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Shoguchi E, Kawachi M, Shinzato C, Beedessee G. Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13238. [PMID: 38444256 PMCID: PMC10915500 DOI: 10.1111/1758-2229.13238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12 ) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaJapan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of TokyoKashiwaJapan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
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Matthews JL, Khalil A, Siboni N, Bougoure J, Guagliardo P, Kuzhiumparambil U, DeMaere M, Le Reun NM, Seymour JR, Suggett DJ, Raina JB. Coral endosymbiont growth is enhanced by metabolic interactions with bacteria. Nat Commun 2023; 14:6864. [PMID: 37891154 PMCID: PMC10611727 DOI: 10.1038/s41467-023-42663-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteria are key contributors to microalgae resource acquisition, competitive performance, and functional diversity, but their potential metabolic interactions with coral microalgal endosymbionts (Symbiodiniaceae) have been largely overlooked. Here, we show that altering the bacterial composition of two widespread Symbiodiniaceae species, during their free-living stage, results in a significant shift in their cellular metabolism. Indeed, the abundance of monosaccharides and the key phytohormone indole-3-acetic acid (IAA) were correlated with the presence of specific bacteria, including members of the Labrenzia (Roseibium) and Marinobacter genera. Single-cell stable isotope tracking revealed that these two bacterial genera are involved in reciprocal exchanges of carbon and nitrogen with Symbiodiniaceae. We identified the provision of IAA by Labrenzia and Marinobacter, and this metabolite caused a significant growth enhancement of Symbiodiniaceae. By unravelling these interkingdom interactions, our work demonstrates how specific bacterial associates fundamentally govern Symbiodiniaceae fitness.
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Affiliation(s)
- Jennifer L Matthews
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Abeeha Khalil
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, 6009, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, University of Western Australia, Perth, WA, 6009, Australia
| | | | - Matthew DeMaere
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nine M Le Reun
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David J Suggett
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
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Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
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Tong H, Zhang F, Sun J, McIlroy SE, Zhang W, Wang Y, Huang H, Zhou G, Qian PY. Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages. MICROBIOME 2023; 11:89. [PMID: 37101227 PMCID: PMC10131396 DOI: 10.1186/s40168-023-01495-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Coral meta-organisms consist of the coral, and its associated Symbiodiniaceae (dinoflagellate algae), bacteria, and other microbes. Corals can acquire photosynthates from Symbiodiniaceae, whilst Symbiodiniaceae uses metabolites from corals. Prokaryotic microbes provide Symbiodiniaceae with nutrients and support the resilience of corals as meta-organisms. Eutrophication is a major cause of coral reef degradation; however, its effects on the transcriptomic response of coral meta-organisms remain unclear, particularly for prokaryotic microbes associated with corals in the larval stage. To understand acclimation of the coral meta-organism to elevated nitrate conditions, we analyzed the physiological and transcriptomic responses of Pocillopora damicornis larvae, an ecologically important scleractinian coral, after 5 days of exposure to elevated nitrate levels (5, 10, 20, and 40 µM). RESULTS The major differentially expressed transcripts in coral, Symbiodiniaceae, and prokaryotic microbes included those related to development, stress response, and transport. The development of Symbiodiniaceae was not affected in the 5 and 20 µM groups but was downregulated in the 10 and 40 µM groups. In contrast, prokaryotic microbe development was upregulated in the 10 and 40 µM groups and downregulated in the 5 and 20 µM groups. Meanwhile, coral larval development was less downregulated in the 10 and 40 µM groups than in the 5 and 20 µM groups. In addition, multiple larval, Symbiodiniaceae, and prokaryotic transcripts were significantly correlated with each other. The core transcripts in correlation networks were related to development, nutrient metabolism, and transport. A generalized linear mixed model, using least absolute shrinkage and selection operator, demonstrated that the Symbiodiniaceae could both benefit and cost coral larval development. Furthermore, the most significantly correlated prokaryotic transcripts maintained negative correlations with the physiological functions of Symbiodiniaceae. CONCLUSIONS Results suggested that Symbiodiniaceae tended to retain more nutrients under elevated nitrate concentrations, thereby shifting the coral-algal association from mutualism towards parasitism. Prokaryotic microbes provided Symbiodiniaceae with essential nutrients and may control Symbiodiniaceae growth through competition, whereby prokaryotes can also restore coral larval development inhibited by Symbiodiniaceae overgrowth. Video Abstract.
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Affiliation(s)
- Haoya Tong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fang Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Shelby E. McIlroy
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yan Wang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Guowei Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Hainan Key Laboratory of Tropical Marine Biotechnology, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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6
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Zhu W, Zhu M, Liu X, Xia J, Wang H, Chen R, Li X. Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress. Front Microbiol 2022; 13:1052776. [PMID: 36425038 PMCID: PMC9678930 DOI: 10.3389/fmicb.2022.1052776] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/18/2022] [Indexed: 02/07/2024] Open
Abstract
Global change and local stressors are simultaneously affecting the nearshore corals, and microbiome flexibility may assist corals in thriving under such multiple stressors. Here, we investigated the effects of various environmental variables on Galaxea fascicularis holobiont from nearshore and offshore reefs. These nearshore reefs were more turbid, eutrophic, and warm than offshore reefs. However, coral physiological parameters did not differ significantly. Corals under stressful nearshore environments had low symbiont diversity and selected more tolerant Symbiodiniaceae. The bacterial diversity of offshore corals was significantly higher, and their community composition varied obviously. Diffusion limitations and environmental heterogeneity were essential in structuring microbial communities. Functional annotation analysis demonstrated significant differences between nearshore and offshore corals in bacterial functional groups. Environmental stress significantly reduced the complexity and connectivity of bacterial networks, and the abundances of keystone taxa altered considerably. These results indicated that corals could thrive nearshore through holobiont plasticity to cope with multiple environmental stresses.
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Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ming Zhu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- College of Marine Science, Hainan University, Haikou, China
| | - Xiangbo Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- College of Marine Science, Hainan University, Haikou, China
| | - Jingquan Xia
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Hao Wang
- College of Marine Science, Hainan University, Haikou, China
| | - Rouwen Chen
- College of Marine Science, Hainan University, Haikou, China
| | - Xiubao Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- College of Marine Science, Hainan University, Haikou, China
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7
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Oliveira CYB, Abreu JL, Santos EP, Matos ÂP, Tribuzi G, Oliveira CDL, Veras BO, Bezerra RS, Müller MN, Gálvez AO. Light induces peridinin and docosahexaenoic acid accumulation in the dinoflagellate Durusdinium glynnii. Appl Microbiol Biotechnol 2022; 106:6263-6276. [PMID: 35972515 DOI: 10.1007/s00253-022-12131-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/02/2022]
Abstract
Peridinin is a light-harvesting carotenoid present in phototrophic dinoflagellates and has great potential for new drug applications and cosmetics development. Herein, the effects of irradiance mediated by light-emitting diodes on growth performance, carotenoid and fatty acid profiles, and antioxidant activity of the endosymbiotic dinoflagellate Durusdinium glynnii were investigated. The results demonstrate that D. glynnii is particularly well adapted to low-light conditions; however, it can be high-light-tolerant. In contrast to other light-harvesting carotenoids, the peridinin accumulation in D. glynnii occurred during high-light exposure. The peridinin to chlorophyll-a ratio varied as a function of irradiance, while the peridinin to total carotenoids ratio remained stable. Under optimal irradiance for growth, there was a peak in docosahexaenoic acid (DHA) bioaccumulation. This study contributes to the understanding of the photoprotective role of peridinin in endosymbiont dinoflagellates and highlights the antioxidant activity of peridinin-rich extracts. KEY POINTS: • Peridinin has a protective role against chlorophyll photo-oxidation • High light conditions induce cellular peridinin accumulation • D. glynnii accumulates high amounts of DHA under optimal light supply.
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Affiliation(s)
- Carlos Yure B Oliveira
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil.
| | - Jéssika L Abreu
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil
| | - Elizabeth P Santos
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil
| | - Ângelo P Matos
- Center of Agricultural Sciences, Federal University of Santa Catarina, Florianópolis, 88034-001, Brazil
| | - Giustino Tribuzi
- Department of Food Science and Technology, Federal University of Santa Catarina, Florianopolis, 88034-801, Brazil
| | - Cicero Diogo L Oliveira
- Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, 57072-900, Brazil
| | - Bruno O Veras
- Department of Biochemistry, Federal University of Pernambuco, Recife, 50740-550, Brazil
| | - Railson S Bezerra
- Department of Biochemistry, Federal University of Pernambuco, Recife, 50740-550, Brazil
| | - Marius N Müller
- Department of Oceanography, Federal University of Pernambuco, Recife, 50740-550, Brazil
| | - Alfredo O Gálvez
- Department of Fishing and Aquaculture, Federal Rural University of Pernambuco, St. Dom Manuel de Medeiros, Dois Irmãos, Recife, 52171-900, Brazil
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Díaz-Almeyda EM, Ryba T, Ohdera AH, Collins SM, Shafer N, Link C, Prado-Zapata M, Ruhnke C, Moore M, González Angel AM, Pollock FJ, Medina M. Thermal Stress Has Minimal Effects on Bacterial Communities of Thermotolerant Symbiodinium Cultures. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.764086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Algae in the dinoflagellate family Symbiodiniaceae are endocellular photosymbionts of corals and other cnidarians. This close relationship is disrupted when seawater temperature increases, causing coral bleaching eventually affecting entire coral reefs. Although the relationship between animal host and photosymbiont has been well-studied, little is known about the bacterial community associated with Symbiodiniaceae in culture. We compared the microbial communities of three isolates from different species of the genus Symbiodinium (formerly known as Symbiodinium clade A) with different ecophysiology, levels of interaction with the animal host, and thermal adaptations. Two species, Symbiodinium microadriaticum and Symbiodinium necroappettens, exhibit intermediate thermotolerance, with a decrease of both growth rate and photochemical efficiency with increased temperature. The third species, Symbiodinium pilosum, has high thermotolerance with no difference in growth rate or photochemical efficiency at 32°C. Microbial communities were characterized after 27 days of growth under control (26°C) and high temperature (32°C). Data shows stronger grouping of bacterial assemblages based on Symbiodinium species than temperature. Microbial communities did not group phylogenetically. We found a shared set of fifteen ASVs belonging to four genera and three families that remained in all three Symbiodiniaceae species. These included Labrenzia, Phycisphaeraceae (SM1A02), Roseovarius, and Muricauda, which are all commonly associated with corals and Symbiodiniaceae cultures. Few ASVs differed significantly by temperature within species. S. pilosum displayed significantly lower levels of microbial diversity and greater individual variability in community composition at 32°C compared to 26°C. These results suggest that bacteria associated or co-cultured with thermotolerant Symbiodinium might play an important role in thermotolerance. Further research on the functional metabolic pathways of these bacteria might hold the key to understanding Symbiodinium’s ability to tolerate thermal stress.
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9
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Coral-microbe interactions: their importance to reef function and survival. Emerg Top Life Sci 2022; 6:33-44. [PMID: 35119475 DOI: 10.1042/etls20210229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
Many different microorganisms associate with the coral host in a single entity known as the holobiont, and their interactions with the host contribute to coral health, thereby making them a fundamental part of reef function, survival, and conservation. As corals continue to be susceptible to bleaching due to environmental stress, coral-associated bacteria may have a potential role in alleviating bleaching. This review provides a synthesis of the various roles bacteria have in coral physiology and development, and explores the possibility that changes in the microbiome with environmental stress could have major implications in how corals acclimatize and survive. Recent studies on the interactions between the coral's algal and bacterial symbionts elucidate how bacteria may stabilize algal health and, therefore, mitigate bleaching. A summary of the innovative tools and experiments to examine host-microbe interactions in other cnidarians (a temperate coral, a jellyfish, two anemones, and a freshwater hydroid) is offered in this review to delineate our current knowledge of mechanisms underlying microbial establishment and maintenance in the animal host. A better understanding of these mechanisms may enhance the success of maintaining probiotics long-term in corals as a conservation strategy.
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10
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Röthig T, Puntin G, Wong JCY, Burian A, McLeod W, Baker DM. Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish. MICROBIOME 2021; 9:127. [PMID: 34078452 PMCID: PMC8173792 DOI: 10.1186/s40168-021-01075-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/07/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnership is highly sensitive to environmental change-including eutrophication-that causes dysbiosis and contributes to global coral reef decline. Yet, some holobionts exhibit resistance to dysbiosis in eutrophic environments, including the obligate photosymbiotic scyphomedusa Cassiopea xamachana. METHODS Our aim was to assess the mechanisms in C. xamachana that stabilize symbiotic relationships. We combined labelled bicarbonate (13C) and nitrate (15N) with metabarcoding approaches to evaluate nutrient cycling and microbial community composition in symbiotic and aposymbiotic medusae. RESULTS C-fixation and cycling by algal Symbiodiniaceae was essential for C. xamachana as even at high heterotrophic feeding rates aposymbiotic medusae continuously lost weight. Heterotrophically acquired C and N were readily shared among host and algae. This was in sharp contrast to nitrate assimilation by Symbiodiniaceae, which appeared to be strongly restricted. Instead, the bacterial microbiome seemed to play a major role in the holobiont's DIN assimilation as uptake rates showed a significant positive relationship with phylogenetic diversity of medusa-associated bacteria. This is corroborated by inferred functional capacity that links the dominant bacterial taxa (~90 %) to nitrogen cycling. Observed bacterial community structure differed between apo- and symbiotic C. xamachana putatively highlighting enrichment of ammonium oxidizers and nitrite reducers and depletion of nitrogen-fixers in symbiotic medusae. CONCLUSION Host, algal symbionts, and bacterial associates contribute to regulated nutrient assimilation and cycling in C. xamachana. We found that the bacterial microbiome of symbiotic medusae was seemingly structured to increase DIN removal and enforce algal N-limitation-a mechanism that would help to stabilize the host-algae relationship even under eutrophic conditions. Video abstract.
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Affiliation(s)
- Till Röthig
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Giulia Puntin
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany
| | - Jane C. Y. Wong
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
| | - Alfred Burian
- Marine Ecology Department, Lurio University, Nampula, Mozambique
- Department of Computational Landscape Ecology, UFZ– Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Wendy McLeod
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
| | - David M. Baker
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
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A Phylogeny-Informed Analysis of the Global Coral-Symbiodiniaceae Interaction Network Reveals that Traits Correlated with Thermal Bleaching Are Specific to Symbiont Transmission Mode. mSystems 2021; 6:6/3/e00266-21. [PMID: 33947806 PMCID: PMC8269218 DOI: 10.1128/msystems.00266-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The complex network of associations between corals and their dinoflagellates (family Symbiodiniaceae) are the basis of coral reef ecosystems but are sensitive to increasing global temperatures. Coral-symbiont interactions are restricted by ecological and evolutionary determinants that constrain partner choice and influence holobiont response to environmental stress; however, little is known about how these processes shape thermal resilience of the holobiont. Here, we built a network of global coral-Symbiodiniaceae associations, mapped species traits (e.g., symbiont transmission mode and biogeography) and phylogenetic relationships of both partners onto the network, and assigned thermotolerance to both host and symbiont nodes. Using network analysis and phylogenetic comparative methods, we determined the contribution of species traits to thermal resilience of the holobiont, while accounting for evolutionary patterns among species. We found that the network shows nonrandom interactions among species, which are shaped by evolutionary history, symbiont transmission mode (horizontally transmitted [HT] or vertically transmitted [VT] corals) and biogeography. Coral phylogeny, but not Symbiodiniaceae phylogeny, symbiont transmission mode, or biogeography, was a good predictor of thermal resilience. Closely related corals have similar Symbiodiniaceae interaction patterns and bleaching susceptibilities. Nevertheless, the association patterns that explain increased host thermal resilience are not generalizable across the entire network but are instead unique to HT and VT corals. Under nonstress conditions, thermally resilient VT coral species associate with thermotolerant phylotypes and limit their number of unique symbionts and overall symbiont thermotolerance diversity, while thermally resilient HT coral species associate with a few host-specific symbiont phylotypes. IMPORTANCE Recent advances have revealed a complex network of interactions between coral and Symbiodiniaceae. Specifically, nonrandom association patterns, which are determined in part by restrictions imposed by symbiont transmission mode, increase the sensitivity of the overall network to thermal stress. However, little is known about the extent to which coral-Symbiodiniaceae network resistance to thermal stress is shaped by host and symbiont species phylogenetic relationships and host and symbiont species traits, such as symbiont transmission mode. We built a frequency-weighted global coral-Symbiodiniaceae network and used network analysis and phylogenetic comparative methods to show that evolutionary relatedness, but not transmission mode, predicts thermal resilience of the coral-Symbiodiniaceae holobiont. Consequently, thermal stress events could result in nonrandom pruning of susceptible lineages and loss of taxonomic diversity with catastrophic effects on community resilience to future events. Our results show that inclusion of the contribution of evolutionary and ecological processes will further our understanding of the fate of coral assemblages under climate change.
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Peixoto RS, Sweet M, Villela HDM, Cardoso P, Thomas T, Voolstra CR, Høj L, Bourne DG. Coral Probiotics: Premise, Promise, Prospects. Annu Rev Anim Biosci 2020; 9:265-288. [PMID: 33321044 DOI: 10.1146/annurev-animal-090120-115444] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.
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Affiliation(s)
- Raquel S Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,IMAM-AquaRio, Rio de Janeiro Aquarium Research Center, Rio de Janeiro, 20220-360, Brazil.,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, United Kingdom
| | - Helena D M Villela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Pedro Cardoso
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil;
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz 78457, Germany.,Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lone Høj
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland 4810, Australia.,College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
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13
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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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14
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15
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Baquiran JIP, Nada MAL, Campos CLD, Sayco SLG, Cabaitan PC, Rosenberg Y, Ayalon I, Levy O, Conaco C. The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light Pollution. Microorganisms 2020; 8:E1566. [PMID: 33053643 PMCID: PMC7601249 DOI: 10.3390/microorganisms8101566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
Corals harbor a great diversity of symbiotic microorganisms that play pivotal roles in host nutrition, reproduction, and development. Changes in the ocean environment, such as increasing exposure to artificial light at night (ALAN), may alter these relationships and result in a decline in coral health. In this study, we examined the microbiome associated with gravid specimens of the reef-building coral Acropora digitifera. We also assessed the temporal effects of ALAN on the coral-associated microbial community using high-throughput sequencing of the 16S rRNA gene V4 hypervariable region. The A. digitifera microbial community was dominated by phyla Proteobacteria, Firmicutes, and Bacteroidetes. Exposure to ALAN had no large-scale effect on the coral microbiome, although taxa affiliated with Rhodobacteraceae, Caulobacteraceae, Burkholderiaceae, Lachnospiraceae, and Ruminococcaceae were significantly enriched in corals subjected to ALAN. We further noted an increase in the relative abundance of the family Endozoicomonadaceae (Endozoicomonas) as the spawning period approached, regardless of light treatment. These findings highlight the stability of the A. digitifera microbial community under short-term artificial light pollution and provide initial insights into the response of the collective holobiont to ALAN.
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Affiliation(s)
- Jake Ivan P. Baquiran
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Michael Angelou L. Nada
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Celine Luisa D. Campos
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Sherry Lyn G. Sayco
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Patrick C. Cabaitan
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Yaeli Rosenberg
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.R.); (I.A.); (O.L.)
| | - Inbal Ayalon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.R.); (I.A.); (O.L.)
- Israel The H. Steinitz Marine Biology Laboratory, The Interuniversity Institute for Marine Sciences of Eilat, P.O. Box 469, Eilat 88103, Israel
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.R.); (I.A.); (O.L.)
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
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16
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Voolstra CR, Ziegler M. Adapting with Microbial Help: Microbiome Flexibility Facilitates Rapid Responses to Environmental Change. Bioessays 2020; 42:e2000004. [DOI: 10.1002/bies.202000004] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/11/2020] [Indexed: 02/06/2023]
Affiliation(s)
| | - Maren Ziegler
- Department of Animal Ecology and SystematicsJustus Liebig University Giessen 35392 Germany
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17
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Camp EF, Kahlke T, Nitschke MR, Varkey D, Fisher NL, Fujise L, Goyen S, Hughes DJ, Lawson CA, Ros M, Woodcock S, Xiao K, Leggat W, Suggett DJ. Revealing changes in the microbiome of Symbiodiniaceae under thermal stress. Environ Microbiol 2020; 22:1294-1309. [DOI: 10.1111/1462-2920.14935] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/08/2020] [Accepted: 01/27/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Emma F. Camp
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Tim Kahlke
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Matthew R. Nitschke
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
- School of Biological SciencesVictoria University of Wellington Wellington New Zealand
| | - Deepa Varkey
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
- Department of Molecular SciencesMacquarie University Sydney NSW 2109 Australia
| | - Nerissa L. Fisher
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Lisa Fujise
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Samantha Goyen
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - David J. Hughes
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Caitlin A. Lawson
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Mickael Ros
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Stephen Woodcock
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Kun Xiao
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - William Leggat
- School of Environmental and Life SciencesUniversity of Newcastle Ourimbah NSW 2308 Australia
| | - David J. Suggett
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
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18
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Morgans CA, Hung JY, Bourne DG, Quigley KM. Symbiodiniaceae probiotics for use in bleaching recovery. Restor Ecol 2020. [DOI: 10.1111/rec.13069] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Carys A. Morgans
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
| | - Julia Y. Hung
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
| | - David G. Bourne
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
- Australian Institute of Marine Science Townsville Queensland 4816 Australia
| | - Kate M. Quigley
- College of Science and EngineeringJames Cook University Townsville Queensland 4814 Australia
- Australian Institute of Marine Science Townsville Queensland 4816 Australia
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19
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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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20
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A Zeaxanthin-Producing Bacterium Isolated from the Algal Phycosphere Protects Coral Endosymbionts from Environmental Stress. mBio 2020; 11:mBio.01019-19. [PMID: 31964724 PMCID: PMC6974559 DOI: 10.1128/mbio.01019-19] [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] [Indexed: 02/06/2023] Open
Abstract
Occupying less than 1% of the seas, coral reefs are estimated to harbor ∼25% of all marine species. However, the destruction of coral reefs has intensified in the face of global climate changes, such as rising seawater temperatures, which induce the overproduction of reactive oxygen species harmful to corals. Although reef-building corals form complex consortia with bacteria and photosynthetic endosymbiotic algae of the family Symbiodiniaceae, the functional roles of coral-associated bacteria remain largely elusive. By manipulating the Symbiodiniaceae bacterial community, we demonstrated that a bacterium that produces an antioxidant carotenoid could mitigate thermal and light stresses in cultured Symbiodiniaceae isolated from a reef-building coral. Therefore, this study illuminates the unexplored roles of coral-associated bacteria under stressful conditions. Reef-building corals form a complex consortium with photosynthetic algae in the family Symbiodiniaceae and bacteria, collectively termed the coral holobiont. These bacteria are hypothesized to be involved in the stress resistance of the coral holobiont, but their functional roles remain largely elusive. Here, we show that cultured Symbiodiniaceae algae isolated from the reef-building coral Galaxea fascicularis are associated with novel bacteria affiliated with the family Flavobacteriaceae. Antibiotic treatment eliminated the bacteria from cultured Symbiodiniaceae, resulting in a decreased maximum quantum yield of PSII (variable fluorescence divided by maximum fluorescence [Fv/Fm]) and an increased production of reactive oxygen species (ROS) under thermal and light stresses. We then isolated this bacterial strain, named GF1. GF1 inoculation in the antibiotic-treated Symbiodiniaceae cultures restored the Fv/Fm and reduced the ROS production. Furthermore, we found that GF1 produces the carotenoid zeaxanthin, which possesses potent antioxidant activity. Zeaxanthin supplementation to cultured Symbiodiniaceae ameliorated the Fv/Fm and ROS production, suggesting that GF1 mitigates thermal and light stresses in cultured Symbiodiniaceae via zeaxanthin production. These findings could advance our understanding of the roles of bacteria in Symbiodiniaceae and the coral holobiont, thereby contributing to the development of novel approaches toward coral protection through the use of symbiotic bacteria and their metabolites.
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21
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Quigley KM, Alvarez Roa C, Torda G, Bourne DG, Willis BL. Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles. Microbiologyopen 2019; 9:e959. [PMID: 31670480 PMCID: PMC7002099 DOI: 10.1002/mbo3.959] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 02/04/2023] Open
Abstract
Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.
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Affiliation(s)
- Kate M Quigley
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | - Greg Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bette L Willis
- College of Marine and Environmental Sciences, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, QLD, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
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22
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Epstein HE, Smith HA, Cantin NE, Mocellin VJL, Torda G, van Oppen MJH. Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect Seasonality. Front Microbiol 2019; 10:1775. [PMID: 31474944 PMCID: PMC6706759 DOI: 10.3389/fmicb.2019.01775] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022] Open
Abstract
The coral microbiome is known to fluctuate in response to environmental variation and has been suggested to vary seasonally. However, most studies to date, particularly studies on bacterial communities, have examined temporal variation over a time frame of less than 1 year, which is insufficient to establish if microbiome variations are indeed seasonal in nature. The present study focused on expanding our understanding of long-term variability in microbial community composition using two common coral species, Acropora hyacinthus, and Acropora spathulata, at two mid-shelf reefs on the Great Barrier Reef. By sampling over a 2-year time period, this study aimed to determine whether temporal variations reflect seasonal cycles. Community composition of both bacteria and Symbiodiniaceae was characterized through 16S rRNA gene and ITS2 rDNA metabarcoding. We observed significant variations in community composition of both bacteria and Symbiodiniaceae among time points for A. hyacinthus and A. spathulata. However, there was no evidence to suggest that temporal variations were cyclical in nature and represented seasonal variation. Clear evidence for differences in the microbial communities found between reefs suggests that reef location and coral species play a larger role than season in driving microbial community composition in corals. In order to identify the basis of temporal patterns in coral microbial community composition, future studies should employ longer time series of sampling at sufficient temporal resolution to identify the environmental correlates of microbiome variation.
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Affiliation(s)
- Hannah E. Epstein
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- AIMS@JCU, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Hillary A. Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Neal E. Cantin
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | - Gergely Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, Townsville, QLD, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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23
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Bernasconi R, Stat M, Koenders A, Paparini A, Bunce M, Huggett MJ. Establishment of Coral-Bacteria Symbioses Reveal Changes in the Core Bacterial Community With Host Ontogeny. Front Microbiol 2019; 10:1529. [PMID: 31338082 PMCID: PMC6629827 DOI: 10.3389/fmicb.2019.01529] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/18/2019] [Indexed: 12/25/2022] Open
Abstract
Bacterial communities are fundamental symbionts of corals. However, the process by which bacterial communities are acquired across the life history of corals, particularly in larval and early juvenile stages, is still poorly characterized. Here, transfer of bacteria of the Scleractinian coral Acropora digitifera from adults to spawned egg-sperm bundles was analyzed, as well as acquisition across early developmental stages (larvae and newly settled spat), and 6-month-old juveniles. Larvae were reared under manipulated environmental conditions to determine the source (maternal, seawater, or sediment) of bacteria likely to establish symbiotic relationships with the host using amplicon sequencing of the 16S rRNA gene. Maternal colonies directly transferred bacteria from the families Rhodobacteraceae, Cryomorphaceae, and Endozoicimonaceae to egg-sperm bundles. Furthermore, significant differences in the microbial community structure were identified across generations, yet the structure of the coral bacterial community across early life history stages was not impacted by different environmental rearing conditions. These data indicate that the uptake and structure of bacterial communities is developmentally, rather than environmentally, regulated. Both maternal coral colonies and ubiquitous bacteria found across environmental substrates represent a potential source of symbionts important in establishing the coral microbiome. Uniquely, we report the presence of variation with ontogeny of both the core and resident bacterial communities, supporting the hypothesis that microbial communities are likely to play specific roles within the distinct life history stages of the coral host.
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Affiliation(s)
- Rachele Bernasconi
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Michael Stat
- Faculty of Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Annette Koenders
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Andrea Paparini
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University, Bentley, WA, Australia
| | - Megan J. Huggett
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
- Faculty of Science, School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW, Australia
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