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Achlatis M, Pernice M, Green K, Guagliardo P, Kilburn MR, Hoegh-Guldberg O, Dove S. Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge. THE ISME JOURNAL 2018; 12:1308-1318. [PMID: 29386628 PMCID: PMC5932049 DOI: 10.1038/s41396-017-0044-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/12/2017] [Indexed: 01/04/2023]
Abstract
Some of the most aggressive coral-excavating sponges host intracellular dinoflagellates from the genus Symbiodinium, which are hypothesized to provide the sponges with autotrophic energy that powers bioerosion. Investigations of the contribution of Symbiodinium to host metabolism and particularly inorganic nutrient recycling are complicated, however, by the presence of alternative prokaryotic candidates for this role. Here, novel methods are used to study nutrient assimilation and transfer within and between the outer-layer cells of the Indopacific bioeroding sponge Cliona orientalis. Combining stable isotope labelling, transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS), we visualize and measure metabolic activity at the individual cell level, tracking the fate of 15N-ammonium and 13C-bicarbonate within the intact holobiont. We found strong uptake of both inorganic sources (especially 13C-bicarbonate) by Symbiodinium cells. Labelled organic nutrients were translocated from Symbiodinium to the Symbiodinium-hosting sponge cells within 6 h, and occasionally to other sponge cells within 3 days. By contrast, prokaryotic symbionts were not observed to participate in inorganic nutrient assimilation in the outer layers of the sponge. Our findings strongly support the metabolic interaction between the sponge and dinoflagellates, shedding light on the ecological advantages and adaptive capacity of photosymbiotic bioeroding sponges in oligotrophic marine habitats.
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Affiliation(s)
- Michelle Achlatis
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St. Lucia, QLD, 4072, Australia.
- Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St. Lucia, QLD, 4072, Australia.
- Global Change Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Matthew R Kilburn
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ove Hoegh-Guldberg
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Global Change Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Sophie Dove
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St. Lucia, QLD, 4072, Australia
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van de Water JAJM, Allemand D, Ferrier-Pagès C. Host-microbe interactions in octocoral holobionts - recent advances and perspectives. MICROBIOME 2018; 6:64. [PMID: 29609655 PMCID: PMC5880021 DOI: 10.1186/s40168-018-0431-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/01/2018] [Indexed: 05/05/2023]
Abstract
Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses.
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Affiliation(s)
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
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Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci Rep 2017; 7:40579. [PMID: 28094347 PMCID: PMC5240137 DOI: 10.1038/srep40579] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/07/2016] [Indexed: 01/22/2023] Open
Abstract
Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.
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Neave MJ, Apprill A, Ferrier-Pagès C, Voolstra CR. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl Microbiol Biotechnol 2016; 100:8315-24. [PMID: 27557714 PMCID: PMC5018254 DOI: 10.1007/s00253-016-7777-0] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 02/01/2023]
Abstract
Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.
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Affiliation(s)
- Matthew J Neave
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Bourne DG, Morrow KM, Webster NS. Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems. Annu Rev Microbiol 2016; 70:317-40. [PMID: 27482741 DOI: 10.1146/annurev-micro-102215-095440] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.
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Affiliation(s)
- David G Bourne
- Marine Biology and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia 4811; .,Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
| | - Kathleen M Morrow
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810.,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia 4810
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Rädecker N, Pogoreutz C, Voolstra CR, Wiedenmann J, Wild C. Nitrogen cycling in corals: the key to understanding holobiont functioning? Trends Microbiol 2015; 23:490-7. [DOI: 10.1016/j.tim.2015.03.008] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/08/2015] [Accepted: 03/18/2015] [Indexed: 01/11/2023]
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