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Hamamoto K, Mizuyama M, Nishijima M, Maeda A, Gibu K, Poliseno A, Iguchi A, Reimer JD. Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan. ENVIRONMENTAL MICROBIOME 2024; 19:54. [PMID: 39080706 PMCID: PMC11290285 DOI: 10.1186/s40793-024-00594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions. RESULTS The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation. CONCLUSION Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.
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Affiliation(s)
- Kohei Hamamoto
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
- Department of Health Informatics, Faculty of Human Health Sciences, Meio University, Nago, Okinawa, 905-8585, Japan
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Ayumi Maeda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-Conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
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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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Galbraith E, Convertino M. The Eco-Evo Mandala: Simplifying Bacterioplankton Complexity into Ecohealth Signatures. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1471. [PMID: 34828169 PMCID: PMC8625105 DOI: 10.3390/e23111471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/30/2021] [Accepted: 11/05/2021] [Indexed: 12/24/2022]
Abstract
The microbiome emits informative signals of biological organization and environmental pressure that aid ecosystem monitoring and prediction. Are the many signals reducible to a habitat-specific portfolio that characterizes ecosystem health? Does an optimally structured microbiome imply a resilient microbiome? To answer these questions, we applied our novel Eco-Evo Mandala to bacterioplankton data from four habitats within the Great Barrier Reef, to explore how patterns in community structure, function and genetics signal habitat-specific organization and departures from theoretical optimality. The Mandala revealed communities departing from optimality in habitat-specific ways, mostly along structural and functional traits related to bacterioplankton abundance and interaction distributions (reflected by ϵ and λ as power law and exponential distribution parameters), which are not linearly associated with each other. River and reef communities were similar in their relatively low abundance and interaction disorganization (low ϵ and λ) due to their protective structured habitats. On the contrary, lagoon and estuarine inshore reefs appeared the most disorganized due to the ocean temperature and biogeochemical stress. Phylogenetic distances (D) were minimally informative in characterizing bacterioplankton organization. However, dominant populations, such as Proteobacteria, Bacteroidetes, and Cyanobacteria, were largely responsible for community patterns, being generalists with a large functional gene repertoire (high D) that increases resilience. The relative balance of these populations was found to be habitat-specific and likely related to systemic environmental stress. The position on the Mandala along the three fundamental traits, as well as fluctuations in this ecological state, conveys information about the microbiome's health (and likely ecosystem health considering bacteria-based multitrophic dependencies) as divergence from the expected relative optimality. The Eco-Evo Mandala emphasizes how habitat and the microbiome's interaction network topology are first- and second-order factors for ecosystem health evaluation over taxonomic species richness. Unhealthy microbiome communities and unbalanced microbes are identified not by macroecological indicators but by mapping their impact on the collective proportion and distribution of interactions, which regulates the microbiome's ecosystem function.
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Affiliation(s)
- Elroy Galbraith
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Matteo Convertino
- bluEco Lab, Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
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Cheutin MC, Villéger S, Hicks CC, Robinson JPW, Graham NAJ, Marconnet C, Restrepo CXO, Bettarel Y, Bouvier T, Auguet JC. Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts. Microorganisms 2021; 9:microorganisms9081711. [PMID: 34442789 PMCID: PMC8398123 DOI: 10.3390/microorganisms9081711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; p = 0.001), especially in herbivorous fishes (R2 = 0.07; p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.
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Affiliation(s)
- Marie-Charlotte Cheutin
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
- Correspondence:
| | - Sébastien Villéger
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Christina C. Hicks
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - James P. W. Robinson
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - Nicholas A. J. Graham
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - Clémence Marconnet
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Claudia Ximena Ortiz Restrepo
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Yvan Bettarel
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Thierry Bouvier
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Jean-Christophe Auguet
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
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Vanwonterghem I, Webster NS. Coral Reef Microorganisms in a Changing Climate. iScience 2020; 23:100972. [PMID: 32208346 PMCID: PMC7096749 DOI: 10.1016/j.isci.2020.100972] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 01/09/2023] Open
Abstract
Coral reefs are one of the most diverse and productive ecosystems on the planet, yet they have suffered tremendous losses due to anthropogenic disturbances and are predicted to be one of the most adversely affected habitats under future climate change conditions. Coral reefs can be viewed as microbially driven ecosystems that rely on the efficient capture, retention, and recycling of nutrients in order to thrive in oligotrophic waters. Microorganisms play vital roles in maintaining holobiont health and ecosystem resilience under environmental stress; however, they are also key players in positive feedback loops that intensify coral reef decline, with cascading effects on biogeochemical cycles and marine food webs. There is an urgent need to develop a fundamental understanding of the complex microbial interactions within coral reefs and their role in ecosystem acclimatization, and it is important to include microorganisms in reef conservation in order to secure a future for these unique environments.
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Affiliation(s)
- Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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Ezzat L, Lamy T, Maher RL, Munsterman KS, Landfield KM, Schmeltzer ER, Clements CS, Vega Thurber RL, Burkepile DE. Parrotfish predation drives distinct microbial communities in reef-building corals. Anim Microbiome 2020; 2:5. [PMID: 33500004 PMCID: PMC7807759 DOI: 10.1186/s42523-020-0024-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Coral-associated microbial communities are sensitive to multiple environmental and biotic stressors that can lead to dysbiosis and mortality. Although the processes contributing to these microbial shifts remain inadequately understood, a number of potential mechanisms have been identified. For example, predation by various corallivore species, including ecologically-important taxa such as parrotfishes, may disrupt coral microbiomes via bite-induced transmission and/or enrichment of potentially opportunistic bacteria. Here, we used a combination of mesocosm experiments and field-based observations to investigate whether parrotfish corallivory can alter coral microbial assemblages directly and to identify the potentially relevant pathways (e.g. direct transmission) that may contribute to these changes. RESULTS Our mesocosm experiment demonstrated that predation by the parrotfish Chlorurus spilurus on Porites lobata corals resulted in a 2-4x increase in bacterial alpha diversity of the coral microbiome and a shift in bacterial community composition after 48 h. These changes corresponded with greater abundance of both potentially beneficial (i.e. Oceanospirillum) and opportunistic bacteria (i.e. Flammeovirgaceae, Rhodobacteraceae) in predated compared to mechanically wounded corals. Importantly, many of these taxa were detectable in C. spilurus mouths, but not in corals prior to predation. When we sampled bitten and unbitten corals in the field, corals bitten by parrotfishes exhibited 3x greater microbial richness and a shift in community composition towards greater abundance of both potential beneficial symbionts (i.e. Ruegeria) and bacterial opportunists (i.e. Rhodospiralles, Glaciecola). Moreover, we observed 4x greater community variability in naturally bitten vs. unbitten corals, a potential indicator of dysbiosis. Interestingly, some of the microbial taxa detected in naturally bitten corals, but not unbitten colonies, were also detected in parrotfish mouths. CONCLUSIONS Our findings suggest that parrotfish corallivory may represent an unrecognized route of bacterial transmission and/or enrichment of rare and distinct bacterial taxa, both of which could impact coral microbiomes and health. More broadly, we highlight how underappreciated pathways, such as corallivory, may contribute to dysbiosis within reef corals, which will be critical for understanding and predicting coral disease dynamics as reefs further degrade.
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Affiliation(s)
- Leïla Ezzat
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Thomas Lamy
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Rebecca L Maher
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Katrina S Munsterman
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Kaitlyn M Landfield
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Cody S Clements
- School of Biological Sciences and Aquatic Chemical Ecology Center, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Deron E Burkepile
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
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Tebbett SB, Bellwood DR. Algal turf sediments on coral reefs: what's known and what's next. MARINE POLLUTION BULLETIN 2019; 149:110542. [PMID: 31542595 DOI: 10.1016/j.marpolbul.2019.110542] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Algal turfs are likely to rise in prominence on coral reefs in the Anthropocene. In these ecosystems the sediments bound within algal turfs will shape ecosystem functions and the services humanity can obtain from reefs. However, while interest is growing in the role of algal turf sediments, studies remain limited. In this review we provide an overview of our knowledge to-date concerning algal turf sediments on coral reefs. Specifically, we highlight what algal turf sediments are, their role in key ecosystem processes, the potential importance of algal turf sediments on Anthropocene reefs, and key knowledge gaps for future research. The evidence suggests that the management of algal turf sediments will be critically important if we are to sustain key functions and services on highly-altered, Anthropocene coral reef configurations.
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Affiliation(s)
- Sterling B Tebbett
- ARC Centre of Excellence for Coral Reef Studies, College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia.
| | - David R Bellwood
- ARC Centre of Excellence for Coral Reef Studies, College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
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