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Methou P, Cueff‐Gauchard V, Michel LN, Gayet N, Pradillon F, Cambon‐Bonavita M. Symbioses of alvinocaridid shrimps from the South West Pacific: No chemosymbiotic diets but conserved gut microbiomes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:614-630. [PMID: 37752716 PMCID: PMC10667644 DOI: 10.1111/1758-2229.13201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Rimicaris exoculata shrimps from hydrothermal vent ecosystems are known to host dense epibiotic communities inside their enlarged heads and digestive systems. Conversely, other shrimps from the family, described as opportunistic feeders have received less attention. We examined the nutrition and bacterial communities colonising 'head' chambers and digestive systems of three other alvinocaridids-Rimicaris variabilis, Nautilocaris saintlaurentae and Manuscaris sp.-using a combination of electron microscopy, stable isotopes and sequencing approaches. Our observations inside 'head' cavities and on mouthparts showed only a really low coverage of bacterial epibionts. In addition, no clear correlation between isotopic ratios and relative abundance of epibionts on mouthparts could be established among shrimp individuals. Altogether, these results suggest that none of these alvinocaridids rely on chemosynthetic epibionts as their main source of nutrition. Our analyses also revealed a substantial presence of several Firmicutes and Deferribacterota lineages within the foreguts and midguts of these shrimps, which closest known lineages were systematically digestive symbionts associated with alvinocaridids, and more broadly for Firmicutes from digestive systems of other crustaceans from marine and terrestrial ecosystems. Overall, our study opens new perspectives not only about chemosynthetic symbioses of vent shrimps but more largely about digestive microbiomes with potential ancient and evolutionarily conserved bacterial partnerships among crustaceans.
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Affiliation(s)
- Pierre Methou
- X‐STARJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Valérie Cueff‐Gauchard
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
| | - Loïc N. Michel
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
- Laboratory of Oceanology, Freshwater, and Oceanic Sciences Unit of reSearch (FOCUS)University of LiègeLiègeBelgium
| | - Nicolas Gayet
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
| | - Florence Pradillon
- Univ BrestIfremer, CNRS, Unité Biologie des Environnements Extrêmes marins ProfondsPlouzanéFrance
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Qi L, Shi M, Zhu FC, Lian CA, He LS. Genomic evidence for the first symbiotic Deferribacterota, a novel gut symbiont from the deep-sea hydrothermal vent shrimp Rimicaris kairei. Front Microbiol 2023; 14:1179935. [PMID: 37455748 PMCID: PMC10344455 DOI: 10.3389/fmicb.2023.1179935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The genus Rimicaris is the dominant organism living in hydrothermal vents. However, little research has been done on the functions of their intestinal flora. Here, we investigated the potential functions of Deferribacterota, which is dominant in the intestine of Rimicaris kairei from the Central Indian Ridge. In total, six metagenome-assembled genomes (MAGs) of Deferribacterota were obtained using the metagenomic approach. The six Deferribacterota MAGs (Def-MAGs) were clustered into a new branch in the phylogenetic tree. The six Def-MAGs were further classified into three species, including one new order and two new genera, based on the results of phylogenetic analysis, relative evolutionary divergence (RED), average nucleotide identity (ANI), average amino acid identity (AAI) and DNA-DNA hybridization (DDH) values. The results of the energy metabolism study showed that these bacteria can use a variety of carbon sources, such as glycogen, sucrose, salicin, arbutin, glucose, cellobiose, and maltose. These bacteria have a type II secretion system and effector proteins that can transport some intracellular toxins to the extracellular compartment and a type V CRISPR-Cas system that can defend against various invasions. In addition, cofactors such as biotin, riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) synthesized by R. kairei gut Deferribacterota may also assist their host in surviving under extreme conditions. Taken together, the potential function of Deferribacterota in the hydrothermal R. kairei gut suggests its long-term coevolution with the host.
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Affiliation(s)
- Li Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengke Shi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang-Chao Zhu
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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Shrimp Antimicrobial Peptides: A Multitude of Possibilities. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10459-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Hui M, Wang A, Cheng J, Sha Z. Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts. PeerJ 2022; 10:e13758. [PMID: 35966925 PMCID: PMC9368993 DOI: 10.7717/peerj.13758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/29/2022] [Indexed: 01/17/2023] Open
Abstract
Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R 2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.
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Affiliation(s)
- Min Hui
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Aiyang Wang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,University of Chinese Academy of Sciences, Beijing, China
| | - Jiao Cheng
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,University of Chinese Academy of Sciences, Beijing, China
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Full-Length Transcriptome Comparison Provides Novel Insights into the Molecular Basis of Adaptation to Different Ecological Niches of the Deep-Sea Hydrothermal Vent in Alvinocaridid Shrimps. DIVERSITY 2022. [DOI: 10.3390/d14050371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The deep-sea hydrothermal vent ecosystem is one of the extreme chemoautotrophic environments. Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, and Alvinocaris longirostris Kikuchi and Ohta, 1995, are typically co-distributed and closely related alvinocaridid shrimps in hydrothermal vent areas with different ecological niches, providing an excellent model for studying the adaptive evolution mechanism of animals in the extreme deep-sea hydrothermal vent environment. The shrimp S. leurokolos lives in close proximity to the chimney vent discharging high-temperature fluid, while A. longirostris inhabits the peripheral areas of hydrothermal vents. In this study, full-length transcriptomes of S. leurokolos and A. longirostris were generated using a combination of single-molecule real-time (SMRT) and Illumina RNA-seq technology. Expression analyses of the transcriptomes showed that among the top 30% of highly expressed genes of each species, more genes related to sulfide and heavy metal metabolism (sulfide: quinone oxidoreductase, SQR; persulfide dioxygenase, ETHE1; thiosulfate sulfurtransferase, TST, and ferritin, FRI) were specifically highly expressed in S. leurokolos, while genes involved in maintaining epibiotic bacteria or pathogen resistance (beta-1,3-glucan-binding protein, BGBP; endochitinase, CHIT; acidic mammalian chitinase, CHIA, and anti-lipopolysaccharide factors, ALPS) were highly expressed in A. longirostris. Gene family expansion analysis revealed that genes related to anti-oxidant metabolism (cytosolic manganese superoxide dismutase, SODM; glutathione S-transferase, GST, and glutathione peroxidase, GPX) and heat stress (heat shock cognate 70 kDa protein, HSP70 and heat shock 70 kDa protein cognate 4, HSP7D) underwent significant expansion in S. leurokolos, while CHIA and CHIT involved in pathogen resistance significantly expanded in A. longirostris. Finally, 66 positively selected genes (PSGs) were identified in the vent shrimp S. leurokolos. Most of the PSGs were involved in DNA repair, antioxidation, immune defense, and heat stress response, suggesting their function in the adaptive evolution of species inhabiting the extreme vent microhabitat. This study provides abundant genetic resources for deep-sea invertebrates, and is expected to lay the foundation for deep decipherment of the adaptive evolution mechanism of shrimps in a deep-sea chemosynthetic ecosystem based on further whole-genome comparison.
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Symbiont Community Composition in Rimicaris kairei Shrimps from Indian Ocean Vents with Notes on Mineralogy. Appl Environ Microbiol 2022; 88:e0018522. [PMID: 35404070 PMCID: PMC9040608 DOI: 10.1128/aem.00185-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Hydrothermal vent ecosystems are home to a wide array of symbioses between animals and chemosynthetic microbes, among which shrimps in the genus Rimicaris is one of the most iconic. So far, studies of Rimicaris symbioses have been restricted to Atlantic species, including Rimicaris exoculata, which is totally reliant on the symbionts for nutrition, and the mixotrophic species Rimicaris chacei. Here, we expand this by investigating and characterizing the symbiosis of the Indian Ocean species Rimicaris kairei using specimens from two vent fields, Kairei and Edmond. We also aimed to evaluate the differences in mineralogy and microbial communities between two cephalothorax color morphs, black and brown, through a combination of 16S metabarcoding, scanning electron microscopy, fluorescent in situ hybridization, energy-dispersive X-ray spectroscopy, and synchrotron near-edge X-ray absorption structure analyses. Overall, our results highlight that R. kairei exhibits similar symbiont lineages to those of its Atlantic congeners, although with a few differences, such as the lack of Zetaproteobacteria. We found distinct mineralization processes behind the two color morphs that were linked to differences in the vent fluid composition, but the symbiotic community composition was surprisingly similar. In R. exoculata, such mineralogical differences have been shown to stem from disparity in the microbial communities, but our results indicate that in R. kairei this is instead due to the shift of dominant metabolisms by the same symbiotic partners. We suggest that a combination of local environmental factors and biogeographic barriers likely contribute to the differences between Atlantic and Indian Ocean Rimicaris symbioses. IMPORTANCE Hydrothermal vent shrimps in the genus Rimicaris are among the most charismatic deep-sea animals of Atlantic and Indian Oceans, often occurring on towering black smokers in dense aggregates of thousands of individuals. Although this dominance is only possible because of symbiosis, no study on the symbiosis of Indian Ocean Rimicaris species has been conducted. Here, we characterize the Rimicaris kairei symbiosis by combining molecular, microscopic, and elemental analyses, making comparisons with those of the Atlantic species possible for the first time. Although most symbiotic partners remained consistent across the two oceans, some differences were recognized in symbiont lineages, as well as in the mechanisms behind the formation of two color morphs with distinct mineralogies. Our results shed new light on relationships among mineralogy, environmental factors, and microbial communities that are useful for understanding other deep-sea symbioses in the future.
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Leinberger J, Milke F, Christodoulou M, Poehlein A, Caraveo-Patiño J, Teske A, Brinkhoff T. Microbial epibiotic community of the deep-sea galatheid squat lobster Munidopsis alvisca. Sci Rep 2022; 12:2675. [PMID: 35177734 PMCID: PMC8854721 DOI: 10.1038/s41598-022-06666-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
Life at hydrothermal vent sites is based on chemosynthetic primary producers that supply heterotrophic microorganisms with substrates and generate biomass for higher trophic levels. Often, chemoautotrophs associate with the hydrothermal vent megafauna. To investigate attached bacterial and archaeal communities on deep-sea squat lobsters, we collected ten specimens from a hydrothermal vent in the Guaymas Basin (Gulf of California). All animals were identified as Munidopsis alvisca via morphological and molecular classification, and intraspecific divergence was determined. Amplicon sequencing of microbial DNA and cDNA revealed significant differences between microbial communities on the carapaces of M. alvisca and those in ambient sea water. Major epibiotic bacterial taxa were chemoautotrophic Gammaproteobacteria, such as Thiotrichaceae and Methylococcaceae, while archaea were almost exclusively represented by sequences affiliated with Ca. Nitrosopumilus. In sea water samples, Marine Group II and III archaea and organoheterotrophic Alphaproteobacteria, Flavobacteriia and Planctomycetacia were more dominant. Based on the identified taxa, we assume that main metabolic processes, carried out by M. alvisca epibiota, include ammonia, methane and sulphide oxidation. Considering that M. alvisca could benefit from sulphide detoxification by its epibiota, and that attached microbes are supplied with a stable habitat in proximity to substrate-rich hydrothermal fluids, a mutualistic host-microbe relationship appears likely.
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Affiliation(s)
- Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Magdalini Christodoulou
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | | | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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Qi L, Lian CA, Zhu FC, Shi M, He LS. Comparative Analysis of Intestinal Microflora Between Two Developmental Stages of Rimicaris kairei, a Hydrothermal Shrimp From the Central Indian Ridge. Front Microbiol 2022; 12:802888. [PMID: 35242112 PMCID: PMC8886129 DOI: 10.3389/fmicb.2021.802888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/28/2021] [Indexed: 01/04/2023] Open
Abstract
Despite extreme physical and chemical characteristics, deep-sea hydrothermal vents provide a place for fauna survival and reproduction. The symbiotic relationship of chemotrophic microorganisms has been investigated in the gill of Rimicaris exoculata, which are endemic to the hydrothermal vents of the Mid-Atlantic Ridge. However, only a few studies have examined intestinal symbiosis. Here, we studied the intestinal fauna in juvenile and adult Rimicaris kairei, another species in the Rimicaris genus that was originally discovered at the Kairei and Edmond hydrothermal vent fields in the Central Indian Ridge. The results showed that there were significant differences between juvenile and adult gut microbiota in terms of species richness, diversity, and evenness. The values of Chao1, observed species, and ASV rarefaction curves indicated almost four times the number of species in adults compared to juveniles. In juveniles, the most abundant phylum was Deferribacterota, at 80%, while in adults, Campilobacterota was the most abundant, at 49%. Beta diversity showed that the intestinal communities of juveniles and adults were clearly classified into two clusters based on the evaluations of Bray-Curtis and weighted UniFrac distance matrices. Deferribacteraceae and Sulfurovum were the main featured bacteria contributing to the difference. Moreover, functional prediction for all of the intestinal microbiota showed that the pathways related to ansamycin synthesis, branched-chain amino acid biosynthesis, lipid metabolism, and cell motility appeared highly abundant in juveniles. However, for adults, the most abundant pathways were those of sulfur transfer, carbohydrate, and biotin metabolism. Taken together, these results indicated large differences in intestinal microbial composition and potential functions between juvenile and adult vent shrimp (R. kairei), which may be related to their physiological needs at different stages of development.
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Affiliation(s)
- Li Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Mengke Shi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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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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Le Bloa S, Boidin-Wichlacz C, Cueff-Gauchard V, Rosa RD, Cuvillier-Hot V, Durand L, Methou P, Pradillon F, Cambon-Bonavita MA, Tasiemski A. Antimicrobial Peptides and Ectosymbiotic Relationships: Involvement of a Novel Type IIa Crustin in the Life Cycle of a Deep-Sea Vent Shrimp. Front Immunol 2020; 11:1511. [PMID: 32765521 PMCID: PMC7381244 DOI: 10.3389/fimmu.2020.01511] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/09/2020] [Indexed: 01/04/2023] Open
Abstract
The symbiotic shrimp Rimicaris exoculata dominates the macrofauna inhabiting the active smokers of the deep-sea mid Atlantic ridge vent fields. We investigated the nature of the host mechanisms controlling the vital and highly specialized ectosymbiotic community confined into its cephalothoracic cavity. R. exoculata belongs to the Pleocyemata, crustacean brooding eggs, usually producing Type I crustins. Unexpectedly, a novel anti-Gram-positive type II crustin was molecularly identified in R. exoculata. Re-crustin is mainly produced by the appendages and the inner surfaces of the cephalothoracic cavity, embedding target epibionts. Symbiosis acquisition and regulating mechanisms are still poorly understood. Yet, symbiotic communities were identified at different steps of the life cycle such as brooding stage, juvenile recruitment and molt cycle, all of which may be crucial for symbiotic acquisition and control. Here, we show a spatio-temporal correlation between the production of Re-crustin and the main ectosymbiosis-related life-cycle events. Overall, our results highlight (i) a novel and unusual AMP sequence from an extremophile organism and (ii) the potential role of AMPs in the establishment of vital ectosymbiosis along the life cycle of deep-sea invertebrates.
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Affiliation(s)
- Simon Le Bloa
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Céline Boidin-Wichlacz
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Valérie Cueff-Gauchard
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Rafael Diego Rosa
- Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Lucile Durand
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Pierre Methou
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Florence Pradillon
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Aurélie Tasiemski
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
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11
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Methou P, Michel LN, Segonzac M, Cambon-Bonavita MA, Pradillon F. Integrative taxonomy revisits the ontogeny and trophic niches of Rimicaris vent shrimps. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200837. [PMID: 32874664 PMCID: PMC7428246 DOI: 10.1098/rsos.200837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Among hydrothermal vent species, Rimicaris exoculata is one of the most emblematic, hosting abundant and diverse ectosymbioses that provide most of its nutrition. Rimicaris exoculata co-occurs in dense aggregates with the much less abundant Rimicaris chacei in many Mid-Atlantic Ridge vent fields. This second shrimp also houses ectosymbiotic microorganisms but has a mixotrophic diet. Recent observations have suggested potential misidentifications between these species at their juvenile stages, which could have led to misinterpretations of their early-life ecology. Here, we confirm erroneous identification of the earliest stages and propose a new set of morphological characters unambiguously identifying juveniles of each species. On the basis of this reassessment, combined use of C, N and S stable isotope ratios reveals distinct ontogenic trophic niche shifts in both species, from photosynthesis-based nutrition before settlement, towards a chemosynthetic diet afterwards. Furthermore, isotopic compositions in the earliest juvenile stages suggest differences in larval histories. Each species thus exhibits specific early-life strategies that would, without our re-examination, have been interpreted as ontogenetic variations. Overall, our results provide a good illustration of the identification issues persisting in deep-sea ecosystems and the importance of integrative taxonomy in providing an accurate view of fundamental aspects of the biology and ecology of species inhabiting these environments.
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Affiliation(s)
- Pierre Methou
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, F-29280 Plouzané, France
- Ifremer, Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), ZI de la pointe du Diable, F-29280 Plouzané, France
| | - Loïc N. Michel
- Ifremer, Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), ZI de la pointe du Diable, F-29280 Plouzané, France
| | - Michel Segonzac
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, case postale 53, 57 rue Cuvier, F-75231 Paris cedex 05, France
| | - Marie-Anne Cambon-Bonavita
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, F-29280 Plouzané, France
| | - Florence Pradillon
- Ifremer, Centre Brest, Laboratoire Environnement Profond (REM/EEP/LEP), ZI de la pointe du Diable, F-29280 Plouzané, France
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" Candidatus Desulfobulbus rimicarensis," an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata. Appl Environ Microbiol 2020; 86:AEM.02549-19. [PMID: 32060020 PMCID: PMC7117923 DOI: 10.1128/aem.02549-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/26/2020] [Indexed: 02/03/2023] Open
Abstract
The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe “Candidatus Desulfobulbus rimicarensis,” an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host. The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name “Candidatus Desulfobulbus rimicarensis” is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps. IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe “Candidatus Desulfobulbus rimicarensis,” an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.
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Li YF, Chen YW, Xu JK, Ding WY, Shao AQ, Zhu YT, Wang C, Liang X, Yang JL. Temperature elevation and Vibrio cyclitrophicus infection reduce the diversity of haemolymph microbiome of the mussel Mytilus coruscus. Sci Rep 2019; 9:16391. [PMID: 31704981 PMCID: PMC6841970 DOI: 10.1038/s41598-019-52752-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
Abstract
Haemolymph microbiome was considered to be unique to healthy invertebrates and beneficial to the host against external pathogens, including disease resistance and maintenance of homeostasis. Here, we investigated the effects of elevated water temperature on infection of haemolymph microbiome of the hard-shelled mussel (Mytilus coruscus). Exposure to Vibrio. cyclitrophicus resulted in high mortality of mussels on day nine at 27 °C. The haemolymph was collected to determine the microbiota by 16 S rRNA gene sequencing. Exposure to waterborne V. cyclitrophicus increased the mortality of mussels that was associated with a reduction in the diversity of their microbial community. Principal coordinate analysis (PCoA) revealed that temperature was an essential factor in shaping microbial communities in mussel haemolymph. Vibrio exposure promoted the proliferation of opportunistic pathogens (e.g., Arcobacter and Francisella) at a lower temperature. A high abundance of Vibrio present in live and dead mussels, at 27 °C might contribute greatly to mortality, as indicated by linear discriminant analysis effect size (LEfSe). These data suggested that the dynamics of microbial community have unique biomarker species in mussel haemolymph that could be used as health indicators. An elevated temperature may reduce the ability of bacterial elimination function against infection in mussel haemolymph.
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Affiliation(s)
- Yi-Feng Li
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yan-Wen Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jia-Kang Xu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Wen-Yang Ding
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - An-Qi Shao
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - You-Ting Zhu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Chong Wang
- Ocean and Fisheries Research Institute of Binzhou, Binzhou, China
| | - Xiao Liang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China. .,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
| | - Jin-Long Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China. .,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
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Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria). ISME JOURNAL 2019; 14:104-122. [PMID: 31562384 PMCID: PMC6908604 DOI: 10.1038/s41396-019-0508-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 11/30/2022]
Abstract
Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.
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Machon J, Krieger J, Meth R, Zbinden M, Ravaux J, Montagné N, Chertemps T, Harzsch S. Neuroanatomy of a hydrothermal vent shrimp provides insights into the evolution of crustacean integrative brain centers. eLife 2019; 8:e47550. [PMID: 31383255 PMCID: PMC6684273 DOI: 10.7554/elife.47550] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/14/2019] [Indexed: 11/13/2022] Open
Abstract
Alvinocaridid shrimps are emblematic representatives of the deep hydrothermal vent fauna at the Mid-Atlantic Ridge. They are adapted to a mostly aphotic habitat with extreme physicochemical conditions in the vicinity of the hydrothermal fluid emissions. Here, we investigated the brain architecture of the vent shrimp Rimicaris exoculata to understand possible adaptations of its nervous system to the hydrothermal sensory landscape. Its brain is modified from the crustacean brain ground pattern by featuring relatively small visual and olfactory neuropils that contrast with well-developed higher integrative centers, the hemiellipsoid bodies. We propose that these structures in vent shrimps may fulfill functions in addition to higher order sensory processing and suggest a role in place memory. Our study promotes vent shrimps as fascinating models to gain insights into sensory adaptations to peculiar environmental conditions, and the evolutionary transformation of specific brain areas in Crustacea.
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Affiliation(s)
- Julia Machon
- Sorbonne Université, UMR CNRS MNHN 7208 Biologie des organismes et écosystèmes aquatiques (BOREA), Equipe Adaptation aux Milieux ExtrêmesParisFrance
| | - Jakob Krieger
- Department of Cytology and Evolutionary BiologyUniversity of Greifswald, Zoological Institute and MuseumGreifswaldGermany
| | - Rebecca Meth
- Department of Cytology and Evolutionary BiologyUniversity of Greifswald, Zoological Institute and MuseumGreifswaldGermany
| | - Magali Zbinden
- Sorbonne Université, UMR CNRS MNHN 7208 Biologie des organismes et écosystèmes aquatiques (BOREA), Equipe Adaptation aux Milieux ExtrêmesParisFrance
| | - Juliette Ravaux
- Sorbonne Université, UMR CNRS MNHN 7208 Biologie des organismes et écosystèmes aquatiques (BOREA), Equipe Adaptation aux Milieux ExtrêmesParisFrance
| | - Nicolas Montagné
- Sorbonne Université, UPEC, Univ Paris Diderot, CNRS, INRA, IRD, Institute of Ecology & Environmental Sciences of Paris (iEES-Paris)ParisFrance
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Univ Paris Diderot, CNRS, INRA, IRD, Institute of Ecology & Environmental Sciences of Paris (iEES-Paris)ParisFrance
| | - Steffen Harzsch
- Department of Cytology and Evolutionary BiologyUniversity of Greifswald, Zoological Institute and MuseumGreifswaldGermany
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16
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Methou P, Hernández-Ávila I, Aube J, Cueff-Gauchard V, Gayet N, Amand L, Shillito B, Pradillon F, Cambon-Bonavita MA. Is It First the Egg or the Shrimp? - Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development. Front Microbiol 2019; 10:808. [PMID: 31057515 PMCID: PMC6478704 DOI: 10.3389/fmicb.2019.00808] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/29/2019] [Indexed: 12/26/2022] Open
Abstract
Rimicaris exoculata is one of the most well-known and emblematic species of endemic vent fauna. Like many other species from these ecosystems, Rimicaris shrimps host important communities of chemosynthetic bacteria living in symbiosis with their host inside the cephalothorax and gut. For many of these symbiotic partners, the mode of transmission remains to be elucidated and the starting point of the symbiotic relationship is not yet defined, but could begin with the egg. In this study, we explored the proliferation of microbial communities on R. exoculata broods through embryonic development using a combination of NGS sequencing and microscopy approaches. Variations in abundance and diversity of egg microbial communities were analyzed in broods at different developmental stages and collected from mothers at two distinct vent fields on the Mid-Atlantic Ridge (TAG and Snake Pit). We also assessed the specificity of the egg microbiome by comparing communities developing on egg surfaces with those developing on the cuticle of pleopods, which are thought to be exposed to similar environmental conditions because the brood is held under the female's abdomen. In terms of abundance, bacterial colonization clearly increases with both egg developmental stage and the position of the egg within the brood: those closest to the exterior having a higher bacterial coverage. Bacterial biomass increase also accompanies an increase of mineral precipitations and thus clearly relates to the degree of exposure to vent fluids. In terms of diversity, most bacterial lineages were found in all samples and were also those found in the cephalothorax of adults. However, significant variation occurs in the relative abundance of these lineages, most of this variation being explained by body surface (egg vs. pleopod), vent field, and developmental stage. The occurrence of symbiont-related lineages of Epsilonbacteraeota, Gammaproteobacteria, Zetaproteobacteria, and Mollicutes provide a basis for discussion on both the acquisition of symbionts and the potential roles of these bacterial communities during egg development.
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Affiliation(s)
- Pierre Methou
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Ivan Hernández-Ávila
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Johanne Aube
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Valérie Cueff-Gauchard
- Univ Brest, CNRS, Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Nicolas Gayet
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Louis Amand
- Unité Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d’Histoire Naturelle, Eq. Adaptations aux Milieux Extrêmes (BOREA), CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Paris, France
| | - Bruce Shillito
- Unité Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d’Histoire Naturelle, Eq. Adaptations aux Milieux Extrêmes (BOREA), CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Paris, France
| | - Florence Pradillon
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
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17
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Liu XL, Ye S, Li HW, Lu B, Yu YQ, Fan YP, Yang WJ, Yang JS. An H-ferritin from the hydrothermal vent shrimp Rimicaris exoculata and its potential role in iron metabolism. Biometals 2019; 32:251-264. [PMID: 30756217 DOI: 10.1007/s10534-019-00174-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/19/2019] [Indexed: 01/17/2023]
Abstract
Rimicaris exoculata (Decapoda: Bresiliidae) is one of the dominant species among hydrothermal vent communities along the Mid-Atlantic Ridge. This shrimp can tolerate high concentrations of heavy metals such as iron, but the mechanisms used for detoxification and utilization of excess metals remain largely unknown. Ferritin is a major iron storage protein in most living organisms. The central heavy subunit of ferritin (H-ferritin) possesses ferroxidase activity and converts iron from Fe2+ to Fe3+, the non-toxic form used for storage. In the present study, the H-ferritin RexFrtH was identified in the hydrothermal vent shrimp R. exoculata, and found to be highly expressed in the gill, the main organ involved in bioaccumulation of metals, at both RNA and protein levels. Accumulation of RexFrtH decreased from efferent to afferent vessels, coinciding with the direction of water flow through the gills. Fe3+ was localized with RexFrtH, and in vitro iron-binding and ferroxidase assays using recombinant RexFrtH confirmed the high affinity for iron. Based on these results, we propose a model of iron metabolism in R. exoculata gills; ferrous iron from ambient hydrothermal water accumulates and is converted and stored in ferric form by RexFrtH as an iron reservoir when needed for metabolism, or excreted as an intermediate to prevent iron overload. The findings expand our understanding of the adaptation strategies used by shrimps inhabiting extreme hydrothermal vents to cope with extremely high heavy metal concentrations.
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Affiliation(s)
- Xiao-Li Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Sen Ye
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Hua-Wei Li
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Bo Lu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Yan-Qin Yu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.,Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Yu-Peng Fan
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
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18
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Apremont V, Cambon-Bonavita MA, Cueff-Gauchard V, François D, Pradillon F, Corbari L, Zbinden M. Gill chamber and gut microbial communities of the hydrothermal shrimp Rimicaris chacei Williams and Rona 1986: A possible symbiosis. PLoS One 2018; 13:e0206084. [PMID: 30388125 PMCID: PMC6214521 DOI: 10.1371/journal.pone.0206084] [Citation(s) in RCA: 18] [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: 04/18/2018] [Accepted: 10/06/2018] [Indexed: 11/18/2022] Open
Abstract
Rimicaris chacei Williams and Rona 1986, formerly named as Chorocaris chacei, is a caridean shrimp living in deep-sea hydrothermal ecosystems. This shrimp is endemic to the Mid Atlantic Ridge (MAR) and lives at the periphery of aggregates of its well-known congeneric R. exoculata Williams and Rona 1986. Contrasting with the very dense and mobile clusters formed by R. exoculata, R. chacei lives in small groups of several individuals that are not very mobile. Although devoid of the characteristic hypertrophied cephalothorax of R. exoculata, which harbors the ectosymbionts, a microbial community has also been reported in the cephalothorax of R. chacei. Previous data on morphology, behavior and isotopic values indicate a diet based on a combination of feeding on its epibiotic bacteria and scavenging or occasional predation. In this study, our objective was to describe, for the first time, the distribution, morphology and phylogeny of the microbial communities associated with R. chacei. This species is significantly less studied than R. exoculata, but nevertheless represents the only other known example of symbiosis in crustaceans of MAR hydrothermal vent sites. Microbial communities have been observed at the same locations as in R. exoculata (mouthparts, branchiostegites and digestive tract). However, in R. chacei, the surfaces occupied by the bacteria are smaller. The main lineages are affiliated to Epsilon and Gammaproteobacteria in the cephalothorax and to Deferribacteres, Mollicutes, Epsilon and Gammaproteobacteria in the digestive tract. Comparison with the well-described bacterial communities of R. exoculata and hypotheses about the role of these communities in R. chacei are discussed.
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Affiliation(s)
- Vincent Apremont
- IFREMER, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Unité Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université, MNHN, CNRS, IRD; Equipe Adaptation aux Milieux Extrêmes (AMEX), 7 Quai St Bernard, Paris, France
| | | | - Valérie Cueff-Gauchard
- IFREMER, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - David François
- IFREMER, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Florence Pradillon
- Ifremer centre Bretagne, ZI de la Pointe du Diable, Laboratoire Environnement Profond, REM/EEP/LEP, Plouzané, France
| | - Laure Corbari
- Muséum National d’Histoire naturelle, Institut de Systématique, Évolution, Biodiversité ISYEB—UMR 7205 –CNRS, MNHN, UPMC, EPHE, Paris, France
| | - Magali Zbinden
- Unité Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université, MNHN, CNRS, IRD; Equipe Adaptation aux Milieux Extrêmes (AMEX), 7 Quai St Bernard, Paris, France
- * E-mail:
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19
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Watsuji TO, Motoki K, Hada E, Nagai Y, Takaki Y, Yamamoto A, Ueda K, Toyofuku T, Yamamoto H, Takai K. Compositional and Functional Shifts in the Epibiotic Bacterial Community of Shinkaia crosnieri Baba & Williams (a Squat Lobster from Hydrothermal Vents) during Methane-Fed Rearing. Microbes Environ 2018; 33:348-356. [PMID: 30333383 PMCID: PMC6308002 DOI: 10.1264/jsme2.me18072] [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] [Indexed: 11/23/2022] Open
Abstract
The hydrothermal vent squat lobster Shinkaia crosnieri Baba & Williams harbors an epibiotic bacterial community, which is numerically and functionally dominated by methanotrophs affiliated with Methylococcaceae and thioautotrophs affiliated with Sulfurovum and Thiotrichaceae. In the present study, shifts in the phylogenetic composition and metabolic function of the epibiont community were investigated using S. crosnieri individuals, which were reared for one year in a tank fed with methane as the energy and carbon source. The results obtained indicated that indigenous predominant thioautotrophic populations, such as Sulfurovum and Thiotrichaceae members, became absent, possibly due to the lack of an energy source, and epibiotic communities were dominated by indigenous Methylococcaceae and betaproteobacterial methylotrophic members that adapted to the conditions present during rearing for 12 months with a supply of methane. Furthermore, the overall phylogenetic composition of the epibiotic community markedly changed from a composition dominated by chemolithotrophs to one enriched with cross-feeding heterotrophs in addition to methanotrophs and methylotrophs. Thus, the composition and function of the S. crosnieri epibiotic bacterial community were strongly affected by the balance between the energy and carbon sources supplied for chemosynthetic production as well as that between the production and consumption of organic compounds.
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Affiliation(s)
- Tomo-O Watsuji
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Kaori Motoki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University.,Present Address: Department of Biological Sciences, Graduate School of Science, the University of Tokyo
| | - Emi Hada
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yukiko Nagai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Asami Yamamoto
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University
| | | | | | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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20
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Bellec L, Cambon-Bonavita MA, Cueff-Gauchard V, Durand L, Gayet N, Zeppilli D. A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship. Front Microbiol 2018; 9:2246. [PMID: 30294317 PMCID: PMC6159746 DOI: 10.3389/fmicb.2018.02246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/03/2018] [Indexed: 12/26/2022] Open
Abstract
Deep-sea hydrothermal vent meiofauna have been the focus of recent research and the discovery of an abundant well-adapted free-living marine nematode on the Mid-Atlantic Ridge offers new perspectives on adaptations to the vent environment. Indeed, knowledge concerning biological interactions of microbes and meiofauna in marine extreme environments is scarce, especially for nematodes. In this study, we used microscopic observations [fluorescence in situ hybridization (FISH) and scanning electron microscopy (SEM)] and metabarcoding of 16S rRNA to characterize the bacterial community of the nematode species Oncholaimus dyvae, an overlooked but ecologically important vent organism. Detection of bacteria in the buccal cavity and on the cuticle (SEM) and epibionts in its intestine (FISH) suggests that O. dyvae harbors its own bacterial community. Molecular results and phylogenetic analysis show that bacteria associated with this species are related to symbiotic lineages typical of hydrothermal vent fauna, such as sulfur-oxidizing bacteria related to Epsilonproteobacteria and Gammaproteobacteria. This multi-approach study suggests a potential symbiotic role of bacteria with its nematode host and opens new research perspectives on vent meiofauna.
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Affiliation(s)
- Laure Bellec
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France.,IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Valérie Cueff-Gauchard
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Lucile Durand
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Nicolas Gayet
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France
| | - Daniela Zeppilli
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France
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Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis. PLoS One 2017; 12:e0187842. [PMID: 29121118 PMCID: PMC5679544 DOI: 10.1371/journal.pone.0187842] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/26/2017] [Indexed: 11/19/2022] Open
Abstract
For deep-sea hydrothermal vent crabs, recent investigations have revealed some epibiotic bacteria, but no study has described the bacterial community associated with the gill and intestine. In this study, the microbiota attached to the gill and intestine of the hydrothermal vent crab Austinograea sp. and two shallow-water crab species (Eriocheir sinensis and Portunus trituberculatus) were compared by high-throughput sequencing of 16S rDNA genes. The highest and lowest diversity in bacterial communities were observed in the gill and intestine of Austinograea sp., respectively. Non-metric multidimensional scaling (NMDS) analysis indicated that Austinograea sp. harbored a distinct microbial community. Operational taxonomic units (OTUs) for phylum Fusobacteria, class Epsilonproteobacteria, and genera Leucothrix, Polaribacter, Fusibacter, etc. were dominant in Austinograea sp. Of these, Leucothrix, Sulfurospirillum, and Arcobacter may be involved in oxidizing reduced sulfur compounds and sulfur metabolism; Marinomonas, Polaribacter adapted to the low temperature, and Fusibacter and Psychrilyobacter may survive well under hypoxic conditions. Bacteria commonly present in seawater were dominant in the gill, whereas anaerobic bacteria showed strikingly high abundance in the intestine. Interestingly, Firmicutes and Epsilonproteobacteria may complement each other in Austinograea sp., forming an internal environment. The diversified microbial community of Austinograea sp. reveals adaptation to the hydrothermal vent environment.
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Zhang J, Sun QL, Luan ZD, Lian C, Sun L. Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent. Sci Rep 2017; 7:2000. [PMID: 28515421 PMCID: PMC5435735 DOI: 10.1038/s41598-017-02073-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 04/05/2017] [Indexed: 11/09/2022] Open
Abstract
Shrimp of the family Alvinocarididae are the predominant megafauna of deep-sea hydrothermal vents. However, genome information on this family is currently unavailable. In the present study, by employing Illumina sequencing, we performed the first de novo transcriptome analysis of the gills of the shrimp Rimicaris sp. from the hydrothermal vent in Desmos, Manus Basin. The analysis was conducted in a comparative manner with the shrimp taken directly from the vent (GR samples) and the shrimp that had been maintained for ten days under normal laboratory condition (mGR samples). Among the 128,938 unigenes identified, a large number of differentially expressed genes (DEGs) between the GR and mGR samples were detected, including 2365 and 1607 genes significantly upregulated and downregulated, respectively, in GR. The DEGs covered diverse functional categories. Most of the DEGs associated with immunity were downregulated in GR, while most of the DEGs associated with sulfur metabolism and detoxification were upregulated in GR. These results provide the first comprehensive transcriptomic resource for hydrothermal vent Rimicaris and revealed varied categories of genes likely involved in deep-sea survival.
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Qing-Lei Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhen-Dong Luan
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Lian
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Abstract
The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.
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Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
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Le Bloa S, Durand L, Cueff- Gauchard V, Le Bars J, Taupin L, Marteau C, Bazire A, Cambon-Bonavita MA. Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers. PLoS One 2017; 12:e0174338. [PMID: 28328982 PMCID: PMC5362221 DOI: 10.1371/journal.pone.0174338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 03/07/2017] [Indexed: 01/26/2023] Open
Abstract
Rimicaris exoculata is a caridean shrimp that dominates the fauna at several hydrothermal vent sites of the Mid-Atlantic Ridge. It has two distinct and stable microbial communities. One of these epibiontic bacterial communities is located in the shrimp gut and has a distribution and role that are poorly understood. The second colonizes its enlarged gill chamber and is involved in host nutrition. It is eliminated after each molt, and has colonization processes reminiscent of those of a biofilm. The presence and expression of genes usually involved in quorum sensing (QS) were then studied. At four sites, Rainbow, TAG, Snake Pit and Logatchev, two lux genes were identified in the R. exoculata epibiontic community at different shrimp molt stages and life stages. RT-PCR experiments highlighted lux gene expression activity at TAG, Snake Pit and Rainbow vent sites. Their potential QS activity and their possible roles in epibiont colonization processes are discussed. Moreover, phylogenetic analysis has shown the presence of three clades for luxS (Epsilonproteobacteria) and four clades for luxR (Gammaproteobacteria) genes, each clade being restricted to a single site. These genes are more divergent than the 16S rRNA one. They could therefore be used as biogeographical genetic markers.
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Affiliation(s)
- Simon Le Bloa
- Ifremer, Centre Bretagne, Laboratoire de Microbiologie des Environnements Extrêmes, REM/EEP/LM2E, UMR 6197 Ifremer-CNRS-UBO, ZI Pointe du Diable, CS, Plouzané, France
- Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
| | - Lucile Durand
- Ifremer, Centre Bretagne, Laboratoire de Microbiologie des Environnements Extrêmes, REM/EEP/LM2E, UMR 6197 Ifremer-CNRS-UBO, ZI Pointe du Diable, CS, Plouzané, France
| | - Valérie Cueff- Gauchard
- Ifremer, Centre Bretagne, Laboratoire de Microbiologie des Environnements Extrêmes, REM/EEP/LM2E, UMR 6197 Ifremer-CNRS-UBO, ZI Pointe du Diable, CS, Plouzané, France
- Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
| | - Josiane Le Bars
- Ifremer, Centre Bretagne, Laboratoire de Microbiologie des Environnements Extrêmes, REM/EEP/LM2E, UMR 6197 Ifremer-CNRS-UBO, ZI Pointe du Diable, CS, Plouzané, France
- Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
| | - Laure Taupin
- Université de Bretagne-Sud, EA 3884, LBCM, Rue de Saint Maudé, Lorient, France
| | - Charlotte Marteau
- Université de Bretagne-Sud, EA 3884, LBCM, Rue de Saint Maudé, Lorient, France
| | - Alexis Bazire
- Université de Bretagne-Sud, EA 3884, LBCM, Rue de Saint Maudé, Lorient, France
| | - Marie-Anne Cambon-Bonavita
- Ifremer, Centre Bretagne, Laboratoire de Microbiologie des Environnements Extrêmes, REM/EEP/LM2E, UMR 6197 Ifremer-CNRS-UBO, ZI Pointe du Diable, CS, Plouzané, France
- Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
- CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 Ifremer-CNRS-UBO, Technopôle Iroise, 4 place Nicolas Copernic, Plouzané, France
- * E-mail:
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Cowart DA, Durand L, Cambon-Bonavita MA, Arnaud-Haond S. Investigation of bacterial communities within the digestive organs of the hydrothermal vent shrimp Rimicaris exoculata provide insights into holobiont geographic clustering. PLoS One 2017; 12:e0172543. [PMID: 28296889 PMCID: PMC5351989 DOI: 10.1371/journal.pone.0172543] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/05/2017] [Indexed: 01/16/2023] Open
Abstract
Prokaryotic communities forming symbiotic relationships with the vent shrimp, Rimicaris exoculata, are well studied components of hydrothermal ecosystems at the Mid-Atlantic Ridge (MAR). Despite the tight link between host and symbiont, the observed lack of spatial genetic structure seen in R. exoculata contrasts with the geographic differentiation detected in specific bacterial ectosymbionts. The geographic clustering of bacterial lineages within a seemingly panmictic host suggests either the presence of finer scale restriction to gene flow not yet detected in the host, horizontal transmission (environmental selection) of its endosymbionts as a consequence of unique vent geochemistry, or vertically transmitted endosymbionts that exhibit genetic differentiation. To identify which hypothesis best fits, we tested whether bacterial assemblages exhibit differentiation across sites or host populations by performing a 16S rRNA metabarcoding survey on R. exoculata digestive prokaryote samples (n = 31) taken from three geochemically distinct vents across MAR: Rainbow, Trans-Atlantic Geotraverse (TAG) and Logatchev. Analysis of communities across two organs (digestive tract, stomach), three molt colors (white, red, black) and three life stages (eggs, juveniles, adults) also provided insights into symbiont transmission mode. Examining both whole communities and operational taxonomic units (OTUs) confirmed the presence of three main epibionts: Epsilonproteobacteria, Mollicutes and Deferribacteres. With these findings, we identified a clear pattern of geographic segregation by vent in OTUs assigned to Epsilonproteobacteria. Additionally, we detected evidence for differentiation among all communities associated to vents and life stages. Overall, results suggest a combination of environmental selection and vertical inheritance of some of the symbiotic lineages.
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Affiliation(s)
- Dominique A. Cowart
- Ifremer (Institut Français de Recherche pour l'Exploitation de la MER) UMR MARBEC (Marine Biodiversity, Exploitation and Conservation) BP 17, Sète - France
| | - Lucile Durand
- Ifremer (Institut Français de Recherche pour l'Exploitation de la MER) Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM) ZI pointe du diable, CS 10070, Plouzané - France
| | - Marie-Anne Cambon-Bonavita
- Ifremer (Institut Français de Recherche pour l'Exploitation de la MER) Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM) ZI pointe du diable, CS 10070, Plouzané - France
- UBO, UMR 6197, UBO, Ifremer, CNRS, IUEM Rue Dumont d'Urville, Plouzané - France
- CNRS, UMR 6197, CNRS, Ifremer, UBO, IUEM Rue Dumont d'Urville, Plouzané - France
| | - Sophie Arnaud-Haond
- Ifremer (Institut Français de Recherche pour l'Exploitation de la MER) UMR MARBEC (Marine Biodiversity, Exploitation and Conservation) BP 17, Sète - France
- * E-mail:
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Sun QL, Zeng ZG, Chen S, Sun L. First Comparative Analysis of the Community Structures and Carbon Metabolic Pathways of the Bacteria Associated with Alvinocaris longirostris in a Hydrothermal Vent of Okinawa Trough. PLoS One 2016; 11:e0154359. [PMID: 27111851 PMCID: PMC4844111 DOI: 10.1371/journal.pone.0154359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/12/2016] [Indexed: 11/19/2022] Open
Abstract
Alvinocaris longirostris is a species of shrimp existing in the hydrothermal fields of Okinawa Trough. To date the structure and function of the microbial community associated with A. longirostris are essentially unknown. In this study, by employment of the techniques of high through-put sequencing and clone library construction and analysis, we compared for the first time the community structures and metabolic profiles of microbes associated with the gill and gut of A. longirostris in a hydrothermal field of Okinawa Trough. Fourteen phyla were detected in the gill and gut communities, of which 11 phyla were shared by both tissues. Proteobacteria made up a substantial proportion in both tissues, while Firmicutes was abundant only in gut. Although gill and gut communities were similar in bacterial diversities, the bacterial community structures in these two tissues were significantly different. Further, we discovered for the first time the existence in the gill and gut communities of A. longirostris the genes (cbbM and aclB) encoding the key enzymes of Calvin-Benson-Bassham (CBB) cycle and the reductive tricarboxylic acid (rTCA) cycle, and that both cbbM and aclB were significantly more abundant in gill than in gut. Taken together, these results provide the first evidence that at least two carbon fixation pathways are present in both the gill and the gut communities of A. longirostris, and that the communities in different tissues likely differ in autotrophic productivity.
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Affiliation(s)
- Qing-lei Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, 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
| | - Zhi-gang Zeng
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Shuai Chen
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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Hansen M, Perner M. Hydrogenase Gene Distribution and H2 Consumption Ability within the Thiomicrospira Lineage. Front Microbiol 2016; 7:99. [PMID: 26903978 PMCID: PMC4744846 DOI: 10.3389/fmicb.2016.00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/18/2016] [Indexed: 01/27/2023] Open
Abstract
Thiomicrospira were originally characterized as sulfur-oxidizing chemolithoautotrophs. Attempts to grow them on hydrogen failed for many years. Only recently we demonstrated hydrogen consumption among two of three tested Thiomicrospira and posited that hydrogen consumption may be more widespread among Thiomicrospira than previously assumed. Here, we investigate and compare the hydrogen consumption ability and the presence of group 1 [NiFe]-hydrogenase genes (enzyme catalyzes H2↔2H+ + 2e-) for sixteen different Thiomicrospira species. Seven of these Thiomicrospira species encoded group 1 [NiFe]-hydrogenase genes and five of these species could also consume hydrogen. All Thiomicrospira species exhibiting hydrogen consumption were from hydrothermal vents along the Mid-Atlantic ridge or Eastern Pacific ridges. The tested Thiomicrospira from Mediterranean and Western Pacific vents could not consume hydrogen. The [NiFe]-hydrogenase genes were categorized into two clusters: those resembling the hydrogenase from Hydrogenovibrio are in cluster I and are related to those from Alpha- and other Gammaproteobacteria. In cluster II, hydrogenases found exclusively in Thiomicrospira crunogena strains are combined and form a monophyletic group with those from Epsilonproteobacteria suggesting they were acquired through horizontal gene transfer. Hydrogen consumption appears to be common among some Thiomicrospira, given that five of the tested sixteen strains carried this trait. The hydrogen consumption ability expands their competitiveness within an environment.
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Affiliation(s)
- Moritz Hansen
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg Hamburg, Germany
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Chen C, Copley JT, Linse K, Rogers AD, Sigwart JD. The heart of a dragon: 3D anatomical reconstruction of the 'scaly-foot gastropod' (Mollusca: Gastropoda: Neomphalina) reveals its extraordinary circulatory system. Front Zool 2015; 12:13. [PMID: 26085836 PMCID: PMC4470333 DOI: 10.1186/s12983-015-0105-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/15/2015] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The 'scaly-foot gastropod' (Chrysomallon squamiferum Chen et al., 2015) from deep-sea hydrothermal vent ecosystems of the Indian Ocean is an active mobile gastropod occurring in locally high densities, and it is distinctive for the dermal scales covering the exterior surface of its foot. These iron-sulfide coated sclerites, and its nutritional dependence on endosymbiotic bacteria, are both noted as adaptations to the extreme environment in the flow of hydrogen sulfide. We present evidence for other adaptations of the 'scaly-foot gastropod' to life in an extreme environment, investigated through dissection and 3D tomographic reconstruction of the internal anatomy. RESULTS Our anatomical investigations of juvenile and adult specimens reveal a large unganglionated nervous system, a simple and reduced digestive system, and that the animal is a simultaneous hermaphrodite. We show that Chrysomallon squamiferum relies on endosymbiotic bacteria throughout post-larval life. Of particular interest is the circulatory system: Chrysomallon has a very large ctenidium supported by extensive blood sinuses filled with haemocoel. The ctenidium provides oxygen for the host but the circulatory system is enlarged beyond the scope of other similar vent gastropods. At the posterior of the ctenidium is a remarkably large and well-developed heart. Based on the volume of the auricle and ventricle, the heart complex represents approximately 4 % of the body volume. This proportionally giant heart primarily sucks blood through the ctenidium and supplies the highly vascularised oesophageal gland. Thus we infer the elaborate cardiovascular system most likely evolved to oxygenate the endosymbionts in an oxygen poor environment and/or to supply hydrogen sulfide to the endosymbionts. CONCLUSIONS This study exemplifies how understanding the autecology of an organism can be enhanced by detailed investigation of internal anatomy. This gastropod is a large and active species that is abundant in its hydrothermal vent field ecosystem. Yet all of its remarkable features-protective dermal sclerites, circulatory system, high fecundity-can be viewed as adaptations beneficial to its endosymbiont microbes. We interpret these results to show that, as a result of specialisation to resolve energetic needs in an extreme chemosynthetic environment, this dramatic dragon-like species has become a carrying vessel for its bacteria.
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Affiliation(s)
- Chong Chen
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS UK
| | - Jonathan T Copley
- Ocean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH UK
| | - Katrin Linse
- British Antarctic Survey, High Cross, Cambridge, CB3 0ET UK
| | - Alex D Rogers
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS UK
| | - Julia D Sigwart
- Queen's University Belfast, Marine Laboratory, Portaferry, BT22 1PF Northern Ireland
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Zwirglmaier K, Reid WDK, Heywood J, Sweeting CJ, Wigham BD, Polunin NVC, Hawkes JA, Connelly DP, Pearce D, Linse K. Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents. Microbiologyopen 2014; 4:136-50. [PMID: 25515351 PMCID: PMC4335981 DOI: 10.1002/mbo3.227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/16/2014] [Accepted: 10/27/2014] [Indexed: 11/12/2022] Open
Abstract
We analyzed the diversity of bacterial epibionts and trophic ecology of a new species of Kiwa yeti crab discovered at two hydrothermal vent fields (E2 and E9) on the East Scotia Ridge (ESR) in the Southern Ocean using a combination of 454 pyrosequencing, Sanger sequencing, and stable isotope analysis. The Kiwa epibiont communities were dominated by Epsilon- and Gammaproteobacteria. About 454 sequencing of the epibionts on 15 individual Kiwa specimen revealed large regional differences between the two hydrothermal vent fields: at E2, the bacterial community on the Kiwa ventral setae was dominated (up to 75%) by Gammaproteobacteria, whereas at E9 Epsilonproteobacteria dominated (up to 98%). Carbon stable isotope analysis of both Kiwa and the bacterial epibionts also showed distinct differences between E2 and E9 in mean and variability. Both stable isotope and sequence data suggest a dominance of different carbon fixation pathways of the epibiont communities at the two vent fields. At E2, epibionts were putatively fixing carbon via the Calvin-Benson-Bassham and reverse tricarboxylic acid cycle, while at E9 the reverse tricarboxylic acid cycle dominated. Co-varying epibiont diversity and isotope values at E2 and E9 also present further support for the hypothesis that epibionts serve as a food source for Kiwa.
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Affiliation(s)
- Katrin Zwirglmaier
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, United Kingdom
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Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents. ISME JOURNAL 2013; 8:1153-65. [PMID: 24351936 PMCID: PMC4030223 DOI: 10.1038/ismej.2013.225] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/07/2013] [Accepted: 11/14/2013] [Indexed: 11/10/2022]
Abstract
Microbial biogeography is influenced by the combined effects of passive dispersal and environmental selection, but the contribution of either factor can be difficult to discern. As thermophilic bacteria cannot grow in the cold seabed, their inactive spores are not subject to environmental selection. We therefore conducted a global experimental survey using thermophilic endospores that are passively deposited by sedimentation to the cold seafloor as tracers to study the effect of dispersal by ocean currents on the biogeography of marine microorganisms. Our analysis of 81 different marine sediments from around the world identified 146 species-level 16S rRNA phylotypes of endospore-forming, thermophilic Firmicutes. Phylotypes showed various patterns of spatial distribution in the world oceans and were dispersal-limited to different degrees. Co-occurrence of several phylotypes in locations separated by great distances (west of Svalbard, the Baltic Sea and the Gulf of California) demonstrated a widespread but not ubiquitous distribution. In contrast, Arctic regions with water masses that are relatively isolated from global ocean circulation (Baffin Bay and east of Svalbard) were characterized by low phylotype richness and different compositions of phylotypes. The observed distribution pattern of thermophilic endospores in marine sediments suggests that the impact of passive dispersal on marine microbial biogeography is controlled by the connectivity of local water masses to ocean circulation.
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Flot JF, Bauermeister J, Brad T, Hillebrand-Voiculescu A, Sarbu SM, Dattagupta S. Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania. Mol Ecol 2013; 23:1405-1417. [PMID: 24044653 PMCID: PMC4282457 DOI: 10.1111/mec.12461] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/06/2013] [Accepted: 07/13/2013] [Indexed: 12/03/2022]
Abstract
Niphargus is a speciose amphipod genus found in groundwater habitats across Europe. Three Niphargus species living in the sulphidic Frasassi caves in Italy harbour sulphur-oxidizing Thiothrix bacterial ectosymbionts. These three species are distantly related, implying that the ability to form ectosymbioses with Thiothrix may be common among Niphargus. Therefore, Niphargus–Thiothrix associations may also be found in sulphidic aquifers other than Frasassi. In this study, we examined this possibility by analysing niphargids of the genera Niphargus and Pontoniphargus collected from the partly sulphidic aquifers of the Southern Dobrogea region of Romania, which are accessible through springs, wells and Movile Cave. Molecular and morphological analyses revealed seven niphargid species in this region. Five of these species occurred occasionally or exclusively in sulphidic locations, whereas the remaining two were restricted to nonsulphidic areas. Thiothrix were detected by PCR on all seven Dobrogean niphargid species and observed using microscopy to be predominantly attached to their hosts' appendages. 16S rRNA gene sequences of the Thiothrix epibionts fell into two main clades, one of which (herein named T4) occurred solely on niphargids collected in sulphidic locations. The other Thiothrix clade was present on niphargids from both sulphidic and nonsulphidic areas and indistinguishable from the T3 ectosymbiont clade previously identified on Frasassi-dwelling Niphargus. Although niphargids from Frasassi and Southern Dobrogea are not closely related, the patterns of their association with Thiothrix are remarkably alike. The finding of similar Niphargus–Thiothrix associations in aquifers located 1200 km apart suggests that they may be widespread in European groundwater ecosystems.
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Affiliation(s)
- Jean-François Flot
- Courant Research Center Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077, Göttingen, Germany; Max Planck Institute for Dynamics and Self-Organization, Biological Physics and Evolutionary Dynamics, Bunsenstraße 10, 37073, Göttingen, Germany
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Quinn RA, Cawthorn RJ, Summerfield RL, Smolowitz R, Chistoserdov AY. Bacterial communities associated with lesions of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) from Atlantic Canada. Can J Microbiol 2013; 59:380-90. [PMID: 23750952 DOI: 10.1139/cjm-2012-0679] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Shell disease is a major threat to the American lobster (Homarus americanus, Milne Edwards) fishery. Here we describe the composition of microbial communities associated with lesions of 2 forms of shell disease in Atlantic Canada, (i) a trauma shell disease (TSD) characterized by massive lesions and (ii) an enzootic shell disease (EnSD) characterized by irregularly shaped lesions with a distinct orange to yellow color. The microbiology of the lesions was described by polymerase chain reaction and denaturing gradient gel electrophoresis of 16S rDNA amplified from scrapings of the shell lesions and was compared with communities of unaffected carapaces and previously described forms of shell diseases. Both TSD and EnSD lesions were dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria, all commonly detected in other forms of shell disease; however, unique members of Epsilonproteobacteria were also present. Two Vibrio spp. and 2 Pseudoalteromonas spp. were dominant in lesions of TSD and a Tenacibaculum sp. and Tenacibaculum ovolyticum were dominant in lesions of EnSD. The TSD and EnSD in this study contained similar taxa as other shell disease forms; however, their microbiology is mostly different and neither resembles that of epizootic shell disease.
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Affiliation(s)
- Robert A Quinn
- P.O. Box 42451, Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504-2451, USA
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Forget NL, Kim Juniper S. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge. Microbiologyopen 2013; 2:259-75. [PMID: 23401293 PMCID: PMC3633350 DOI: 10.1002/mbo3.70] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/19/2012] [Accepted: 01/07/2013] [Indexed: 02/01/2023] Open
Abstract
We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.
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Affiliation(s)
- Nathalie L Forget
- Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, British Columbia, Canada V8P 5C2.
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Bauermeister J, Ramette A, Dattagupta S. Repeatedly evolved host-specific ectosymbioses between sulfur-oxidizing bacteria and amphipods living in a cave ecosystem. PLoS One 2012; 7:e50254. [PMID: 23209690 PMCID: PMC3510229 DOI: 10.1371/journal.pone.0050254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 10/17/2012] [Indexed: 11/18/2022] Open
Abstract
Ectosymbioses between invertebrates and sulfur-oxidizing bacteria are widespread in sulfidic marine environments and have evolved independently in several invertebrate phyla. The first example from a freshwater habitat, involving Niphargus ictus amphipods and filamentous Thiothrix ectosymbionts, was recently reported from the sulfide-rich Frasassi caves in Italy. Subsequently, two new Niphargus species, N. frasassianus and N. montanarius, were discovered within Frasassi and found to co-occur with N. ictus. Using a variety of microscopic and molecular techniques, we found that all three Frasassi-dwelling Niphargus species harbor Thiothrix ectosymbionts, which belong to three distinct phylogenetic clades (named T1, T2, and T3). T1 and T3 Thiothrix dominate the N. frasassianus ectosymbiont community, whereas T2 and T3 are prevalent on N. ictus and N. montanarius. Relative distribution patterns of the three ectosymbionts are host species-specific and consistent over different sampling locations and collection years. Free-living counterparts of T1-T3 are rare or absent in Frasassi cave microbial mats, suggesting that ectosymbiont transmission among Niphargus occurs primarily through inter- or intraspecific inoculations. Phylogenetic analyses indicate that the Niphargus-Thiothrix association has evolved independently at least two times. While ectosymbioses with T1 and T2 may have been established within Frasassi, T3 ectosymbionts seem to have been introduced to the cave system by Niphargus.
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Affiliation(s)
- Jan Bauermeister
- Geomicrobiology and Symbiosis Group, Courant Research Center Geobiology, University of Göttingen, Göttingen, Germany
| | - Alban Ramette
- HGF-MPG Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sharmishtha Dattagupta
- Geomicrobiology and Symbiosis Group, Courant Research Center Geobiology, University of Göttingen, Göttingen, Germany
- * E-mail:
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Inorganic carbon fixation by chemosynthetic ectosymbionts and nutritional transfers to the hydrothermal vent host-shrimp Rimicaris exoculata. ISME JOURNAL 2012; 7:96-109. [PMID: 22914596 DOI: 10.1038/ismej.2012.87] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The shrimp Rimicaris exoculata dominates several hydrothermal vent ecosystems of the Mid-Atlantic Ridge and is thought to be a primary consumer harbouring a chemoautotrophic bacterial community in its gill chamber. The aim of the present study was to test current hypotheses concerning the epibiont's chemoautotrophy, and the mutualistic character of this association. In-vivo experiments were carried out in a pressurised aquarium with isotope-labelled inorganic carbon (NaH(13)CO(3) and NaH(14)CO(3)) in the presence of two different electron donors (Na(2)S(2)O(3) and Fe(2+)) and with radiolabelled organic compounds ((14)C-acetate and (3)H-lysine) chosen as potential bacterial substrates and/or metabolic by-products in experiments mimicking transfer of small biomolecules from epibionts to host. The bacterial epibionts were found to assimilate inorganic carbon by chemoautotrophy, but many of them (thick filaments of epsilonproteobacteria) appeared versatile and able to switch between electron donors, including organic compounds (heterotrophic acetate and lysine uptake). At least some of them (thin filamentous gammaproteobacteria) also seem capable of internal energy storage that could supply chemosynthetic metabolism for hours under conditions of electron donor deprivation. As direct nutritional transfer from bacteria to host was detected, the association appears as true mutualism. Import of soluble bacterial products occurs by permeation across the gill chamber integument, rather than via the digestive tract. This first demonstration of such capabilities in a decapod crustacean supports the previously discarded hypothesis of transtegumental absorption of dissolved organic matter or carbon as a common nutritional pathway.
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The transcriptome of Bathymodiolus azoricus gill reveals expression of genes from endosymbionts and free-living deep-sea bacteria. Mar Drugs 2012; 10:1765-1783. [PMID: 23015773 PMCID: PMC3447338 DOI: 10.3390/md10081765] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/26/2012] [Accepted: 07/31/2012] [Indexed: 12/21/2022] Open
Abstract
Deep-sea environments are largely unexplored habitats where a surprising number of species may be found in large communities, thriving regardless of the darkness, extreme cold, and high pressure. Their unique geochemical features result in reducing environments rich in methane and sulfides, sustaining complex chemosynthetic ecosystems that represent one of the most surprising findings in oceans in the last 40 years. The deep-sea Lucky Strike hydrothermal vent field, located in the Mid Atlantic Ridge, is home to large vent mussel communities where Bathymodiolus azoricus represents the dominant faunal biomass, owing its survival to symbiotic associations with methylotrophic or methanotrophic and thiotrophic bacteria. The recent transcriptome sequencing and analysis of gill tissues from B. azoricus revealed a number of genes of bacterial origin, hereby analyzed to provide a functional insight into the gill microbial community. The transcripts supported a metabolically active microbiome and a variety of mechanisms and pathways, evidencing also the sulfur and methane metabolisms. Taxonomic affiliation of transcripts and 16S rRNA community profiling revealed a microbial community dominated by thiotrophic and methanotrophic endosymbionts of B. azoricus and the presence of a Sulfurovum-like epsilonbacterium.
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van der Heijden K, Petersen JM, Dubilier N, Borowski C. Genetic connectivity between north and south Mid-Atlantic Ridge chemosynthetic bivalves and their symbionts. PLoS One 2012; 7:e39994. [PMID: 22792208 PMCID: PMC3391212 DOI: 10.1371/journal.pone.0039994] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 06/04/2012] [Indexed: 11/18/2022] Open
Abstract
Transform faults are geological structures that interrupt the continuity of mid-ocean ridges and can act as dispersal barriers for hydrothermal vent organisms. In the equatorial Atlantic Ocean, it has been hypothesized that long transform faults impede gene flow between the northern and the southern Mid-Atlantic Ridge (MAR) and disconnect a northern from a southern biogeographic province. To test if there is a barrier effect in the equatorial Atlantic, we examined phylogenetic relationships of chemosynthetic bivalves and their bacterial symbionts from the recently discovered southern MAR hydrothermal vents at 5°S and 9°S. We examined Bathymodiolus spp. mussels and Abyssogena southwardae clams using the mitochondrial cytochrome c oxidase subunit I (COI) gene as a phylogenetic marker for the hosts and the bacterial 16S rRNA gene as a marker for the symbionts. Bathymodiolus spp. from the two southern sites were genetically divergent from the northern MAR species B. azoricus and B. puteoserpentis but all four host lineages form a monophyletic group indicating that they radiated after divergence from their northern Atlantic sister group, the B. boomerang species complex. This suggests dispersal of Bathymodiolus species from north to south across the equatorial belt. 16S rRNA genealogies of chemoautotrophic and methanotrophic symbionts of Bathymodiolus spp. were inconsistent and did not match the host COI genealogy indicating disconnected biogeography patterns. The vesicomyid clam Abyssogena southwardae from 5°S shared an identical COI haplotype with A. southwardae from the Logatchev vent field on the northern MAR and their symbionts shared identical 16S phylotypes, suggesting gene flow across the Equator. Our results indicate genetic connectivity between the northern and southern MAR and suggest that a strict dispersal barrier does not exist.
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Affiliation(s)
| | - Jillian M. Petersen
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicole Dubilier
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christian Borowski
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
- * E-mail:
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Thurber AR, Jones WJ, Schnabel K. Dancing for food in the deep sea: bacterial farming by a new species of Yeti crab. PLoS One 2011; 6:e26243. [PMID: 22140426 PMCID: PMC3227565 DOI: 10.1371/journal.pone.0026243] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 09/23/2011] [Indexed: 11/24/2022] Open
Abstract
Vent and seep animals harness chemosynthetic energy to thrive far from the sun's energy. While symbiont-derived energy fuels many taxa, vent crustaceans have remained an enigma; these shrimps, crabs, and barnacles possess a phylogenetically distinct group of chemosynthetic bacterial epibionts, yet the role of these bacteria has remained unclear. We test whether a new species of Yeti crab, which we describe as Kiwa puravida n. sp, farms the epibiotic bacteria that it grows on its chelipeds (claws), chelipeds that the crab waves in fluid escaping from a deep-sea methane seep. Lipid and isotope analyses provide evidence that epibiotic bacteria are the crab's main food source and K. puravida n. sp. has highly-modified setae (hairs) on its 3(rd) maxilliped (a mouth appendage) which it uses to harvest these bacteria. The ε- and γ- proteobacteria that this methane-seep species farms are closely related to hydrothermal-vent decapod epibionts. We hypothesize that this species waves its arm in reducing fluid to increase the productivity of its epibionts by removing boundary layers which may otherwise limit carbon fixation. The discovery of this new species, only the second within a family described in 2005, stresses how much remains undiscovered on our continental margins.
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Affiliation(s)
- Andrew R Thurber
- Integrative Oceanography Division, Scripps Institution of Oceanography, La Jolla, California, United States of America.
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Guri M, Durand L, Cueff-Gauchard V, Zbinden M, Crassous P, Shillito B, Cambon-Bonavita MA. Acquisition of epibiotic bacteria along the life cycle of the hydrothermal shrimp Rimicaris exoculata. ISME JOURNAL 2011; 6:597-609. [PMID: 21993397 DOI: 10.1038/ismej.2011.133] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The caridean shrimp Rimicaris exoculata dominates the fauna at several Mid-Atlantic Ridge hydrothermal vent sites. This shrimp has an enlarged gill chamber, harboring a dense ectosymbiotic community of chemoautotrophic bacteria associated with mineral oxide deposits. Until now, their acquisition is not fully understood. At three hydrothermal vent sites, we analyzed the epibionts diversity at different moult stages and also in the first stages of the shrimp life (eggs, hatched eggs (with larvae) and juveniles). Hatched eggs associated with young larvae were collected for the first time directly from gravid females at the Logachev vent site during the Serpentine cruise. An approach using 16S rRNA clone libraries, scanning and transmission electron microscopy, and fluorescent in situ hybridization was used. Molecular results and microscope observations indicated a switch in the composition of the bacterial community between early R. exoculata life cycle stage (egg libraries dominated by the Gammaproteobacteria) and later stages (juvenile/adult libraries dominated by the Epsilonproteobacteria). We hypothesized that the epibiotic phylotype composition could vary according to the life stage of the shrimp. Our results confirmed the occurrence of a symbiosis with Gammaproteobacteria and Epsilonproteobacteria, but more complex than previously assumed. We revealed the presence of active type-I methanotrophic bacteria colonizing the cephalothorax of shrimps from the Rainbow site. They were also present on the eggs from the Logachev site. This could be the first 'epibiotic' association between methanotrophic bacteria and hydrothermal vent crustacean. We discuss possible transmission pathways for epibionts linked to the shrimp life cycle.
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Hydrogen is an energy source for hydrothermal vent symbioses. Nature 2011; 476:176-80. [PMID: 21833083 DOI: 10.1038/nature10325] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 06/20/2011] [Indexed: 11/08/2022]
Abstract
The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.
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Hügler M, Petersen JM, Dubilier N, Imhoff JF, Sievert SM. Pathways of carbon and energy metabolism of the epibiotic community associated with the deep-sea hydrothermal vent shrimp Rimicaris exoculata. PLoS One 2011; 6:e16018. [PMID: 21249205 PMCID: PMC3017555 DOI: 10.1371/journal.pone.0016018] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Accepted: 12/03/2010] [Indexed: 12/03/2022] Open
Abstract
Background The shrimp Rimicaris exoculata dominates the faunal biomass at many deep-sea hydrothermal vent sites at the Mid-Atlantic Ridge. In its enlarged gill chamber it harbors a specialized epibiotic bacterial community for which a nutritional role has been proposed. Methodology/Principal Findings We analyzed specimens from the Snake Pit hydrothermal vent field on the Mid-Atlantic Ridge by complementing a 16S rRNA gene survey with the analysis of genes involved in carbon, sulfur and hydrogen metabolism. In addition to Epsilon- and Gammaproteobacteria, the epibiotic community unexpectedly also consists of Deltaproteobacteria of a single phylotype, closely related to the genus Desulfocapsa. The association of these phylogenetic groups with the shrimp was confirmed by fluorescence in situ hybridization. Based on functional gene analyses, we hypothesize that the Gamma- and Epsilonproteobacteria are capable of autotrophic growth by oxidizing reduced sulfur compounds, and that the Deltaproteobacteria are also involved in sulfur metabolism. In addition, the detection of proteobacterial hydrogenases indicates the potential for hydrogen oxidation in these communities. Interestingly, the frequency of these phylotypes in 16S rRNA gene clone libraries from the mouthparts differ from that of the inner lining of the gill chamber, indicating potential functional compartmentalization. Conclusions Our data show the specific association of autotrophic bacteria with Rimicaris exoculata from the Snake Pit hydrothermal vent field, and suggest that autotrophic carbon fixation is contributing to the productivity of the epibiotic community with the reductive tricarboxylic acid cycle as one important carbon fixation pathway. This has not been considered in previous studies of carbon fixation and stable carbon isotope composition of the shrimp and its epibionts. Furthermore, the co-occurrence of sulfur-oxidizing and sulfur-reducing epibionts raises the possibility that both may be involved in the syntrophic exchange of sulfur compounds, which could increase the overall efficiency of this epibiotic community.
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Affiliation(s)
- Michael Hügler
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
- Leibniz Institute of Marine Sciences, IFM- GEOMAR, Kiel, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Stefan M. Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
- * E-mail:
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Ruehland C, Dubilier N. Gamma- and epsilonproteobacterial ectosymbionts of a shallow-water marine worm are related to deep-sea hydrothermal vent ectosymbionts. Environ Microbiol 2010; 12:2312-26. [PMID: 21966922 DOI: 10.1111/j.1462-2920.2010.02256.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The marine oligochaete worm Tubificoides benedii is often found in high numbers in eutrophic coastal sediments with low oxygen and high sulfide concentrations. A dense biofilm of filamentous bacteria on the worm's tail end were morphologically described over 20 years ago, but no further studies of these epibiotic associations were done. In this study, we used fluorescence in situ hybridization and comparative sequence analysis of 16S rRNA and protein-coding genes to characterize the microbial community of the worm's tail ends. The presence of genes involved in chemoautotrophy (cbbL and cbbM) and sulfur metabolism (aprA) indicated the potential of the T. benedii microbial community for chemosynthesis. Two filamentous ectosymbionts were specific to the worm's tail ends: one belonged to the Leucothrix mucor clade within the Gammaproteobacteria and the other to the Thiovulgaceae within the Epsilonproteobacteria. Both T. benedii ectosymbionts belonged to clades that consisted almost exclusively of bacteria associated with invertebrates from deep-sea hydrothermal vents. Such close relationships between symbionts from shallow-water and deep-sea hosts that are not closely related to each other are unusual, and indicate that biogeography and host affiliation did not play a role in these associations. Instead, similarities between the dynamic environments of vents and organic-rich mudflats with their strong fluctuations in reductants and oxidants may have been the driving force behind the establishment and evolution of these symbioses.
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Affiliation(s)
- Caroline Ruehland
- Symbiosis Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
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