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Silva DP, Villela HDM, Santos HF, Duarte GAS, Ribeiro JR, Ghizelini AM, Vilela CLS, Rosado PM, Fazolato CS, Santoro EP, Carmo FL, Ximenes DS, Soriano AU, Rachid CTCC, Vega Thurber RL, Peixoto RS. Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites. MICROBIOME 2021; 9:118. [PMID: 34020712 PMCID: PMC8138999 DOI: 10.1186/s40168-021-01041-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/22/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities. RESULTS The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome. CONCLUSIONS Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.
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Affiliation(s)
- Denise P Silva
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Helena D M Villela
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Henrique F Santos
- Department of Marine Biology, Fluminense Federal University (UFF), Niterói, Brazil
| | - Gustavo A S Duarte
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - José Roberto Ribeiro
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Angela M Ghizelini
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Caren L S Vilela
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Phillipe M Rosado
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carolline S Fazolato
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Erika P Santoro
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Flavia L Carmo
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Dalton S Ximenes
- Processes Laboratory, Leopoldo Américo Miguez de Mello Research Center (CENPES), Petrobras, Rio de Janeiro, Brazil
| | - Adriana U Soriano
- Environmental Treatments, Wastes and Water Resources, Leopoldo Américo Miguez de Mello Research Center (CENPES), Petrobras, Rio de Janeiro, Brazil
| | - Caio T C C Rachid
- LABEM, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Rebecca L Vega Thurber
- Department of Microbiology, Oregon State University, Nash Hall 226, OSU, Corvallis, OR, 97331, USA.
| | - Raquel S Peixoto
- LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Marchese P, Garzoli L, Young R, Allcock L, Barry F, Tuohy M, Murphy M. Fungi populate deep-sea coral gardens as well as marine sediments in the Irish Atlantic Ocean. Environ Microbiol 2021; 23:4168-4184. [PMID: 33939869 DOI: 10.1111/1462-2920.15560] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/06/2021] [Accepted: 05/02/2021] [Indexed: 02/06/2023]
Abstract
Fungi populate deep Oceans in extreme habitats characterized by high hydrostatic pressure, low temperature and absence of sunlight. Marine fungi are potential major contributors to biogeochemical events, critical for marine communities and food web equilibrium under climate change conditions and a valuable source of novel extremozymes and small molecules. Despite their ecophysiological and biotechnological relevance, fungal deep-sea biodiversity has not yet been thoroughly characterized. In this study, we describe the culturable mycobiota associated with the deepest margin of the European Western Continental Shelf: sediments sampled at the Porcupine Bank and deep-water corals and sponges sampled in the Whittard Canyon. Eighty-seven strains were isolated, belonging to 43 taxa and mainly Ascomycota. Ten species and four genera were detected for the first time in the marine environment and a possible new species of Arachnomyces was isolated from sediments. The genera Cladosporium and Penicillium were the most frequent and detected on both substrates, followed by Candida and Emericellopsis. Our results showed two different fungal communities: sediment-associated taxa which were predominantly saprotrophic and animal-associated taxa which were predominantly symbiotic. This survey supports selective fungal biodiversity in the deep North Atlantic, encouraging further mycological studies on cold water coral gardens, often overexploited marine habitats.
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Affiliation(s)
- Pietro Marchese
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Laura Garzoli
- MEG-Molecular Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, 28922, Italy
| | - Ryan Young
- Martin Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Louise Allcock
- Martin Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Frank Barry
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Maria Tuohy
- Molecular Glycobiotechnology, School of Natural Sciences, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Mary Murphy
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, H91TK33, Ireland
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Doering T, Wall M, Putchim L, Rattanawongwan T, Schroeder R, Hentschel U, Roik A. Towards enhancing coral heat tolerance: a "microbiome transplantation" treatment using inoculations of homogenized coral tissues. MICROBIOME 2021; 9:102. [PMID: 33957989 PMCID: PMC8103578 DOI: 10.1186/s40168-021-01053-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/18/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding. RESULTS Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context. CONCLUSIONS Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. Video abstract.
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Affiliation(s)
- Talisa Doering
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Marlene Wall
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Lalita Putchim
- Phuket Marine Biological Center (PMBC), Phuket, Thailand
| | | | | | - Ute Hentschel
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
| | - Anna Roik
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany.
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Michán C, Blasco J, Alhama J. High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments. Microb Biotechnol 2021; 14:870-885. [PMID: 33559398 PMCID: PMC8085945 DOI: 10.1111/1751-7915.13763] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
| | - Julián Blasco
- Department of Ecology and Coastal ManagementICMAN‐CSICCampus Rio San PedroPuerto Real (Cádiz)E‐11510Spain
| | - José Alhama
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
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Antwis RE, Beresford NA, Jackson JA, Fawkes R, Barnett CL, Potter E, Walker L, Gaschak S, Wood MD. Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone. J Anim Ecol 2021; 90:2172-2187. [PMID: 33901301 DOI: 10.1111/1365-2656.13507] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/11/2021] [Indexed: 12/19/2022]
Abstract
Environmental impacts of the 1986 Chernobyl Nuclear Power Plant accident are much debated, but the effects of radiation on host microbiomes have received little attention to date. We present the first analysis of small mammal gut microbiomes from the Chernobyl Exclusion Zone in relation to total absorbed dose rate, including both caecum and faeces samples. We provide novel evidence that host species determines fungal community composition, and that associations between microbiome (both bacterial and fungal) communities and radiation exposure vary between host species. Using ambient versus total weighted absorbed dose rates in analyses produced different results, with the latter more robust for interpreting microbiome changes at the individual level. We found considerable variation between results for faecal and gut samples of bank voles, suggesting faecal samples are not an accurate indicator of gut composition. Associations between radiation exposure and microbiome composition of gut samples were not robust against geographical variation, although we identified families of bacteria (Lachnospiraceae and Muribaculaceae) and fungi (Steccherinaceae and Strophariaceae) in the guts of bank voles that may serve as biomarkers of radiation exposure. Further studies considering a range of small mammal species are needed to establish the robustness of these potential biomarkers.
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Affiliation(s)
- Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nicholas A Beresford
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Joseph A Jackson
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ross Fawkes
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Catherine L Barnett
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Elaine Potter
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Lee Walker
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Sergey Gaschak
- Chornobyl Center for Nuclear Safety, Radioactive Waste and Radioecology, International Radioecology Laboratory, Slavutych, Ukraine
| | - Michael D Wood
- School of Science, Engineering and Environment, University of Salford, Salford, UK
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Mutalipassi M, Riccio G, Mazzella V, Galasso C, Somma E, Chiarore A, de Pascale D, Zupo V. Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives. Mar Drugs 2021; 19:227. [PMID: 33923826 PMCID: PMC8074062 DOI: 10.3390/md19040227] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023] Open
Abstract
Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.
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Affiliation(s)
- Mirko Mutalipassi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Gennaro Riccio
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Mazzella
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Christian Galasso
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Emanuele Somma
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri, 34127 Trieste, Italy;
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
| | - Antonia Chiarore
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy;
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Zupo
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
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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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Su H, Xiao Z, Yu K, Zhang Q, Lu C, Wang G, Wang Y, Liang J, Huang W, Huang X, Wei F. High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals. Int J Mol Sci 2021; 22:ijms22073523. [PMID: 33805379 PMCID: PMC8037212 DOI: 10.3390/ijms22073523] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/08/2023] Open
Abstract
β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.
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Affiliation(s)
- Hongfei Su
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Zhenlun Xiao
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China
- Correspondence:
| | - Qi Zhang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Chunrong Lu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Guanghua Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Yinghui Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Wen Huang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Xueyong Huang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Fen Wei
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
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Keller-Costa T, Lago-Lestón A, Saraiva JP, Toscan R, Silva SG, Gonçalves J, Cox CJ, Kyrpides N, Nunes da Rocha U, Costa R. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. MICROBIOME 2021; 9:72. [PMID: 33766108 PMCID: PMC7993494 DOI: 10.1186/s40168-021-01031-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/08/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. RESULTS Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system. CONCLUSIONS This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.
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Affiliation(s)
- T. Keller-Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- División de Biología Experimental y Aplicada (DBEA), Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carr. Ensenada-Tijuana 3918, Zona Playitas, C.P 22860 Ensenada, Baja California Mexico
| | - J. P. Saraiva
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Toscan
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - S. G. Silva
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - J. Gonçalves
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - C. J. Cox
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - N. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - U. Nunes da Rocha
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
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Fox MD, Nelson CE, Oliver TA, Quinlan ZA, Remple K, Glanz J, Smith JE, Putnam HM. Differential resistance and acclimation of two coral species to chronic nutrient enrichment reflect life‐history traits. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Michael D. Fox
- Center for Marine Biodiversity and Conservation Scripps Institution of Oceanography University of California San Diego San Diego CA USA
| | - Craig E. Nelson
- Department of Oceanography and Sea Grant College Program Center for Microbial Oceanography: Research and Education University of Hawai‘i at Mānoa Honolulu HI USA
| | - Thomas A. Oliver
- Pacific Islands Fisheries Science Center NOAA Inouye Regional Center Honolulu HI USA
| | - Zachary A. Quinlan
- Department of Oceanography and Sea Grant College Program Center for Microbial Oceanography: Research and Education University of Hawai‘i at Mānoa Honolulu HI USA
- Department of Biology San Diego State University San Diego CA USA
| | - Kristina Remple
- Department of Oceanography and Sea Grant College Program Center for Microbial Oceanography: Research and Education University of Hawai‘i at Mānoa Honolulu HI USA
| | - Jess Glanz
- Department of Biology California State University Northridge Northridge CA USA
| | - Jennifer E. Smith
- Center for Marine Biodiversity and Conservation Scripps Institution of Oceanography University of California San Diego San Diego CA USA
| | - Hollie M. Putnam
- Department of Biological Sciences University of Rhode Island Kingston RI USA
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Rodríguez-Gómez C, Durán-Riveroll LM, Okolodkov YB, Oliart-Ros RM, García-Casillas AM, Cembella AD. Diversity of Bacterioplankton and Bacteriobenthos from the Veracruz Reef System, Southwestern Gulf of Mexico. Microorganisms 2021; 9:619. [PMID: 33802890 PMCID: PMC8002828 DOI: 10.3390/microorganisms9030619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.
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Affiliation(s)
- Citlali Rodríguez-Gómez
- Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, Veracruz 91897, Mexico; (C.R.-G.); (R.M.O.-R.)
| | - Lorena María Durán-Riveroll
- CONACYT—Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Tijuana-Ensenada 3918, Ensenada 22860, Baja California, Mexico
- Alfred-Wegener-Institut, Helmholtz Zentrum für Polar-und Meeresforschung, 27570 Bremerhaven, Germany
| | - Yuri B. Okolodkov
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Mar Mediterráneo 314, Fracc. Costa Verde, Boca del Río 94294, Veracruz, Mexico;
| | - Rosa María Oliart-Ros
- Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, Veracruz 91897, Mexico; (C.R.-G.); (R.M.O.-R.)
| | | | - Allan D. Cembella
- Alfred-Wegener-Institut, Helmholtz Zentrum für Polar-und Meeresforschung, 27570 Bremerhaven, Germany
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Putnam HM. Avenues of reef-building coral acclimatization in response to rapid environmental change. J Exp Biol 2021; 224:224/Suppl_1/jeb239319. [DOI: 10.1242/jeb.239319] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABSTRACT
The swiftly changing climate presents a challenge to organismal fitness by creating a mismatch between the current environment and phenotypes adapted to historic conditions. Acclimatory mechanisms may be especially crucial for sessile benthic marine taxa, such as reef-building corals, where climate change factors including ocean acidification and increasing temperature elicit strong negative physiological responses such as bleaching, disease and mortality. Here, within the context of multiple stressors threatening marine organisms, I describe the wealth of metaorganism response mechanisms to rapid ocean change and the ontogenetic shifts in organism interactions with the environment that can generate plasticity. I then highlight the need to consider the interactions of rapid and evolutionary responses in an adaptive (epi)genetic continuum. Building on the definitions of these mechanisms and continuum, I also present how the interplay of the microbiome, epigenetics and parental effects creates additional avenues for rapid acclimatization. To consider under what conditions epigenetic inheritance has a more substantial role, I propose investigation into the offset of timing of gametogenesis leading to different environmental integration times between eggs and sperm and the consequences of this for gamete epigenetic compatibility. Collectively, non-genetic, yet heritable phenotypic plasticity will have significant ecological and evolutionary implications for sessile marine organism persistence under rapid climate change. As such, reef-building corals present ideal and time-sensitive models for further development of our understanding of adaptive feedback loops in a multi-player (epi)genetic continuum.
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Affiliation(s)
- Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
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63
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Vilela CLS, Villela HDM, Duarte GAS, Santoro EP, Rachid CTCC, Peixoto RS. Estrogen induces shift in abundances of specific groups of the coral microbiome. Sci Rep 2021; 11:2767. [PMID: 33531587 PMCID: PMC7854615 DOI: 10.1038/s41598-021-82387-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Synthetic estrogens such as ethinylestradiol (EE2) are persistent micropollutants that are not effectively removed from wastewater by conventional treatments. These contaminants are released into waterbodies, where they disrupt endocrine systems of organisms and cause harmful effects such as feminization, infertility, reproduction problems and genital malformations. The consequences of this pollution for key marine ecosystems such as coral reefs and their associated microbiomes are underexplored. We evaluated the effects of EE2 concentrations of 100 ng L-1 and 100 µg L-1 on the coral metaorganism Mussismilia harttii. The results indicated no effects on visible bleaching or Fv/Fm ratios in the corals during a 17-day microcosm experiment. However, next-generation sequencing of 16S rDNA revealed a statistically significant effect of high EE2 concentrations on OTU richness, and shifts in specific microbial groups after treatments with or without EE2. These groups might be bioindicators of early shifts in the metaorganism composition caused by EE2 contamination.
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Affiliation(s)
- Caren L S Vilela
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Helena D M Villela
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo A S Duarte
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Erika P Santoro
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Caio T C C Rachid
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel S Peixoto
- Department of General Microbiology, Paulo de Goes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuval, Saudi Arabia.
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64
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Lawson CA, Raina JB, Deschaseaux E, Hrebien V, Possell M, Seymour JR, Suggett DJ. Heat stress decreases the diversity, abundance and functional potential of coral gas emissions. GLOBAL CHANGE BIOLOGY 2021; 27:879-891. [PMID: 33253484 DOI: 10.1111/gcb.15446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/13/2020] [Accepted: 10/29/2020] [Indexed: 06/12/2023]
Abstract
Terrestrial ecosystems emit large quantities of biogenic volatile organic compounds (BVOCs), many of which play important roles in abiotic stress responses, pathogen and grazing defences, inter- and intra-species communications, and climate regulation. Conversely, comparatively little is known about the diversity and functional potential of BVOCs produced in the marine environment, especially in highly productive coral reefs. Here we describe the first 'volatilomes' of two common reef-building corals, Acropora intermedia and Pocillopora damicornis, and how the functional potential of their gaseous emissions is altered by heat stress events that are driving rapid deterioration of coral reef ecosystems worldwide. A total of 87 BVOCs were detected from the two species and the chemical richness of both coral volatilomes-particularly the chemical classes of alkanes and carboxylic acids-decreased during heat stress by 41% and 62% in A. intermedia and P. damicornis, respectively. Across both coral species, the abundance of individual compounds changed significantly during heat stress, with the majority (>86%) significantly decreasing compared to control conditions. Additionally, almost 60% of the coral volatilome (or 52 BVOCs) could be assigned to four key functional groups based on their activities in other species or systems, including stress response, chemical signalling, climate regulation and antimicrobial activity. The total number of compounds assigned to these functions decreased significantly under heat stress for both A. intermedia (by 35%) and P. damicornis (by 64%), with most dramatic losses found for climatically active BVOCs in P. damicornis and antimicrobial BVOCs in A. intermedia. Together, our observations suggest that future heat stress events predicted for coral reefs will reduce the diversity, quantity and functional potential of BVOCs emitted by reef-building corals, potentially further compromising the healthy functioning of these ecosystems.
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Affiliation(s)
- Caitlin A Lawson
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
- School of Environment and Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Elisabeth Deschaseaux
- Centre for Coastal Biogeochemistry, Southern Cross University, Lismore, NSW, Australia
| | - Victoria Hrebien
- Centre for Coastal Biogeochemistry, Southern Cross University, Lismore, NSW, Australia
| | - Malcolm Possell
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
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Tracing the Trophic Plasticity of the Coral-Dinoflagellate Symbiosis Using Amino Acid Compound-Specific Stable Isotope Analysis. Microorganisms 2021; 9:microorganisms9010182. [PMID: 33466994 PMCID: PMC7830491 DOI: 10.3390/microorganisms9010182] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 12/21/2022] Open
Abstract
The association between corals and photosynthetic dinoflagellates is one of the most well-known nutritional symbioses, but nowadays it is threatened by global changes. Nutritional exchanges are critical to understanding the performance of this symbiosis under stress conditions. Here, compound-specific δ15N and δ13C values of amino acids (δ15NAA and δ13CAA) were assessed in autotrophic, mixotrophic and heterotrophic holobionts as diagnostic tools to follow nutritional interactions between the partners. Contrary to what was expected, heterotrophy was mainly traced through the δ15N of the symbiont’s amino acids (AAs), suggesting that symbionts directly profit from host heterotrophy. The trophic index (TP) ranged from 1.1 to 2.3 from autotrophic to heterotrophic symbionts. In addition, changes in TP across conditions were more significant in the symbionts than in the host. The similar δ13C-AAs signatures of host and symbionts further suggests that symbiont-derived photosynthates are the main source of carbon for AAs synthesis. Symbionts, therefore, appear to be a key component in the AAs biosynthetic pathways, and might, via this obligatory function, play an essential role in the capacity of corals to withstand environmental stress. These novel findings highlight important aspects of the nutritional exchanges in the coral–dinoflagellates symbiosis. In addition, they feature δ15NAA as a useful tool for studies regarding the nutritional exchanges within the coral–symbiodiniaceae symbiosis.
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66
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Boilard A, Dubé CE, Gruet C, Mercière A, Hernandez-Agreda A, Derome N. Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont. Microorganisms 2020; 8:microorganisms8111682. [PMID: 33138319 PMCID: PMC7692791 DOI: 10.3390/microorganisms8111682] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.
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Affiliation(s)
- Aurélie Boilard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Caroline E. Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA;
- Correspondence: (C.E.D.); (N.D.)
| | - Cécile Gruet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
| | - Alexandre Mercière
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan CEDEX, France;
- Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea, French Polynesia
| | | | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.B.); (C.G.)
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Correspondence: (C.E.D.); (N.D.)
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Maher RL, Schmeltzer ER, Meiling S, McMinds R, Ezzat L, Shantz AA, Adam TC, Schmitt RJ, Holbrook SJ, Burkepile DE, Vega Thurber R. Coral Microbiomes Demonstrate Flexibility and Resilience Through a Reduction in Community Diversity Following a Thermal Stress Event. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.555698] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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68
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Massé A, Tribollet A, Meziane T, Bourguet-Kondracki ML, Yéprémian C, Sève C, Thiney N, Longeon A, Couté A, Domart-Coulon I. Functional diversity of microboring Ostreobium algae isolated from corals. Environ Microbiol 2020; 22:4825-4846. [PMID: 32990394 DOI: 10.1111/1462-2920.15256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 09/09/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022]
Abstract
The filamentous chlorophyte Ostreobium sp. dominates shallow marine carbonate microboring communities, and is one of the major agents of reef bioerosion. While its large genetic diversity has emerged, its physiology remains little known, with unexplored relationship between genotypes and phenotypes (endolithic versus free-living growth forms). Here, we isolated nine strains affiliated to two lineages of Ostreobium (>8% sequence divergence of the plastid gene rbcL), one of which was assigned to the family Odoaceae, from the fast-growing coral host Pocillopora acuta Lamarck 1816. Free-living isolates maintained their bioerosive potential, colonizing pre-bleached coral carbonate skeletons. We compared phenotypes, highlighting shifts in pigment and fatty acid compositions, carbon to nitrogen ratios and stable isotope compositions (δ13 C and δ15 N). Our data show a pattern of higher chlorophyll b and lower arachidonic acid (20:4ω6) content in endolithic versus free-living Ostreobium. Photosynthetic carbon fixation and nitrate uptake, quantified via 8 h pulse-labeling with 13 C-bicarbonate and 15 N-nitrate, showed lower isotopic enrichment in endolithic compared to free-living filaments. Our results highlight the functional plasticity of Ostreobium phenotypes. The isotope tracer approach opens the way to further study the biogeochemical cycling and trophic ecology of these cryptic algae at coral holobiont and reef scales.
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Affiliation(s)
- Anaïs Massé
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France.,IRD-Sorbonne Université (UPMC-CNRS-MNHN), Laboratoire IPSL-LOCEAN, 4 Place Jussieu, Tour 46-00, 5éme étage, Paris Cedex, 75005, France
| | - Aline Tribollet
- IRD-Sorbonne Université (UPMC-CNRS-MNHN), Laboratoire IPSL-LOCEAN, 4 Place Jussieu, Tour 46-00, 5éme étage, Paris Cedex, 75005, France
| | - Tarik Meziane
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle (MNHN), SU, UNICAEN, UA, CNRS (UMR7208), IRD; CP53, 61 rue Buffon, Paris, 75005, France
| | - Marie-Lise Bourguet-Kondracki
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Claude Yéprémian
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Charlotte Sève
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Najet Thiney
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle (MNHN), SU, UNICAEN, UA, CNRS (UMR7208), IRD; CP53, 61 rue Buffon, Paris, 75005, France
| | - Arlette Longeon
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Alain Couté
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Isabelle Domart-Coulon
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
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Pascelli C, Laffy PW, Botté E, Kupresanin M, Rattei T, Lurgi M, Ravasi T, Webster NS. Viral ecogenomics across the Porifera. MICROBIOME 2020; 8:144. [PMID: 33008461 PMCID: PMC7532657 DOI: 10.1186/s40168-020-00919-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/08/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. RESULTS Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. CONCLUSIONS Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract.
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Affiliation(s)
- Cecília Pascelli
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
- James Cook University, Townsville, Australia
| | - Patrick W Laffy
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Emmanuelle Botté
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Marija Kupresanin
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Miguel Lurgi
- Biosciences Department, University of Swansea, Swansea, Wales
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Nicole S Webster
- AIMS@JCU, Townsville, Queensland, Australia.
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia.
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia.
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70
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Cárdenas A, Ye J, Ziegler M, Payet JP, McMinds R, Vega Thurber R, Voolstra CR. Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity. Front Microbiol 2020; 11:572534. [PMID: 33117317 PMCID: PMC7561429 DOI: 10.3389/fmicb.2020.572534] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022] Open
Abstract
Coral reefs are highly diverse marine ecosystems increasingly threatened on a global scale. The foundation species of reef ecosystems are stony corals that depend on their symbiotic microalgae and bacteria for aspects of their metabolism, immunity, and environmental adaptation. Conversely, the function of viruses in coral biology is less well understood, and we are missing an understanding of the diversity and function of coral viruses, particularly in understudied regions such as the Red Sea. Here we characterized coral-associated viruses using a large metagenomic and metatranscriptomic survey across 101 cnidarian samples from the central Red Sea. While DNA and RNA viral composition was different across coral hosts, biological traits such as coral life history strategy correlated with patterns of viral diversity. Coral holobionts were broadly associated with Mimiviridae and Phycodnaviridae that presumably infect protists and algal cells, respectively. Further, Myoviridae and Siphoviridae presumably target members of the bacterial phyla Actinobacteria, Firmicutes, and Proteobacteria, whereas Hepadnaviridae and Retroviridae might infect the coral host. Genes involved in bacterial virulence and auxiliary metabolic genes were common among the viral sequences, corroborating a contribution of viruses to the holobiont’s genetic diversity. Our work provides a first insight into Red Sea coral DNA and RNA viral assemblages and reveals that viral diversity is consistent with global coral virome patterns.
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Affiliation(s)
- Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jin Ye
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Jérôme P Payet
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Ryan McMinds
- Center of Modeling, Simulation and Interactions, Université Côte d'Azur, Nice, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz, Germany.,Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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71
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Goulet TL, Erill I, Ascunce MS, Finley SJ, Javan GT. Conceptualization of the Holobiont Paradigm as It Pertains to Corals. Front Physiol 2020; 11:566968. [PMID: 33071821 PMCID: PMC7538806 DOI: 10.3389/fphys.2020.566968] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
Corals' obligate association with unicellular dinoflagellates, family Symbiodiniaceae form the foundation of coral reefs. For nearly a century, researchers have delved into understanding the coral-algal mutualism from multiple levels of resolution and perspectives, and the questions and scope have evolved with each iteration of new techniques. Advances in genetic technologies not only aided in distinguishing between the multitude of Symbiodiniaceae but also illuminated the existence and diversity of other organisms constituting the coral microbiome. The coral therefore is a meta-organism, often referred to as the coral holobiont. In this review, we address the importance of including a holistic perspective to understanding the coral holobiont. We also discuss the ramifications of how different genotypic combinations of the coral consortium affect the holobiont entity. We highlight the paucity of data on most of the coral microbiome. Using Symbiodiniaceae data, we present evidence that the holobiont properties are not necessarily the sum of its parts. We then discuss the consequences of the holobiont attributes to the fitness of the holobiont and the myriad of organisms that contribute to it. Considering the complexity of host-symbiont genotypic combinations will aid in our understanding of coral resilience, robustness, acclimation, and/or adaptation in the face of environmental change and increasing perturbations.
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Affiliation(s)
- Tamar L Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Marina S Ascunce
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Sheree J Finley
- Department of Physical Sciences and Forensic Science Programs, Alabama State University, Montgomery, AL, United States
| | - Gulnaz T Javan
- Department of Physical Sciences and Forensic Science Programs, Alabama State University, Montgomery, AL, United States
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72
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Zanotti AA, Gregoracci GB, Capel KCC, Kitahara MV. Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis. Anim Microbiome 2020; 2:29. [PMID: 33499978 PMCID: PMC7807860 DOI: 10.1186/s42523-020-00047-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022] Open
Abstract
Background Commonly known as sun-coral, Tubastraea tagusensis is an azooxanthellate scleractinian coral that successfully invaded the Southwestern Atlantic causing significant seascape changes. Today it is reported to over 3500 km along the Brazilian coast, with several rocky shores displaying high substrate coverage. Apart from its singular invasiveness capacity, the documentation and, therefore, understanding of the role of symbiotic microorganisms in the sun-coral invasion is still scarce. However, in general, the broad and constant relationship between corals and microorganisms led to the development of co-evolution hypotheses. As such, it has been shown that the microbial community responds to environmental factors, adjustment of the holobiont, adapting its microbiome, and improving the hosts’ fitness in a short space of time. Here we describe the microbial community (i.e. Bacteria) associated with sun-coral larvae and adult colonies from a locality displaying a high invasion development. Results The usage of high throughput sequencing indicates a great diversity of Bacteria associated with T. tagusensis, with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, and Firmicutes corresponding to the majority of the microbiome in all samples. However, T. tagusensis’ microbial core consists of only eight genera for colonies, and, within them, three are also present in the sequenced larvae. Overall, the microbiome from colonies sampled at different depths did not show significant differences. The microbiome of the larvae suggests a partial vertical transfer of the microbial core in this species. Conclusion Although diverse, the microbiome core of adult Tubastraea tagusensis is composed of only eight genera, of which three are transferred from the mother colony to their larvae. The remaining bacteria genera are acquired from the seawater, indicating that they might play a role in the host fitness and, therefore, facilitate the sun-coral invasion in the Southwestern Atlantic.
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Affiliation(s)
- Aline Aparecida Zanotti
- Programa de Pós Graduação em Sistemas Costeiros e Oceânicos (PGSISCO), Universidade Federal do Paraná (UFPR), Pontal do Paraná, Brazil. .,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo (USP), São Sebastião, Brazil.
| | - Gustavo Bueno Gregoracci
- Departamento de Ciências do Mar (DCMar), Universidade Federal de São Paulo (UNIFESP), Santos, Brazil
| | | | - Marcelo Visentini Kitahara
- Programa de Pós Graduação em Sistemas Costeiros e Oceânicos (PGSISCO), Universidade Federal do Paraná (UFPR), Pontal do Paraná, Brazil.,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo (USP), São Sebastião, Brazil.,Departamento de Ciências do Mar (DCMar), Universidade Federal de São Paulo (UNIFESP), Santos, Brazil
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73
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Lifshitz N, Hazanov L, Fine M, Yarden O. Seasonal Variations in the Culturable Mycobiome of Acropora loripes along a Depth Gradient. Microorganisms 2020; 8:E1139. [PMID: 32731457 PMCID: PMC7464153 DOI: 10.3390/microorganisms8081139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/12/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Coral associated fungi are widespread, highly diverse and are part and parcel of the coral holobiont. To study how environmental conditions prevailing near the coral-host may affect fungal diversity, the culturable (isolated on potato dextrose agar) mycobiome associated with Acropora loripes colonies was seasonally sampled along a depth gradient in the Gulf of Aqaba. Fragments were sampled from both apparently healthy coral colonies as well as those exhibiting observable lesions. Based on phylogenetic analysis of 197 fungal sequences, Ascomycota were the most prevalent (91.9%). The abundance of fungi increased with increasing water depth, where corals sampled at 25 m yielded up to 70% more fungal colony forming units (CFUs) than those isolated at 6 m. Fungal diversity at 25 m was also markedly higher, with over 2-fold more fungal families represented. Diversity was also higher in lesioned coral samples, when compared to apparently healthy colonies. In winter, concurrent with water column mixing and increased levels of available nutrients, at the shallow depths, Saccharomytacea and Sporidiobolacea were more prevalent, while in spring and fall Trichocomacea (overall, the most prevalent family isolated throughout this study) were the most abundant taxa isolated at these depths as well as at deeper sampling sites. Our results highlight the dynamic nature of the culturable coral mycobiome and its sensitivity to environmental conditions and coral health.
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Affiliation(s)
- Nofar Lifshitz
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel;
- The Interuniversity Institute for Marine Science, P.O.B. 469, Eilat 88103, Israel; (L.H.); (M.F.)
| | - Lena Hazanov
- The Interuniversity Institute for Marine Science, P.O.B. 469, Eilat 88103, Israel; (L.H.); (M.F.)
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Maoz Fine
- The Interuniversity Institute for Marine Science, P.O.B. 469, Eilat 88103, Israel; (L.H.); (M.F.)
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel;
- The Interuniversity Institute for Marine Science, P.O.B. 469, Eilat 88103, Israel; (L.H.); (M.F.)
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74
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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75
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Liang J, Yu K, Wang Y, Huang X, Huang W, Qin Z, Wang G, Su H, Chen B, Wu Z. Diazotroph Diversity Associated With Scleractinian Corals and Its Relationships With Environmental Variables in the South China Sea. Front Physiol 2020; 11:615. [PMID: 32625112 PMCID: PMC7314963 DOI: 10.3389/fphys.2020.00615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
Coral reef ecosystems cannot operate normally without an effective nitrogen cycle. For oligotrophic coral reef areas, coral-associated diazotrophs are indispensable participants in the nitrogen cycle. However, the distribution of these diazotrophs and the correlation with the physical and chemical variables of the surrounding seawater remain unclear. To this end, 68 scleractinian coral colonies were sampled from 6 coral reef areas with different environmental variables in the South China Sea to investigate the composition of associated diazotrophs based on nifH gene amplification using high-throughput sequencing. The six coral reefs can be clearly divided into two types (fringing reefs and island reefs), are affected by varying degrees of human activities and are located at different latitudes from 9°20’06”N to 22°34’55”N with different seawater temperatures. Alpha- and beta-diversity analyses showed that the distribution of diazotrophs among coral reefs exhibited significant geographical fluctuations (p ≤ 0.05) and non-significant interspecific fluctuations (p > 0.05). The predominant bacterial phyla included Proteobacteria, Chlorobi, Cyanobacteria, and two unclassified phyla. Chlorobi exhibited a relative abundance of 47–96% in coral samples from the high-latitude Daya Bay fringing reef affected by eutrophication. Unclassified bacteria II, with a relative abundance of 28–87%, was found in all coral samples from the midlatitude Luhuitou fringing reef affected by eutrophication. However, unclassified bacteria I and Proteobacteria dominated (>80% relative abundance) in most of the coral samples from the Weizhou Island fringing reef, which is far from land, and three island reefs (Huangyan Island, Xinyi Reef, and Sanjiao Reef) at relatively low latitudes. At the genus level, some core diazotrophs were found in different coral sample groups. In addition, correlation analysis with various environmental variables revealed that the variables were positively or negatively correlated with different diazotrophic genera. Coral-associated diazotrophs were common among coral individuals. However, their composition was closely related to the different environmental variables. These results provide insights into the geographical distribution characteristics of coral-associated diazotrophs and their evolutionary trends in response to environmental change in the South China Sea.
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Affiliation(s)
- Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Yinghui Wang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Xueyong Huang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Wen Huang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Guanghua Wang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Hongfei Su
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhengchao Wu
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Roach TNF, Little M, Arts MGI, Huckeba J, Haas AF, George EE, Quinn RA, Cobián-Güemes AG, Naliboff DS, Silveira CB, Vermeij MJA, Kelly LW, Dorrestein PC, Rohwer F. A multiomic analysis of in situ coral-turf algal interactions. Proc Natl Acad Sci U S A 2020; 117:13588-13595. [PMID: 32482859 PMCID: PMC7306781 DOI: 10.1073/pnas.1915455117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.
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Affiliation(s)
- Ty N F Roach
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744;
- Biosphere 2, University of Arizona, Oracle, AZ 85739
- Department of Biology, San Diego State University, San Diego, CA 92182
- Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA 92182
- Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Milou G I Arts
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, Amsterdam, The Netherlands
- Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, 1790 AB, Den Burg, Texel, The Netherlands
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Joel Huckeba
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, Amsterdam, The Netherlands
| | - Andreas F Haas
- Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, 1790 AB, Den Burg, Texel, The Netherlands
| | - Emma E George
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T1Z4
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823
| | | | | | - Cynthia B Silveira
- Department of Biology, San Diego State University, San Diego, CA 92182
- Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Mark J A Vermeij
- Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, 1790 AB, Den Burg, Texel, The Netherlands
- Caribbean Research and Management of Biodiversity (CARMABI), Willemstad, Curaçao
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA 92182;
- Viral Information Institute, San Diego State University, San Diego, CA 92182
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77
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McCauley M, Jackson CR, Goulet TL. Microbiomes of Caribbean Octocorals Vary Over Time but Are Resistant to Environmental Change. Front Microbiol 2020; 11:1272. [PMID: 32595627 PMCID: PMC7304229 DOI: 10.3389/fmicb.2020.01272] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
The bacterial microbiome is an essential component of many corals, although knowledge of the microbiomes in scleractinian corals far exceeds that for octocorals. This study characterized the bacterial communities present in shallow water Caribbean gorgonian octocorals over time and space, in addition to determining the bacterial assemblages in gorgonians exposed to environmental perturbations. We found that seven shallow water Caribbean gorgonian species maintained distinct microbiomes and predominantly harbored two bacterial genera, Mycoplasma and Endozoicomonas. Representatives of these taxa accounted for over 70% of the sequences recovered, made up the three most common operational taxonomic units (OTUs), and were present in most of the gorgonian species. Gorgonian species sampled in different seasons and/or in different years, exhibited significant shifts in the abundances of these bacterial OTUs, though there were few changes to overall bacterial diversity, or to the specific OTUs present. These shifts had minimal impact on the relative abundance of inferred functional proteins within the gorgonian corals. Sequences identified as Escherichia were ubiquitous in gorgonian colonies sampled from a lagoon but not in colonies sampled from a back reef. Exposure to increased temperature and/or ultraviolet radiation (UVR) or nutrient enrichment led to few significant changes in the gorgonian coral microbiomes. While there were some shifts in the abundance of the prevalent bacteria, more commonly observed was “microbial switching” between different OTUs identified within the same bacterial genus. The relative stability of gorgonian coral bacterial microbiome may potentially explain some of the resistance and resilience of Caribbean gorgonian corals against changing environmental conditions.
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Affiliation(s)
- Mark McCauley
- Department of Biology, The University of Mississippi, University, MS, United States
| | - Colin R Jackson
- Department of Biology, The University of Mississippi, University, MS, United States
| | - Tamar L Goulet
- Department of Biology, The University of Mississippi, University, MS, United States
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78
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Analysis of Fungal Composition in Mine-Contaminated Soils in Hechi City. Curr Microbiol 2020; 77:2685-2693. [PMID: 32472261 DOI: 10.1007/s00284-020-02044-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022]
Abstract
Fungi play an important role in bioremediation of contaminated soil. However, the diversity of fungal populations in four mine-contaminated soils located in Hechi City has remained unexplored. In this study, high-throughput sequencing of ITS was performed to investigate the diversity and abundance of fungal communities in four mine-contaminated soils in Hechi city. Phylogenetic taxonomy showed that the fungal communities included five phyla. Ascomycota and Basidiomycota were the most abundant phyla in four samples. The most abundant fungi included Agaricomycetes, Nectriaceae, Eurotiomycetes, Mortierellaceae, Incertae sedis, Trichocomaceae, Sordariomycetes, and Fusarium. Various fungi with the potential of bioremediation and industrial application were discussed. The results of fungal composition will provide a clue for isolation of new fungi with the potential of bioremediation and industrial application. Furthermore, this study will lay a good foundation for modifying the indigenous fungi by genetic engineering in the future.
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79
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Guibert I, Lecellier G, Torda G, Pochon X, Berteaux-Lecellier V. Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima. MICROBIOME 2020; 8:57. [PMID: 32317019 PMCID: PMC7175534 DOI: 10.1186/s40168-020-00835-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics. RESULTS Our results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima. CONCLUSIONS Altogether, our results suggest that at least three microbiotypes naturally exist in the studied clam populations, regardless of water temperature. These microbiotypes plausibly provide similar functions to the clam host via alternate molecular pathways as well as microbiotype-specific functions. This redundancy in functions among microbiotypes together with their specificities provides hope that giant clam populations can tolerate some levels of environmental variation such as increased temperature. Importantly, the composition of the benthic assemblage could make clams susceptible to infections by Vibrionaceae, especially when water temperature increases. Video abstract.
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Affiliation(s)
- Isis Guibert
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, SAR China
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
- USR3278 PSL CRIOBE CNRS-EPHE-UPVD, Papetoai, Moorea, French Polynesia
| | - Gael Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
- UVSQ, Université de Paris-Saclay, 45 Avenue des Etats-Unis, Versailles Cedex, France
| | - Gergely Torda
- ARC, Centre of Excellence for Coral Reef Studies, James Cook University, QLD, Townsville, 4811 Australia
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson, 7042 New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth, 0941 New Zealand
| | - Véronique Berteaux-Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-UR, Promenade Roger-Laroque, Sorbonne Université, Noumea Cedex, New Caledonia France
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80
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Sun F, Yang H, Wang G, Shi Q. Combination Analysis of Metatranscriptome and Metagenome Reveal the Composition and Functional Response of Coral Symbionts to Bleaching During an El Niño Event. Front Microbiol 2020; 11:448. [PMID: 32265879 PMCID: PMC7104784 DOI: 10.3389/fmicb.2020.00448] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/02/2020] [Indexed: 01/12/2023] Open
Abstract
With the abnormal rise in ocean temperatures globally in recent years, coral bleaching is becoming common and serious. However, the response mechanisms and processes of coral symbionts to bleaching are not well understood. In this study, metagenomics and metatranscriptomics were used to explore the composition of coral symbionts and their functions in response to coral bleaching. All four bleaching coral species displayed a significant reduction of the abundance and function of Dinophyceae-like eukaryotes at the DNA and RNA levels. However, different species of bleaching coral have their own characteristic symbiotic components. Bleaching Acropora tenuis and Goniastrea minuta corals exhibited a very high abundance of prokaryotes and associated gene functions, especially for opportunistic bacteria. In contrast, algae and fungi were identified as the main microbial associate components and had relatively high RNA abundance in bleaching Pocillopora verrucosa and Pocillopora meandrina. Different coral species, whether unbleached or bleaching, have the same symbiotic taxa that perform the same biological functions in vivo. Different stages of bleaching, or transitional states, were identified by different genome content and functional gene abundance among bleaching corals. These stages should be considered in future coral bleaching studies to accurately determine symbiont structure and function. An implicit hypothesis is that there is a causal relationship between the stability of eukaryotic communities and coral bleaching.
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Affiliation(s)
- Fulin Sun
- South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Hongqiang Yang
- South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Nansha Marine Ecological and Environmental Research Station, Chinese Academy of Sciences, Sansha, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Guan Wang
- South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Qi Shi
- South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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81
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Karcher DB, Roth F, Carvalho S, El-Khaled YC, Tilstra A, Kürten B, Struck U, Jones BH, Wild C. Nitrogen eutrophication particularly promotes turf algae in coral reefs of the central Red Sea. PeerJ 2020; 8:e8737. [PMID: 32274261 PMCID: PMC7130110 DOI: 10.7717/peerj.8737] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/12/2020] [Indexed: 11/20/2022] Open
Abstract
While various sources increasingly release nutrients to the Red Sea, knowledge about their effects on benthic coral reef communities is scarce. Here, we provide the first comparative assessment of the response of all major benthic groups (hard and soft corals, turf algae and reef sands—together accounting for 80% of the benthic reef community) to in-situ eutrophication in a central Red Sea coral reef. For 8 weeks, dissolved inorganic nitrogen (DIN) concentrations were experimentally increased 3-fold above environmental background concentrations around natural benthic reef communities using a slow release fertilizer with 15% total nitrogen (N) content. We investigated which major functional groups took up the available N, and how this changed organic carbon (Corg) and N contents using elemental and stable isotope measurements. Findings revealed that hard corals (in their tissue), soft corals and turf algae incorporated fertilizer N as indicated by significant increases in δ15N by 8%, 27% and 28%, respectively. Among the investigated groups, Corg content significantly increased in sediments (+24%) and in turf algae (+33%). Altogether, this suggests that among the benthic organisms only turf algae were limited by N availability and thus benefited most from N addition. Thereby, based on higher Corg content, turf algae potentially gained competitive advantage over, for example, hard corals. Local management should, thus, particularly address DIN eutrophication by coastal development and consider the role of turf algae as potential bioindicator for eutrophication.
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Affiliation(s)
- Denis B Karcher
- 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 (KAUST), Thuwal, Saudi Arabia.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden.,Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Susana Carvalho
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yusuf C El-Khaled
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Arjen Tilstra
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Benjamin Kürten
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Project Management Jülich, Jülich Research Centre, Rostock, Germany
| | - Ulrich Struck
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Burton H Jones
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian Wild
- Marine Ecology Department, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
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82
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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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83
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Lima LFO, Weissman M, Reed M, Papudeshi B, Alker AT, Morris MM, Edwards RA, de Putron SJ, Vaidya NK, Dinsdale EA. Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network. mBio 2020; 11:e02691-19. [PMID: 32127450 PMCID: PMC7064765 DOI: 10.1128/mbio.02691-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
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Affiliation(s)
- Laís F O Lima
- Department of Biology, San Diego State University, San Diego, California, USA
- College of Biological Sciences, University of California Davis, Davis, California, USA
| | - Maya Weissman
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
| | - Micheal Reed
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Pervasive Institute of Technology, Indiana University, Bloomington, Indiana, USA
| | - Amanda T Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Megan M Morris
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | | | - Naveen K Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
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84
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Valouzi H, Hashemi SS, Wylie SJ, Ahadiyat A, Golnaraghi A. Wisteria Vein Mosaic Virus Detected for the First Time in Iran from an Unknown Host by Analysis of Aphid Vectors. THE PLANT PATHOLOGY JOURNAL 2020; 36:87-97. [PMID: 32089664 PMCID: PMC7012578 DOI: 10.5423/ppj.oa.10.2019.0268] [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: 10/29/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
The development of reverse transcription-polymerase chain reaction using degenerate primers against conserved regions of most potyviral genomes enabled sampling of the potyvirome. However, these assays usually involve sampling potential host plants, but identifying infected plants when they are asymptomatic is challenging, and many plants, especially wild ones, contain inhibitors to DNA amplification. We used an alternative approach which utilized aphid vectors and indicator plants to identify potyviruses capable of infecting common bean (Phaseolus vulgaris). Aphids were collected from a range of asymptomatic leguminous weeds and trees in Iran, and transferred to bean seedlings under controlled conditions. Bean plants were tested serologically for potyvirus infections four-weeks post-inoculation. The serological assay and symptomatology together indicated the presence of one potyvirus, and symptomology alone implied the presence of an unidentified virus. The partial genome of the potyvirus, encompassing the complete coat protein gene, was amplified using generic potyvirus primers. Sequence analysis of the amplicon confirmed the presence of an isolate of Wisteria vein mosaic virus (WVMV), a virus species not previously identified from Western Asia. Phylogenetic analyses of available WVMV sequences categorized them into five groups: East Asian-1 to 3, North American and World. The Iranian isolate clustered with those in the World group. Multiple sequence alignment indicated the presence of some genogroup-specific amino acid substitutions among the isolates studied. Chinese isolates were sister groups of other isolates and showed higher nucleotide distances as compared with the others, suggesting a possible Eastern-Asian origin of WVMV, the main region where Wisteria might have originated.
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Affiliation(s)
- Hajar Valouzi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Seyedeh-Shahrzad Hashemi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Stephen J. Wylie
- Plant Biotechnology Research Group – Virology, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150,
Australia
| | - Ali Ahadiyat
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Alireza Golnaraghi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
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85
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Matthews JL, Raina J, Kahlke T, Seymour JR, Oppen MJH, Suggett DJ. Symbiodiniaceae‐bacteria interactions: rethinking metabolite exchange in reef‐building corals as multi‐partner metabolic networks. Environ Microbiol 2020; 22:1675-1687. [DOI: 10.1111/1462-2920.14918] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer L. Matthews
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Jean‐Baptiste Raina
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Tim Kahlke
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Justin R. Seymour
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Madeleine J. H. Oppen
- The University of Melbourne Parkville 3010 Victoria Australia
- Australian Institute of Marine Science PMB No 3 Townsville MC 4810 QLD Australia
| | - David J. Suggett
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
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86
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Tamang JP, Cotter PD, Endo A, Han NS, Kort R, Liu SQ, Mayo B, Westerik N, Hutkins R. Fermented foods in a global age: East meets West. Compr Rev Food Sci Food Saf 2020; 19:184-217. [PMID: 33319517 DOI: 10.1111/1541-4337.12520] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]
Abstract
Fermented foods and alcoholic beverages have long been an important part of the human diet in nearly every culture on every continent. These foods are often well-preserved and serve as stable and significant sources of proteins, vitamins, minerals, and other nutrients. Despite these common features, however, many differences exist with respect to substrates and products and the types of microbes involved in the manufacture of fermented foods and beverages produced globally. In this review, we describe these differences and consider the influence of geography and industrialization on fermented foods manufacture. Whereas fermented foods produced in Europe, North America, Australia, and New Zealand usually depend on defined starter cultures, those made in Asia and Africa often rely on spontaneous fermentation. Likewise, in developing countries, fermented foods are not often commercially produced on an industrial scale. Although many fermented products rely on autochthonous microbes present in the raw material, for other products, the introduction of starter culture technology has led to greater consistency, safety, and quality. The diversity and function of microbes present in a wide range of fermented foods can now be examined in detail using molecular and other omic approaches. The nutritional value of fermented foods is now well-appreciated, especially in resource-poor regions where yoghurt and other fermented foods can improve public health and provide opportunities for economic development. Manufacturers of fermented foods, whether small or large, should follow Good Manufacturing Practices and have sustainable development goals. Ultimately, preferences for fermented foods and beverages depend on dietary habits of consumers, as well as regional agricultural conditions and availability of resources.
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Affiliation(s)
- Jyoti Prakash Tamang
- DAICENTER and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, Sikkim, India
| | - Paul D Cotter
- Food Biosciences, Principal Research Officer, Teagasc Food Research Centre, Moorepark, Fermoy and APC Microbiome Ireland, Cork, Ireland
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Tokyo, Japan
| | - Nam Soo Han
- Department of Food Science and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Remco Kort
- Department of Molecular Cell Biology, VU University Amsterdam, The Netherlands.,Yoba for Life foundation, Amsterdam, The Netherlands
| | - Shao Quan Liu
- Food Science and Technology Programme, National University of Singapore
| | - Baltasar Mayo
- Department of Microbiology and Chemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Nieke Westerik
- Department of Molecular Cell Biology, VU University Amsterdam, The Netherlands.,Yoba for Life foundation, Amsterdam, The Netherlands
| | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska
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87
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Mhuantong W, Nuryadi H, Trianto A, Sabdono A, Tangphatsornruang S, Eurwilaichitr L, Kanokratana P, Champreda V. Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea. PeerJ 2019; 7:e8137. [PMID: 31875145 PMCID: PMC6925950 DOI: 10.7717/peerj.8137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/01/2019] [Indexed: 01/22/2023] Open
Abstract
Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.
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Affiliation(s)
- Wuttichai Mhuantong
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Handung Nuryadi
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Agus Trianto
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Agus Sabdono
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | | | - Lily Eurwilaichitr
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Pattanop Kanokratana
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Verawat Champreda
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
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88
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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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89
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Ricci F, Rossetto Marcelino V, Blackall LL, Kühl M, Medina M, Verbruggen H. Beneath the surface: community assembly and functions of the coral skeleton microbiome. MICROBIOME 2019; 7:159. [PMID: 31831078 PMCID: PMC6909473 DOI: 10.1186/s40168-019-0762-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/17/2019] [Indexed: 05/24/2023]
Abstract
Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.
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Affiliation(s)
- Francesco Ricci
- School of BioSciences, University of Melbourne, Parkville, 3010 Australia
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia
| | - Linda L. Blackall
- School of BioSciences, University of Melbourne, Parkville, 3010 Australia
| | - Michael Kühl
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Mónica Medina
- Pennsylvania State University, University Park, PA 16802 USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, 3010 Australia
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90
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Yun HS, Kim YS, Yoon HS. Illumina MiSeq Analysis and Comparison of Freshwater Microalgal Communities on Ulleungdo and Dokdo Islands. Pol J Microbiol 2019; 68:527-539. [PMID: 31880896 PMCID: PMC7261877 DOI: 10.33073/pjm-2019-053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 11/05/2022] Open
Abstract
Ulleungdo and Dokdo are volcanic islands with an oceanic climate located off the eastern coast of South Korea. In the present study, we used barcoded Illumina MiSeq to analyze eukaryotic microalgal genera collected from Seonginbong, the highest peak on Ulleungdo, and from groundwater sites on Dongdo and Seodo Islands, which are part of Dokdo. Species richness was significantly greater in the Seonginbong samples than in the Dongdo and Seodo samples, with 834 operational taxonomic units (OTUs) identified from Seonginbong compared with 203 OTUs and 182 OTUs from Dongdo and Seodo, respectively. Taxonomic composition analysis was also used to identify the dominant microalgal phyla at each of the three sites, with Chlorophyta (green algae) the most abundant phyla on Seonginbong and Dongdo, and Bacillariophyta (diatoms) the most abundant on Seodo. These findings suggest that differences in the abundances of Chlorophyta and Bacillariophyta species in the Seonginbong, Dongdo, and Seodo samples are due to variations in species richness and freshwater resources at each sampling location. To the best of our knowledge, this is the first report to detail freshwater microalgal communities on Ulleungdo and Dokdo. As such, the number of species identified in the Seonginbong, Dongdo, and Seodo samples might be an indicator of the ecological differences among these sites and varying characteristics of their microbial communities. Information regarding the microalgal communities also provides a basis for understanding the ecological interactions between microalgae species and other eukaryotic microorganisms. Ulleungdo and Dokdo are volcanic islands with an oceanic climate located off the eastern coast of South Korea. In the present study, we used barcoded Illumina MiSeq to analyze eukaryotic microalgal genera collected from Seonginbong, the highest peak on Ulleungdo, and from groundwater sites on Dongdo and Seodo Islands, which are part of Dokdo. Species richness was significantly greater in the Seonginbong samples than in the Dongdo and Seodo samples, with 834 operational taxonomic units (OTUs) identified from Seonginbong compared with 203 OTUs and 182 OTUs from Dongdo and Seodo, respectively. Taxonomic composition analysis was also used to identify the dominant microalgal phyla at each of the three sites, with Chlorophyta (green algae) the most abundant phyla on Seonginbong and Dongdo, and Bacillariophyta (diatoms) the most abundant on Seodo. These findings suggest that differences in the abundances of Chlorophyta and Bacillariophyta species in the Seonginbong, Dongdo, and Seodo samples are due to variations in species richness and freshwater resources at each sampling location. To the best of our knowledge, this is the first report to detail freshwater microalgal communities on Ulleungdo and Dokdo. As such, the number of species identified in the Seonginbong, Dongdo, and Seodo samples might be an indicator of the ecological differences among these sites and varying characteristics of their microbial communities. Information regarding the microalgal communities also provides a basis for understanding the ecological interactions between microalgae species and other eukaryotic microorganisms.
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Affiliation(s)
- Hyun-Sik Yun
- Department of Biology, College of Natural Sciences, Kyungpook National University , Daegu , South Korea ; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University , Daegu , South Korea
| | - Young-Saeng Kim
- Research Institute of Ulleung-do & Dok-do, Kyungpook National University , Daegu , South Korea
| | - Ho-Sung Yoon
- Department of Biology, College of Natural Sciences, Kyungpook National University , Daegu , South Korea ; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University , Daegu , South Korea
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91
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Rice MM, Maher RL, Vega Thurber R, Burkepile DE. Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral. PeerJ 2019; 7:e8056. [PMID: 31741802 PMCID: PMC6859885 DOI: 10.7717/peerj.8056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 10/18/2019] [Indexed: 11/20/2022] Open
Abstract
Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals' response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment.
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Affiliation(s)
- Mallory M Rice
- 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
| | | | - 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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92
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Pernice M, Raina JB, Rädecker N, Cárdenas A, Pogoreutz C, Voolstra CR. Down to the bone: the role of overlooked endolithic microbiomes in reef coral health. ISME JOURNAL 2019; 14:325-334. [PMID: 31690886 PMCID: PMC6976677 DOI: 10.1038/s41396-019-0548-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 10/17/2019] [Accepted: 10/28/2019] [Indexed: 01/10/2023]
Abstract
Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2–3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the “overlooked” coral skeleton.
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Affiliation(s)
- 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.
| | - Nils Rädecker
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anny Cárdenas
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Claudia Pogoreutz
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. .,Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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93
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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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94
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Vargas-Gastélum L, Chong-Robles J, Lago-Lestón A, Darcy JL, Amend AS, Riquelme M. Targeted ITS1 sequencing unravels the mycodiversity of deep-sea sediments from the Gulf of Mexico. Environ Microbiol 2019; 21:4046-4061. [PMID: 31336033 DOI: 10.1111/1462-2920.14754] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022]
Abstract
Fungi from marine environments have been significantly less studied than terrestrial fungi. This study describes distribution patterns and associated habitat characteristics of the mycobiota of deep-sea sediments collected from the Mexican exclusive economic zone (EEZ) of the Gulf of Mexico (GoM), ranging between 1000 and > 3500 m depth. Internal Transcribed Spacer 1 (ITS1) amplicons were sequenced by Illumina MiSeq. From 29 stations sampled across three annual campaigns, a total of 4421 operational taxonomic units (OTUs) were obtained, indicating a high fungal richness. Most OTUs assignments corresponded to Ascomycota, unidentified fungi and Basidiomycota. The majority of the stations shared a mere 31 OTUs, including the worldwide reported genera Penicillium, Rhodotorula and Cladosporium. Both a transient and a conserved community were identified, suggesting their dependence on or adaptation to the habitat dynamics, respectively. The differences found in fungal richness and taxonomic compositions were correlated principally with latitude, carbon and carbonates content, and terrigenous content, which could be the potential drivers that delimit fungal distribution. This study represents an expansion of our current knowledge on the biogeography of the fungal community from deep-sea sediments, and identifies the geographic and physicochemical properties that delimit fungal composition and distribution in the GoM.
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Affiliation(s)
- Lluvia Vargas-Gastélum
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Ensenada, Baja California, 22860, Mexico
| | - Jennyfers Chong-Robles
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Ensenada, Baja California, 22860, Mexico
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Ensenada, Baja California, 22860, Mexico
| | - John L Darcy
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Anthony S Amend
- Botany Department, University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Meritxell Riquelme
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Ensenada, Baja California, 22860, Mexico
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95
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van Oppen MJH, Blackall LL. Coral microbiome dynamics, functions and design in a changing world. Nat Rev Microbiol 2019; 17:557-567. [DOI: 10.1038/s41579-019-0223-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
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96
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Agyirifo DS, Wamalwa M, Otwe EP, Galyuon I, Runo S, Takrama J, Ngeranwa J. Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities. Heliyon 2019; 5:e02170. [PMID: 31388591 PMCID: PMC6667825 DOI: 10.1016/j.heliyon.2019.e02170] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/05/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Fermentation of Theobroma cacao L. beans is the most critical stage in the production of cocoa products such as chocolates and its derivatives. There is a limited understanding of the complex response of microbial diversity during cocoa bean fermentation. The aim of the present study was to investigate microbial communities in the cocoa bean fermentation heap using a culture-independent approach to elucidate microbial diversity, structure, functional annotation and mapping unto metabolic pathways. Genomic DNA was extracted and purified from a sample of cocoa beans fermentation heap and was followed by library preparations. Sequence data was generated on Illumina Hiseq 2000 paired-end technology (Macrogen Inc). Taxonomic analysis based on genes predicted from the metagenome identified a high percentage of Bacteria (90.0%), Yeast (9%), and bacteriophages (1%) from the cocoa microbiome. Lactobacillus (20%), Gluconacetobacter (9%), Acetobacter (7%) and Gluconobacter (6%) dominated this study. The mean species diversity, measured by Shannon alpha-diversity index, was estimated at 142.81. Assignment of metagenomic sequences to SEED database categories at 97% sequence similarity identified a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates and aromatic amino acids. Metabolism of aromatic compounds, amino acids and their derivatives and carbohydrates occupied 0.6%, 8% and 13% respectively. Overall, these results provide insights into the cocoa microbiome, identifying fermentation processes carried out broadly by complex microbial communities and metabolic pathways encoding aromatic compounds such as phenylacetaldehyde, butanediol, acetoin, and theobromine that are required for flavour and aroma production. The results obtained will help develop targeted inoculations to produce desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compounds formation.
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Affiliation(s)
- Daniel S. Agyirifo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Mark Wamalwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
- International Livestock Research Institute-Bioscience East and Central Africa, Kenya
| | - Emmanuel Plas Otwe
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Isaac Galyuon
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Steven Runo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
| | - Jemmy Takrama
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
- Cocoa Research Institute of Ghana, Ghana
| | - Joseph Ngeranwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
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97
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Kellogg CA. Microbiomes of stony and soft deep-sea corals share rare core bacteria. MICROBIOME 2019; 7:90. [PMID: 31182168 PMCID: PMC6558771 DOI: 10.1186/s40168-019-0697-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/19/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis. RESULTS Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians. CONCLUSIONS Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts' phylogeny.
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Affiliation(s)
- Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, 600 4th Street South, St. Petersburg, FL, 33701, USA.
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98
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Kelly LW, Nelson CE, Haas AF, Naliboff DS, Calhoun S, Carlson CA, Edwards RA, Fox MD, Hatay M, Johnson MD, Kelly ELA, Lim YW, Macherla S, Quinlan ZA, Silva GGZ, Vermeij MJA, Zgliczynski B, Sandin SA, Smith JE, Rohwer F. Diel population and functional synchrony of microbial communities on coral reefs. Nat Commun 2019; 10:1691. [PMID: 30979882 PMCID: PMC6461649 DOI: 10.1038/s41467-019-09419-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 02/28/2019] [Indexed: 12/28/2022] Open
Abstract
On coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing microbial communities in the water column overlying 16 remote forereef sites over a diel cycle. Our results show that microbial community composition is more dissimilar between day and night samples collected from the same site than between day or night samples collected across geographically distant reefs. Diel community differentiation is largely driven by the flux of Psychrobacter sp., which is two-orders of magnitude more abundant during the day. Nighttime communities are enriched with species of Roseobacter, Halomonas, and Alteromonas encoding a greater variety of pathways for carbohydrate catabolism, further illustrating temporal patterns of energetic provisioning between different marine microbes. Dynamic diel fluctuations of microbial populations could also support the efficient trophic transfer of energy posited in coral reef food webs.
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Affiliation(s)
- Linda Wegley Kelly
- Department of Biology, San Diego State University, San Diego, 92182, USA.
| | - Craig E Nelson
- Department of Oceanography and Sea Grant College Program, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, 96822, USA
| | - Andreas F Haas
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Texel, The Netherlands
| | - Douglas S Naliboff
- Department of Biology, San Diego State University, San Diego, 92182, USA
| | - Sandi Calhoun
- Department of Biology, San Diego State University, San Diego, 92182, USA
| | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, 93106, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, 92182, USA
| | - Michael D Fox
- Scripps Institution of Oceanography, University of California, San Diego, 92093, USA
| | - Mark Hatay
- Department of Biology, San Diego State University, San Diego, 92182, USA
| | - Maggie D Johnson
- Scripps Institution of Oceanography, University of California, San Diego, 92093, USA.,Smithsonian Marine Station, Ft. Pierce, FL, 34949, USA
| | - Emily L A Kelly
- Scripps Institution of Oceanography, University of California, San Diego, 92093, USA
| | - Yan Wei Lim
- Department of Biology, San Diego State University, San Diego, 92182, USA
| | | | - Zachary A Quinlan
- Department of Oceanography and Sea Grant College Program, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, 96822, USA
| | | | - Mark J A Vermeij
- Caribbean Marine Biological Institute (CARMABI), Willemstad, Curaçao.,Aquatic Microbiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Brian Zgliczynski
- Scripps Institution of Oceanography, University of California, San Diego, 92093, USA
| | - Stuart A Sandin
- Scripps Institution of Oceanography, University of California, San Diego, 92093, USA
| | - Jennifer E Smith
- Scripps Institution of Oceanography, University of California, San Diego, 92093, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, 92182, USA.,Viral Information Institute, San Diego State University, San Diego, 92182, USA
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99
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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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100
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Zhang XY, Hao HL, Lau SCK, Wang HY, Han Y, Dong LM, Huang RM. Biodiversity and antifouling activity of fungi associated with two soft corals from the South China Sea. Arch Microbiol 2019; 201:757-767. [PMID: 30840101 DOI: 10.1007/s00203-019-01639-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/07/2019] [Accepted: 02/19/2019] [Indexed: 11/28/2022]
Abstract
Bacteria in corals have been studied in detail in the past decades. However, the biodiversity and bioactivity of fungi in corals are still poorly understood. This study investigated the biodiversity and antifouling activity of fungi in soft corals Cladiella krempfi and Sarcophyton tortuosum from the South China Sea. A high diverse and abundant fungal community was found in the two soft corals. Furthermore, five isolates shared 83-95% similarity with their closest relatives, indicating that they might be novel species in genera Phaeoshaeria and Mucor. In addition, approximately 50% of the representative isolates exhibited distinct antifouling activity. In particular, isolates Fungal sp. SCAU132 and Fungal sp. SCAU133 displayed very strong antifouling activity against Bugula neritina, suggesting they can provide a potential resource for further investigation on isolation of novel antifouling metabolites. To our knowledge, this study is the first report to investigate the biodiversity and antifouling activity of fungi in C. krempfi and S. tortuosum.
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Affiliation(s)
- Xiao-Yong Zhang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bior-esource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Hui-Li Hao
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, 510642, Guangzhou, China
| | - Stanley Chun Kwan Lau
- Department of Ocean Science, Hong Kong University of Science and Technology, Clearwater Bay, 999077, Kowloon, Hong Kong, China
| | - Huai-You Wang
- Division of Life Science and Center for Chinese Medicine, Hong Kong University of Science and Technology, Clearwater Bay, 999077, Kowloon, Hong Kong, China
| | - Yu Han
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, 510642, Guangzhou, China
| | - Li-Mei Dong
- College of Forestry and Landscape Architecture, South China Agricultural University, 510642, Guangzhou, China.
| | - Ri-Ming Huang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, 510642, Guangzhou, China.
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