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Béziat NS, Duperron S, Gros O. Environmental Transmission of Symbionts in the Mangrove Crabs Aratus pisonii and Minuca rapax: Acquisition of the Bacterial Community through Larval Development to Juvenile Stage. Microorganisms 2024; 12:652. [PMID: 38674597 PMCID: PMC11052079 DOI: 10.3390/microorganisms12040652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 04/28/2024] Open
Abstract
Aratus pisonii and Minuca rapax are two brachyuran crabs living with bacterial ectosymbionts located on gill lamellae. One previous study has shown that several rod-shaped bacterial morphotypes are present and the community is dominated by Alphaproteobacteria and Bacteroidota. This study aims to identify the mode of transmission of the symbionts to the new host generations and to identify the bacterial community colonizing the gills of juveniles. We tested for the presence of bacteria using PCR with universal primers targeting the 16S rRNA encoding gene from gonads, eggs, and different larval stages either obtained in laboratory conditions or from the field. The presence of bacteria on juvenile gills was also characterized by scanning electron microscopy, and subsequently identified by metabarcoding analysis. Gonads, eggs, and larvae were negative to PCR tests, suggesting that bacteria are not present at these stages in significant densities. On the other hand, juveniles of both species display three rod-shaped bacterial morphotypes on gill lamellae, and sequencing revealed that the community is dominated by Bacteroidota and Alphaproteobacteria on A. pisonii juveniles, and by Alphaprotobacteria, Bacteroidota, and Acidimicrobia on M. rapax juveniles. Despite the fact that juveniles of both species co-occur in the same biotope, no shared bacterial phylotype was identified. However, some of the most abundant bacteria present in adults are also present in juveniles of the same species, suggesting that juvenile-associated communities resemble those of adults. Because some of these bacteria were also found in crab burrow water, we hypothesize that the bacterial community is established gradually during the life of the crab starting from the megalopa stage and involves epibiosis-competent bacteria that occur in the environment.
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Affiliation(s)
- Naëma Schanendra Béziat
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Campus de Fouillole, 97110 Pointe-à-Pitre, France;
- Caribaea Initiative, Université des Antilles, 97110 Pointe-à-Pitre, France
| | - Sébastien Duperron
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d’Histoire Naturelle, UMR 7245, CNRS, 57 Rue Cuvier (CP54), 75005 Paris, France;
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Campus de Fouillole, 97110 Pointe-à-Pitre, France;
- C3MAG, UFR des Sciences Exactes et Naturelles, Université des Antilles, 97110 Pointe-à-Pitre, France
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2
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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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Methou P, Chen C, Kayama Watanabe H, Cambon MA, Pradillon F. Reproduction in deep-sea vent shrimps is influenced by diet, with rhythms apparently unlinked to surface production. Ecol Evol 2022; 12:e9076. [PMID: 35866019 PMCID: PMC9288886 DOI: 10.1002/ece3.9076] [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: 02/12/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022] Open
Abstract
Variations in offspring production according to feeding strategies or food supply have been recognized in many animals from various ecosystems. Despite an unusual trophic structure based on non-photosynthetic primary production, these relationships remain largely under-studied in chemosynthetic ecosystems. Here, we use Rimicaris shrimps as a study case to explore relationships between reproduction, diets, and food supply in these environments. For that, we compared reproductive outputs of three congeneric shrimps differing by their diets. They inhabit vents located under oligotrophic waters of tropical gyres with opposed latitudes, allowing us to also examine the prevalence of phylogenetic vs environmental drivers in their reproductive rhythms. For this, we used both our original data and a compilation of published observations on the presence of ovigerous females covering various seasons over the past 35 years. We report distinct egg production trends between Rimicaris species relying solely on chemosymbiosis-R. exoculata and R. kairei-and one relying on mixotrophy, R. chacei. Besides, our data suggest a reproductive periodicity that does not correspond to seasonal variations in surface production, with substantial proportions of brooding females during the same months of the year, despite those months corresponding to either boreal winter or austral summer depending on the hemisphere. These observations contrast with the long-standing paradigm in deep-sea species for which periodic reproductive patterns have always been attributed to seasonal variations of photosynthetic production sinking from the surface. Our results suggest the presence of an intrinsic basis for biological rhythms in the deep sea, and bring to light the importance of having year-round observations in order to understand the life history of vent animals.
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Affiliation(s)
- Pierre Methou
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds Plouzané France.,X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka Japan
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka Japan
| | | | - Marie-Anne Cambon
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds Plouzané France
| | - Florence Pradillon
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds Plouzané France
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Giraud C, Callac N, Boulo V, Lam JS, Pham D, Selmaoui-Folcher N, Wabete N. The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission. Front Microbiol 2022; 13:886752. [PMID: 35633721 PMCID: PMC9133551 DOI: 10.3389/fmicb.2022.886752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
The many ecological niches present in an organism harbor distinct microorganisms called microbiota. Different factors can influence the establishment of these commensal microbial communities. In a previous article, we have concluded that some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission. The present study was conducted in order to investigate this hypothesis. Using HiSeq sequencing of the V4 region of 16S rRNA gene, we analyzed the active microbiota associated with the eggs and the nauplii of L. stylirsotris as well as with the reproductive organs of their breeders. Microbial communities associated with the rearing water were also considered to discriminate environmental microbial lineages. Using these analyses, we highlight a set of core bacterial families present in all samples and composed of members of Colwelliaceae, Alteromonadaceae, Pseudoalteromonadaceae, Saccharospirillaceae, Oceanospirillaceae, Vibrionaceae, Burkholderiaceae, Rhodobacteraceae, Flavobacteraceae, and Corynebacteriaceae; showing the importance of the environment in the establishment of the larval microbiota. We also present specific bacteria affiliated to the Arcobacteraceae, Rhodobacteraceae, Comamonadaceae, and Colwelliaceae families, which were only found in the breeders and their offspring strengthening the hypothesis of a potential vertical transmission shaping the active microbiota of the eggs and the nauplii of L. stylirostris.
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Affiliation(s)
- Carolane Giraud
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
- *Correspondence: Carolane Giraud,
| | - Nolwenn Callac
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Nolwenn Callac,
| | - Viviane Boulo
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | | | - Dominique Pham
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | - Nazha Selmaoui-Folcher
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Nelly Wabete
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
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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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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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7
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Giraud C, Callac N, Beauvais M, Mailliez JR, Ansquer D, Selmaoui-Folcher N, Pham D, Wabete N, Boulo V. Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris: possible influence of the rearing water and more. PeerJ 2021; 9:e12241. [PMID: 34820157 PMCID: PMC8601056 DOI: 10.7717/peerj.12241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management. METHOD In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp (Litopenaeus stylirostris) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method. RESULTS We found a core microbiota made of taxa related to Aestuariibacter, Alteromonas, Vibrio, SAR11, HIMB11, AEGEAN 169 marine group and Candidatus Endobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.
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Affiliation(s)
- Carolane Giraud
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
- University of New Caledonia, Institut des Sciences Exactes et Appliquées (ISEA), Noumea, New Caledonia
| | - Nolwenn Callac
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Maxime Beauvais
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
- Sorbonne Université, UMR 7261, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, CNRS, Banyuls-sur-Mer, France
| | - Jean-René Mailliez
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Dominique Ansquer
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Nazha Selmaoui-Folcher
- University of New Caledonia, Institut des Sciences Exactes et Appliquées (ISEA), Noumea, New Caledonia
| | - Dominique Pham
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Nelly Wabete
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Viviane Boulo
- Ifremer, IRD, Université de la Nouvelle-Calédonie, Université de La Réunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan via Domitia, Montpellier, France
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Wale M, Daffonchio D, Fusi M, Marasco R, Garuglieri E, Diele K. The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. Front Microbiol 2021; 12:770245. [PMID: 34721372 PMCID: PMC8555880 DOI: 10.3389/fmicb.2021.770245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Matthew Wale
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Daniele Daffonchio
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marco Fusi
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Ramona Marasco
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Karen Diele
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
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Carrier TJ, Beaulieu SE, Mills SW, Mullineaux LS, Reitzel AM. Larvae of Deep-Sea Invertebrates Harbor Low-Diversity Bacterial Communities. THE BIOLOGICAL BULLETIN 2021; 241:65-76. [PMID: 34436969 DOI: 10.1086/715669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
AbstractMicrobial symbionts are a common life-history character of marine invertebrates and their developmental stages. Communities of bacteria that associate with the eggs, embryos, and larvae of coastal marine invertebrates tend to be species specific and correlate with aspects of host biology and ecology. The richness of bacteria associated with the developmental stages of coastal marine invertebrates spans four orders of magnitude, from single mutualists to thousands of unique taxa. This understanding stems predominately from the developmental stages of coastal species. If they are broadly representative of marine invertebrates, then we may expect deep-sea species to associate with bacterial communities that are similar in diversity. To test this, we used amplicon sequencing to profile the bacterial communities of invertebrate larvae from multiple taxonomic groups (annelids, molluscs, crustaceans) collected from 2500 to 3670 m in depth in near-bottom waters near hydrothermal vents in 3 different regions of the Pacific Ocean (the East Pacific Rise, the Mariana Back-Arc, and the Pescadero Basin). We find that larvae of deep-sea invertebrates associate with low-diversity bacterial communities (~30 bacterial taxa) that lack specificity between taxonomic groups. The diversity of these communities is estimated to be ~7.9 times lower than that of coastal invertebrate larvae, but this result depends on the taxonomic group. Associating with a low-diversity community may imply that deep-sea invertebrate larvae do not have a strong reliance on a microbiome and that the hypothesized lack of symbiotic contributions would differ from expectations for larvae of coastal marine invertebrates.
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10
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Li M, Chen H, Wang M, Zhong Z, Wang H, Zhou L, Zhang H, Li C. A Toll-like receptor identified in Gigantidas platifrons and its potential role in the immune recognition of endosymbiotic methane oxidation bacteria. PeerJ 2021; 9:e11282. [PMID: 33986997 PMCID: PMC8092104 DOI: 10.7717/peerj.11282] [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: 01/04/2021] [Accepted: 03/24/2021] [Indexed: 11/20/2022] Open
Abstract
Symbiosis with chemosynthetic bacteria is an important ecological strategy for the deep-sea megafaunas including mollusks, tubeworms and crustacean to obtain nutrients in hydrothermal vents and cold seeps. How the megafaunas recognize symbionts and establish the symbiosis has attracted much attention. Bathymodiolinae mussels are endemic species in both hydrothermal vents and cold seeps while the immune recognition mechanism underlying the symbiosis is not well understood due to the nonculturable symbionts. In previous study, a lipopolysaccharide (LPS) pull-down assay was conducted in Gigantidas platifrons to screen the pattern recognition receptors potentially involved in the recognition of symbiotic methane-oxidizing bacteria (MOB). Consequently, a total of 208 proteins including GpTLR13 were identified. Here the molecular structure, expression pattern and immune function of GpTLR13 were further analyzed. It was found that GpTLR13 could bind intensively with the lipid A structure of LPS through surface plasmon resonance analysis. The expression alternations of GpTLR13 transcripts during a 28-day of symbiont-depletion assay were investigated by real-time qPCR. As a result, a robust decrease of GpTLR13 transcripts was observed accompanying with the loss of symbionts, implying its participation in symbiosis. In addition, GpTLR13 transcripts were found expressed exclusively in the bacteriocytes of gills of G. platifrons by in situ hybridization. It was therefore speculated that GpTLR13 may be involved in the immune recognition of symbiotic methane-oxidizing bacteria by specifically recognizing the lipid A structure of LPS. However, the interaction between GpTLR13 and symbiotic MOB was failed to be addressed due to the nonculturable symbionts. Nevertheless, the present result has provided with a promising candidate as well as a new approach for the identification of symbiont-related genes in Bathymodiolinae mussels.
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Affiliation(s)
- Mengna Li
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Chen
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhaoshan Zhong
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Hao Wang
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Li Zhou
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Huan Zhang
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chaolun Li
- Center of Deep Sea Research and Key Laboratory of Marine Ecology & Environmental Sciences (CODR and KLMEES), Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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11
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Nyholm SV. In the beginning: egg-microbe interactions and consequences for animal hosts. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190593. [PMID: 32772674 PMCID: PMC7435154 DOI: 10.1098/rstb.2019.0593] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
Microorganisms are associated with the eggs of many animals. For some hosts, the egg serves as the ideal environment for the vertical transmission of beneficial symbionts between generations, while some bacteria use the egg to parasitize their hosts. In a number of animal groups, egg microbiomes often perform other essential functions. The eggs of aquatic and some terrestrial animals are especially susceptible to fouling and disease since they are exposed to high densities of microorganisms. To overcome this challenge, some hosts form beneficial associations with microorganisms, directly incorporating microbes and/or microbial products on or in their eggs to inhibit pathogens and biofouling. Other functional roles for egg-associated microbiomes are hypothesized to involve oxygen and nutrient acquisition. Although some egg-associated microbiomes are correlated with increased host fitness and are essential for successful development, the mechanisms that lead to such outcomes are often not well understood. This review article will discuss different functions of egg microbiomes and how these associations have influenced the biology and evolution of animal hosts. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269USA
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12
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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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13
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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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