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Voolstra CR, Raina JB, Dörr M, Cárdenas A, Pogoreutz C, Silveira CB, Mohamed AR, Bourne DG, Luo H, Amin SA, Peixoto RS. The coral microbiome in sickness, in health and in a changing world. Nat Rev Microbiol 2024; 22:460-475. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/06/2024]
Abstract
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
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Affiliation(s)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Melanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, American University, Washington, DC, USA
| | - Claudia Pogoreutz
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | | | - Amin R Mohamed
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Haiwei Luo
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC) and Computational Biology Research Center (CBRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Messer LF, Bourne DG, Robbins SJ, Clay M, Bell SC, McIlroy SJ, Tyson GW. A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience. Nat Commun 2024; 15:2902. [PMID: 38575584 PMCID: PMC10995205 DOI: 10.1038/s41467-024-46905-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.
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Affiliation(s)
- Lauren F Messer
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia.
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Megan Clay
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia
| | - Sara C Bell
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia.
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Montaño-Salazar S, Quintanilla E, Sánchez JA. Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level. Sci Rep 2023; 13:22049. [PMID: 38087002 PMCID: PMC10716379 DOI: 10.1038/s41598-023-49049-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.
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Affiliation(s)
- Sandra Montaño-Salazar
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Elena Quintanilla
- Department of Soil and Water Sciences, University of Florida, 2033 Mowry Rd, Gainesville, FL, 32610, USA.
| | - Juan A Sánchez
- Laboratory of Marine Molecular Biology (BIOMMAR), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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4
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Xiang N, Meyer A, Pogoreutz C, Rädecker N, Voolstra CR, Wild C, Gärdes A. Excess labile carbon promotes diazotroph abundance in heat-stressed octocorals. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221268. [PMID: 36938541 PMCID: PMC10014249 DOI: 10.1098/rsos.221268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen limitation is the foundation of stable coral-algal symbioses. Diazotrophs, prokaryotes capable of fixing N2 into ammonia, support the productivity of corals in oligotrophic waters, but could contribute to the destabilization of holobiont functioning when overstimulated. Recent studies on reef-building corals have shown that labile dissolved organic carbon (DOC) enrichment or heat stress increases diazotroph abundance and activity, thereby increasing nitrogen availability and destabilizing the coral-algal symbiosis. However, the (a)biotic drivers of diazotrophs in octocorals are still poorly understood. We investigated diazotroph abundance (via relative quantification of nifH gene copy numbers) in two symbiotic octocorals, the more mixotrophic soft coral Xenia umbellata and the more autotrophic gorgonian Pinnigorgia flava, under (i) labile DOC enrichment for 21 days, followed by (ii) combined labile DOC enrichment and heat stress for 24 days. Without heat stress, relative diazotroph abundances in X. umbellata and P. flava were unaffected by DOC enrichment. During heat stress, DOC enrichment (20 and 40 mg glucose l-1) increased the relative abundances of diazotrophs by sixfold in X. umbellata and fourfold in P. flava, compared with their counterparts without excess DOC. Our data suggest that labile DOC enrichment and concomitant heat stress could disrupt the nitrogen limitation in octocorals by stimulating diazotroph proliferation. Ultimately, the disruption of nitrogen cycling may further compromise octocoral fitness by destabilizing symbiotic nutrient cycling. Therefore, improving local wastewater facilities to reduce labile DOC input into vulnerable coastal ecosystems may help octocorals cope with ocean warming.
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Affiliation(s)
- Nan Xiang
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen Bremen 28359, Germany
- Section of Polar Biological Oceanography, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Leibniz Center for Tropical Marine Research (ZMT), Bremen 28359, Germany
| | - Achim Meyer
- Leibniz Center for Tropical Marine Research (ZMT), Bremen 28359, Germany
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen Bremen 28359, Germany
| | - Astrid Gärdes
- Section of Polar Biological Oceanography, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
- Leibniz Center for Tropical Marine Research (ZMT), Bremen 28359, Germany
- Hochschule Bremerhaven, Fachbereich 1, An der Karlstadt 8, Bremerhaven 27568, Germany
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Xiang N, Rädecker N, Pogoreutz C, Cárdenas A, Meibom A, Wild C, Gärdes A, Voolstra CR. Presence of algal symbionts affects denitrifying bacterial communities in the sea anemone Aiptasia coral model. ISME COMMUNICATIONS 2022; 2:105. [PMID: 37938763 PMCID: PMC9723753 DOI: 10.1038/s43705-022-00190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2023]
Abstract
The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.
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Affiliation(s)
- Nan Xiang
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany.
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany.
| | - Nils Rädecker
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Center for Advanced Surface Analysis (CASA), Institute of Earth Science, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
| | - Astrid Gärdes
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Hochschule Bremerhaven, Fachbereich 1, An der Karlstadt 8, 27568, Bremerhaven, Germany
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Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022; 16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
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7
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Morrow KM, Pankey MS, Lesser MP. Community structure of coral microbiomes is dependent on host morphology. MICROBIOME 2022; 10:113. [PMID: 35902906 PMCID: PMC9331152 DOI: 10.1186/s40168-022-01308-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities. RESULTS The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community. CONCLUSIONS The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.
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Affiliation(s)
- Kathleen M Morrow
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
- Present address: Thomas Jefferson High School for Science and Technology, 6560 Braddock Rd, Alexandria, VA, 22312, USA
| | - M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Michael P Lesser
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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Glaze TD, Erler DV, Siljanen HMP. Microbially facilitated nitrogen cycling in tropical corals. THE ISME JOURNAL 2022; 16:68-77. [PMID: 34226659 PMCID: PMC8692614 DOI: 10.1038/s41396-021-01038-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023]
Abstract
Tropical scleractinian corals support a diverse assemblage of microbial symbionts. This 'microbiome' possesses the requisite functional diversity to conduct a range of nitrogen (N) transformations including denitrification, nitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Very little direct evidence has been presented to date verifying that these processes are active within tropical corals. Here we use a combination of stable isotope techniques, nutrient uptake calculations and captured metagenomics to quantify rates of nitrogen cycling processes in a selection of tropical scleractinian corals. Denitrification activity was detected in all species, albeit with very low rates, signifying limited importance in holobiont N removal. Relatively greater nitrogen fixation activity confirms that corals are net N importers to reef systems. Low net nitrification activity suggests limited N regeneration capacity; however substantial gross nitrification activity may be concealed through nitrate consumption. Based on nrfA gene abundance and measured inorganic N fluxes, we calculated significant DNRA activity in the studied corals, which has important implications for coral reef N cycling and warrants more targeted investigation. Through the quantification and characterisation of all relevant N-cycling processes, this study provides clarity on the subject of tropical coral-associated biogeochemical N-cycling.
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Affiliation(s)
- Thomas D Glaze
- Centre for Coastal Biogeochemistry Research, School of Environment Science and Engineering, Southern Cross University, Lismore, NSW, Australia.
| | - Dirk V Erler
- Centre for Coastal Biogeochemistry Research, School of Environment Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Henri M P Siljanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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Moynihan MA, Goodkin NF, Morgan KM, Kho PYY, Lopes Dos Santos A, Lauro FM, Baker DM, Martin P. Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef. THE ISME JOURNAL 2022; 16:233-246. [PMID: 34294880 PMCID: PMC8692400 DOI: 10.1038/s41396-021-01054-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The role of diazotrophs in coral physiology and reef biogeochemistry remains poorly understood, in part because N2 fixation rates and diazotrophic community composition have only been jointly analyzed in the tissue of one tropical coral species. We performed field-based 15N2 tracer incubations during nutrient-replete conditions to measure diazotroph-derived nitrogen (DDN) assimilation into three species of scleractinian coral (Pocillopora acuta, Goniopora columna, Platygyra sinensis). Using multi-marker metabarcoding (16S rRNA, nifH, 18S rRNA), we analyzed DNA- and RNA-based communities in coral tissue and skeleton. Despite low N2 fixation rates, DDN assimilation supplied up to 6% of the holobiont's N demand. Active coral-associated diazotrophs were chiefly Cluster I (aerobes or facultative anaerobes), suggesting that oxygen may control coral-associated diazotrophy. Highest N2 fixation rates were observed in the endolithic community (0.20 µg N cm-2 per day). While the diazotrophic community was similar between the tissue and skeleton, RNA:DNA ratios indicate potential differences in relative diazotrophic activity between these compartments. In Pocillopora, DDN was found in endolithic, host, and symbiont compartments, while diazotrophic nifH sequences were only observed in the endolithic layer, suggesting a possible DDN exchange between the endolithic community and the overlying coral tissue. Our findings demonstrate that coral-associated diazotrophy is significant, even in nutrient-rich waters, and suggest that endolithic microbes are major contributors to coral nitrogen cycling on reefs.
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Affiliation(s)
- Molly A Moynihan
- Earth Observatory of Singapore, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore.
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore.
| | - Nathalie F Goodkin
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- Earth Observatory of Singapore, Nanyang Technological University, Singapore, Singapore
- American Museum of Natural History, New York, NY, USA
| | - Kyle M Morgan
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Phyllis Y Y Kho
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | | | - Federico M Lauro
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - David M Baker
- Division for Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong, PR China
- The Swire Institute of Marine Science, University of Hong Kong, Hong Kong, PR China
| | - Patrick Martin
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
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Barreto MM, Ziegler M, Venn A, Tambutté E, Zoccola D, Tambutté S, Allemand D, Antony CP, Voolstra CR, Aranda M. Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata. Front Microbiol 2021; 12:707674. [PMID: 34899619 PMCID: PMC8656159 DOI: 10.3389/fmicb.2021.707674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.
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Affiliation(s)
- Marcelle Muniz Barreto
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | | | - Chakkiath Paul Antony
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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11
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Rädecker N, Pogoreutz C, Gegner HM, Cárdenas A, Perna G, Geißler L, Roth F, Bougoure J, Guagliardo P, Struck U, Wild C, Pernice M, Raina JB, Meibom A, Voolstra CR. Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling. THE ISME JOURNAL 2021; 16:1110-1118. [PMID: 34857934 PMCID: PMC8941099 DOI: 10.1038/s41396-021-01158-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/22/2022]
Abstract
Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.
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Affiliation(s)
- Nils Rädecker
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. .,Department of Biology, University of Konstanz, Konstanz, Germany. .,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Claudia Pogoreutz
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Hagen M Gegner
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Metabolomics Core Technology Platform, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Anny Cárdenas
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gabriela Perna
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Laura Geißler
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Florian Roth
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Faculty of Biological and Environmental Sciences, Tvärminne Zoological Station, University of Helsinki, Helsinki, Finland
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, Australia
| | - Ulrich Struck
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Christian Wild
- Faculty of Biology and Chemistry, Marine Ecology Department, University of Bremen, Bremen, Germany
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - 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, Université de Lausanne, Lausanne, Switzerland
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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12
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Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming. Appl Environ Microbiol 2021; 88:e0188621. [PMID: 34788073 PMCID: PMC8788706 DOI: 10.1128/aem.01886-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms; however, little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. Although bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift toward Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava but decreased by 1 order of magnitude in X. umbellata under excess DOC, likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes based on N availability, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment. IMPORTANCE Octocorals are important members of reef-associated benthic communities that can rapidly replace scleractinian corals as the dominant ecosystem engineers on degraded reefs. Considering the substantial change in the (a)biotic environment that is commonly driving reef degradation, maintaining a dynamic and metabolically diverse microbial community might contribute to octocoral acclimatization. Nitrogen (N) cycling microbes, in particular denitrifying prokaryotes, may support holobiont functioning by limiting internal N availability, but little is known about the identity and (a)biotic drivers of octocoral-associated denitrifiers. Here, we show contrasting dynamics of bacterial communities associated with two common octocoral species, the soft coral Xenia umbellata and the gorgonian Pinnigorgia flava after a 6-week exposure to excess dissolved organic carbon under concomitant warming conditions. The specific responses of denitrifier communities of the two octocoral species aligned with the nutritional status of holobiont members. This suggests a passive regulation based on N availability in the coral holobiont.
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13
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Dubé CE, Ziegler M, Mercière A, Boissin E, Planes S, Bourmaud CAF, Voolstra CR. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun 2021; 12:6402. [PMID: 34737272 PMCID: PMC8568919 DOI: 10.1038/s41467-021-26543-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.
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Affiliation(s)
- C. E. Dubé
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia ,grid.23856.3a0000 0004 1936 8390Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, G1V 0A6 Canada
| | - M. Ziegler
- grid.8664.c0000 0001 2165 8627Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, 35392 Giessen, Germany ,grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia
| | - A. Mercière
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - E. Boissin
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - S. Planes
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. A. -F. Bourmaud
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. R. Voolstra
- grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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14
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Meunier V, Geissler L, Bonnet S, Rädecker N, Perna G, Grosso O, Lambert C, Rodolfo-Metalpa R, Voolstra CR, Houlbrèque F. Microbes support enhanced nitrogen requirements of coral holobionts in a high CO 2 environment. Mol Ecol 2021; 30:5888-5899. [PMID: 34473860 DOI: 10.1111/mec.16163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022]
Abstract
Ocean acidification is posing a threat to calcifying organisms due to the increased energy requirements of calcification under high CO2 conditions. The ability of scleractinian corals to cope with future ocean conditions will thus depend on their ability to fulfil their carbon requirement. However, the primary productivity of coral holobionts is limited by low nitrogen (N) availability in coral reef waters. Here, we employed CO2 seeps of Tutum Bay (Papua New Guinea) as a natural laboratory to understand how coral holobionts offset their increased energy requirements under high CO2 conditions. Our results demonstrate for the first time that under high pCO2 conditions, N assimilation pathways of Pocillopora damicornis are jointly modified. We found that diazotroph-derived N assimilation rates in the Symbiodiniaceae were significantly higher in comparison to an ambient CO2 control site, concomitant with a restructured diazotroph community and the specific prevalence of an alpha-proteobacterium. Further, corals at the high CO2 site also had increased feeding rates on picoplankton and in particular exhibited selective feeding on Synechococcus sp., known to be rich in N. Given the high abundance of picoplankton in oligotrophic waters at large, our results suggest that corals exhibiting flexible diazotrophic communities and capable of exploiting N-rich picoplankton sources to offset their increased N requirements may be able to cope better in a high pCO2 world.
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Affiliation(s)
- Valentine Meunier
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
| | - Laura Geissler
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sophie Bonnet
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Marseille, France
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz, Germany.,Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gabriela Perna
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Olivier Grosso
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, Marseille, France
| | | | - Riccardo Rodolfo-Metalpa
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
| | | | - Fanny Houlbrèque
- Centre IRD Nouméa, UMR ENTROPIE (IRD, Université de La Réunion, CNRS, Université de La Nouvelle-Calédonie, Ifremer), Nouméa, New Caledonia
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15
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El-Khaled YC, Roth F, Rädecker N, Tilstra A, Karcher DB, Kürten B, Jones BH, Voolstra CR, Wild C. Nitrogen fixation and denitrification activity differ between coral- and algae-dominated Red Sea reefs. Sci Rep 2021; 11:11820. [PMID: 34083565 PMCID: PMC8175748 DOI: 10.1038/s41598-021-90204-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
Coral reefs experience phase shifts from coral- to algae-dominated benthic communities, which could affect the interplay between processes introducing and removing bioavailable nitrogen. However, the magnitude of such processes, i.e., dinitrogen (N2) fixation and denitrification levels, and their responses to phase shifts remain unknown in coral reefs. We assessed both processes for the dominant species of six benthic categories (hard corals, soft corals, turf algae, coral rubble, biogenic rock, and reef sands) accounting for > 98% of the benthic cover of a central Red Sea coral reef. Rates were extrapolated to the relative benthic cover of the studied organisms in co-occurring coral- and algae-dominated areas of the same reef. In general, benthic categories with high N2 fixation exhibited low denitrification activity. Extrapolated to the respective reef area, turf algae and coral rubble accounted for > 90% of overall N2 fixation, whereas corals contributed to more than half of reef denitrification. Total N2 fixation was twice as high in algae- compared to coral-dominated areas, whereas denitrification levels were similar. We conclude that algae-dominated reefs promote new nitrogen input through enhanced N2 fixation and comparatively low denitrification. The subsequent increased nitrogen availability could support net productivity, resulting in a positive feedback loop that increases the competitive advantage of algae over corals in reefs that experienced a phase shift.
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Affiliation(s)
- Yusuf C El-Khaled
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany.
| | - Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Baltic Sea Centre, Stockholm University, 10691, Stockholm, Sweden
- Faculty of Biological and Environmental Sciences, Tvärminne Zoological Station, University of Helsinki, 00014, Helsinki, Finland
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Arjen Tilstra
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
| | - Denis B Karcher
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
- Australian National Centre for the Public Awareness of Science, Australian National University, ACT, Canberra, 2601, Australia
| | - Benjamin Kürten
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Project Management Jülich, Jülich Research Centre GmbH, 18069, Rostock, Germany
| | - Burton H Jones
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23995, Saudi Arabia
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, 28359, Bremen, Germany
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16
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Tilstra A, Roth F, El-Khaled YC, Pogoreutz C, Rädecker N, Voolstra CR, Wild C. Relative abundance of nitrogen cycling microbes in coral holobionts reflects environmental nitrate availability. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201835. [PMID: 34109033 PMCID: PMC8170195 DOI: 10.1098/rsos.201835] [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: 10/15/2020] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Recent research suggests that nitrogen (N) cycling microbes are important for coral holobiont functioning. In particular, coral holobionts may acquire bioavailable N via prokaryotic dinitrogen (N2) fixation or remove excess N via denitrification activity. However, our understanding of environmental drivers on these processes in hospite remains limited. Employing the strong seasonality of the central Red Sea, this study assessed the effects of environmental parameters on the proportional abundances of N cycling microbes associated with the hard corals Acropora hemprichii and Stylophora pistillata. Specifically, we quantified changes in the relative ratio between nirS and nifH gene copy numbers, as a proxy for seasonal shifts in denitrification and N2 fixation potential in corals, respectively. In addition, we assessed coral tissue-associated Symbiodiniaceae cell densities and monitored environmental parameters to provide a holobiont and environmental context, respectively. While ratios of nirS to nifH gene copy numbers varied between seasons, they revealed similar seasonal patterns in both coral species, with ratios closely following patterns in environmental nitrate availability. Symbiodiniaceae cell densities aligned with environmental nitrate availability, suggesting that the seasonal shifts in nirS to nifH gene abundance ratios were probably driven by nitrate availability in the coral holobiont. Thereby, our results suggest that N cycling in coral holobionts probably adjusts to environmental conditions by increasing and/or decreasing denitrification and N2 fixation potential according to environmental nitrate availability. Microbial N cycling may, thus, extenuate the effects of changes in environmental nitrate availability on coral holobionts to support the maintenance of the coral-Symbiodiniaceae symbiosis.
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Affiliation(s)
- Arjen Tilstra
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Yusuf C. El-Khaled
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Claudia Pogoreutz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian R. Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
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17
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Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals. THE ISME JOURNAL 2021; 15:1222-1235. [PMID: 33342999 PMCID: PMC8115149 DOI: 10.1038/s41396-020-00845-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 01/29/2023]
Abstract
Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm-2 d-1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.
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18
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Tilstra A, El-Khaled YC, Roth F, Rädecker N, Pogoreutz C, Voolstra CR, Wild C. Denitrification Aligns with N 2 Fixation in Red Sea Corals. Sci Rep 2019; 9:19460. [PMID: 31857601 PMCID: PMC6923481 DOI: 10.1038/s41598-019-55408-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/26/2019] [Indexed: 12/27/2022] Open
Abstract
Denitrification may potentially alleviate excess nitrogen (N) availability in coral holobionts to maintain a favourable N to phosphorous ratio in the coral tissue. However, little is known about the abundance and activity of denitrifiers in the coral holobiont. The present study used the nirS marker gene as a proxy for denitrification potential along with measurements of denitrification rates in a comparative coral taxonomic framework from the Red Sea: Acropora hemprichii, Millepora dichotoma, and Pleuractis granulosa. Relative nirS gene copy numbers associated with the tissues of these common corals were assessed and compared with denitrification rates on the holobiont level. In addition, dinitrogen (N2) fixation rates, Symbiodiniaceae cell density, and oxygen evolution were assessed to provide an environmental context for denitrification. We found that relative abundances of the nirS gene were 16- and 17-fold higher in A. hemprichii compared to M. dichotoma and P. granulosa, respectively. In concordance, highest denitrification rates were measured in A. hemprichii, followed by M. dichotoma and P. granulosa. Denitrification rates were positively correlated with N2 fixation rates and Symbiodiniaceae cell densities. Our results suggest that denitrification may counterbalance the N input from N2 fixation in the coral holobiont, and we hypothesize that these processes may be limited by photosynthates released by the Symbiodiniaceae.
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Affiliation(s)
- Arjen Tilstra
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, 28359, Germany.
| | - Yusuf C El-Khaled
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, 28359, Germany
| | - Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Claudia Pogoreutz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, 28359, Germany
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19
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A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol 2019; 3:1509-1520. [PMID: 31636428 DOI: 10.1038/s41559-019-0999-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and the environment or their hosts - termed the 'holobiont'. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.
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20
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Wada N, Ishimochi M, Matsui T, Pollock FJ, Tang SL, Ainsworth TD, Willis BL, Mano N, Bourne DG. Characterization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus. Sci Rep 2019; 9:14662. [PMID: 31601819 PMCID: PMC6787259 DOI: 10.1038/s41598-019-49651-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 08/29/2019] [Indexed: 01/28/2023] Open
Abstract
Bacterial diversity associated with corals has been studied extensively, however, localization of bacterial associations within the holobiont is still poorly resolved. Here we provide novel insight into the localization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus. In total, 318 and 308 CAMAs were characterized via histological and fluorescent in situ hybridization (FISH) approaches respectively, and shown to be distributed extensively throughout coral tissues collected from five sites in Japan and Australia. The densities of CAMAs within the tissues were negatively correlated with the distance from the coastline (i.e. lowest densities at offshore sites). CAMAs were randomly distributed across the six coral tissue regions investigated. Within each CAMA, bacterial cells had similar morphological characteristics, but bacterial morphologies varied among CAMAs, with at least five distinct types identified. Identifying the location of microorganisms associated with the coral host is a prerequisite for understanding their contributions to fitness. Localization of tissue-specific communities housed within CAMAs is particularly important, as these communities are potentially important contributors to vital metabolic functions of the holobiont.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Nangang, 11529, Taipei, Taiwan
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, 252-0813, Kanagawa, Japan
- AIMS@JCU, Townsville, 4811, QLD, Australia
| | - Mizuki Ishimochi
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, 252-0813, Kanagawa, Japan
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Taeko Matsui
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, 252-0813, Kanagawa, Japan
| | - F Joseph Pollock
- The Nature Conservancy, Caribbean Division, Coral Gables, FL, 33134, USA
- AIMS@JCU, Townsville, 4811, QLD, Australia
- Department of Biology, The Pennsylvania State University, State College, 16802, PA, USA
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Nangang, 11529, Taipei, Taiwan
| | - Tracy D Ainsworth
- School of Biological, Earth and Environmental Science, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Bette L Willis
- College of Science and Engineering, James Cook University, Townsville, 4811, QLD, Australia
- AIMS@JCU, Townsville, 4811, QLD, Australia
| | - Nobuhiro Mano
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, 252-0813, Kanagawa, Japan.
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, 4811, QLD, Australia.
- AIMS@JCU, Townsville, 4811, QLD, Australia.
- Australian Institute of Marine Science, Townsville, 4810, QLD, Australia.
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21
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A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat Microbiol 2019; 4:2090-2100. [DOI: 10.1038/s41564-019-0532-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/05/2019] [Indexed: 11/09/2022]
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Morris LA, Voolstra CR, Quigley KM, Bourne DG, Bay LK. Nutrient Availability and Metabolism Affect the Stability of Coral-Symbiodiniaceae Symbioses. Trends Microbiol 2019; 27:678-689. [PMID: 30987816 DOI: 10.1016/j.tim.2019.03.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/28/2019] [Accepted: 03/13/2019] [Indexed: 01/19/2023]
Abstract
Coral reefs rely upon the highly optimized coral-Symbiodiniaceae symbiosis, making them sensitive to environmental change and susceptible to anthropogenic stress. Coral bleaching is predominantly attributed to photo-oxidative stress, yet nutrient availability and metabolism underpin the stability of symbioses. Recent studies link symbiont proliferation under nutrient enrichment to bleaching; however, the interactions between nutrients and symbiotic stability are nuanced. Here, we demonstrate how bleaching is regulated by the forms and ratios of available nutrients and their impacts on autotrophic carbon metabolism, rather than algal symbiont growth. By extension, historical nutrient conditions mediate host-symbiont compatibility and bleaching tolerance over proximate and evolutionary timescales. Renewed investigations into the coral nutrient metabolism will be required to truly elucidate the cellular mechanisms leading to coral bleaching.
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Affiliation(s)
- Luke A Morris
- AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, Australia; Australian Institute of Marine Science, Townsville, Australia; College of Science and Engineering, James Cook University, Townsville, Australia. https://twitter.com/ReefLuke
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. https://twitter.com/reefgenomics
| | - Kate M Quigley
- AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, Australia; Australian Institute of Marine Science, Townsville, Australia. https://twitter.com/la__cientifica
| | - David G Bourne
- AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, Australia; Australian Institute of Marine Science, Townsville, Australia; College of Science and Engineering, James Cook University, Townsville, Australia
| | - Line K Bay
- AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, Australia; Australian Institute of Marine Science, Townsville, Australia.
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23
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Bernasconi R, Stat M, Koenders A, Huggett MJ. Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont. MICROBIAL ECOLOGY 2019; 77:794-807. [PMID: 30218130 DOI: 10.1007/s00248-018-1255-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/29/2018] [Indexed: 05/12/2023]
Abstract
Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.
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Affiliation(s)
- Rachele Bernasconi
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia.
| | - Michael Stat
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University, Bentley, 6102, Western Australia
- Department of Biological Sciences, Macquarie University, Sydney, 2109, Australia
| | - Annette Koenders
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia
| | - Megan J Huggett
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, Western Australia, 6027, Australia
- School of Environmental and Life Sciences, Faculty of Science, The University of Newcastle, PO Box 127, Ourimbah, New South Wales, 2258, Australia
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Chen J, Shen W, Xu H, Li Y, Luo T. The Composition of Nitrogen-Fixing Microorganisms Correlates With Soil Nitrogen Content During Reforestation: A Comparison Between Legume and Non-legume Plantations. Front Microbiol 2019; 10:508. [PMID: 30930882 PMCID: PMC6427063 DOI: 10.3389/fmicb.2019.00508] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/27/2019] [Indexed: 12/02/2022] Open
Abstract
Numerous reforestation projects have been conducted to improve soil fertility in degraded forests, often causing alterations to the soil microbial communities. However, it remains unclear whether microbial functional groups are affected and how these groups correlate with an increase in the nutrient contents during reforestation. We investigated the abundance and composition of free-living nitrogen-fixing microorganisms (diazotrophs) by quantifying and sequencing the marker gene nifH in bulk soils from five reforestation approaches, including legumes and non-legumes, in subtropical China. The relationships between diazotrophic community attributes and soil nitrogen (N) content [NO3 -, NH4 +, and microbial biomass N (MBN)] were examined under various approaches. Abundance of diazotrophs was highest in the native tree plantation (Schima spp. and Michelia macclurei) and Acacia mangium monoculture (AM), and lowest in the Pinus massoniana monoculture. The diazotrophic abundance correlated positively with soil organic matter and water content while there was a negative correlation to pH. The composition of diazotrophic community differed significantly among the five reforestation approaches examined and was closely correlated with variations in soil pH, NH4 + and water content. Diazotrophic community composition was closely related to soil NH4 + content, whereas abundance was not. The AM contained higher NH4 +, NO3 - and MBN contents than the other reforestation approaches, which may be associated with the indicator species of diazotrophs (Actinobacteria, Proteobacteria, and Firmicutes). However, there were more indicator species of Proteobacteria in the mixed Acacia plantation (Acacia mangium and Acacia crassicarpa) than in AM, which might have contributed to the remarkedly lower N content compared to AM. Overall, the soil N content under reforestation appeared to be more related to the composition of diazotroph community than to the abundance of diazotrophs.
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Affiliation(s)
- Jie Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Weijun Shen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Han Xu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yide Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Tushou Luo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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25
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Chen J, Shen W, Xu H, Li Y, Luo T. The Composition of Nitrogen-Fixing Microorganisms Correlates With Soil Nitrogen Content During Reforestation: A Comparison Between Legume and Non-legume Plantations. Front Microbiol 2019. [DOI: 10.10.3389/fmicb.2019.00508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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26
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Tilstra A, van Hoytema N, Cardini U, Bednarz VN, Rix L, Naumann MS, Al-Horani FA, Wild C. Effects of Water Column Mixing and Stratification on Planktonic Primary Production and Dinitrogen Fixation on a Northern Red Sea Coral Reef. Front Microbiol 2018; 9:2351. [PMID: 30327648 PMCID: PMC6174798 DOI: 10.3389/fmicb.2018.02351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/12/2018] [Indexed: 11/13/2022] Open
Abstract
The northern Red Sea experiences strong annual differences in environmental conditions due to its relative high-latitude location for coral reefs. This allows the study of regulatory effects by key environmental parameters (i.e., temperature, inorganic nutrient, and organic matter concentrations) on reef primary production and dinitrogen (N2) fixation, but related knowledge is scarce. Therefore, this study measured environmental parameters, primary production and N2 fixation of phytoplankton groups in the water overlying a coral reef in the Gulf of Aqaba. To this end, we used a comparative approach between mixed and stratified water column scenarios in a full year of seasonal observations. Findings revealed that inorganic nutrient concentrations were significantly higher in the mixed compared to the stratified period. While gross photosynthesis and N2 fixation rates remained similar, net photosynthesis decreased from mixed to stratified period. Net heterotrophic activity of the planktonic community increased significantly during the stratified compared to the mixed period. While inorganic nitrogen (N) availability was correlated with net photosynthesis over the year, N2 fixation only correlated with N availability during the mixed period. This emphasizes the complexity of planktonic trophodynamics in northern Red Sea coral reefs. Comparing mixed and stratified planktonic N2 fixation rates with those of benthic organisms and substrates revealed a close seasonal activity similarity between free-living pelagic and benthic diazotrophs. During the mixed period, N2 fixation potentially contributed up to 3% of planktonic primary production N demand. This contribution increased by ca. one order of magnitude to 21% during the stratified period. Planktonic N2 fixation is likely a significant N source for phytoplankton to maintain high photosynthesis under oligotrophic conditions in coral reefs, especially during stratified conditions.
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Affiliation(s)
- Arjen Tilstra
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Nanne van Hoytema
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Ulisse Cardini
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research, Bremen, Germany
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Vanessa N. Bednarz
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research, Bremen, Germany
- Centre Scientifique de Monaco, Monaco, Monaco
| | - Laura Rix
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research, Bremen, Germany
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Malik S. Naumann
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | | | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
- Coral Reef Ecology Group, Leibniz Centre for Tropical Marine Research, Bremen, Germany
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27
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? ZOOLOGY 2018; 127:1-19. [DOI: 10.1016/j.zool.2018.02.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
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28
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Pogoreutz C, Rädecker N, Cárdenas A, Gärdes A, Wild C, Voolstra CR. Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome. Ecol Evol 2018; 8:2240-2252. [PMID: 29468040 PMCID: PMC5817147 DOI: 10.1002/ece3.3830] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/11/2017] [Accepted: 12/17/2017] [Indexed: 01/04/2023] Open
Abstract
The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora-associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.
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Affiliation(s)
- Claudia Pogoreutz
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Marine Ecology GroupFaculty of Biology and ChemistryUniversity of BremenBremenGermany
- Coral Reef Ecology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Nils Rädecker
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Anny Cárdenas
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Tropical Marine Microbiology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Astrid Gärdes
- Tropical Marine Microbiology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Christian Wild
- Marine Ecology GroupFaculty of Biology and ChemistryUniversity of BremenBremenGermany
- Coral Reef Ecology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Christian R. Voolstra
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef. ISME JOURNAL 2017; 12:813-824. [PMID: 29222444 DOI: 10.1038/s41396-017-0008-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/15/2017] [Accepted: 10/20/2017] [Indexed: 12/30/2022]
Abstract
Diazotrophs, both Bacteria and Archaea, capable of fixing nitrogen (N2), are present in the tissues and mucous, of corals and can supplement the coral holobiont nitrogen budget with fixed nitrogen (N) in the form of ammonia (NH3). Stylophora pistillata from Heron Island on the Great Barrier Reef collected at 5 and 15 m, and experimentally manipulated in the laboratory, showed that the rates of net photosynthesis, steady state quantum yields of photosystem II (PSII) fluorescence (∆Fv/Fm') and calcification varied based on irradiance as expected. Rates of N2 fixation were, however, invariant across treatments while the amount of fixed N contributing to Symbiodinium spp. N demand is irradiance dependent. Additionally, both the Symbiodinium and diazotrophic communities are significantly different based on depth, and novel Cluster V nifH gene phylotypes, which are not known to fix nitrogen, were recovered. A functional analysis using PICRUSt also showed that shallow corals were enriched in genes involved in nitrogen metabolism, and N2 fixation specifically. Corals have evolved a number of strategies to derive nitrogen from organic (e.g., heterotrophic feeding) and inorganic sources (e.g., N2 fixation) to maintain critical pathways such as protein synthesis to succeed ecologically in nitrogen-limited habitats.
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Association of coral algal symbionts with a diverse viral community responsive to heat shock. BMC Microbiol 2017; 17:174. [PMID: 28818037 PMCID: PMC5561611 DOI: 10.1186/s12866-017-1084-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Stony corals provide the structural foundation of coral reef ecosystems and are termed holobionts given they engage in symbioses, in particular with photosynthetic dinoflagellates of the genus Symbiodinium. Besides Symbiodinium, corals also engage with bacteria affecting metabolism, immunity, and resilience of the coral holobiont, but the role of associated viruses is largely unknown. In this regard, the increase of studies using RNA sequencing (RNA-Seq) to assess gene expression provides an opportunity to elucidate viral signatures encompassed within the data via careful delineation of sequence reads and their source of origin. RESULTS Here, we re-analyzed an RNA-Seq dataset from a cultured coral symbiont (Symbiodinium microadriaticum, Clade A1) across four experimental treatments (control, cold shock, heat shock, dark shock) to characterize associated viral diversity, abundance, and gene expression. Our approach comprised the filtering and removal of host sequence reads, subsequent phylogenetic assignment of sequence reads of putative viral origin, and the assembly and analysis of differentially expressed viral genes. About 15.46% (123 million) of all sequence reads were non-host-related, of which <1% could be classified as archaea, bacteria, or virus. Of these, 18.78% were annotated as virus and comprised a diverse community consistent across experimental treatments. Further, non-host related sequence reads assembled into 56,064 contigs, including 4856 contigs of putative viral origin that featured 43 differentially expressed genes during heat shock. The differentially expressed genes included viral kinases, ubiquitin, and ankyrin repeat proteins (amongst others), which are suggested to help the virus proliferate and inhibit the algal host's antiviral response. CONCLUSION Our results suggest that a diverse viral community is associated with coral algal endosymbionts of the genus Symbiodinium, which prompts further research on their ecological role in coral health and resilience.
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