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Feng W, Wang M, Dong D, Hui M, Zhang H, Fu L, Zhong Z, Xu Z, Li C. Variation in epibiotic bacteria on two squat lobster species of Munidopsidae. Front Microbiol 2023; 14:1197476. [PMID: 37448572 PMCID: PMC10336205 DOI: 10.3389/fmicb.2023.1197476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 07/15/2023] Open
Abstract
The relationships between epibiotic bacteria on deep-sea hosts and host lifestyle factors are of particular interest in the field of deep-sea chemoautotrophic environmental adaptations. The squat lobsters Shinkaia crosnieri and Munidopsis verrilli are both dominant species in cold-seep ecosystems, and they have different distributions and feeding behaviors. These species may have evolved to have distinct epibiotic microbiota. Here, we compared the epibiotic bacterial communities on the M. verrilli carapace (MVcarapace), S. crosnieri carapace (SCcarapace), and S. crosnieri ventral plumose setae (SCsetae). The epibiotic bacteria on SCsetae were dense and diverse and had a multi-layer configuration, while those on MVcarapace and SCcarapace were sparse and had a monolayer configuration. Chemoautotrophic bacteria had the highest relative abundance in all epibiotic bacterial communities. The relative abundance of amplicon sequence variant 3 (ASV3; unknown species in order Thiotrichales), which is associated with sulfide oxidation, was significantly higher in SCsetae than MVcarapace and SCcarapace. Thiotrichales species seemed to be specifically enriched on SCsetae, potentially due to the synthetic substrate supply, adhesion preference, and host behaviors. We hypothesize that the S. crosnieri episymbionts use chemical fluxes near cold seeps more efficiently, thereby supporting the host's nutrient strategies, resulting in a different distribution of the two species of squat lobster.
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Affiliation(s)
- Wenze Feng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Dong
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Min Hui
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Huan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lulu Fu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhaoshan Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zheng Xu
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Chaolun Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Sen A, Tanguy G, Galand PE, Andersen AC, Hourdez S. Bacterial symbiont diversity in Arctic seep Oligobrachia siboglinids. Anim Microbiome 2023; 5:30. [PMID: 37264469 DOI: 10.1186/s42523-023-00251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/15/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND High latitude seeps are dominated by Oligobrachia siboglinid worms. Since these worms are often the sole chemosymbiotrophic taxon present (they host chemosynthetic bacteria within the trophosome organ in their trunk region), a key question in the study of high latitude seep ecology has been whether they harbor methanotrophic symbionts. This debate has manifested due to the mismatch between stable carbon isotope signatures of the worms (lower than -50‰ and usually indicative of methanotrophic symbioses) and the lack of molecular or microscopic evidence for methanotrophic symbionts. Two hypotheses have circulated to explain this paradox: (1) the uptake of sediment carbon compounds with depleted δC13 values from the seep environment, and (2) a small, but significant and difficult to detect population of methanotrophic symbionts. We conducted 16S rRNA amplicon sequencing of the V3-V4 regions on two species of northern seep Oligobrachia (Oligobrachia webbi and Oligobrachia sp. CPL-clade), from four different high latitude sites, to investigate the latter hypothesis. We also visually checked the worms' symbiotic bacteria within the symbiont-hosting organ, the trophosome, through transmission electron microscopy. RESULTS The vast majority of the obtained reads corresponded to sulfide-oxidizers and only a very small proportion of the reads pertained to methane-oxidizers, which suggests a lack of methanotrophic symbionts. A number of sulfur oxidizing bacterial strains were recovered from the different worms, however, host individuals tended to possess a single strain, or sometimes two closely-related strains. However, strains did not correspond specifically with either of the two Oligobrachia species we investigated. Water depth could play a role in determining local sediment bacterial communities that were opportunistically taken up by the worms. Bacteria were abundant in non-trophosome (and thereby symbiont-free) tissue and are likely epibiotic or tube bacterial communities. CONCLUSIONS The absence of methanotrophic bacterial sequences in the trophosome of Arctic and north Atlantic seep Oligobrachia likely indicates a lack of methanotrophic symbionts in these worms, which suggests that nutrition is sulfur-based. This is turn implies that sediment carbon uptake is responsible for the low δ13C values of these animals. Furthermore, endosymbiotic partners could be locally determined, and possibly only represent a fraction of all bacterial sequences obtained from tissues of these (and other) species of frenulates.
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Affiliation(s)
- Arunima Sen
- Department of Arctic Biology, The University Centre in Svalbard (UNIS), Longyearbyen, Norway.
- Faculty of Bioscience and Aquaculture, Nord University, Bodø, Norway.
| | - Gwenn Tanguy
- FR2424 Sorbonne Université-CNRS, Genomer, Station Biologique de Roscoff, Roscoff, France
| | - Pierre E Galand
- UMR8222 Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), CNRS-Sorbonne Université, Observatoire Océanologique, Banyuls-Sur-Mer, France
| | - Ann C Andersen
- UMR7144 Laboratoire Adaptation et Diversité en Milieu Marin (AD2M), Sorbonne Université-CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Stéphane Hourdez
- UMR8222 Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), CNRS-Sorbonne Université, Observatoire Océanologique, Banyuls-Sur-Mer, France
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Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps. mSystems 2022; 7:e0032022. [PMID: 35938718 PMCID: PMC9426478 DOI: 10.1128/msystems.00320-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.
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Kato N, Chen C, Watanabe HK, Yamamoto M, Shimomura M. The First Bopyrid Isopod from Hydrothermal Vents: Pleurocryptella shinkai sp. nov. (Isopoda: Epicaridea) Parasitizing Shinkaia crosnieri (Decapoda: Anomura). Zoolog Sci 2022; 39:293. [DOI: 10.2108/zs210117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/09/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Noeru Kato
- Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Hiromi Kayama Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Masahiro Yamamoto
- Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Michitaka Shimomura
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan
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Metatranscriptomics by
In Situ
RNA Stabilization Directly and Comprehensively Revealed Episymbiotic Microbial Communities of Deep-Sea Squat Lobsters. mSystems 2020; 5:5/5/e00551-20. [PMID: 33024051 PMCID: PMC8534475 DOI: 10.1128/msystems.00551-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shinkaia crosnieri is an invertebrate that inhabits an area around deep-sea hydrothermal vents in the Okinawa Trough in Japan by harboring episymbiotic microbes as the primary nutrition. To reveal physiology and phylogenetic composition of the active episymbiotic populations, metatranscriptomics is expected to be a powerful approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. Here, we conducted direct metatranscriptomic analysis of S. crosnieri episymbionts by applying in situ RNA stabilization equipment. As expected, we obtained RNA expression profiles that were substantially different from those obtained by conventional metatranscriptomics (i.e., stabilization after retrieval). The episymbiotic community members were dominated by three orders, namely, Thiotrichales, Methylococcales, and Campylobacterales, and the Campylobacterales members were mostly dominated by the Sulfurovum genus. At a finer phylogenetic scale, the episymbiotic communities on different host individuals shared many species, indicating that the episymbionts on each host individual are not descendants of a few founder cells but are horizontally exchanged. Furthermore, our analysis revealed the key metabolisms of the community: two carbon fixation pathways, a formaldehyde assimilation pathway, and utilization of five electron donors (sulfide, thiosulfate, sulfur, methane, and ammonia) and two electron accepters (oxygen and nitrate/nitrite). Importantly, it was suggested that Thiotrichales episymbionts can utilize intercellular sulfur globules even when sulfur compounds are not usable, possibly also in a detached and free-living state. IMPORTANCE Deep-sea hydrothermal vent ecosystems remain mysterious. To depict in detail the enigmatic life of chemosynthetic microbes, which are key primary producers in these ecosystems, metatranscriptomic analysis is expected to be a promising approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. In this study, we conducted direct metatranscriptome analysis of microbial episymbionts of deep-sea squat lobsters (Shinkaia crosnieri) by applying in situ RNA stabilization equipment. Compared to conventional metatranscriptomics (i.e., RNA stabilization after retrieval), our method provided substantially different RNA expression profiles. Moreover, we discovered that S. crosnieri and its episymbiotic microbes constitute complex and resilient ecosystems, where closely related but various episymbionts are stably maintained by horizontal exchange and partly by their sulfur storage ability for survival even when sulfur compounds are not usable, likely also in a detached and free-living state.
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Takai K. Recent Topics on Deep-Sea Microbial Communities in Microbes and Environments. Microbes Environ 2020; 34:345-346. [PMID: 31902911 PMCID: PMC6934399 DOI: 10.1264/jsme2.me3404rh] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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Miyazaki J, Ikuta T, Watsuji TO, Abe M, Yamamoto M, Nakagawa S, Takaki Y, Nakamura K, Takai K. Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica. ISME JOURNAL 2020; 14:1273-1289. [PMID: 32051527 PMCID: PMC7174374 DOI: 10.1038/s41396-020-0605-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastropod Alviniconcha marisindica in the Kairei and Edmond fields (kAlv and eAlv populations, respectively) of the Indian Ocean, utilize H2 in response to their physical and environmental H2 conditions, although the 16S rRNA gene sequence of both the endosymbionts shared 99.6% identity. A thermodynamic calculation using in situ H2 and hydrogen sulfide (H2S) concentrations indicated that chemosynthetic symbiosis could be supported by metabolic energy via H2 oxidation, particularly for the kAlv holobiont. Metabolic activity measurements showed that both the living individuals and the gill tissues consumed H2 and H2S at similar levels. Moreover, a combination of fluorescence in situ hybridization, quantitative transcript analyses, and enzymatic activity measurements showed that the kAlv endosymbiont expressed the genes and enzymes for both H2- and sulfur-oxidations. These results suggest that both H2 and H2S could serve as the primary energy sources for the kAlv holobiont. The eAlv holobiont had the ability to utilize H2, but the gene expression and enzyme activity for hydrogenases were much lower than for sulfur-oxidation enzymes. These results suggest that the energy acquisitions of A. marisindica holobionts are dependent on H2- and sulfur-oxidation in the H2-enriched Kairei field and that the mechanism of dual metabolism is controlled by the in situ H2 concentration.
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Affiliation(s)
- Junichi Miyazaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Tetsuro Ikuta
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Tomo-O Watsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kitakyusyu, 803-0846, Japan
| | - Mariko Abe
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Satoshi Nakagawa
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Kentaro Nakamura
- Department of Systems Innovation, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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