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Sun F, Yang H, Zhang X, Tan F, Wang G, Shi Q. Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching. MARINE ENVIRONMENTAL RESEARCH 2024; 201:106694. [PMID: 39163656 DOI: 10.1016/j.marenvres.2024.106694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/12/2024] [Accepted: 08/13/2024] [Indexed: 08/22/2024]
Abstract
Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.
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Affiliation(s)
- Fulin Sun
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hongqiang Yang
- South China Sea Institute of Oceanology, 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.
| | - Xiyang Zhang
- South China Sea Institute of Oceanology, 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
| | - Fei Tan
- South China Sea Institute of Oceanology, 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
| | - Guan Wang
- South China Sea Institute of Oceanology, 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
| | - Qi Shi
- South China Sea Institute of Oceanology, 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
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Hulver AM, Carbonne C, Teixidó N, Comeau S, Kemp DW, Keister EF, Gattuso JP, Grottoli AG. Elevated heterotrophic capacity as a strategy for Mediterranean corals to cope with low pH at CO2 vents. PLoS One 2024; 19:e0306725. [PMID: 39078831 PMCID: PMC11288460 DOI: 10.1371/journal.pone.0306725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 06/21/2024] [Indexed: 08/02/2024] Open
Abstract
The global increase in anthropogenic CO2 is leading to ocean warming and acidification, which is threatening corals. In Ischia, Italy, two species of Mediterranean scleractinian corals-the symbiotic Cladocora caespitosa and the asymbiotic Astroides calycularis-were collected from ambient pH sites (average pHT = 8.05) and adjacent CO2 vent sites (average pHT = 7.8) to evaluate their response to ocean acidification. Coral colonies from both sites were reared in a laboratory setting for six months at present day pH (pHT ~ 8.08) or low pH (pHT ~7.72). Previous work showed that these corals were tolerant of low pH and maintained positive calcification rates throughout the experiment. We hypothesized that these corals cope with low pH by increasing their heterotrophic capacity (i.e., feeding and/or proportion of heterotrophically derived compounds incorporated in their tissues), irrespective of site of origin, which was quantified indirectly by measuring δ13C, δ15N, and sterols. To further characterize coral health, we quantified energy reserves by measuring biomass, total lipids, and lipid classes. Additional analysis for C. caespitosa included carbohydrates (an energy reserve) and chlorophyll a (an indicator of photosynthetic capacity). Isotopic evidence shows that ambient-sourced Mediterranean corals, of both species, decreased heterotrophy in response to six months of low pH. Despite maintaining energy reserves, lower net photosynthesis (C. caespitosa) and a trend of declining calcification (A. calycularis) suggest a long-term cost to low heterotrophy under ocean acidification conditions. Conversely, vent-sourced corals maintained moderate (C. caespitosa) or high (A. calycularis) heterotrophic capacity and increased photosynthesis rates (C. caespitosa) in response to six months at low pH, allowing them to sustain themselves physiologically. Provided there is sufficient zooplankton and/or organic matter to meet their heterotrophic needs, vent-sourced corals are more likely to persist this century and potentially be a source for new corals in the Mediterranean.
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Affiliation(s)
- Ann Marie Hulver
- School of Earth Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Chloé Carbonne
- CNRS-INSU, Laboratoire d’Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | - Nuria Teixidó
- CNRS-INSU, Laboratoire d’Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn, Ischia Marine Center, Ischia, Naples, Italy
| | - Steeve Comeau
- CNRS-INSU, Laboratoire d’Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | - Dustin W. Kemp
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elise F. Keister
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jean-Pierre Gattuso
- CNRS-INSU, Laboratoire d’Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
- Institute for Sustainable Development and International Relations, Sciences Po, Paris, France
| | - Andréa G. Grottoli
- School of Earth Sciences, The Ohio State University, Columbus, Ohio, United States of America
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Lin Z, Zheng X, Chen J. Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis. MICROBIAL ECOLOGY 2023; 86:1856-1868. [PMID: 36719456 DOI: 10.1007/s00248-023-02183-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.
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Affiliation(s)
- Zhenyue Lin
- Fujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
- Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350001, China.
| | - Xinqing Zheng
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, 356015, China
| | - Jianming Chen
- Fujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
- Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350001, China.
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Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host. mSystems 2023; 8:e0092122. [PMID: 36688656 PMCID: PMC9948713 DOI: 10.1128/msystems.00921-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Beneficial microorganisms for corals (BMCs) have been demonstrated to be effective probiotics to alleviate bleaching and mitigate coral mortality in vivo. The selection of putative BMCs is traditionally performed manually, using an array of biochemical and molecular tests for putative BMC traits. We present a comprehensive genetic survey of BMC traits using a genome-based framework for the identification of alternative mechanisms that can be used for future in silico selection of BMC strains. We identify exclusive BMC traits associated with specific strains and propose new BMC mechanisms, such as the synthesis of glycine betaine and ectoines. Our roadmap facilitates the selection of BMC strains while increasing the array of genetic targets that can be included in the selection of putative BMC strains to be tested as coral probiotics. IMPORTANCE Probiotics are currently the main hope as a potential medicine for corals, organisms that are considered the marine "canaries of the coal mine" and that are threatened with extinction. Our experiments have proved the concept that probiotics mitigate coral bleaching and can also prevent coral mortality. Here, we present a comprehensive genetic survey of probiotic traits using a genome-based framework. The main outcomes are a roadmap that facilitates the selection of coral probiotic strains while increasing the array of mechanisms that can be included in the selection of coral probiotics.
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Bove CB, Ingersoll MV, Davies SW. Help Me, Symbionts, You're My Only Hope: Approaches to Accelerate our Understanding of Coral Holobiont Interactions. Integr Comp Biol 2022; 62:1756-1769. [PMID: 36099871 DOI: 10.1093/icb/icac141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023] Open
Abstract
Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont-the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome-that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian-Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.
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Affiliation(s)
- Colleen B Bove
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA 02215, USA
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Palladino G, Caroselli E, Tavella T, D'Amico F, Prada F, Mancuso A, Franzellitti S, Rampelli S, Candela M, Goffredo S, Biagi E. Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO 2 gradient. ISME COMMUNICATIONS 2022; 2:65. [PMID: 37938252 PMCID: PMC9723718 DOI: 10.1038/s43705-022-00152-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 05/13/2023]
Abstract
Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.
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Affiliation(s)
- Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
| | - Erik Caroselli
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Teresa Tavella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Fiorella Prada
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Arianna Mancuso
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Silvia Franzellitti
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Sant'Alberto 163, 48123, Ravenna, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy.
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy.
| | - Stefano Goffredo
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy.
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126, Bologna, Italy.
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
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Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China. Microorganisms 2022; 10:microorganisms10081507. [PMID: 35893564 PMCID: PMC9330434 DOI: 10.3390/microorganisms10081507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.
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Williams SD, Klinges JG, Zinman S, Clark AS, Bartels E, Villoch Diaz Maurino M, Muller EM. Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida's Coral Reef. PeerJ 2022; 10:e13574. [PMID: 35729906 PMCID: PMC9206844 DOI: 10.7717/peerj.13574] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/22/2022] [Indexed: 01/17/2023] Open
Abstract
Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida's Coral Reef and sampled after residing within Mote Marine Laboratory's in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.
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Affiliation(s)
| | - J. Grace Klinges
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America
| | - Samara Zinman
- Nova Southeastern University, Dania Beach, FL, United States of America
| | - Abigail S. Clark
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America,The College of the Florida Keys, Key West, FL, United States of America
| | - Erich Bartels
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America
| | - Marina Villoch Diaz Maurino
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America
| | - Erinn M. Muller
- Mote Marine Laboratory, Sarasota, FL, United States of America
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Dermawan D, Wang YF, You SJ, Jiang JJ, Hsieh YK. Impact of climatic and non-climatic stressors on ocean life and human health: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153387. [PMID: 35081412 DOI: 10.1016/j.scitotenv.2022.153387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Ocean life forms are fundamentally well adapted to natural environmental variations, and they can even tolerate extreme conditions for a short time. However, several anthropogenic stressors are causing such drastic changes in the ocean ecosystem. First, the review attempts to outline the impact of climatic and non-climatic stressors on ocean life, and it also outlines the synergistic impact of both stressors. Then the impact on human health caused by the damage of the marine ecosystem has been discussed. Furthermore, the type of prior studies and current mitigation adaptation programs have been presented. Finally, some perspectives about future research and mitigation adaptation are offered.
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Affiliation(s)
- Denny Dermawan
- Department of Environmental Engineering, Chung Yuan Christian University, Chung-Li 320, Taiwan; Department of Civil Engineering, Chung Yuan Christian University, Chung-Li 320, Taiwan
| | - Ya-Fen Wang
- Department of Environmental Engineering, Chung Yuan Christian University, Chung-Li 320, Taiwan; Center for Environmental Risk Management, Chung Yuan Christian University, Chung-Li 32023, Taiwan
| | - Sheng-Jie You
- Department of Environmental Engineering, Chung Yuan Christian University, Chung-Li 320, Taiwan; Center for Environmental Risk Management, Chung Yuan Christian University, Chung-Li 32023, Taiwan
| | - Jheng-Jie Jiang
- Department of Environmental Engineering, Chung Yuan Christian University, Chung-Li 320, Taiwan; Center for Environmental Risk Management, Chung Yuan Christian University, Chung-Li 32023, Taiwan
| | - Yen-Kung Hsieh
- Marine Ecology and Conservation Research Center, National Academy of Marine Research, Kaohsiung 80661, Taiwan; Department of Environmental Science and Occupational Safety and Health, Tajen University, Pingtung, Taiwan.
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Wu B, Luo S, Luo H, Huang H, Xu F, Feng S, Xu H. Improved phytoremediation of heavy metal contaminated soils by Miscanthus floridulus under a varied rhizosphere ecological characteristic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151995. [PMID: 34856269 DOI: 10.1016/j.scitotenv.2021.151995] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/02/2021] [Accepted: 11/22/2021] [Indexed: 05/21/2023]
Abstract
Miscanthus floridulus is a plant with high biomass and heavy metal tolerance, which is a good candidate for phytoremediation. It is essential to explore how to improve its remediation ability, especially the rhizosphere ecological characteristics which are significant for phytoremediation efficiency. Therefore, the heavy metals accumulation of M. floridulus, rhizosphere soil physicochemical properties, enzyme activities, and bacterial community of different distances from the tailing were measured, focusing on the relationship between phytoremediation ability and rhizosphere ecological characteristics. The results show that the stronger the phytoremediation ability is, the better is the soil environment, and the higher the coverage with plants. Soil rhizosphere environment and the phytoremediation ability are shaped by heavy metals. Rhizosphere microecology may regulate phytoremediation by improving soil nutrients and enzyme activities, alleviating heavy metal toxicity, changing rhizosphere microbial community structure, increasing beneficial microbial abundance, promoting heavy metals accumulation by plants. This study not only clarified the relationship between rhizosphere ecological factors, but also elucidated the phytoremediation regulatory mechanism. Some of microbial taxa might developed as biological bioinoculants, providing the possibility to promote the growth of plants with ecological restoration ability and improve the phytoremediation efficiency.
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Affiliation(s)
- Bohan Wu
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Shihua Luo
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Huanyan Luo
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Huayan Huang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Fei Xu
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Su Feng
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.
| | - Heng Xu
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Key Laboratory of Environment Protection, Soil Ecological Protection and Pollution Control, Sichuan University & Department of Ecology and Environment of Sichuan, Chengdu 610065, Sichuan, PR China.
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11
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Chapron L, Galand PE, Pruski AM, Peru E, Vétion G, Robin S, Lartaud F. Resilience of cold-water coral holobionts to thermal stress. Proc Biol Sci 2021; 288:20212117. [PMID: 34905712 PMCID: PMC8670956 DOI: 10.1098/rspb.2021.2117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/23/2021] [Indexed: 12/24/2022] Open
Abstract
Cold-water corals are threatened by global warming, especially in the Mediterranean Sea where they live close to their upper known thermal limit (i.e. 13°C), yet their response to rising temperatures is not well known. Here, temperature effects on Lophelia pertusa and Madrepora oculata holobionts (i.e. the host and its associated microbiome) were investigated. We found that at warmer seawater temperature (+2°C), L. pertusa showed a modification of its microbiome prior to a change in behaviour, leading to lower energy reserves and skeletal growth, whereas M. oculata was more resilient. At extreme temperature (+4°C), both species quickly lost their specific bacterial signature followed by lower physiological activity prior to death. In addition, our results showing the holobionts' negative response to colder temperatures (-3°C), suggest that Mediterranean corals live close to their thermal optimum. The species-specific response to temperature change highlights that global warming may affect dramatically the main deep-sea reef-builders, which would alter the associated biodiversity and related ecosystem services.
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Affiliation(s)
- Leila Chapron
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Pierre E. Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Audrey M. Pruski
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Erwan Peru
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Gilles Vétion
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Sarah Robin
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Franck Lartaud
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Observatoire Océanologique, 66650, Banyuls/Mer, France
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12
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Barreto MM, Ziegler M, Venn A, Tambutté E, Zoccola D, Tambutté S, Allemand D, Antony CP, Voolstra CR, Aranda M. Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata. Front Microbiol 2021; 12:707674. [PMID: 34899619 PMCID: PMC8656159 DOI: 10.3389/fmicb.2021.707674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.
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Affiliation(s)
- Marcelle Muniz Barreto
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | | | - Chakkiath Paul Antony
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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13
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Zhou G, Tong H, Cai L, Huang H. Transgenerational Effects on the Coral Pocillopora damicornis Microbiome Under Ocean Acidification. MICROBIAL ECOLOGY 2021; 82:572-580. [PMID: 33576852 DOI: 10.1007/s00248-021-01690-2] [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: 08/24/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Reef-building corals are inhabited by functionally diverse microorganisms which play important roles in coral health and persistence in the Anthropocene. However, our understanding of the complex associations within coral holobionts is largely limited, particularly transgenerational exposure to environmental stress, like ocean acidification. Here we investigated the microbiome development of an ecologically important coral Pocillopora damicornis following transgenerational exposure to moderate and high pCO2 (partial pressure of CO2) levels, using amplicon sequencing and analysis. Our results showed that the Symbiodiniaceae community structures in adult and juvenile had similar patterns, all of which were dominated by Durusdinium spp., previously known as clade D. Conversely, prokaryotic communities varied between adults and juveniles, possibly driven by the effect of host development. Surprisingly, there were no significant changes in both Symbiodiniaceae and prokaryotic communities with different pCO2 treatments, which was independent of the life history stage. This study shows that ocean acidification has no significant effect on P. damicornis microbiome, and warrants further research to test whether transgenerational acclimation exists in coral holobiont to projected future climate change.
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Affiliation(s)
- Guowei Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, China.
- Sanya National Marine Ecosystem Research Station and Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China.
| | - Haoya Tong
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, China
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, SAR, China
| | - Lin Cai
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, SAR, China
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, China.
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research and Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, China.
- Sanya National Marine Ecosystem Research Station and Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China.
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14
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Cross-Linked Regulation of Coral-Associated Dinoflagellates and Bacteria in Pocillopora sp. during High-Temperature Stress and Recovery. Microorganisms 2021; 9:microorganisms9091972. [PMID: 34576867 PMCID: PMC8468813 DOI: 10.3390/microorganisms9091972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
As the problem of ocean warming worsens, the environmental adaptation potential of symbiotic Symbiodiniaceae and bacteria is directly related to the future and fate of corals. This study aimed to analyse the comprehensive community dynamics and physiology of these two groups of organisms in the coral Pocillopora sp. through indoor simulations of heat stress (which involved manually adjusting the temperature between both 26 °C and 34 °C). Heat treatment (≥30 °C) significantly reduced the abundance of Symbiodiniaceae and bacteria by more than 70%. After the temperature was returned to 26 °C for one month, the Symbiodiniaceae density was still low, while the absolute number of bacteria quickly recovered to 55% of that of the control. At this time point, the Fv/Fm value rose to 91% of the pretemperature value. The content of chlorophyll b associated with Cyanobacteria increased by 50% compared with that under the control conditions. Moreover, analysis of the Symbiodiniaceae subclade composition suggested that the relative abundance of C1c.C45, C1, and C1ca increased during heat treatment, indicating that they might constitute heat-resistant subgroups. We suggest that the increase in the absolute number of bacteria during the recovery period could be an important indicator of coral holobiont recovery after heat stress. This study provides insight into the cross-linked regulation of key symbiotic microbes in the coral Pocillopora sp. during high-temperature stress and recovery and provides a scientific basis for exploring the mechanism underlying coral adaptation to global warming.
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15
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Yu H, Zheng X, Weng W, Yan X, Chen P, Liu X, Peng T, Zhong Q, Xu K, Wang C, Shu L, Yang T, Xiao F, He Z, Yan Q. Synergistic effects of antimony and arsenic contaminations on bacterial, archaeal and fungal communities in the rhizosphere of Miscanthus sinensis: Insights for nitrification and carbon mineralization. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125094. [PMID: 33486227 DOI: 10.1016/j.jhazmat.2021.125094] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
The impacts of metal(loids) on soil microbial communities are research focuses to understand nutrient cycling in heavy metal-contaminated environments. However, how antimony (Sb) and arsenic (As) contaminations synergistically affect microbially-driven ecological processes in the rhizosphere of plants is poorly understood. Here we examined the synergistic effects of Sb and As contaminations on bacterial, archaeal and fungal communities in the rhizosphere of a pioneer plant (Miscanthus sinensis) by focusing on soil carbon and nitrogen cycle. High contamination (HC) soils showed significantly lower levels of soil enzymatic activities, carbon mineralization and nitrification potential than low contamination (LC) environments. Multivariate analysis indicated that Sb and As fractions, pH and available phosphorus (AP) were the main factors affecting the structure and assembly of microbial communities, while Sb and As contaminations reduced the microbial alpha-diversity and interspecific interactions. Random forest analysis showed that microbial keystone taxa provided better predictions for soil carbon mineralization and nitrification under Sb and As contaminations. Partial least squares path modeling indicated that Sb and As contaminations could reduce the carbon mineralization and nitrification by influencing the microbial biomass, alpha-diversity and soil enzyme activities. This study enhances our understanding of microbial carbon and nitrogen cycling affected by Sb and As contaminations.
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Affiliation(s)
- Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Wanlin Weng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xizhe Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Pubo Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Tao Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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16
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Lamim VB, Procópio L. Influence of Acidification and Warming of Seawater on Biofouling by Bacteria Grown over API 5L Steel. Indian J Microbiol 2021; 61:151-159. [PMID: 33927456 DOI: 10.1007/s12088-021-00925-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
The acidification and warming of seawater have several impacts on marine organisms, including over microorganisms. The influence of acidification and warming of seawater on biofilms grown on API 5L steel surfaces was evaluated by sequencing the 16S ribosomal gene. For this, three microcosms were designed, the first simulating the natural marine environment (MCC), the second with a decrease in pH from 8.1 to 7.9, and an increase in temperature by 2 °C (MMS), and the third with pH in around 7.7 and an increase in temperature of 4 °C (MES). The results showed that MCC was dominated by the Gammaproteobacteria class, mainly members of the Alteromonadales Order. The second most abundant group was Alphaproteobacteria, with a predominance of Rhodobacterales and Oceanospirillales. In the MMS system there was a balance between representatives of the Gammaproteobacteria and Alphaproteobacteria classes. In MES there was an inversion in the representations of the most prevalent classes previously described in MCC. In this condition, there was a predominance of members of the Alphaproteobacteria Class, in contrast to the decrease in the abundance of Gammaproteobacteria members. These results suggest that possible future climate changes may influence the dynamics of the biofouling process in surface metals. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00925-7.
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Affiliation(s)
- Victória Brigido Lamim
- Microbial Corrosion Laboratory, Estácio University (UNESA), Bispo Street, 83, Room, AG405, Rio de Janeiro, Rio de Janeiro 20261-063 Brazil
| | - Luciano Procópio
- Microbial Corrosion Laboratory, Estácio University (UNESA), Bispo Street, 83, Room, AG405, Rio de Janeiro, Rio de Janeiro 20261-063 Brazil
- Industrial Microbiology and Bioremediation Department, Federal University of Rio de Janeiro (UFRJ), Estrada de Xerém, 27, Duque de Caxias, Rio de Janeiro Brazil
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17
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Kerfahi D, Harvey BP, Agostini S, Kon K, Huang R, Adams JM, Hall-Spencer JM. Responses of Intertidal Bacterial Biofilm Communities to Increasing pCO 2. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:727-738. [PMID: 32185542 DOI: 10.1007/s10126-020-09958-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/21/2020] [Indexed: 06/10/2023]
Abstract
The effects of ocean acidification on ecosystems remain poorly understood, because it is difficult to simulate the effects of elevated CO2 on entire marine communities. Natural systems enriched in CO2 are being used to help understand the long-term effects of ocean acidification in situ. Here, we compared biofilm bacterial communities on intertidal cobbles/boulders and bedrock along a seawater CO2 gradient off Japan. Samples sequenced for 16S rRNA showed differences in bacterial communities with different pCO2 and between habitat types. In both habitats, bacterial diversity increased in the acidified conditions. Differences in pCO2 were associated with differences in the relative abundance of the dominant phyla. However, despite the differences in community composition, there was no indication that these changes would be significant for nutrient cycling and ecosystem function. As well as direct effects of seawater chemistry on the biofilm, increased microalgal growth and decreased grazing may contribute to the shift in bacterial composition at high CO2, as documented by other studies. Thus, the effects of changes in bacterial community composition due to globally increasing pCO2 levels require further investigation to assess the implications for marine ecosystem function. However, the apparent lack of functional shifts in biofilms along the pCO2 gradient is a reassuring indicator of stability of their ecosystem functions in shallow ocean margins.
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Affiliation(s)
- Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, 42601, Republic of Korea
| | - Ben P Harvey
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, Japan
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, Japan
| | - Koetsu Kon
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, Japan
| | - Ruiping Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361100, Fujian, China
| | - Jonathan M Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, 210008, China.
| | - Jason M Hall-Spencer
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, Japan
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
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18
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Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific. Sci Rep 2020; 10:19990. [PMID: 33203914 PMCID: PMC7672225 DOI: 10.1038/s41598-020-76792-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/30/2020] [Indexed: 12/28/2022] Open
Abstract
Corals are dependent upon lipids as energy reserves to mount a metabolic response to biotic and abiotic challenges. This study profiled lipids, fatty acids, and microbial communities of healthy and white syndrome (WS) diseased colonies of Acropora hyacinthus sampled from reefs in Western Australia, the Great Barrier Reef, and Palmyra Atoll. Total lipid levels varied significantly among locations, though a consistent stepwise decrease from healthy tissues from healthy colonies (HH) to healthy tissue on WS-diseased colonies (HD; i.e. preceding the lesion boundary) to diseased tissue on diseased colonies (DD; i.e. lesion front) was observed, demonstrating a reduction in energy reserves. Lipids in HH tissues were comprised of high energy lipid classes, while HD and DD tissues contained greater proportions of structural lipids. Bacterial profiling through 16S rRNA gene sequencing and histology showed no bacterial taxa linked to WS causation. However, the relative abundance of Rhodobacteraceae-affiliated sequences increased in DD tissues, suggesting opportunistic proliferation of these taxa. While the cause of WS remains inconclusive, this study demonstrates that the lipid profiles of HD tissues was more similar to DD tissues than to HH tissues, reflecting a colony-wide systemic effect and provides insight into the metabolic immune response of WS-infected Indo-Pacific corals.
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19
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Thinesh T, Meenatchi R, Lipton AN, Anandham R, Jose PA, Tang SL, Seghal Kiran G, Selvin J. Metagenomic sequencing reveals altered bacterial abundance during coral-sponge interaction: Insights into the invasive process of coral-killing sponge Terpios hoshinota. Microbiol Res 2020; 240:126553. [PMID: 32711340 DOI: 10.1016/j.micres.2020.126553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/26/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023]
Abstract
The coral-killing invasive sponge, Terpios hoshinota, causes extensive mortality to live corals and is a potential threat to reefs at different geographical locations. However, to date, the invasive mechanism remains largely unknown. In this study, we aimed to understand the bacterial competition between sponge and coral hosted bacteria when sponge outcompetes corals. We analysed the bacterial community of Terpios-invaded coral tissue, and the adjacent healthy tissue of sponge-invaded Favites colonies from Palk bay reef (South East Asia) of the Indian Ocean by using next-generation sequencing. Comparative analysis revealed similar bacterial diversity in both healthy and sponge covered coral tissues. However, relative abundance found to be differed between the groups. Terpios covered coral tissue had higher bacterial abundance than the healthy coral tissue. Bacterial phyla such as Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia live both in sponge covered and healthy coral tissue. Notably, many of the lower abundant bacteria in healthy coral tissue (abundance <1%) became the most abundant in sponge-invaded tissue. In particular, the genus Neisseria, Bacteroides, and members of Pseudoalteromonas predominant in sponge-invaded tissue. Similar bacterial diversity between normal and and sponge-invaded coral tissues suggest that bacteria follow an exploitative competition, which might favoured sponge growth over corals.
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Affiliation(s)
- T Thinesh
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - R Meenatchi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Anuj Nishanth Lipton
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu 625 104, India
| | - Polpass Arul Jose
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu 625 104, India
| | - Sen-Lin Tang
- Biodiversity Research Centre, Academia sinica, Taiwan
| | - G Seghal Kiran
- Department of Food Science and Technology, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
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20
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Biagi E, Caroselli E, Barone M, Pezzimenti M, Teixido N, Soverini M, Rampelli S, Turroni S, Gambi MC, Brigidi P, Goffredo S, Candela M. Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138048. [PMID: 32251879 DOI: 10.1016/j.scitotenv.2020.138048] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
Coral microbiomes, the complex microbial communities associated with the different anatomic compartments of the coral, provide important functions for the host's survival, such as nutrient cycling at the host's surface, prevention of pathogens colonization, and promotion of nutrient uptake. Microbiomes are generally referred to as plastic entities, able to adapt their composition and functionality in response to environmental change, with a possible impact on coral acclimatization to phenomena related to climate change, such as ocean acidification. Ocean sites characterized by natural gradients of pCO2 provide models for investigating the ability of marine organisms to acclimatize to decreasing seawater pH. Here we compared the microbiome of the temperate, shallow water, non-symbiotic solitary coral Astroides calycularis that naturally lives at a volcanic CO2 vent in Ischia Island (Naples, Italy), with that of corals living in non-acidified sites at the same island. Bacterial DNA associated with the different anatomic compartments (mucus, tissue and skeleton) of A. calycularis was differentially extracted and a total of 68 samples were analyzed by 16S rRNA gene sequencing. In terms of phylogenetic composition, the microbiomes associated with the different coral anatomic compartments were different from each other and from the microbial communities of the surrounding seawater. Of all the anatomic compartments, the mucus-associated microbiome differed the most between the control and acidified sites. The differences detected in the microbial communities associated to the three anatomic compartments included a general increase in subdominant bacterial groups, some of which are known to be involved in different stages of the nitrogen cycle, such as potential nitrogen fixing bacteria and bacteria able to degrade organic nitrogen. Our data therefore suggests a potential increase of nitrogen fixation and recycling in A. calycularis living close to the CO2 vent system.
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Affiliation(s)
- Elena Biagi
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Erik Caroselli
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032 Fano, Pesaro Urbino, Italy
| | - Monica Barone
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Martina Pezzimenti
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Nuria Teixido
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, 181 chemin du Lazaret, F-06230 Villefranche-sur-Mer, France; Villa Dohrn-Benthic Ecology Center, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80077 Ischia (Naples), Italy
| | - Matteo Soverini
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Simone Rampelli
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Silvia Turroni
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Maria Cristina Gambi
- Villa Dohrn-Benthic Ecology Center, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80077 Ischia (Naples), Italy
| | - Patrizia Brigidi
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Stefano Goffredo
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032 Fano, Pesaro Urbino, Italy.
| | - Marco Candela
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032 Fano, Pesaro Urbino, Italy.
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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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22
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Meron D, Maor-Landaw K, Eyal G, Elifantz H, Banin E, Loya Y, Levy O. The Complexity of the Holobiont in the Red Sea Coral Euphyllia paradivisa under Heat Stress. Microorganisms 2020; 8:E372. [PMID: 32155796 PMCID: PMC7143197 DOI: 10.3390/microorganisms8030372] [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: 02/11/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 11/16/2022] Open
Abstract
The recognition of the microbiota complexity and their role in the evolution of their host is leading to the popularization of the holobiont concept. However, the coral holobiont (host and its microbiota) is still enigmatic and unclear. Here, we explore the complex relations between different holobiont members of a mesophotic coral Euphyllia paradivisa. We subjected two lines of the coral-with photosymbionts, and without photosymbionts (apo-symbiotic)-to increasing temperatures and to antibiotics. The different symbiotic states were characterized using transcriptomics, microbiology and physiology techniques. The bacterial community's composition is dominated by bacteroidetes, alphaproteobacteria, and gammaproteobacteria, but is dependent upon the symbiont state, colony, temperature treatment, and antibiotic exposure. Overall, the most important parameter determining the response was whether the coral was a symbiont/apo-symbiotic, while the colony and bacterial composition were secondary factors. Enrichment Gene Ontology analysis of coral host's differentially expressed genes demonstrated the cellular differences between symbiotic and apo-symbiotic samples. Our results demonstrate the significance of each component of the holobiont consortium and imply a coherent link between them, which dramatically impacts the molecular and cellular processes of the coral host, which possibly affect its fitness, particularly under environmental stress.
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Affiliation(s)
- Dalit Meron
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- Morris Kahn Marine Research Station, University of Haifa, Haifa 3498838, Israel
| | - Keren Maor-Landaw
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gal Eyal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland St. Lucia, Qld 4072, Australia
| | - Hila Elifantz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- The Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yossi Loya
- Department of Zoology, Tel-Aviv University, Tel Aviv 6997801, Israel;
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
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23
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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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24
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Changes in the metabolic potential of the sponge microbiome under ocean acidification. Nat Commun 2019; 10:4134. [PMID: 31515490 PMCID: PMC6742649 DOI: 10.1038/s41467-019-12156-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/15/2019] [Indexed: 01/05/2023] Open
Abstract
Anthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of marine organisms. Here we assess the possible effects of ocean acidification on the metabolic potential of sponge symbionts, inferred by metagenomic analyses of the microbiomes of two sponge species sampled at a shallow volcanic CO2 seep and a nearby control reef. When comparing microbial functions between the seep and control sites, the microbiome of the sponge Stylissa flabelliformis (which is more abundant at the control site) exhibits at the seep reduced potential for uptake of exogenous carbohydrates and amino acids, and for degradation of host-derived creatine, creatinine and taurine. The microbiome of Coelocarteria singaporensis (which is more abundant at the seep) exhibits reduced potential for carbohydrate import at the seep, but greater capacity for archaeal carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate pathway, as well as archaeal and bacterial urea production and ammonia assimilation from arginine and creatine catabolism. Together these metabolic features might contribute to enhanced tolerance of the sponge symbionts, and possibly their host, to ocean acidification.
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25
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Chan WY, Peplow LM, Menéndez P, Hoffmann AA, Oppen MJH. The roles of age, parentage and environment on bacterial and algal endosymbiont communities in
Acropora
corals. Mol Ecol 2019; 28:3830-3843. [DOI: 10.1111/mec.15187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/28/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Wing Yan Chan
- Australian Institute of Marine Science Townsville Qld Australia
- School of BioSciences University of Melbourne Parkville Vic. Australia
| | - Lesa M. Peplow
- Australian Institute of Marine Science Townsville Qld Australia
| | - Patricia Menéndez
- Australian Institute of Marine Science Townsville Qld Australia
- Department of Econometrics and Business Statistics, School of Mathematics and Physics Monash University Clayton Vic. Australia
| | - Ary A. Hoffmann
- Bio21 Institute University of Melbourne Parkville Vic. Australia
| | - Madeleine J. H. Oppen
- Australian Institute of Marine Science Townsville Qld Australia
- School of BioSciences University of Melbourne Parkville Vic. Australia
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26
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Ahmed HI, Herrera M, Liew YJ, Aranda M. Long-Term Temperature Stress in the Coral Model Aiptasia Supports the "Anna Karenina Principle" for Bacterial Microbiomes. Front Microbiol 2019; 10:975. [PMID: 31139158 PMCID: PMC6517863 DOI: 10.3389/fmicb.2019.00975] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
The understanding of host-microbial partnerships has become a hot topic during the last decade as it has been shown that associated microbiota play critical roles in the host physiological functions and susceptibility to diseases. Moreover, the microbiome may contribute to host resilience to environmental stressors. The sea anemone Aiptasia is a good laboratory model system to study corals and their microbial symbiosis. In this regard, studying its bacterial microbiota provides a better understanding of cnidarian metaorganisms as a whole. Here, we investigated the bacterial communities of different Aiptasia host-symbiont combinations under long-term heat stress in laboratory conditions. Following a 16S rRNA gene sequencing approach we were able to detect significant differences in the bacterial composition and structure of Aiptasia reared at different temperatures. A higher number of taxa (i.e., species richness), and consequently increased α-diversity and β-dispersion, were observed in the microbiomes of heat-stressed individuals across all host strains and experimental batches. Our findings are in line with the recently proposed Anna Karenina principle (AKP) for animal microbiomes, which states that dysbiotic or stressed organisms have a more variable and unstable microbiome than healthy ones. Microbial interactions affect the fitness and survival of their hosts, thus exploring the AKP effect on animal microbiomes is important to understand host resilience. Our data contributes to the current knowledge of the Aiptasia holobiont and to the growing field of study of host-associated microbiomes.
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Affiliation(s)
| | | | | | - Manuel Aranda
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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27
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Wang N, Wang A, Xie J, He M. Responses of soil fungal and archaeal communities to environmental factors in an ongoing antimony mine area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 652:1030-1039. [PMID: 30586790 DOI: 10.1016/j.scitotenv.2018.10.300] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Microorganisms are vital to biogeochemical cycles. However, heavy metal contamination has been implicated in altering the microbial community. Antimony (Sb) and arsenic (As) in soils can alter soil bacterial community composition in previous studies and, therefore, may have effects on soil fungal and archaeal community composition. The aim of this study was to assess the microbial activity and fungal and archaeal community composition in long-term Sb and As contamination areas. We analyzed soil respiration rates from 247.91 μg C/kg SDW h to 1372.93 μg C/kg SDW h, which revealed a positive correlation with concentrations of antimony (r = 0.79). The microbial diversity indices (Shannon and Simpson indices) showed that the abundances of the fungal and archaeal communities were more sensitive to As. Redundancy analysis (RDA) revealed that soil properties and contamination are drivers controlling the fungal and archaeal community. All of these two microbial groups responded strongly to pH. However, the dominant drivers for fungal and archaeal community composition were very different. These differences were related to limiting conditions for different species, with fungal community composition affected strongly by pH, TC, TSb, RI and SbDGT, while archaeal community composition was mainly affected by the pH, AsDGT and TAs. Furthermore, soil respiration showed a very strong relationship with fungal community composition with r2 = 0,60, p < 0.01. These results showed that microbial responses to contamination gradients of Sb and As were heterogeneous due to the limiting environmental conditions of different microbial taxa.
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Affiliation(s)
- Ningning Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Aihuan Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jun Xie
- Environmental Monitoring Station of Lenshuijiang City, Lenshuijiang 417500, Hunan, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
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28
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O’Brien PA, Smith HA, Fallon S, Fabricius K, Willis BL, Morrow KM, Bourne DG. Elevated CO 2 Has Little Influence on the Bacterial Communities Associated With the pH-Tolerant Coral, Massive Porites spp. Front Microbiol 2018; 9:2621. [PMID: 30443242 PMCID: PMC6221987 DOI: 10.3389/fmicb.2018.02621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Ocean acidification (OA) as a result of increased anthropogenic CO2 input into the atmosphere carries consequences for all ocean life. Low pH can cause a shift in coral-associated microbial communities of pCO2-sensitive corals, however, it remains unknown whether the microbial community is also influenced in corals known to be more tolerant to high pCO2/low pH. This study profiles the bacterial communities associated with the tissues of the pCO2-tolerant coral, massive Porites spp., from two natural CO2 seep sites in Papua New Guinea. Amplicon sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene revealed that microbial communities remained stable across CO2 seep sites (pH = 7.44-7.85) and adjacent control sites (ambient pH = 8.0-8.1). Microbial communities were more significantly influenced by reef location than pH, with the relative abundance of dominant microbial taxa differing between reefs. These results directly contrast with previous findings that increased CO2 has a strong effect on structuring microbial communities. The stable structure of microbial communities associated with the tissues of massive Porites spp. under high pCO2/low pH conditions confirms a high degree of tolerance by the whole Porites holobiont to OA, and suggest that pH tolerant corals such as Porites may dominate reef assemblages in an increasingly acidic ocean.
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Affiliation(s)
- Paul A. O’Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Hillary A. Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Stewart Fallon
- Research School of Earth Sciences, The Australian National University, Canberra, ACT, Australia
| | | | - Bette L. Willis
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Kathleen M. Morrow
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States
| | - David G. Bourne
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States
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29
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Franzellitti S, Airi V, Calbucci D, Caroselli E, Prada F, Voolstra CR, Mass T, Falini G, Fabbri E, Goffredo S. Transcriptional response of the heat shock gene hsp70 aligns with differences in stress susceptibility of shallow-water corals from the Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2018; 140:444-454. [PMID: 30055833 DOI: 10.1016/j.marenvres.2018.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Shallow-water corals of the Mediterranean Sea are facing a dramatic increase in water temperature due to climate change, predicted to increase the frequency of bleaching and mass mortality events. However, supposedly not all corals are affected equally, as they show differences in stress susceptibility, as suggested by physiological outputs of corals along temperature gradients and under controlled conditions in terms of reproduction, demography, growth, calcification, and photosynthetic efficiency. In this study, gene expression and induction of a 70-kDa heat shock protein (HSP70) was analyzed in five common shallow-water hard corals in the Mediterranean Sea, namely Astroides calycularis, Balanophyllia europaea, Caryophyllia inornata, Cladocora caespitosa, and Leptopsammia pruvoti. The main aim was to assess the contribution of this evolutionary conserved cytoprotective mechanism to the physiological plasticity of these species that possess different growth modes (solitary vs colonial) and trophic strategies (zooxanthellate vs azooxanthellate). Using quantitative real-time PCR, in situ hsp70 baseline levels and expression profiles after a heat-shock exposure were assessed. Levels of hsp70 and heat stress induction were higher in zooxanthellate than in azooxanthellate species, and different heat stress transcriptional profiles were observed between colonial and solitary zooxanthellate corals. On the whole, the hsp70 transcriptional response to heat stress aligns with stress susceptibility of the species and suggests a contribution of trophic strategy and morphology in shaping coral resilience to stress. Understanding these molecular processes may contribute to assess the potential effects and relative resilience of Mediterranean corals under climate change.
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Affiliation(s)
- Silvia Franzellitti
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via S. Alberto 163, I-48123, Ravenna, Italy.
| | - Valentina Airi
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
| | - Diana Calbucci
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via S. Alberto 163, I-48123, Ravenna, Italy
| | - Erik Caroselli
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
| | - Fiorella Prada
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Multi Purpose Boulevard, Mt. Carmel, Haifa, 3498838, Israel
| | - Giuseppe Falini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, via F. Selmi 2, I-40126, Bologna, Italy
| | - Elena Fabbri
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences, University of Bologna, via S. Alberto 163, I-48123, Ravenna, Italy
| | - Stefano Goffredo
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via F. Selmi 3, I-40126, Bologna, Italy
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30
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Äijö T, Müller CL, Bonneau R. Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. Bioinformatics 2018; 34:372-380. [PMID: 28968799 PMCID: PMC5860357 DOI: 10.1093/bioinformatics/btx549] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 08/01/2017] [Accepted: 09/12/2017] [Indexed: 12/28/2022] Open
Abstract
Motivation The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis. Results To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence and environmental noise models. Availability and implementation A Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome. Contact taijo@flatironinstitute.org or rb113@nyu.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | | | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
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31
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Rubio-Portillo E, Kersting DK, Linares C, Ramos-Esplá AA, Antón J. Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea. Front Microbiol 2018; 9:22. [PMID: 29410656 PMCID: PMC5787083 DOI: 10.3389/fmicb.2018.00022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/05/2018] [Indexed: 12/21/2022] Open
Abstract
The endemic Mediterranean zooxanthellate scleractinian reef-builder Cladocora caespitosa is among the organisms most affected by warming-related mass mortality events in the Mediterranean Sea. Corals are known to contain a diverse microbiota that plays a key role in their physiology and health. Here we report the first study that examines the microbiome and pathobiome associated with C. caespitosa in three different Mediterranean locations (i.e., Genova, Columbretes Islands, and Tabarca Island). The microbial communities associated with this species showed biogeographical differences, but shared a common core microbiome that probably plays a key role in the coral holobiont. The putatively pathogenic microbial assemblage (i.e., pathobiome) of C. caespitosa also seemed to depend on geographic location and the human footprint. In locations near the coast and with higher human influence, the pathobiome was entirely constituted by Vibrio species, including the well-known coral pathogens Vibrio coralliilyticus and V. mediterranei. However, in the Columbretes Islands, located off the coast and the most pristine of the analyzed locations, no changes among microbial communities associated to healthy and necrosed samples were detected. Hence, our results provide new insights into the microbiome of the temperate corals and its role in coral health status, highlighting its dependence on the local environmental conditions and the human footprint.
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Affiliation(s)
- Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Diego K Kersting
- Working Group on Geobiology and Anthropocene Research, Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany.,Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
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32
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Grottoli AG, Dalcin Martins P, Wilkins MJ, Johnston MD, Warner ME, Cai WJ, Melman TF, Hoadley KD, Pettay DT, Levas S, Schoepf V. Coral physiology and microbiome dynamics under combined warming and ocean acidification. PLoS One 2018; 13:e0191156. [PMID: 29338021 PMCID: PMC5770069 DOI: 10.1371/journal.pone.0191156] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/01/2018] [Indexed: 11/23/2022] Open
Abstract
Rising seawater temperature and ocean acidification threaten the survival of coral reefs. The relationship between coral physiology and its microbiome may reveal why some corals are more resilient to these global change conditions. Here, we conducted the first experiment to simultaneously investigate changes in the coral microbiome and coral physiology in response to the dual stress of elevated seawater temperature and ocean acidification expected by the end of this century. Two species of corals, Acropora millepora containing the thermally sensitive endosymbiont C21a and Turbinaria reniformis containing the thermally tolerant endosymbiont Symbiodinium trenchi, were exposed to control (26.5°C and pCO2 of 364 μatm) and treatment (29.0°C and pCO2 of 750 μatm) conditions for 24 days, after which we measured the microbial community composition. These microbial findings were interpreted within the context of previously published physiological measurements from the exact same corals in this study (calcification, organic carbon flux, ratio of photosynthesis to respiration, photosystem II maximal efficiency, total lipids, soluble animal protein, soluble animal carbohydrates, soluble algal protein, soluble algal carbohydrate, biomass, endosymbiotic algal density, and chlorophyll a). Overall, dually stressed A. millepora had reduced microbial diversity, experienced large changes in microbial community composition, and experienced dramatic physiological declines in calcification, photosystem II maximal efficiency, and algal carbohydrates. In contrast, the dually stressed coral T. reniformis experienced a stable and more diverse microbiome community with minimal physiological decline, coupled with very high total energy reserves and particulate organic carbon release rates. Thus, the microbiome changed and microbial diversity decreased in the physiologically sensitive coral with the thermally sensitive endosymbiotic algae but not in the physiologically tolerant coral with the thermally tolerant endosymbiont. Our results confirm recent findings that temperature-stress tolerant corals have a more stable microbiome, and demonstrate for the first time that this is also the case under the dual stresses of ocean warming and acidification. We propose that coral with a stable microbiome are also more physiologically resilient and thus more likely to persist in the future, and shape the coral species diversity of future reef ecosystems.
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Affiliation(s)
- Andréa G. Grottoli
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
- * E-mail:
| | - Paula Dalcin Martins
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Michael J. Wilkins
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Michael D. Johnston
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - Wei-Jun Cai
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - Todd F. Melman
- Reef Systems Coral Farm, New Albany, OH, United States of America
| | - Kenneth D. Hoadley
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - D. Tye Pettay
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America
| | - Stephen Levas
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Verena Schoepf
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States of America
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Wang N, Zhang S, He M. Bacterial community profile of contaminated soils in a typical antimony mining site. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:141-152. [PMID: 28039624 DOI: 10.1007/s11356-016-8159-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, SbDGT, AsDGT, potential ecological risk index (RI), TC, TN), among which pH, SbDGT, and AsDGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.
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Affiliation(s)
- Ningning Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Suhuan Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China.
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Marcelino VR, Morrow KM, Oppen MJH, Bourne DG, Verbruggen H. Diversity and stability of coral endolithic microbial communities at a naturally high
p
CO
2
reef. Mol Ecol 2017; 26:5344-5357. [DOI: 10.1111/mec.14268] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 12/15/2022]
Affiliation(s)
| | - Kathleen M. Morrow
- Department of Molecular, Cellular and Biomedical Sciences University of New Hampshire Durham NH USA
- Australian Institute of Marine Science Townsville Qld Australia
| | - Madeleine J. H. Oppen
- School of Biosciences University of Melbourne Melbourne Vic. Australia
- Australian Institute of Marine Science Townsville Qld Australia
| | - David G. Bourne
- Australian Institute of Marine Science Townsville Qld Australia
- College of Science and Engineering James Cook University Townville Qld Australia
| | - Heroen Verbruggen
- School of Biosciences University of Melbourne Melbourne Vic. Australia
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Zhou G, Cai L, Yuan T, Tian R, Tong H, Zhang W, Jiang L, Guo M, Liu S, Qian PY, Huang H. Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO 2. Environ Microbiol 2017. [PMID: 28631353 DOI: 10.1111/1462-2920.13840] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Reef-building corals are complex holobionts, harbouring diverse microorganisms that play essential roles in maintaining coral health. However, microbiome development in early life stages of corals remains poorly understood. Here, microbiomes of Acropora gemmifera were analysed during spawning and early developmental stages, and also under different seawater partial pressure of CO2 (pCO2 ) conditions, using amplicon sequencing of 16S rRNA gene for bacteria and archaea and of ITS2 for Symbiodinium. No remarkable microbiome shift was observed in adults before and after spawning. Moreover, microbiomes in eggs were highly similar to those in spawned adults, possibly suggesting a vertical transmission from parents to offspring. However, significant stage-specific changes were found in coral microbiome during development, indicating that host development played a dominant role in shaping coral microbiome. Specifically, Cyanobacteria were particularly abundant in 6-day-old juveniles, but decreased largely in 31-day-old juveniles with a possible subclade shift in Symbiodinium dominance from C2r to D17. Larval microbiome showed changes in elevated pCO2 , while juvenile microbiomes remained rather stable in response to higher pCO2 . This study provides novel insights into the microbiome development during the critical life stages of coral.
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Affiliation(s)
- Guowei Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, Hainan, China.,Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Lin Cai
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Tao Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Renmao Tian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Haoya Tong
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Weipeng Zhang
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Lei Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Minglan Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Sheng Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Pei-Yuan Qian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, Hainan, China
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36
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Carrier TJ, Reitzel AM. The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire. Front Microbiol 2017; 8:802. [PMID: 28553264 PMCID: PMC5425589 DOI: 10.3389/fmicb.2017.00802] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 04/19/2017] [Indexed: 12/20/2022] Open
Abstract
Our understanding of the diverse interactions between hosts and microbes has grown profoundly over the past two decades and, as a product, has revolutionized our knowledge of the life sciences. Through primarily laboratory experiments, the current framework for holobionts and their respective hologenomes aims to decipher the underpinnings and implications of symbioses between host and microbiome. However, the laboratory setting restricts the full spectrum of host-associated symbionts as compared to those found in nature; thus, limiting the potential for a holistic interpretation of the functional roles the microbiome plays in host biology. When holobionts are studied in nature, associated microbial communities vary considerably between conditions, resulting in more microbial associates as part of the "hologenome" across environments than in either environment alone. We review and synthesize empirical evidence suggesting that hosts may associate with a larger microbial network that, in part, corresponds to experiencing diverse environmental conditions. To conceptualize the interactions between host and microbiome in an ecological context, we suggest the "host-associated microbial repertoire," which is the sum of microbial species a host may associate with over the course of its life-history under all encountered environmental circumstances. Furthermore, using examples from both terrestrial and marine ecosystems, we discuss how this concept may be used as a framework to compare the ability of the holobiont to acclimate and adapt to environmental variation, and propose three "signatures" of the concept.
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Affiliation(s)
- Tyler J Carrier
- Department of Biological Sciences, University of North Charlotte at CharlotteCharlotte, NC, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Charlotte at CharlotteCharlotte, NC, USA
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37
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Weber L, DeForce E, Apprill A. Optimization of DNA extraction for advancing coral microbiota investigations. MICROBIOME 2017; 5:18. [PMID: 28179023 PMCID: PMC5299696 DOI: 10.1186/s40168-017-0229-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/04/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND DNA-based sequencing approaches are commonly used to identify microorganisms and their genes and document trends in microbial community diversity in environmental samples. However, extraction of microbial DNA from complex environmental samples like corals can be technically challenging, and extraction methods may impart biases on microbial community structure. METHODS We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition. During phase I, total DNA was extracted from seven coral species in a replicated experimental design using four different MO BIO Laboratories, Inc., DNA Isolation kits: PowerSoil®, PowerPlant® Pro, PowerBiofilm®, and UltraClean® Tissue & Cells (with three homogenization permutations). Technical performance of the treatments was evaluated using DNA yield and amplification efficiency of small subunit ribosomal RNA (SSU ribosomal RNA (rRNA)) genes. During phase II, potential extraction biases were examined via microbial community analysis of SSU rRNA gene sequences amplified from the most successful DNA extraction treatments. RESULTS In phase I of the study, the PowerSoil® and PowerPlant® Pro extracts contained low DNA concentrations, amplified poorly, and were not investigated further. Extracts from PowerBiofilm® and UltraClean® Tissue and Cells permutations were further investigated in phase II, and analysis of sequences demonstrated that overall microbial community composition was dictated by coral species and not extraction treatment. Finer pairwise comparisons of sequences obtained from Orbicella faveolata, Orbicella annularis, and Acropora humilis corals revealed subtle differences in community composition between the treatments; PowerBiofilm®-associated sequences generally had higher microbial richness and the highest coverage of dominant microbial groups in comparison to the UltraClean® Tissue and Cells treatments, a result likely arising from using a combination of different beads during homogenization. CONCLUSIONS Both the PowerBiofilm® and UltraClean® Tissue and Cells treatments are appropriate for large-scale analyses of coral microbiota. However, studies interested in detecting cryptic microbial members may benefit from using the PowerBiofilm® DNA treatment because of the likely enhanced lysis efficiency of microbial cells attributed to using a variety of beads during homogenization. Consideration of the methodology involved with microbial DNA extraction is particularly important for studies investigating complex host-associated microbiota.
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Affiliation(s)
- Laura Weber
- Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge, MA 02139 USA
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543 USA
| | | | - Amy Apprill
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543 USA
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38
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Scott JJ, Glazer BT, Emerson D. Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō'ihi Seamount. Environ Microbiol 2016; 19:301-316. [PMID: 27871143 DOI: 10.1111/1462-2920.13607] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 01/22/2023]
Abstract
Thirty kilometers south of the island of Hawai'i lies the Lō'ihi Seamount, an active submarine volcano that hosts a network of low-temperature hydrothermal vents enriched in ferrous iron that supports extensive microbial mats. These mats, which can be a half a meter deep, are composed of ferric iron bound to organic polymers - the metabolic byproduct of iron-oxidizing Zetaproteobacteria. Though the role of Zetaproteobacteria in mat formation is well established, we have a limited understanding of how differences in diversity are related to mat morphology. We used Minimum Entropy Decomposition and ZetaOtu classification to demonstrate cryptic diversity between closely related Zetaproteobacteria while showing habitat and geographic specificity. Veiled mats, common structures at Lō'ihi, exhibit distinct community composition and contain diversity not detected in other mat types, including specific Zetaproteobacteria and an unclassified Gammaproteobacteria. Our analyses also indicate that diversity can change dramatically across small spatial transects from points of active venting, yet we found comparatively few differences between major sampling sites. This study provides a better picture of the microbiome responsible for iron mat production at Lō'ihi and has broad implications for our understanding of these globally distributed communities.
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Affiliation(s)
- Jarrod J Scott
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
| | - Brian T Glazer
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd. Honolulu, HI, 96822, USA
| | - David Emerson
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
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39
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Carlos C, Pereira LB, Ottoboni LMM. Comparative genomics of Paracoccus sp. SM22M-07 isolated from coral mucus: insights into bacteria-host interactions. Curr Genet 2016; 63:509-518. [PMID: 27796486 DOI: 10.1007/s00294-016-0658-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
One of the main goals of coral microbiology is to understand the ways in which coral-bacteria associations are established and maintained. This work describes the sequencing of the genome of Paracoccus sp. SM22M-07 isolated from the mucus of the endemic Brazilian coral species Mussismilia hispida. Comparative analysis was used to identify unique genomic features of SM22M-07 that might be involved in its adaptation to the marine ecosystem and the nutrient-rich environment provided by coral mucus, as well as in the establishment and strengthening of the interaction with the host. These features included genes related to the type IV protein secretion system, erythritol catabolism, and succinoglycan biosynthesis. We experimentally confirmed the production of succinoglycan by Paracoccus sp. SM22M-07 and we hypothesize that it may be involved in the association of the bacterium with coral surfaces.
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Affiliation(s)
- Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53703, USA.
| | - Letícia Bianca Pereira
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), C. P. 6010, Campinas, SP, 13083-875, Brazil
| | - Laura Maria Mariscal Ottoboni
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), C. P. 6010, Campinas, SP, 13083-875, Brazil
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40
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Zhou G, Yuan T, Cai L, Zhang W, Tian R, Tong H, Jiang L, Yuan X, Liu S, Qian P, Huang H. Changes in microbial communities, photosynthesis and calcification of the coral Acropora gemmifera in response to ocean acidification. Sci Rep 2016; 6:35971. [PMID: 27786309 PMCID: PMC5082368 DOI: 10.1038/srep35971] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 10/10/2016] [Indexed: 12/24/2022] Open
Abstract
With the increasing anthropogenic CO2 concentration, ocean acidification (OA) can have dramatic effects on coral reefs. However, the effects of OA on coral physiology and the associated microbes remain largely unknown. In the present study, reef-building coral Acropora gemmifera collected from a reef flat with highly fluctuating environmental condition in the South China Sea were exposed to three levels of partial pressure of carbon dioxide (pCO2) (i.e., 421, 923, and 2070 μatm) for four weeks. The microbial community structures associated with A. gemmifera under these treatments were analyzed using 16S rRNA gene barcode sequencing. The results revealed that the microbial community associated with A. gemmifera was highly diverse at the genus level and dominated by Alphaproteobacteria. More importantly, the microbial community structure remained rather stable under different pCO2 treatments. Photosynthesis and calcification in A. gemmifera, as indicated by enrichment of δ18O and increased depletion of δ13C in the coral skeleton, were significantly impaired only at the high pCO2 (2070 μatm). These results suggest that A. gemmifera can maintain a high degree of stable microbial communities despite of significant physiological changes in response to extremely high pCO2.
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Affiliation(s)
- Guowei Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, China.,Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Tao Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Lin Cai
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Weipeng Zhang
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Renmao Tian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Haoya Tong
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Lei Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Xiangcheng Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Sheng Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Peiyuan Qian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, China
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41
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Kellogg CA, Ross SW, Brooke SD. Bacterial community diversity of the deep-sea octocoral Paramuricea placomus. PeerJ 2016; 4:e2529. [PMID: 27703865 PMCID: PMC5047221 DOI: 10.7717/peerj.2529] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/05/2016] [Indexed: 01/08/2023] Open
Abstract
Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth) in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each) and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.
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Affiliation(s)
- Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, US Geological Survey , St. Petersburg , FL , United States of America
| | - Steve W Ross
- Center for Marine Science, University of North Carolina at Wilmington , Wilmington , NC , United States of America
| | - Sandra D Brooke
- Coastal and Marine Laboratory, Florida State University , St. Teresa , FL , United States of America
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42
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Lawler SN, Kellogg CA, France SC, Clostio RW, Brooke SD, Ross SW. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species. Front Microbiol 2016; 7:458. [PMID: 27092120 PMCID: PMC4820459 DOI: 10.3389/fmicb.2016.00458] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/21/2016] [Indexed: 12/19/2022] Open
Abstract
Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.
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Affiliation(s)
- Stephanie N Lawler
- College of Marine Science, University of South Florida, St. Petersburg FL, USA
| | - Christina A Kellogg
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg FL, USA
| | - Scott C France
- Department of Biology, University of Louisiana at Lafayette Lafayette, LA, USA
| | - Rachel W Clostio
- Department of Biology, University of Louisiana at Lafayette Lafayette, LA, USA
| | - Sandra D Brooke
- Coastal and Marine Laboratory, Florida State University, St. Teresa FL, USA
| | - Steve W Ross
- Center for Marine Science, University of North Carolina Wilmington Wilmington, NC, USA
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43
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Röthig T, Ochsenkühn MA, Roik A, van der Merwe R, Voolstra CR. Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome. Mol Ecol 2016; 25:1308-23. [PMID: 26840035 PMCID: PMC4804745 DOI: 10.1111/mec.13567] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 01/03/2023]
Abstract
Scleractinian corals are assumed to be stenohaline osmoconformers, although they are frequently subjected to variations in seawater salinity due to precipitation, freshwater run-off and other processes. Observed responses to altered salinity levels include differences in photosynthetic performance, respiration and increased bleaching and mortality of the coral host and its algal symbiont, but a study looking at bacterial community changes is lacking. Here, we exposed the coral Fungia granulosa to strongly increased salinity levels in short- and long-term experiments to disentangle temporal and compartment effects of the coral holobiont (i.e. coral host, symbiotic algae and associated bacteria). Our results show a significant reduction in calcification and photosynthesis, but a stable microbiome after short-term exposure to high-salinity levels. By comparison, long-term exposure yielded unchanged photosynthesis levels and visually healthy coral colonies indicating long-term acclimation to high-salinity levels that were accompanied by a major coral microbiome restructuring. Importantly, a bacterium in the family Rhodobacteraceae was succeeded by Pseudomonas veronii as the numerically most abundant taxon. Further, taxonomy-based functional profiling indicates a shift in the bacterial community towards increased osmolyte production, sulphur oxidation and nitrogen fixation. Our study highlights that bacterial community composition in corals can change within days to weeks under altered environmental conditions, where shifts in the microbiome may enable adjustment of the coral to a more advantageous holobiont composition.
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Affiliation(s)
- Till Röthig
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Michael A Ochsenkühn
- Biological and Organometallic Catalysis Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Anna Roik
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Riaan van der Merwe
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Zhang YY, Ling J, Yang QS, Wang YS, Sun CC, Sun HY, Feng JB, Jiang YF, Zhang YZ, Wu ML, Dong JD. The diversity of coral associated bacteria and the environmental factors affect their community variation. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1467-1477. [PMID: 25833806 DOI: 10.1007/s10646-015-1454-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 06/04/2023]
Abstract
Coral associated bacterial community potentially has functions relating to coral health, nutrition and disease. Culture-free, 16S rRNA based techniques were used to compare the bacterial community of coral tissue, mucus and seawater around coral, and to investigate the relationship between the coral-associated bacterial communities and environmental variables. The diversity of coral associated bacterial communities was very high, and their composition different from seawater. Coral tissue and mucus had a coral associated bacterial community with higher abundances of Gammaproteobacteria. However, bacterial community in seawater had a higher abundance of Cyanobacteria. Different populations were also found in mucus and tissue from the same coral fragment, and the abundant bacterial species associated with coral tissue was very different from those found in coral mucus. The microbial diversity and OTUs of coral tissue were much higher than those of coral mucus. Bacterial communities of corals from more human activities site have higher diversity and evenness; and the structure of bacterial communities were significantly different from the corals collected from other sites. The composition of bacterial communities associated with same coral species varied with season's changes, geographic differences, and coastal pollution. Unique bacterial groups found in the coral samples from more human activities location were significant positively correlated to chemical oxygen demand. These coral specific bacteria lead to coral disease or adjust to form new function structure for the adaption of different surrounding needs further research.
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Affiliation(s)
- Yan-Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Qing-Song Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hong-Yan Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Jing-Bin Feng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Yu-Feng Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan-Zhou Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jun-De Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
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Bier RL, Bernhardt ES, Boot CM, Graham EB, Hall EK, Lennon JT, Nemergut DR, Osborne BB, Ruiz-González C, Schimel JP, Waldrop MP, Wallenstein MD. Linking microbial community structure and microbial processes: an empirical and conceptual overview. FEMS Microbiol Ecol 2015; 91:fiv113. [DOI: 10.1093/femsec/fiv113] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 01/20/2023] Open
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46
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Krediet CJ, DeNofrio JC, Caruso C, Burriesci MS, Cella K, Pringle JR. Rapid, Precise, and Accurate Counts of Symbiodinium Cells Using the Guava Flow Cytometer, and a Comparison to Other Methods. PLoS One 2015; 10:e0135725. [PMID: 26291447 PMCID: PMC4546242 DOI: 10.1371/journal.pone.0135725] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/25/2015] [Indexed: 11/23/2022] Open
Abstract
In studies of both the establishment and breakdown of cnidarian-dinoflagellate symbiosis, it is often necessary to determine the number of Symbiodinium cells relative to the quantity of host tissue. Ideally, the methods used should be rapid, precise, and accurate. In this study, we systematically evaluated methods for sample preparation and storage and the counting of algal cells using the hemocytometer, a custom image-analysis program for automated counting of the fluorescent algal cells, the Coulter Counter, or the Millipore Guava flow-cytometer. We found that although other methods may have value in particular applications, for most purposes, the Guava flow cytometer provided by far the best combination of precision, accuracy, and efficient use of investigator time (due to the instrument's automated sample handling), while also allowing counts of algal numbers over a wide range and in small volumes of tissue homogenate. We also found that either of two assays of total homogenate protein provided a precise and seemingly accurate basis for normalization of algal counts to the total amount of holobiont tissue.
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Affiliation(s)
- Cory J. Krediet
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jan C. DeNofrio
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Carlo Caruso
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Matthew S. Burriesci
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kristen Cella
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - John R. Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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47
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Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens. Sci Rep 2015; 5:11903. [PMID: 26144865 PMCID: PMC4491727 DOI: 10.1038/srep11903] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/09/2015] [Indexed: 11/29/2022] Open
Abstract
By cultivating turf algae and aggressively defending their territories, territorial damselfishes in the genus Stegastes play a major role in shaping coral-algal dynamics on coral reefs. The epilithic algal matrix (EAM) inside Stegastes’ territories is known to harbor high abundances of potential coral disease pathogens. To determine the impact of territorial grazers on coral microbial assemblages, we established a coral transplant inside and outside of Stegastes’ territories. Over the course of one year, the percent mortality of transplanted corals was monitored and coral samples were collected for microbial analysis. As compared to outside damselfish territories, Stegastes were associated with a higher rate of mortality of transplanted corals. However, 16S rDNA sequencing revealed that territorial grazers do not differentially impact the microbial assemblage of corals exposed to the EAM. Regardless of Stegastes presence or absence, coral transplantation resulted in a shift in the coral-associated microbial community and an increase in coral disease associated potential pathogens. Further, transplanted corals that suffer low to high mortality undergo a microbial transition from a microbiome similar to that of healthy corals to that resembling the EAM. These findings demonstrate that coral transplantation significantly impacts coral microbial communities, and transplantation may increase susceptibility to coral disease.
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48
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Hao YQ, Zhao XF, Zhang DY. Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities. Environ Microbiol 2015; 18:1730-9. [PMID: 25809418 DOI: 10.1111/1462-2920.12858] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/07/2015] [Indexed: 11/29/2022]
Abstract
To assess the relative importance of environmental selection, dispersal and stochastic processes in structuring ecological communities, we conducted a bacterial community assembly experiment using microcosms filled with sterile liquid medium under field conditions in the Inner Mongolian grasslands. Multiple replicate microcosms containing different carbon substrates were placed at nine locations across three spatial scales (10, 300 and 10 000 m distance between locations) in such a way that the environment of microcosms varies independently of the geographical distance. The operational taxonomic units within the experimental communities were assessed via the terminal restriction fragment length polymorphism techniques on the 10th and 17th days after the onset of the experiment. We found no evidence of distance decay in community similarity, and communities within a given location were more similar to each other regardless of environment than communities at other locations within the same spatial scale. Variance partitioning indicated that location explained more compositional variation in microbial communities than environment, particularly on the 17th day, despite that environment and location in combination could only explain less than half of the total variation. These results suggest that bacterial dispersal is not limited by distance in this experiment, and community assembly in microcosms is not environmentally determined but governed by stochastic processes.
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Affiliation(s)
- Yi-Qi Hao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xin-Feng Zhao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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49
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Morrow KM, Bourne DG, Humphrey C, Botté ES, Laffy P, Zaneveld J, Uthicke S, Fabricius KE, Webster NS. Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges. ISME JOURNAL 2015; 9:894-908. [PMID: 25325380 PMCID: PMC4817704 DOI: 10.1038/ismej.2014.188] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/18/2014] [Accepted: 08/21/2014] [Indexed: 01/26/2023]
Abstract
Atmospheric carbon dioxide (CO2) levels are rapidly rising causing an increase in the partial pressure of CO2 (pCO2) in the ocean and a reduction in pH known as ocean acidification (OA). Natural volcanic seeps in Papua New Guinea expel 99% pure CO2 and thereby offer a unique opportunity to explore the effects of OA in situ. The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away. A primary driver of microbial differences in A. millepora was a 50% reduction of symbiotic Endozoicomonas. This loss of symbiotic taxa from corals at the CO2 seep highlights a potential hurdle for corals to overcome if they are to adapt to and survive OA. In contrast, the two sponges Coelocarteria singaporensis and Cinachyra sp. were ∼40-fold more abundant at the seep and hosted a significantly higher relative abundance of Synechococcus than sponges at control sites. The increase in photosynthetic microbes at the seep potentially provides these species with a nutritional benefit and enhanced scope for growth under future climate scenarios (thus, flexibility in symbiosis may lead to a larger niche breadth). The microbial community in the apparently pCO2-sensitive sponge species S. massa was not significantly different between sites. These data show that responses to elevated pCO2 are species-specific and that the stability and flexibility of microbial partnerships may have an important role in shaping and contributing to the fitness and success of some hosts.
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Affiliation(s)
- Kathleen M Morrow
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
| | - David G Bourne
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
| | - Craig Humphrey
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
| | - Emmanuelle S Botté
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
| | - Patrick Laffy
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
| | - Jesse Zaneveld
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
| | - Sven Uthicke
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
| | | | - Nicole S Webster
- Australian Institute of Marine Science, P.M.B. 3, Townville, Queensland, Australia
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50
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Natural high pCO2 increases autotrophy in Anemonia viridis (Anthozoa) as revealed from stable isotope (C, N) analysis. Sci Rep 2015; 5:8779. [PMID: 25739995 PMCID: PMC4350107 DOI: 10.1038/srep08779] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/03/2015] [Indexed: 11/23/2022] Open
Abstract
Contemporary cnidarian-algae symbioses are challenged by increasing CO2 concentrations (ocean warming and acidification) affecting organisms' biological performance. We examined the natural variability of carbon and nitrogen isotopes in the symbiotic sea anemone Anemonia viridis to investigate dietary shifts (autotrophy/heterotrophy) along a natural pCO2 gradient at the island of Vulcano, Italy. δ13C values for both algal symbionts (Symbiodinium) and host tissue of A. viridis became significantly lighter with increasing seawater pCO2. Together with a decrease in the difference between δ13C values of both fractions at the higher pCO2 sites, these results indicate there is a greater net autotrophic input to the A. viridis carbon budget under high pCO2 conditions. δ15N values and C/N ratios did not change in Symbiodinium and host tissue along the pCO2 gradient. Additional physiological parameters revealed anemone protein and Symbiodinium chlorophyll a remained unaltered among sites. Symbiodinium density was similar among sites yet their mitotic index increased in anemones under elevated pCO2. Overall, our findings show that A. viridis is characterized by a higher autotrophic/heterotrophic ratio as pCO2 increases. The unique trophic flexibility of this species may give it a competitive advantage and enable its potential acclimation and ecological success in the future under increased ocean acidification.
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