affiliation(s)
- Alex D Rogers
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
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32
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Mapping the resilience of chemosynthetic communities in hydrothermal vent fields. Sci Rep 2018; 8:9364. [PMID: 29921902 PMCID: PMC6008444 DOI: 10.1038/s41598-018-27596-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/04/2018] [Indexed: 11/29/2022] Open
Abstract
Hydrothermal vent fields are vulnerable to natural disturbances, such as volcanic activity, and are currently being considered as targets for mineral mining. Local vent communities are linked by pelagic larval dispersal and form regional metacommunities, nested within a number of biogeographic provinces. Larval supply depends on the connectivity of the dispersal networks, and affects recoverability of communities from disturbances. However, it is unclear how the dispersal networks contribute to recoverability of local communities. Here, we integrated a population dynamics model and estimation of large scale dispersal networks. By simulating disturbances to vent fields, we mapped recoverability of communities in 131 hydrothermal vent fields in the western Pacific Ocean. Our analysis showed substantial variation in recovery time due to variation in regional connectivity between known vent fields, and was not qualitatively affected by potential larval recruitment from unknown vent fields. In certain cases, simultaneous disturbance of a series of vent fields either delayed or wholly prevented recovery. Our approach is applicable to a dispersal network estimated from genetic diversity. Our method not only reveals distribution of recoverability of chemosynthetic communities in hydrothermal vent fields, but is also a practical tool for planning conservation strategies.
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33
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Heads M. Metapopulation vicariance explains old endemics on young volcanic islands. Cladistics 2018; 34:292-311. [PMID: 34645077 DOI: 10.1111/cla.12204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 01/15/2023] Open
Abstract
Terrestrial plants and animals on oceanic islands occupy zones of volcanism found at intraplate localities and along island arcs at subduction zones. The organisms often survive as metapopulations, or populations of separate sub-populations connected by dispersal. Although the individual islands and their local subpopulations are ephemeral and unstable, the ecosystem dynamism enables metapopulations to persist in a region, more or less in situ, for periods of up to tens of millions of years. As well as surviving on systems of young volcanic islands, metapopulations can also evolve there; tectonic changes can break up widespread insular metapopulations and produce endemics restricted to fewer islands or even a single island. These processes explain the presence of old endemic clades on young islands, which is often reported in molecular clock studies, and the many distribution patterns in island life that are spatially correlated with tectonic features. Metapopulations can be ruptured by sea floor subsidence, and this occurs with volcanic loading in zones of active volcanism and with sea floor cooling following its production at mid-ocean ridges. Metapopulation vicariance will also result if an active zone of volcanism is rifted apart. This can be caused by the migration of an arc (by slab rollback) away from a continent or from another subduction zone, by the offset of an arc at transform faults and by sea floor spreading at mid-ocean ridges. These mechanisms are illustrated with examples from islands in the Caribbean and the Pacific. Endemism on oceanic islands has usually been attributed to chance, long-distance dispersal, but the processes discussed here will generate endemism on young volcanic islands by vicariance.
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Affiliation(s)
- Michael Heads
- Buffalo Museum of Science, 1020 Humboldt Parkway, Buffalo, NY, 14211-1293, USA
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34
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Eilertsen MH, Georgieva MN, Kongsrud JA, Linse K, Wiklund H, Glover AG, Rapp HT. Genetic connectivity from the Arctic to the Antarctic: Sclerolinum contortum and Nicomache lokii (Annelida) are both widespread in reducing environments. Sci Rep 2018; 8:4810. [PMID: 29556042 PMCID: PMC5859262 DOI: 10.1038/s41598-018-23076-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/06/2018] [Indexed: 11/23/2022] Open
Abstract
The paradigm of large geographic ranges in the deep sea has been challenged by genetic studies, which often reveal putatively widespread species to be several taxa with more restricted ranges. Recently, a phylogeographic study revealed that the tubeworm Sclerolinum contortum (Siboglinidae) inhabits vents and seeps from the Arctic to the Antarctic. Here, we further test the conspecificity of the same populations of S. contortum with additional mitochondrial and nuclear markers. We also investigate the genetic connectivity of another species with putatively the same wide geographic range - Nicomache lokii (Maldanidae). Our results support the present range of S. contortum, and the range of N. lokii is extended from vents and seeps in the Nordic Seas to mud volcanoes in the Barbados Trench and Antarctic vents. Sclerolinum contortum shows more pronounced geographic structure than N. lokii, but whether this is due to different dispersal capacities or reflects the geographic isolation of the sampled localities is unclear. Two distinct mitochondrial lineages of N. lokii are present in the Antarctic, which may result from two independent colonization events. The environmental conditions inhabited by the two species and implications for their distinct habitat preference is discussed.
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Affiliation(s)
- Mari H Eilertsen
- Department of Biological Sciences, University of Bergen, PO Box 7800, N-5020, Bergen, Norway. .,K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, PO Box 7803, N-5020, Bergen, Norway.
| | - Magdalena N Georgieva
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jon A Kongsrud
- Department of Natural History, University Museum of Bergen, PO Box 7800, N-5020, Bergen, Norway
| | - Katrin Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Helena Wiklund
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Adrian G Glover
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Hans T Rapp
- Department of Biological Sciences, University of Bergen, PO Box 7800, N-5020, Bergen, Norway.,K.G. Jebsen Centre for Deep-Sea Research, University of Bergen, PO Box 7803, N-5020, Bergen, Norway.,Uni Research, Uni Environment, PO Box 7810, N-5020, Bergen, Norway
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35
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Roterman CN, Lee WK, Liu X, Lin R, Li X, Won YJ. A new yeti crab phylogeny: Vent origins with indications of regional extinction in the East Pacific. PLoS One 2018; 13:e0194696. [PMID: 29547631 PMCID: PMC5856415 DOI: 10.1371/journal.pone.0194696] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/07/2018] [Indexed: 11/19/2022] Open
Abstract
The recent discovery of two new species of kiwaid squat lobsters on hydrothermal vents in the Pacific Ocean and in the Pacific sector of the Southern Ocean has prompted a re-analysis of Kiwaid biogeographical history. Using a larger alignment with more fossil calibrated nodes than previously, we consider the precise relationship between Kiwaidae, Chirostylidae and Eumunididae within Chirostyloidea (Decapoda: Anomura) to be still unresolved at present. Additionally, the placement of both new species within a new “Bristly” clade along with the seep-associated Kiwa puravida is most parsimoniously interpreted as supporting a vent origin for the family, rather than a seep-to-vent progression. Fossil-calibrated divergence analysis indicates an origin for the clade around the Eocene-Oligocene boundary in the eastern Pacific ~33–38 Ma, coincident with a lowering of bottom temperatures and increased ventilation in the Pacific deep sea. Likewise, the mid-Miocene (~10–16 Ma) rapid radiation of the new Bristly clade also coincides with a similar cooling event in the tropical East Pacific. The distribution, diversity, tree topology and divergence timing of Kiwaidae in the East Pacific is most consistent with a pattern of extinctions, recolonisations and radiations along fast-spreading ridges in this region and may have been punctuated by large-scale fluctuations in deep-water ventilation and temperature during the Cenozoic; further affecting the viability of Kiwaidae populations along portions of mid-ocean ridge.
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Affiliation(s)
| | - Won-Kyung Lee
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
- Deep-sea and Seabed Mineral Resources Research Center, Korea Institute of Ocean Science & Technology, Ansan, Republic of Korea
| | - Xinming Liu
- Guangxi Academy of Oceanography, Nanning, China
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Rongcheng Lin
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yong-Jin Won
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
- * E-mail:
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36
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Guinot D, Segonzac M. A review of the brachyuran deep-sea vent community of the western Pacific, with two new species of Austinograea Hessler & Martin, 1989 (Crustacea, Decapoda, Brachyura, Bythograeidae) from the Lau and North Fiji Back-Arc Basins. ZOOSYSTEMA 2018. [DOI: 10.5252/zoosystema2018v40a5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Danièle Guinot
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNR
| | - Michel Segonzac
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNR
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37
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Miyazaki J, Kawagucci S, Makabe A, Takahashi A, Kitada K, Torimoto J, Matsui Y, Tasumi E, Shibuya T, Nakamura K, Horai S, Sato S, Ishibashi JI, Kanzaki H, Nakagawa S, Hirai M, Takaki Y, Okino K, Watanabe HK, Kumagai H, Chen C. Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171570. [PMID: 29308272 PMCID: PMC5750039 DOI: 10.1098/rsos.171570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
Since the initial discovery of hydrothermal vents in 1977, these 'extreme' chemosynthetic systems have been a focus of interdisciplinary research. The Okinawa Trough (OT), located in the semi-enclosed East China Sea between the Eurasian continent and the Ryukyu arc, hosts more than 20 known vent sites but all within a relatively narrow depth range (600-1880 m). Depth is a significant factor in determining fluid temperature and chemistry, as well as biological composition. However, due to the narrow depth range of known sites, the actual influence of depth here has been poorly resolved. Here, the Yokosuka site (2190 m), the first OT vent exceeding 2000 m depth is reported. A highly active hydrothermal vent site centred around four active vent chimneys reaching 364°C in temperature, it is the hottest in the OT. Notable Cl depletion (130 mM) and both high H2 and CH4 concentrations (approx. 10 mM) probably result from subcritical phase separation and thermal decomposition of sedimentary organic matter. Microbiota and fauna were generally similar to other sites in the OT, although with some different characteristics. In terms of microbiota, the H2-rich vent fluids in Neuschwanstein chimney resulted in the dominance of hydrogenotrophic chemolithoautotrophs such as Thioreductor and Desulfobacterium. For fauna, the dominance of the deep-sea mussel Bathymodiolus aduloides is surprising given other nearby vent sites are usually dominated by B. platifrons and/or B. japonicus, and a sponge field in the periphery dominated by Poecilosclerida is unusual for OT vents. Our insights from the Yokosuka site implies that although the distribution of animal species may be linked to depth, the constraint is perhaps not water pressure and resulting chemical properties of the vent fluid but instead physical properties of the surrounding seawater. The potential significance of these preliminary results and prospect for future research on this unique site are discussed.
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Affiliation(s)
- Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Institute of Geochemistry and Petrology, ETH Zürich, Clausiusstrasse 25, 8092 Zürich, Switzerland
| | - Akiko Makabe
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ayu Takahashi
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kazuya Kitada
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Junji Torimoto
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yohei Matsui
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takazo Shibuya
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kentaro Nakamura
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Department of Systems Innovation, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shunsuke Horai
- Department of Earth and Planetary Sciences, School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shun Sato
- Department of Earth and Planetary Sciences, School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Jun-ichiro Ishibashi
- Department of Earth and Planetary Sciences, School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hayato Kanzaki
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Nakagawa
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), 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
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Research and Development Center for Marine Biosciences, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kyoko Okino
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8564, Japan
| | - Hiromi Kayama Watanabe
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Department of Marine Biodiversity Research (BIO-DIVE), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hidenori Kumagai
- Research and Development Center for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Chong Chen
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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38
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Taylor ML, Roterman CN. Invertebrate population genetics across Earth's largest habitat: The deep-sea floor. Mol Ecol 2017; 26:4872-4896. [PMID: 28833857 DOI: 10.1111/mec.14237] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/04/2023]
Abstract
Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made.
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Affiliation(s)
- M L Taylor
- Department of Zoology, University of Oxford, Oxford, UK
| | - C N Roterman
- Department of Zoology, University of Oxford, Oxford, UK
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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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Gollner S, Kaiser S, Menzel L, Jones DOB, Brown A, Mestre NC, van Oevelen D, Menot L, Colaço A, Canals M, Cuvelier D, Durden JM, Gebruk A, Egho GA, Haeckel M, Marcon Y, Mevenkamp L, Morato T, Pham CK, Purser A, Sanchez-Vidal A, Vanreusel A, Vink A, Martinez Arbizu P. Resilience of benthic deep-sea fauna to mining activities. MARINE ENVIRONMENTAL RESEARCH 2017; 129:76-101. [PMID: 28487161 DOI: 10.1016/j.marenvres.2017.04.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 05/21/2023]
Abstract
With increasing demand for mineral resources, extraction of polymetallic sulphides at hydrothermal vents, cobalt-rich ferromanganese crusts at seamounts, and polymetallic nodules on abyssal plains may be imminent. Here, we shortly introduce ecosystem characteristics of mining areas, report on recent mining developments, and identify potential stress and disturbances created by mining. We analyze species' potential resistance to future mining and perform meta-analyses on population density and diversity recovery after disturbances most similar to mining: volcanic eruptions at vents, fisheries on seamounts, and experiments that mimic nodule mining on abyssal plains. We report wide variation in recovery rates among taxa, size, and mobility of fauna. While densities and diversities of some taxa can recover to or even exceed pre-disturbance levels, community composition remains affected after decades. The loss of hard substrata or alteration of substrata composition may cause substantial community shifts that persist over geological timescales at mined sites.
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Affiliation(s)
- Sabine Gollner
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany; Royal Netherlands Institute for Sea Research (NIOZ), Ocean Systems (OCS), 't Horntje (Texel), The Netherlands.
| | - Stefanie Kaiser
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany.
| | - Lena Menzel
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany.
| | - Daniel O B Jones
- National Oceanography Centre (NOC), University of Southampton Waterfront Campus, Southampton, United Kingdom.
| | - Alastair Brown
- University of Southampton, Ocean and Earth Science, National Oceanography Centre Southampton, Southampton, United Kingdom.
| | - Nelia C Mestre
- CIMA, Faculty of Science and Technology, University of Algarve, Portugal.
| | - Dick van Oevelen
- Royal Netherlands Institute for Sea Research (NIOZ), Estuarine and Delta Systems (EDS), Yerseke, The Netherlands.
| | - Lenaick Menot
- IFREMER, Institut français de recherche pour l'exploitation de la mer, Plouzane, France.
| | - Ana Colaço
- IMAR Department of Oceanography and Fisheries, Horta, Açores, Portugal; MARE - Marine and Environmental Sciences Centre Universidade dos Açores, Departamento de Oceanografia e Pescas, Horta, Açores, Portugal.
| | - Miquel Canals
- GRC Marine Geosciences, Department of Earth and Ocean Dynamics, Faculty of Earth Sciences, University of Barcelona, Barcelona, Spain.
| | - Daphne Cuvelier
- IMAR Department of Oceanography and Fisheries, Horta, Açores, Portugal; MARE - Marine and Environmental Sciences Centre Universidade dos Açores, Departamento de Oceanografia e Pescas, Horta, Açores, Portugal.
| | - Jennifer M Durden
- National Oceanography Centre (NOC), University of Southampton Waterfront Campus, Southampton, United Kingdom.
| | - Andrey Gebruk
- P.P. Shirshov Institute of Oceanology, Moscow, Russia.
| | - Great A Egho
- Marine Biology Research Group, Ghent University, Ghent, Belgium.
| | | | - Yann Marcon
- Alfred Wegener Institute (AWI), Bremerhaven, Germany; MARUM Center for Marine Environmental Sciences, Bremen, Germany.
| | - Lisa Mevenkamp
- Marine Biology Research Group, Ghent University, Ghent, Belgium.
| | - Telmo Morato
- IMAR Department of Oceanography and Fisheries, Horta, Açores, Portugal; MARE - Marine and Environmental Sciences Centre Universidade dos Açores, Departamento de Oceanografia e Pescas, Horta, Açores, Portugal.
| | - Christopher K Pham
- IMAR Department of Oceanography and Fisheries, Horta, Açores, Portugal; MARE - Marine and Environmental Sciences Centre Universidade dos Açores, Departamento de Oceanografia e Pescas, Horta, Açores, Portugal.
| | - Autun Purser
- Alfred Wegener Institute (AWI), Bremerhaven, Germany.
| | - Anna Sanchez-Vidal
- GRC Marine Geosciences, Department of Earth and Ocean Dynamics, Faculty of Earth Sciences, University of Barcelona, Barcelona, Spain.
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium.
| | - Annemiek Vink
- Bundesanstalt für Geowissenschaften und Rohstoffe, Hannover, Germany.
| | - Pedro Martinez Arbizu
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany.
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Goffredi SK, Johnson S, Tunnicliffe V, Caress D, Clague D, Escobar E, Lundsten L, Paduan JB, Rouse G, Salcedo DL, Soto LA, Spelz-Madero R, Zierenberg R, Vrijenhoek R. Hydrothermal vent fields discovered in the southern Gulf of California clarify role of habitat in augmenting regional diversity. Proc Biol Sci 2017; 284:20170817. [PMID: 28724734 PMCID: PMC5543219 DOI: 10.1098/rspb.2017.0817] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/16/2017] [Indexed: 11/12/2022] Open
Abstract
Hydrothermal vent communities are distributed along mid-ocean spreading ridges as isolated patches. While distance is a key factor influencing connectivity among sites, habitat characteristics are also critical. The Pescadero Basin (PB) and Alarcón Rise (AR) vent fields, recently discovered in the southern Gulf of California, are bounded by previously known vent localities (e.g. Guaymas Basin and 21° N East Pacific Rise); yet, the newly discovered vents differ markedly in substrata and vent fluid attributes. Out of 116 macrofaunal species observed or collected, only three species are shared among all four vent fields, while 73 occur at only one locality. Foundation species at basalt-hosted sulfide chimneys on the AR differ from the functional equivalents inhabiting sediment-hosted carbonate chimneys in the PB, only 75 km away. The dominant species of symbiont-hosting tubeworms and clams, and peripheral suspension-feeding taxa, differ between the sites. Notably, the PB vents host a limited and specialized fauna in which 17 of 26 species are unknown at other regional vents and many are new species. Rare sightings and captured larvae of the 'missing' species revealed that dispersal limitation is not responsible for differences in community composition at the neighbouring vent localities. Instead, larval recruitment-limiting habitat suitability probably favours species differentially. As scenarios develop to design conservation strategies around mining of seafloor sulfide deposits, these results illustrate that models encompassing habitat characteristics are needed to predict metacommunity structure.
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Affiliation(s)
- Shana K Goffredi
- Department of Biology, Occidental College, Los Angeles, CA, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Shannon Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Verena Tunnicliffe
- School of Ocean Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - David Caress
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - David Clague
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Elva Escobar
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lonny Lundsten
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | - Greg Rouse
- Scripps Institution of Oceanography, La Jolla, CA, USA
| | - Diana L Salcedo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis A Soto
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ronald Spelz-Madero
- Department of Geology, Universidad Autónoma de Baja California, Mexico City, Mexico
| | - Robert Zierenberg
- Earth and Planetary Sciences, University of California, Davis, Davis, CA, USA
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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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Miller KJ, Gunasekera RM. A comparison of genetic connectivity in two deep sea corals to examine whether seamounts are isolated islands or stepping stones for dispersal. Sci Rep 2017; 7:46103. [PMID: 28393887 PMCID: PMC5385499 DOI: 10.1038/srep46103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/10/2017] [Indexed: 11/09/2022] Open
Abstract
Ecological processes in the deep sea are poorly understood due to the logistical constraints of sampling thousands of metres below the ocean’s surface and remote from most land masses. Under such circumstances, genetic data provides unparalleled insight into biological and ecological relationships. We use microsatellite DNA to compare the population structure, reproductive mode and dispersal capacity in two deep sea corals from seamounts in the Southern Ocean. The solitary coral Desmophyllum dianthus has widespread dispersal consistent with its global distribution and resilience to disturbance. In contrast, for the matrix-forming colonial coral Solenosmilia variabilis asexual reproduction is important and the dispersal of sexually produced larvae is negligible, resulting in isolated populations. Interestingly, despite the recognised impacts of fishing on seamount communities, genetic diversity on fished and unfished seamounts was similar for both species, suggesting that evolutionary resilience remains despite reductions in biomass. Our results provide empirical evidence that a group of seamounts can function either as isolated islands or stepping stones for dispersal for different taxa. Furthermore different strategies will be required to protect the two sympatric corals and consequently the recently declared marine reserves in this region may function as a network for D. dianthus, but not for S. variabilis.
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Affiliation(s)
- Karen J Miller
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, The University of Western Australia (MO96), 35 Stirling Hwy, Crawley, Western Australia 6009, Australia
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44
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Chen C, Uematsu K, Linse K, Sigwart JD. By more ways than one: Rapid convergence at hydrothermal vents shown by 3D anatomical reconstruction of Gigantopelta (Mollusca: Neomphalina). BMC Evol Biol 2017; 17:62. [PMID: 28249568 PMCID: PMC5333402 DOI: 10.1186/s12862-017-0917-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/17/2017] [Indexed: 02/03/2023] Open
Abstract
Background Extreme environments prompt the evolution of characteristic adaptations. Yet questions remain about whether radiations in extreme environments originate from a single lineage that masters a key adaptive pathway, or if the same features can arise in parallel through convergence. Species endemic to deep-sea hydrothermal vents must accommodate high temperature and low pH. The most successful vent species share a constrained pathway to successful energy exploitation: hosting symbionts. The vent-endemic gastropod genus Gigantopelta, from the Southern and Indian Oceans, shares unusual features with a co-occurring peltospirid, the ‘scaly-foot gastropod’ Chrysomallon squamiferum. Both are unusually large for the clade and share other adaptive features such as a prominent enlarged trophosome-like oesophageal gland, not found in any other vent molluscs. Results Transmission electron microscopy confirmed endosymbiont bacteria in the oesophageal gland of Gigantopelta, as also seen in Chrysomallon. They are the only known members of their phylum in vent ecosystems hosting internal endosymbionts; other vent molluscs host endosymbionts in or on their gills, or in the mantle cavity. A five-gene phylogenetic reconstruction demonstrated that Gigantopelta and Chrysomallon are not phylogenetically sister-taxa, despite their superficial similarity. Both genera have specialist adaptations to accommodate internalised endosymbionts, but with anatomical differences that indicate separate evolutionary origins. Hosting endosymbionts in an internal organ within the host means that all resources required by the bacteria must be supplied by the animal, rather than directly by the vent fluid. Unlike Chrysomallon, which has an enlarged oesophageal gland throughout post-settlement life, the oesophageal gland in Gigantopelta is proportionally much smaller in juveniles and the animals likely undergo a trophic shift during ontogeny. The circulatory system is hypertrophied in both but the overall size is smaller in Gigantopelta. In contrast with Chrysomallon, Gigantopelta possesses true ganglia and is gonochoristic. Conclusions Key anatomical differences between Gigantopelta and Chrysomallon demonstrate these two genera acquired a similar way of life through independent and convergent adaptive pathways. What appear to be the holobiont’s adaptations to an extreme environment, are driven by optimising bacteria’s access to vent nutrients. By comparing Gigantopelta and Chrysomallon, we show that metazoans are capable of rapidly and repeatedly evolving equivalent anatomical adaptations and close-knit relationships with chemoautotrophic bacteria, achieving the same end-product through parallel evolutionary trajectories. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0917-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chong Chen
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry, Northern Ireland. .,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
| | - Katrin Linse
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry, Northern Ireland.,Berkeley, Museum of Paleontology, University of California, VLSB 1101, Berkeley, CA, 94720, USA
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45
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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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Meyer KS. Islands in a Sea of Mud: Insights From Terrestrial Island Theory for Community Assembly on Insular Marine Substrata. ADVANCES IN MARINE BIOLOGY 2016; 76:1-40. [PMID: 28065293 DOI: 10.1016/bs.amb.2016.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Most marine hard-bottom habitats are isolated, separated from other similar habitats by sand or mud flats, and can be considered analogous to terrestrial islands. The extensive scientific literature on terrestrial islands provides a theoretical framework for the analysis of isolated marine habitats. More individuals and higher species richness occur on larger marine substrata, a pattern that resembles terrestrial islands. However, while larger terrestrial islands have greater habitat diversity and productivity, the higher species richness on larger marine hard substrata can be explained by simple surface area and hydrodynamic phenomena: larger substrata extend further into the benthic boundary, exposing fauna to faster current and higher food supply. Marine island-like communities are also influenced by their distance to similar habitats, but investigations into the reproductive biology and dispersal ability of individual species are required for a more complete understanding of population connectivity. On terrestrial islands, nonrandom co-occurrence patterns have been attributed to interspecific competition, but while nonrandom co-occurrence patterns have been found for marine fauna, different mechanisms are responsible, including epibiontism. Major knowledge gaps for community assembly in isolated marine habitats include the degree of connectivity between isolated habitats, mechanisms of succession, and the extent of competition on hard substrata, particularly in the deep sea. Anthropogenic hard substrata of known age can be used opportunistically as "natural" laboratories to begin answering these questions.
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Affiliation(s)
- K S Meyer
- Oregon Institute of Marine Biology, Charleston, OR, United States.
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47
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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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48
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Jang SJ, Park E, Lee WK, Johnson SB, Vrijenhoek RC, Won YJ. Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries. BMC Evol Biol 2016; 16:235. [PMID: 27793079 PMCID: PMC5084463 DOI: 10.1186/s12862-016-0807-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/14/2016] [Indexed: 11/29/2022] Open
Abstract
Background The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinella pompejana. DNA sequences from one mitochondrial and eleven nuclear genes were examined in samples collected from ten vent localities that comprise the species’ known range from 23°N latitude on the East Pacific Rise to 38°S latitude on the Pacific Antarctic Ridge. Results Multi-locus genotypes inferred from these sequences clustered the individual worms into three metapopulation segments — the northern East Pacific Rise (NEPR), southern East Pacific Rise (SEPR), and northeastern Pacific Antarctic Ridge (PAR) — separated by the Equator and Easter Microplate boundaries. Genetic diversity estimators were negatively correlated with tectonic spreading rates. Application of the isolation-with-migration (IMa2) model provided information about divergence times and demographic parameters. The PAR and NEPR metapopulation segments were estimated to have split roughly 4.20 million years ago (Mya) (2.42–33.42 Mya, 95 % highest posterior density, (HPD)), followed by splitting of the SEPR and NEPR segments about 0.79 Mya (0.07–6.67 Mya, 95 % HPD). Estimates of gene flow between the neighboring regions were mostly low (2 Nm < 1). Estimates of effective population size decreased with southern latitudes: NEPR > SEPR > PAR. Conclusions Highly effective dispersal capabilities allow A. pompejana to overcome the temporal instability and intermittent distribution of active hydrothermal vents in the eastern Pacific Ocean. Consequently, the species exhibits very high levels of genetic diversity compared with many co-distributed vent annelids and mollusks. Nonetheless, its levels of genetic diversity in partially isolated populations are inversely correlated with tectonic spreading rates. As for many other vent taxa, this pioneering colonizer is similarly affected by local rates of habitat turnover and by major dispersal filters associated with the Equator and the Easter Microplate region. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0807-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sook-Jin Jang
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, South Korea
| | - Eunji Park
- Division of Ecoscience, Ewha Womans University, Seoul, South Korea
| | - Won-Kyung Lee
- Division of Ecoscience, Ewha Womans University, Seoul, South Korea
| | - Shannon B Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039-9644, USA
| | | | - Yong-Jin Won
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, South Korea. .,Division of Ecoscience, Ewha Womans University, Seoul, South Korea.
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Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans. PLoS One 2016; 11:e0163776. [PMID: 27732624 PMCID: PMC5061364 DOI: 10.1371/journal.pone.0163776] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/05/2016] [Indexed: 11/19/2022] Open
Abstract
Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid populations are generally large and continuously undergoing population growth. Benthic and pelagic species abundance data support these findings.
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Huang C, Schaeffer SW, Fisher CR, Cowart DA. Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci. PeerJ 2016; 4:e2366. [PMID: 27635334 PMCID: PMC5012325 DOI: 10.7717/peerj.2366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 07/25/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp. could be amplified in the GoM seep tubeworm, Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation of S. jonesi. METHODS Seventy-seven S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed for Escarpia laminata (18 loci) and Escarpia southwardae (30 loci) were tested to determine if they were homologous and polymorphic in S. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring in S. jonesi. RESULTS Microsatellite pre-screening identified 13 (27%) of the Escarpia loci were homologous and polymorphic in S. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongst S. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci on S. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents. DISCUSSION The ability to develop "universal" microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.
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Affiliation(s)
- Chunya Huang
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Stephen W. Schaeffer
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Charles R. Fisher
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Dominique A. Cowart
- Department of Biology, Pennsylvania State University, University Park, PA, United States
- Current affiliation: Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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