1
|
Haydon TD, Suggett DJ, Siboni N, Kahlke T, Camp EF, Seymour JR. Temporal Variation in the Microbiome of Tropical and Temperate Octocorals. MICROBIAL ECOLOGY 2022; 83:1073-1087. [PMID: 34331071 DOI: 10.1007/s00248-021-01823-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.
Collapse
Affiliation(s)
- Trent D Haydon
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Emma F Camp
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| |
Collapse
|
2
|
Watson SA, Neo ML. Conserving threatened species during rapid environmental change: using biological responses to inform management strategies of giant clams. CONSERVATION PHYSIOLOGY 2021; 9:coab082. [PMID: 34912564 PMCID: PMC8666801 DOI: 10.1093/conphys/coab082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
Giant clams are threatened by overexploitation for human consumption, their valuable shells and the aquarium trade. Consequently, these iconic coral reef megafauna are extinct in some former areas of their range and are included in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and Convention on International Trade in Endangered Species of Wild Fauna and Flora. Now, giant clams are also threatened by rapid environmental change from both a suite of local and regional scale stressors and global change, including climate change, global warming, marine heatwaves and ocean acidification. The interplay between local- to regional-scale and global-scale drivers is likely to cause an array of lethal and sub-lethal effects on giant clams, potentially limiting their depth distribution on coral reefs and decreasing suitable habitat area within natural ranges of species. Global change stressors, pervasive both in unprotected and protected areas, threaten to diminish conservation efforts to date. International efforts urgently need to reduce carbon dioxide emissions to avoid lethal and sub-lethal effects of global change on giant clams. Meanwhile, knowledge of giant clam physiological and ecological responses to local-regional and global stressors could play a critical role in conservation strategies of these threatened species through rapid environmental change. Further work on how biological responses translate into habitat requirements as global change progresses, selective breeding for resilience, the capacity for rapid adaptive responses of the giant clam holobiont and valuing tourism potential, including recognizing giant clams as a flagship species for coral reefs, may help improve the prospects of these charismatic megafauna over the coming decades.
Collapse
Affiliation(s)
- Sue-Ann Watson
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum Network, 70-102 Flinders Street, Townsville, Queensland, 4810, Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 1 James Cook Drive, Townsville, Queensland, 4811, Australia
| | - Mei Lin Neo
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| |
Collapse
|
3
|
Abstract
Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Eslam O Osman
- Biology Department, Eberly College, Pennsylvania State University, State College, Pennsylvania, USA; .,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Biology Lab, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Alexis M Weinnig
- Biology Department, Temple University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
4
|
Bennion M, Ross P, Howells J, McDonald IR, Lane H. Characterisation and distribution of the bacterial genus Endozoicomonas in a threatened surf clam. DISEASES OF AQUATIC ORGANISMS 2021; 146:91-105. [PMID: 34617515 DOI: 10.3354/dao03626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The toheroa Paphies ventricosa is a large Aotearoa New Zealand (ANZ) endemic surf clam of cultural importance to many Māori, the Indigenous people of ANZ. Extensive commercial and recreational harvesting in the 20th century dramatically reduced populations, leading to the collapse and closure of the fishery. Despite being protected for >40 yr, toheroa have inexplicably failed to recover. In 2017, intracellular microcolonies (IMCs) of bacteria were detected in 'sick' toheroa in northern ANZ. Numerous mass mortality events (MMEs) have recently been recorded in ANZ shellfish, with many events linked by the presence of IMCs resembling Rickettsia-like organisms (RLOs). While similar IMCs have been implicated in MMEs in surf clams elsewhere, the impact of these IMCs on the health or recovery of toheroa is unknown. A critical first step towards understanding the significance of a pathogen in a host population is pathogen identification and characterisation. To begin this process, we examined 16S rRNA gene sequences of the putative IMCs from 4 toheroa populations that showed 97% homology to Endozoicomonas spp. sequences held in GenBank. Phylogenetic analysis identified closely related Endozoicomonas strains from the North and South Island, ANZ, and in situ hybridization, using 16S rRNA gene probes, confirmed the presence of the sequenced IMC gene in the gill and digestive gland tissues of toheroa. Quantitative PCR revealed site-specific and seasonal abundance patterns of Endozoicomonas spp. in toheroa populations. Although implicated in disease outbreaks elsewhere, the role of Endozoicomonas spp. within the ANZ shellfish mortality landscape remains uncertain.
Collapse
Affiliation(s)
- Matthew Bennion
- Environmental Research Institute, University of Waikato, Tauranga 3110, New Zealand
| | | | | | | | | |
Collapse
|
5
|
Costa RM, Cárdenas A, Loussert-Fonta C, Toullec G, Meibom A, Voolstra CR. Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia. Front Microbiol 2021; 12:637834. [PMID: 33897642 PMCID: PMC8060496 DOI: 10.3389/fmicb.2021.637834] [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: 12/04/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.
Collapse
Affiliation(s)
- Rúben M Costa
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Céline Loussert-Fonta
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Christian R Voolstra
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
6
|
Guibert I, Bourdreux F, Bonnard I, Pochon X, Dubousquet V, Raharivelomanana P, Berteaux-Lecellier V, Lecellier G. Dimethylsulfoniopropionate concentration in coral reef invertebrates varies according to species assemblages. Sci Rep 2020; 10:9922. [PMID: 32555283 PMCID: PMC7303174 DOI: 10.1038/s41598-020-66290-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/18/2020] [Indexed: 11/28/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is a key compound in the marine sulfur cycle, and is produced in large quantities in coral reefs. In addition to Symbiodiniaceae, corals and associated bacteria have recently been shown to play a role in DMSP metabolism. Numerous ecological studies have focused on DMSP concentrations in corals, which led to the hypothesis that increases in DMSP levels might be a general response to stress. Here we used multiple species assemblages of three common Indo-Pacific holobionts, the scleractinian corals Pocillopora damicornis and Acropora cytherea, and the giant clam Tridacna maxima and examined the DMSP concentrations associated with each species within different assemblages and thermal conditions. Results showed that the concentration of DMSP in A. cytherea and T. maxima is modulated according to the complexity of species assemblages. To determine the potential importance of symbiotic dinoflagellates in DMSP production, we then explored the relative abundance of Symbiodiniaceae clades in relation to DMSP levels using metabarcoding, and found no significant correlation between these factors. Finally, this study also revealed the existence of homologs involved in DMSP production in giant clams, suggesting for the first time that, like corals, they may also contribute to DMSP production. Taken together, our results demonstrated that corals and giant clams play important roles in the sulfur cycle. Because DMSP production varies in response to specific species-environment interactions, this study offers new perspectives for future global sulfur cycling research.
Collapse
Affiliation(s)
- Isis Guibert
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong S.A.R, China.
- Sorbonne Université, UMR250/9220 ENTROPIE IRD-CNRS-UR-IFREMER-UNC, Promenade Roger-Laroque, Noumea cedex, New Caledonia, France.
- USR3278 PSL CRIOBE CNRS-EPHE-UPVD, LabEx CORAIL, Papetoai, Moorea, French Polynesia.
| | - Flavien Bourdreux
- Université de Paris-Saclay, UVSQ, 45 avenue des Etats-Unis, Versailles Cedex, France
- Institut Lavoisier de Versailles, UMR CNRS 8180, 45 avenue des Etats-Unis, Versailles Cedex, France
| | - Isabelle Bonnard
- USR3278 PSL CRIOBE CNRS-EPHE-UPVD, LabEx CORAIL, Université de Perpignan, 58 avenue Paul Alduy, 66860, Perpignan, France
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941, New Zealand
| | - Vaimiti Dubousquet
- Délégation à la recherche, Government of French Polynesia BP 20981, 98713, Papeete, Tahiti, French Polynesia
| | - Phila Raharivelomanana
- UMR 241 EIO, Université de la Polynésie Française, BP 6570 Faaa, 98702, Faaa, Tahiti, French Polynesia
| | - Véronique Berteaux-Lecellier
- USR3278 PSL CRIOBE CNRS-EPHE-UPVD, LabEx CORAIL, Papetoai, Moorea, French Polynesia
- UMR250/9220 ENTROPIE IRD-CNRS-UR-IFREMER-UNC, Promenade Roger-Laroque, Noumea cedex, New Caledonia, France
| | - Gael Lecellier
- Université de Paris-Saclay, UVSQ, 45 avenue des Etats-Unis, Versailles Cedex, France
- UMR250/9220 ENTROPIE IRD-CNRS-UR-IFREMER-UNC, Promenade Roger-Laroque, Noumea cedex, New Caledonia, France
| |
Collapse
|
7
|
Guibert I, Lecellier G, Torda G, Pochon X, Berteaux-Lecellier V. Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima. MICROBIOME 2020; 8:57. [PMID: 32317019 PMCID: PMC7175534 DOI: 10.1186/s40168-020-00835-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics. RESULTS Our results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima. CONCLUSIONS Altogether, our results suggest that at least three microbiotypes naturally exist in the studied clam populations, regardless of water temperature. These microbiotypes plausibly provide similar functions to the clam host via alternate molecular pathways as well as microbiotype-specific functions. This redundancy in functions among microbiotypes together with their specificities provides hope that giant clam populations can tolerate some levels of environmental variation such as increased temperature. Importantly, the composition of the benthic assemblage could make clams susceptible to infections by Vibrionaceae, especially when water temperature increases. Video abstract.
Collapse
Affiliation(s)
- Isis Guibert
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, SAR China
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
- USR3278 PSL CRIOBE CNRS-EPHE-UPVD, Papetoai, Moorea, French Polynesia
| | - Gael Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
- UVSQ, Université de Paris-Saclay, 45 Avenue des Etats-Unis, Versailles Cedex, France
| | - Gergely Torda
- ARC, Centre of Excellence for Coral Reef Studies, James Cook University, QLD, Townsville, 4811 Australia
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson, 7042 New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941 New Zealand
| | - Véronique Berteaux-Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
| |
Collapse
|