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Shoguchi E, Kawachi M, Shinzato C, Beedessee G. Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13238. [PMID: 38444256 PMCID: PMC10915500 DOI: 10.1111/1758-2229.13238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12 ) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaJapan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of TokyoKashiwaJapan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate UniversityOnnaJapan
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
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2
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Sparagon WJ, Arts MGI, Quinlan ZA, Wegley Kelly L, Koester I, Comstock J, Bullington JA, Carlson CA, Dorrestein PC, Aluwihare LI, Haas AF, Nelson CE. Coral thermal stress and bleaching enrich and restructure reef microbial communities via altered organic matter exudation. Commun Biol 2024; 7:160. [PMID: 38351328 PMCID: PMC10864316 DOI: 10.1038/s42003-023-05730-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/16/2023] [Indexed: 02/16/2024] Open
Abstract
Coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, yet there has been relatively little research on the implications for reef water column microbiology and biogeochemistry. A mesocosm heating experiment and bottle incubation compared how unbleached and bleached corals alter dissolved organic matter (DOM) exudation in response to thermal stress and subsequent effects on microbial growth and community structure in the water column. Thermal stress of healthy corals tripled DOM flux relative to ambient corals. DOM exudates from stressed corals (heated and/or previously bleached) were compositionally distinct from healthy corals and significantly increased growth of bacterioplankton, enriching copiotrophs and putative pathogens. Together these results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend into the water column, with altered coral DOM exudation driving microbial feedbacks that influence how coral reefs respond to and recover from mass bleaching events.
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Affiliation(s)
- Wesley J Sparagon
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Milou G I Arts
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Zachary A Quinlan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- San Diego State University, San Diego, USA
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- San Diego State University, San Diego, USA
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology, The Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | - Jessica A Bullington
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology, The Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | | | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Andreas F Haas
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- San Diego State University, San Diego, USA
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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3
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Shakya AW, Allgeier JE. Water column contributions to coral reef productivity: overcoming challenges of context dependence. Biol Rev Camb Philos Soc 2023; 98:1812-1828. [PMID: 37315947 DOI: 10.1111/brv.12984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/16/2023]
Abstract
Coral reefs are declining at an unprecedented rate. Effective management and conservation initiatives necessitate improved understanding of the drivers of production because the high rates found in these ecosystems are the foundation of the many services they provide. The water column is the nexus of coral reef ecosystem dynamics, and functions as the interface through which essentially all energy and nutrients are transferred to fuel both new and recycled production. Substantial research has described many aspects of water column dynamics, often focusing on specific components because water column dynamics are highly spatially and temporally context dependent. Although necessary, a cost of this approach is that these dynamics are often not well linked to the broader ecosystem or across systems. To help overcome the challenge of context dependence, we provide a comprehensive review of this literature, and synthesise it through the perspective of ecosystem ecology. Specifically, we provide a framework to organise the drivers of temporal and spatial variation in production dynamics, structured around five primary state factors. These state factors are used to deconstruct the environmental contexts in which three water column sub-food webs mediate 'new' and 'recycled' production. We then highlight critical pathways by which global change drivers are altering coral reefs via the water column. We end by discussing four key knowledge gaps hindering understanding of the role of the water column for mediating coral reef production, and how overcoming these could improve conservation and management strategies. Throughout, we identify areas of extensive research and those where studies remain lacking and provide a database of 84 published studies. Improved integration of water column dynamics into models of coral reef ecosystem function is imperative to achieve the understanding of ecosystem production necessary to develop effective conservation and management strategies needed to stem global coral loss.
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Affiliation(s)
- Anjali W Shakya
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI, 48109, USA
| | - Jacob E Allgeier
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI, 48109, USA
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McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
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Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
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5
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Silveira CB, Luque A, Haas AF, Roach TNF, George EE, Knowles B, Little M, Sullivan CJ, Varona NS, Wegley Kelly L, Brainard R, Rohwer F, Bailey B. Viral predation pressure on coral reefs. BMC Biol 2023; 21:77. [PMID: 37038111 PMCID: PMC10088212 DOI: 10.1186/s12915-023-01571-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/17/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs' biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health. RESULTS Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m-2) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations. CONCLUSIONS The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA.
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA
| | - Andreas F Haas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ty N F Roach
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Emma E George
- Botany Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ben Knowles
- Department of Ecology and Evolutionary Biology, UC Los Angeles, Los Angeles, CA, 90095, USA
| | - Mark Little
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | | | - Natascha S Varona
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - Russel Brainard
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
- Pacific Islands Fisheries Science Center, National Oceanic & Atmospheric Administration, Honolulu, HI, 96818, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Barbara Bailey
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA.
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA.
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Borbee EM, Ayu IP, Carvalho P, Restiana E, Setiawan F, Subhan B, Humphries AT, Madduppa H, Lane CE. Rubble fields shape planktonic protist communities in Indonesia at a local scale. J Eukaryot Microbiol 2023; 70:e12954. [PMID: 36401815 DOI: 10.1111/jeu.12954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]
Abstract
The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fields of coral rubble. While the impacts of disturbances in these ecosystems are well documented on metazoans, we have a poor understanding of their impact on microbial communities at the base of the food web. We use metabarcoding to characterize protist community composition in sites of varying fisheries management schemes and benthic profiles across the island of Lombok, Indonesia. Our study shows that rubble coverage and net primary productivity are the strongest explainers of variation in protist communities across Lombok. More specifically, rubble fields are characterized by increases in small heterotrophic protists, including ciliates and cercozoans. In addition to shifts in heterotrophic protist communities, we also observed increases in diatom relative abundance in rubble fields, which corresponded to sites with higher net primary productivity. These results are the first to characterize protist communities in tropical marine rubble fields and provide insight on environmental factors potentially driving these shifts on a local scale.
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Affiliation(s)
- Erin M Borbee
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Inna Puspa Ayu
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Paul Carvalho
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ester Restiana
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia.,Department of Fisheries, University of Jambi, Jambi, Indonesia
| | - Fahkrizal Setiawan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Austin T Humphries
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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7
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Nelson CE, Wegley Kelly L, Haas AF. Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:431-460. [PMID: 36100218 DOI: 10.1146/annurev-marine-042121-080917] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.
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Affiliation(s)
- Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, and Sea Grant College Program, School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA;
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA;
| | - Andreas F Haas
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands;
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8
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Trophic provisioning and parental trade-offs lead to successful reproductive performance in corals after a bleaching event. Sci Rep 2022; 12:18702. [PMID: 36333369 PMCID: PMC9636168 DOI: 10.1038/s41598-022-21998-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Warming ocean temperatures are severely compromising the health and resilience of coral reefs worldwide. Coral bleaching can affect coral physiology and the energy available for corals to reproduce. Mechanisms associated with reproductive allocation in corals are poorly understood, especially after a bleaching event occurs. Using isotopic labeling techniques, we traced the acquisition and allocation of carbon from adults to gametes by autotrophy and heterotrophy in previously bleached and non-bleached Montipora capitata and Porites compressa corals. Experiments revealed that both species: (1) relied only on autotrophy to allocate carbon to gametes, while heterotrophy was less relied upon as a carbon source; (2) experienced a trade-off with less carbon available for adult tissues when provisioning gametes, especially when previously bleached; and (3) used different strategies for allocating carbon to gametes. Over time, M. capitata allocated 10% more carbon to gametes despite bleaching by limiting the allocation of carbon to adult tissues, with 50-80% less carbon allocated to bleached compared to non-bleached colonies. Over the same time period, P. compressa maintained carbon allocation to adult tissues, before allocating carbon to gametes. Our study highlights the importance of autotrophy for carbon allocation from adult corals to gametes, and species-specific differences in carbon allocation depending on bleaching susceptibility.
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Weber L, Soule MK, Longnecker K, Becker CC, Huntley N, Kujawinski EB, Apprill A. Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs. ISME COMMUNICATIONS 2022; 2:101. [PMID: 37938276 PMCID: PMC9723752 DOI: 10.1038/s43705-022-00184-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 09/02/2023]
Abstract
Benthic organisms are the architectural framework supporting coral reef ecosystems, but their community composition has recently shifted on many reefs. Little is known about the metabolites released from these benthic organisms and how compositional shifts may influence other reef life, including prolific microorganisms. To investigate the metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting alga, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial abundances and community composition using 16 S rRNA gene sequencing in relation to exudate source and three specific metabolites. Exudates were enriched in amino acids, nucleosides, vitamins, and indole-based metabolites, showing that benthic organisms contribute labile organic matter to reefs. Furthermore, exudate compositions were species-specific, and riboflavin and pantothenic acid emerged as significant coral-produced metabolites, while caffeine emerged as a significant invasive algal-produced metabolite. Microbial abundances and individual microbial taxa responded differently to exudates from stony corals and octocorals, demonstrating that exudate mixtures released from different coral species select for specific bacteria. In contrast, microbial communities did not respond to individual additions of riboflavin, pantothenic acid, or caffeine. This work indicates that recent shifts in benthic organisms alter exudate composition and likely impact microbial communities on coral reefs.
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Affiliation(s)
- Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
| | - Melissa Kido Soule
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Krista Longnecker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Cynthia C Becker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA
| | - Naomi Huntley
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Marine and Environmental Science Department, University of the Virgin Islands, Charlotte Amalie West, St Thomas, Charlotte Amalie, VI, 00802, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Elizabeth B Kujawinski
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
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10
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Lima LFO, Alker AT, Papudeshi B, Morris MM, Edwards RA, de Putron SJ, Dinsdale EA. Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02094-6. [PMID: 35965269 DOI: 10.1007/s00248-022-02094-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.
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Affiliation(s)
- Laís F O Lima
- Department of Biology, San Diego State University, San Diego, CA, USA
- College of Biological Sciences, University of California Davis, Davis, CA, USA
| | - Amanda T Alker
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Bhavya Papudeshi
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Megan M Morris
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | | | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, San Diego, CA, USA.
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.
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11
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Interaction and Assembly of Bacterial Communities in High-Latitude Coral Habitat Associated Seawater. Microorganisms 2022; 10:microorganisms10030558. [PMID: 35336132 PMCID: PMC8955259 DOI: 10.3390/microorganisms10030558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Threatened by climate change and ocean warming, coral reef ecosystems have been shifting in geographic ranges toward a higher latitude area. The water-associated microbial communities and their potential role in primary production contribution are well studied in tropical coral reefs, but poorly defined in high-latitude coral habitats to date. In this study, amplicon sequencing of 16S rRNA and cbbL gene, co-occurrence network, and βNTI were used. The community structure of bacterial and carbon-fixation bacterial communities showed a significant difference between the center of coral, transitional, and non-coral area. Nitrite, DOC, pH, and coral coverage ratio significantly impacted the β-diversity of bacterial and carbon-fixation communities. The interaction of heterotrophs and autotrophic carbon-fixers was more complex in the bottom than in surface water. Carbon-fixers correlated with diverse heterotrophs in surface water but fewer lineages of heterotrophic taxa in the bottom. Bacterial community assembly showed an increase by deterministic process with decrease of coral coverage in bottom water, which may correlate with the gradient of nitrite and pH in the habitat. A deterministic process dominated the assembly of carbon-fixation bacterial community in surface water, while stochastic process dominated t the bottom. In conclusion, the structure and assembly of bacterial and carbon-fixer community were affected by multi-environmental variables in high-latitude coral habitat-associated seawater.
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12
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Manikandan B, Thomas AM, Shetye SS, Balamurugan S, Mohandass C, Nandakumar K. Macroalgal release of dissolved organic carbon in coral reef and its interaction with the bacteria associated with the coral Porites lutea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:66998-67010. [PMID: 34240306 DOI: 10.1007/s11356-021-15096-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Macroalgae supersede corals in the reefs worldwide, converting the coral-dominant systems into algal-dominant ones. Dissolved organic carbon (DOC) released by macroalgae play a prominent role in degrading the coral reefs by stimulating the bacterial growth and metabolism. However, the long-term remineralization of macroalgal DOC and their contribution to the carbon pool are least studied. In this study, we quantified the DOC released by five species of macroalgae that affected live corals through their physical contact and their subsequent remineralization for 100 days by coral mucus bacteria. Also, we analyzed the changes in bacterial community structure after 30 days of exposure to the macroalgal DOC. All the macroalgae released a significant amount of DOC ranging from 2.2 ± 0.17 to 8.1 ± 0.36 μmol C g-1 h-1 (mean ± SD). After 100 days, between 9.2 and 30.9% of the macroalgal DOC remained recalcitrant to bacterial remineralization. There was no apparent change in the dominant bacterial groups exposed to the DOC released by the green macroalgae Caulerpa racemosa and Halimeda sp. In comparison, the Proteobacteria group decreased with a prominent increase in the Firmicutes, Planctomycetes, and Bacteroidetes group in the samples exposed to DOC released by the brown macroalgae Turbinaria ornata, Sargassum tenerrimum, and Padina gymnospora. These inclusive data suggest that the DOC released by different species of macroalgae differed on their lability to microbial mineralization and highlight the comparable patterns in microbial responses to macroalgal exudates across different species.
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Affiliation(s)
| | - Alen Mariyam Thomas
- College of Climate Change and Environmental Science, Kerala Agricultural University, Thrissur, 680656, India
| | | | | | - Chellandi Mohandass
- CSIR-National Institute of Oceanography, Regional Center, Mumbai, 400053, India
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13
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Glasl B, Haskell JB, Aires T, Serrão EA, Bourne DG, Webster NS, Frade PR. Microbial Surface Biofilm Responds to the Growth-Reproduction-Senescence Cycle of the Dominant Coral Reef Macroalgae Sargassum spp. Life (Basel) 2021; 11:life11111199. [PMID: 34833075 PMCID: PMC8621314 DOI: 10.3390/life11111199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Macroalgae play an intricate role in microbial-mediated coral reef degradation processes due to the release of dissolved nutrients. However, temporal variabilities of macroalgal surface biofilms and their implication on the wider reef system remain poorly characterized. Here, we study the microbial biofilm of the dominant reef macroalgae Sargassum over a period of one year at an inshore Great Barrier Reef site (Magnetic Island, Australia). Monthly sampling of the Sargassum biofilm links the temporal taxonomic and putative functional metabolic microbiome changes, examined using 16S rRNA gene amplicon and metagenomic sequencing, to the pronounced growth-reproduction-senescence cycle of the host. Overall, the macroalgal biofilm was dominated by the heterotrophic phyla Firmicutes (35% ± 5.9% SD) and Bacteroidetes (12% ± 0.6% SD); their relative abundance ratio shifted significantly along the annual growth-reproduction-senescence cycle of Sargassum. For example, Firmicutes were 1.7 to 3.9 times more abundant during host growth and reproduction cycles than Bacteroidetes. Both phyla varied in their carbohydrate degradation capabilities; hence, temporal fluctuations in the carbohydrate availability are potentially linked to the observed shift. Dominant heterotrophic macroalgal biofilm members, such as Firmicutes and Bacteroidetes, are implicated in exacerbating or ameliorating the release of dissolved nutrients into the ambient environment, though their contribution to microbial-mediated reef degradation processes remains to be determined.
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Affiliation(s)
- Bettina Glasl
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030 Vienna, Austria
- Correspondence:
| | - Jasmine B. Haskell
- CCMAR-Centre of Marine Sciences, CIMAR, University of Algarve, 8005-139 Faro, Portugal; (J.B.H.); (T.A.); (E.A.S.)
| | - Tania Aires
- CCMAR-Centre of Marine Sciences, CIMAR, University of Algarve, 8005-139 Faro, Portugal; (J.B.H.); (T.A.); (E.A.S.)
| | - Ester A. Serrão
- CCMAR-Centre of Marine Sciences, CIMAR, University of Algarve, 8005-139 Faro, Portugal; (J.B.H.); (T.A.); (E.A.S.)
| | - David G. Bourne
- Australian Institute of Marine Science, Townsville 4810, Australia
- College of Science and Engineering, James Cook University, Townsville 4811, Australia;
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville 4810, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane 4072, Australia
- Australian Antarctic Division, Hobart 7050, Australia;
| | - Pedro R. Frade
- CCMAR-Centre of Marine Sciences, CIMAR, University of Algarve, 8005-139 Faro, Portugal; (J.B.H.); (T.A.); (E.A.S.)
- Zoological Department III, Natural History Museum Vienna, 1010 Vienna, Austria;
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14
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Varasteh T, Tschoeke D, Silva-Lima AW, Thompson C, Thompson F. Transcriptome of the coral Mussismilia braziliensis symbiont Sargassococcus simulans. Mar Genomics 2021; 61:100912. [PMID: 34710723 DOI: 10.1016/j.margen.2021.100912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
A transcriptomic profile of Sargassococcus simulans 103B3, isolated from the coral Mussismilia braziliensis in Abrolhos, Brazil, is presented. A total of 631.3 Mbp transcriptomic sequences were obtained. The transcriptomic analysis disclosed transcripts coding for enzymes relevant for holobiont health including genes involved in I. Light harvesting complex (LHC), II. Organic matter utilization and III. Oxidative stress and microbial defense (Oxidoreductases) enzymes. The isolate exhibited transcripts for uptake and utilization of a variety of carbon sources, such as sugars, oligopeptides, and amino acids by ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) type transporters. Collectively, these enzymes indicate a mixotrophic metabolism in S. simulans with metabolic capabilities for the degradation of an array of organic carbon compounds in the coral Mussismilia and light harvesting within the low-light environments of Abrolhos.
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Affiliation(s)
- Tooba Varasteh
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Diogo Tschoeke
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Arthur W Silva-Lima
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Thompson
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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15
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Cheutin MC, Villéger S, Hicks CC, Robinson JPW, Graham NAJ, Marconnet C, Restrepo CXO, Bettarel Y, Bouvier T, Auguet JC. Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts. Microorganisms 2021; 9:microorganisms9081711. [PMID: 34442789 PMCID: PMC8398123 DOI: 10.3390/microorganisms9081711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; p = 0.001), especially in herbivorous fishes (R2 = 0.07; p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions.
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Affiliation(s)
- Marie-Charlotte Cheutin
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
- Correspondence:
| | - Sébastien Villéger
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Christina C. Hicks
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - James P. W. Robinson
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - Nicholas A. J. Graham
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; (C.C.H.); (J.P.W.R.); (N.A.J.G.)
| | - Clémence Marconnet
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Claudia Ximena Ortiz Restrepo
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Yvan Bettarel
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Thierry Bouvier
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
| | - Jean-Christophe Auguet
- UMR MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34095 Montpellier, France; (S.V.); (C.M.); (C.X.O.R.); (Y.B.); (T.B.); (J.-C.A.)
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16
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Wambua S, Gourlé H, de Villiers EP, Karlsson-Lindsjö O, Wambiji N, Macdonald A, Bongcam-Rudloff E, de Villiers S. Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean. Front Microbiol 2021; 12:673128. [PMID: 34248882 PMCID: PMC8260691 DOI: 10.3389/fmicb.2021.673128] [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: 02/26/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations.
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Affiliation(s)
- Sammy Wambua
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, Kenya.,Department of Biological Sciences, Pwani University, Kilifi, Kenya
| | - Hadrien Gourlé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Etienne P de Villiers
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oskar Karlsson-Lindsjö
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nina Wambiji
- Kenya Marine and Fisheries Research Institute, Mombasa, Kenya
| | - Angus Macdonald
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Santie de Villiers
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, Kenya.,Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
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17
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Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
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Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
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18
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Su H, Xiao Z, Yu K, Zhang Q, Lu C, Wang G, Wang Y, Liang J, Huang W, Huang X, Wei F. High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals. Int J Mol Sci 2021; 22:ijms22073523. [PMID: 33805379 PMCID: PMC8037212 DOI: 10.3390/ijms22073523] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/08/2023] Open
Abstract
β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.
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Affiliation(s)
- Hongfei Su
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Zhenlun Xiao
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China
- Correspondence:
| | - Qi Zhang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Chunrong Lu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Guanghua Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Yinghui Wang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Wen Huang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Xueyong Huang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
| | - Fen Wei
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning 530004, China; (H.S.); (Z.X.); (Q.Z.); (C.L.); (G.W.); (Y.W.); (J.L.); (W.H.); (X.H.); (F.W.)
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19
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Calegario G, Freitas L, Appolinario LR, Venas T, Arruda T, Otsuki K, Masi B, Omachi C, Moreira AP, Soares AC, Rezende CE, Garcia G, Tschoeke D, Thompson C, Thompson FL. Conserved rhodolith microbiomes across environmental gradients of the Great Amazon Reef. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143411. [PMID: 33243513 DOI: 10.1016/j.scitotenv.2020.143411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
The Great Amazon Reef System (GARS) covers an estimated area of 56,000 km2 off the mouth of the Amazon River. Living rhodolith holobionts are major benthic components of the GARS. However, it is unclear whether environmental conditions modulate the rhodolith microbiomes. Previous studies suggest that environmental parameters such as light, temperature, depth, and nutrients are drivers of rhodolith health. However, it is unclear whether rhodoliths from different sectors (northern, central, and southern) from the GARS have different microbiomes. We analysed metagenomes of rhodoliths (n = 10) and seawater (n = 6), obtained from the three sectors, by illumina shotgun sequencing (total read counts: 25.73 million). Suspended particulate material and isotopic composition of dissolved organic carbon (δ13C) indicated a strong influence of the Amazon river plume over the entire study area. However, photosynthetically active radiation at the bottom (PARb) was higher in the southern sector reefs, ranging from 10.1 to 14.3 E.m-2 day-1. The coralline calcareous red algae (CCA) Corallina caespitosa, Corallina officinalis, Lithophyllum cabiochiae, and Hapalidiales were present in the three sectors and in most rhodolith samples. Rhodolith microbiomes were very homogeneous across the studied area and differed significantly from seawater microbiomes. However, some subtle differences were found when comparing the rhodolith microbiomes from the northern and central sectors to the ones from the southern. Consistent with the higher light availability, two phyla were more abundant in rhodolith microbiomes from southern sites (Bacteroidetes, and Cyanobacteria). In addition, two functional categories were enhanced in southern rhodolith microbiomes (iron acquisition and metabolism, and photosynthesis). Phycobiliprotein-coding genes were also more abundant in southern locations, while the functional categories of respiration and sulfur metabolism were enhanced in northern and central rhodolith microbiomes, consistent with higher nutrient loads. The results confirm the conserved nature of rhodolith microbiomes even under pronounced environmental gradients. Subtle taxonomic and functional differences observed in rhodolith microbiomes may enable rhodoliths to thrive in changing environmental conditions.
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Affiliation(s)
- Gabriela Calegario
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lucas Freitas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciana Reis Appolinario
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Taina Venas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tatiane Arruda
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Koko Otsuki
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno Masi
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Claudia Omachi
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Universidade de São Paulo, Instituto Oceanográfico, Laboratório de Indicadores Ambientais, São Paulo, Brazil
| | - Ana Paula Moreira
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ana Carolina Soares
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carlos E Rezende
- Laboratório de Ciências Ambientais, Universidade Estadual Norte Fluminense (UENF), Campos, Brazil
| | - Gizele Garcia
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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20
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Varasteh T, Tschoeke D, Garcia G, Lima AS, Moreira APB, Thompson C, Thompson F. Insights into the genomic repertoire of Aquimarina litoralis CCMR20, a symbiont of coral Mussismilia braziliensis. Arch Microbiol 2021; 203:2743-2746. [PMID: 33675372 DOI: 10.1007/s00203-021-02194-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/12/2021] [Accepted: 02/04/2021] [Indexed: 11/25/2022]
Abstract
Aquimarina litoralis CCMR20 originated from the coral Mussismilia braziliensis (Sebastião Gomes Reef, Brazil, summer 2010). To gain new insights into the genomic repertoire associated with symbioses, we obtained the genome sequence of this strains using Illumina sequencing. CCMR20 has a genome size of 6.3 Mb, 32.6%GC, and 5513 genes (37 tRNA and 4 rRNA). A more fine-grained examination of the gene repertoire of CCMR20 disclosed genes engaged with symbiosis (heterotrophic carbon metabolism, CAZymes, B-vitamins group, carotenoid pigment and antioxidant molecules production). Genomic evidence further expand the possible relevance of this symbiont in the health of Mussismilia holobiont.Whole Genome Shotgun project has been deposited at DDBJ/ENA/GeneBank under the accession number WEKL00000000.
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Affiliation(s)
- Tooba Varasteh
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Diogo Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Gizele Garcia
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
- Departamento de Ensino de Graduação, Universidade Federal Do Rio de Janeiro, Campus UFRJ, Macae' Professor Aloisio Teixeira, Macae', Rio de Janeiro, RJ, 27930-480, Brazil
| | - Arthur Silva Lima
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Ana Paula B Moreira
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Fabiano Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil.
- SAGE, COPPE, Centro de Gestão Tecnológica-CT2, Rio de Janeiro, RJ, Brazil.
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21
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Liang Z, Fang W, Luo Y, Lu Q, Juneau P, He Z, Wang S. Mechanistic insights into organic carbon-driven water blackening and odorization of urban rivers. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124663. [PMID: 33278726 DOI: 10.1016/j.jhazmat.2020.124663] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/21/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
With rapid global urbanization, massive anthropogenic inputs of organic matter and inorganic nutrients are resulting in severe pollution of urban rivers and consequently altering the structure and function of their aquatic microbial communities. In contrast to nutrient-induced eutrophication of freshwaters, water blackening and odorization of urban rivers, as well as their microbial communities, are poorly understood at a mechanistic level. Here, in a one-year field study on the taxonomic composition, predicted function and spatiotemporal dynamics of water and sediment microbial communities in seven black-odorous urban rivers in a megacity in southern China, combined with laboratory water-sediment column experiments, we pinpointed organic carbon as a key parameter driving the overgrowth of aquatic heterogeneous microorganisms. These microorganisms are major constituents of suspended black flocs that mediate methanogenic digestion of organic carbon and consequent water blackening and odorization. Source tracking analysis revealed a strikingly high contribution of sewage communities to black-odorous water microbial communities, in which emerging pathogens are enriched. Our results provide mechanistic insight into organic carbon-driven water blackening and odorization of urban rivers, which brings up current remediation strategies in questioning and sheds light on the future sustainable management of urban aquatic ecosystems.
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Affiliation(s)
- Zhiwei Liang
- 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
| | - Wenwen Fang
- 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
| | - Yukui Luo
- 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
| | - Qihong Lu
- 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
| | - Philippe Juneau
- Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Université du Québec à Montréal, Montréal H3C 3P8, QC, Canada
| | - 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; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, China
| | - Shanquan 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; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510006, China.
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22
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Varasteh T, Hamerski L, Tschoeke D, Lima AS, Garcia G, Cosenza CAN, Thompson C, Thompson F. Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis. MICROBIAL ECOLOGY 2021; 81:267-277. [PMID: 32681284 DOI: 10.1007/s00248-020-01551-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.
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Affiliation(s)
- Tooba Varasteh
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Lidilhone Hamerski
- Instituto de Pesquisas de Produtos Naturais, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Diogo Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Arthur Silva Lima
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Gizele Garcia
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
- Departamento de Ensino de Graduação, Universidade Federal do Rio de Janeiro - Campus UFRJ - Macaé Professor Aloisio Teixeira, Macaé, Rio de Janeiro, RJ, 27930-480, Brazil
| | | | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Fabiano Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil.
- SAGE - COPPE, Centro de Gestão Tecnológica - CT2, Rio de Janeiro, RJ, Brazil.
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23
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Walter JM, Coutinho FH, Leomil L, Hargreaves PI, Campeão ME, Vieira VV, Silva BS, Fistarol GO, Salomon PS, Sawabe T, Mino S, Hosokawa M, Miyashita H, Maruyama F, van Verk MC, Dutilh BE, Thompson CC, Thompson FL. Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia. MICROBIAL ECOLOGY 2020; 80:249-265. [PMID: 32060621 DOI: 10.1007/s00248-019-01480-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.
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Affiliation(s)
- Juline M Walter
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Felipe H Coutinho
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Luciana Leomil
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Paulo I Hargreaves
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mariana E Campeão
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Beatriz S Silva
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Giovana O Fistarol
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Paulo S Salomon
- Marine Phytoplankton Laboratory, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tomoo Sawabe
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Masashi Hosokawa
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Hideaki Miyashita
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 739-8530, Hiroshima, Japan
| | - Fumito Maruyama
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, 739-8530, Hiroshima, Japan
| | - Marcel C van Verk
- Plant-Microbe Interactions, Bioinformatics, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Bas E Dutilh
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Cristiane C Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, 373, CCS-IB-Biomar, Lab. de Microbiologia, Bloco A3, (Anexo), sl. 102, Cidade Universitária, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
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24
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Villela H. Microbiome Flexibility Provides New Perspectives in Coral Research. Bioessays 2020; 42:e2000088. [PMID: 32483815 DOI: 10.1002/bies.202000088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Helena Villela
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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25
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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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26
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Lima LFO, Weissman M, Reed M, Papudeshi B, Alker AT, Morris MM, Edwards RA, de Putron SJ, Vaidya NK, Dinsdale EA. Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network. mBio 2020; 11:e02691-19. [PMID: 32127450 PMCID: PMC7064765 DOI: 10.1128/mbio.02691-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
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Affiliation(s)
- Laís F O Lima
- Department of Biology, San Diego State University, San Diego, California, USA
- College of Biological Sciences, University of California Davis, Davis, California, USA
| | - Maya Weissman
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
| | - Micheal Reed
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Pervasive Institute of Technology, Indiana University, Bloomington, Indiana, USA
| | - Amanda T Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Megan M Morris
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | | | - Naveen K Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
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27
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Silveira CB, Coutinho FH, Cavalcanti GS, Benler S, Doane MP, Dinsdale EA, Edwards RA, Francini-Filho RB, Thompson CC, Luque A, Rohwer FL, Thompson F. Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. BMC Genomics 2020; 21:126. [PMID: 32024463 PMCID: PMC7003362 DOI: 10.1186/s12864-020-6523-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bacteriophages encode genes that modify bacterial functions during infection. The acquisition of phage-encoded virulence genes is a major mechanism for the rise of bacterial pathogens. In coral reefs, high bacterial density and lysogeny has been proposed to exacerbate reef decline through the transfer of phage-encoded virulence genes. However, the functions and distribution of these genes in phage virions on the reef remain unknown. Results Here, over 28,000 assembled viral genomes from the free viral community in Atlantic and Pacific Ocean coral reefs were queried against a curated database of virulence genes. The diversity of virulence genes encoded in the viral genomes was tested for relationships with host taxonomy and bacterial density in the environment. These analyses showed that bacterial density predicted the profile of virulence genes encoded by phages. The Shannon diversity of virulence-encoding phages was negatively related with bacterial density, leading to dominance of fewer genes at high bacterial abundances. A statistical learning analysis showed that reefs with high microbial density were enriched in viruses encoding genes enabling bacterial recognition and invasion of metazoan epithelium. Over 60% of phages could not have their hosts identified due to limitations of host prediction tools; for those which hosts were identified, host taxonomy was not an indicator of the presence of virulence genes. Conclusions This study described bacterial virulence factors encoded in the genomes of bacteriophages at the community level. The results showed that the increase in microbial densities that occurs during coral reef degradation is associated with a change in the genomic repertoire of bacteriophages, specifically in the diversity and distribution of bacterial virulence genes. This suggests that phages are implicated in the rise of pathogens in disturbed marine ecosystems.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA. .,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA. .,Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, FL, 33146, USA.
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, 03550, San Juan de Alicante, Spain
| | - Giselle S Cavalcanti
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Sean Benler
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Michael P Doane
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Ronaldo B Francini-Filho
- Centro de Biologia Marinha, Universidade de São Paulo, Rodovia Manoel Hypólito do Rego, Km 131,50, São Sebastião, SP, 11600-000, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941- 599, Brazil
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Forest L Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Fabiano Thompson
- SAGE/COPPE, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941- 599, Brazil
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28
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Matthews JL, Raina J, Kahlke T, Seymour JR, Oppen MJH, Suggett DJ. Symbiodiniaceae‐bacteria interactions: rethinking metabolite exchange in reef‐building corals as multi‐partner metabolic networks. Environ Microbiol 2020; 22:1675-1687. [DOI: 10.1111/1462-2920.14918] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer L. Matthews
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Jean‐Baptiste Raina
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Tim Kahlke
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Justin R. Seymour
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Madeleine J. H. Oppen
- The University of Melbourne Parkville 3010 Victoria Australia
- Australian Institute of Marine Science PMB No 3 Townsville MC 4810 QLD Australia
| | - David J. Suggett
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
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29
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Achlatis M, Pernice M, Green K, de Goeij JM, Guagliardo P, Kilburn MR, Hoegh-Guldberg O, Dove S. Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter. Proc Biol Sci 2019; 286:20192153. [PMID: 31795848 DOI: 10.1098/rspb.2019.2153] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track 15N- and 13C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.
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Affiliation(s)
- Michelle Achlatis
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland 4072, Australia.,Global Change Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics, 1090 GE Amsterdam, The Netherlands
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Matthew R Kilburn
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ove Hoegh-Guldberg
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland 4072, Australia.,Global Change Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sophie Dove
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland 4072, Australia
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30
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Silveira CB, Luque A, Roach TN, Villela H, Barno A, Green K, Reyes B, Rubio-Portillo E, Le T, Mead S, Hatay M, Vermeij MJ, Takeshita Y, Haas A, Bailey B, Rohwer F. Biophysical and physiological processes causing oxygen loss from coral reefs. eLife 2019; 8:49114. [PMID: 31793432 PMCID: PMC6890468 DOI: 10.7554/elife.49114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/27/2019] [Indexed: 12/25/2022] Open
Abstract
The microbialization of coral reefs predicts that microbial oxygen consumption will cause reef deoxygenation. Here we tested this hypothesis by analyzing reef microbial and primary producer oxygen metabolisms. Metagenomic data and in vitro incubations of bacteria with primary producer exudates showed that fleshy algae stimulate incomplete carbon oxidation metabolisms in heterotrophic bacteria. These metabolisms lead to increased cell sizes and abundances, resulting in bacteria consuming 10 times more oxygen than in coral incubations. Experiments probing the dissolved and gaseous oxygen with primary producers and bacteria together indicated the loss of oxygen through ebullition caused by heterogenous nucleation on algae surfaces. A model incorporating experimental production and loss rates predicted that microbes and ebullition can cause the loss of up to 67% of gross benthic oxygen production. This study indicates that microbial respiration and ebullition are increasingly relevant to reef deoxygenation as reefs become dominated by fleshy algae. Rising water temperatures, pollution and other factors are increasingly threatening corals and the entire reef ecosystems they build. The potential for corals to resist and recover from the stress these factors cause ultimately depends on their ability to compete against fast-growing fleshy algae that can rapidly take over the reefs. Living on the fleshy algae, the coral and in the surrounding water are communities of bacteria and other microbes that help maintain the health of the coral reef. Both corals and algae modify the chemical and physical environment of the reef to alter the composition of the microbial communities for their own benefit. Algae, for instance, release large amounts of sugars and other molecules of organic carbon into the water. These carbon molecules are then taken up by the bacteria, along with oxygen, to produce chemical energy via a process called respiration. This could cause the levels of oxygen in the water to decrease, potentially damaging the corals and creating more open space for the algae. Previous studies have revealed how communities of microbes on coral reefs use organic carbon, but it remains unclear how they affect the levels of oxygen in the reefs. To address this question, Silveira et al. used an approach called metagenomics to analyze the bacteria in samples of water from 87 reefs across the Pacific and the Caribbean, and also performed experiments with reef bacteria grown in the laboratory. The experiments showed that bacteria growing in the presence of fleshy algae became larger and more abundant than bacteria growing near corals, resulting in the water containing lower levels of oxygen. Furthermore, the fleshy algae produced bubbles of oxygen that were released from the water. Silveira et al. developed a mathematical model that predicted that these bubbles, combined with the respiration of bacteria that live near algae, caused the loss of 67% of the oxygen in the water surrounding the reef. These findings represent a fundamental step towards understanding how changes in the levels of oxygen in water affect the ability of coral reefs to resist and recover from stress.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, United States.,Computational Science Research Center, San Diego State University, San Diego, United States.,Department of Mathematics and Statistics, San Diego State University, San Diego, United States
| | - Ty Nf Roach
- Hawaii Institute of Marine Biology, University of Hawaii at Mānoa, Kāneohe, United States
| | - Helena Villela
- Department of Microbiology, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Adam Barno
- Department of Microbiology, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Kevin Green
- Department of Biology, San Diego State University, San Diego, United States
| | - Brandon Reyes
- Department of Biology, San Diego State University, San Diego, United States
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Tram Le
- Department of Biology, San Diego State University, San Diego, United States
| | - Spencer Mead
- Department of Biology, San Diego State University, San Diego, United States
| | - Mark Hatay
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Mark Ja Vermeij
- CARMABI Foundation, Willemstad, Curaçao.,Department of Freshwater and Marine Ecology, Institute for Biodiversity andEcosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | | | - Andreas Haas
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Barbara Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, United States
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
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31
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Zgliczynski BJ, Williams GJ, Hamilton SL, Cordner EG, Fox MD, Eynaud Y, Michener RH, Kaufman LS, Sandin SA. Foraging consistency of coral reef fishes across environmental gradients in the central Pacific. Oecologia 2019; 191:433-445. [PMID: 31485849 DOI: 10.1007/s00442-019-04496-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 08/24/2019] [Indexed: 11/30/2022]
Abstract
We take advantage of a natural gradient of human exploitation and oceanic primary production across five central Pacific coral reefs to examine foraging patterns in common coral reef fishes. Using stomach content and stable isotope (δ15N and δ13C) analyses, we examined consistency across islands in estimated foraging patterns. Surprisingly, species within the piscivore-invertivore group exhibited the clearest pattern of foraging consistency across all five islands despite there being a considerable difference in mean body mass (14 g-1.4 kg) and prey size (0.03-3.8 g). In contrast, the diets and isotopic values of the grazer-detritivores varied considerably and exhibited no consistent patterns across islands. When examining foraging patterns across environmental contexts, we found that δ15N values of species of piscivore-invertivore and planktivore closely tracked gradients in oceanic primary production; again, no comparable patterns existed for the grazer-detritivores. The inter-island consistency in foraging patterns within the species of piscivore-invertivore and planktivore and the lack of consistency among species of grazer-detritivores suggests a linkage to different sources of primary production among reef fish functional groups. Our findings suggest that piscivore-invertivores and planktivores are likely linked to well-mixed and isotopically constrained allochthonous oceanic primary production, while grazer-detritivores are likely linked to sources of benthic primary production and autochthonous recycling. Further, our findings suggest that species of piscivore-invertivore, independent of body size, converge toward consuming low trophic level prey, with a hypothesized result of reducing the number of steps between trophic levels and increasing the trophic efficiency at a community level.
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Affiliation(s)
- Brian J Zgliczynski
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA.
| | | | | | - Elisabeth G Cordner
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Michael D Fox
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Yoan Eynaud
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | | | - Les S Kaufman
- Department of Biology, Boston University, Boston, MA, USA
| | - Stuart A Sandin
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
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32
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Bell JJ, Rovellini A, Davy SK, Taylor MW, Fulton EA, Dunn MR, Bennett HM, Kandler NM, Luter HM, Webster NS. Climate change alterations to ecosystem dominance: how might sponge-dominated reefs function? Ecology 2018; 99:1920-1931. [PMID: 29989167 DOI: 10.1002/ecy.2446] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/29/2018] [Accepted: 06/18/2018] [Indexed: 11/10/2022]
Abstract
Anthropogenic stressors are impacting ecological systems across the world. Of particular concern are the recent rapid changes occurring in coral reef systems. With ongoing degradation from both local and global stressors, future reefs are likely to function differently from current coral-dominated ecosystems. Determining key attributes of future reef states is critical to reliably predict outcomes for ecosystem service provision. Here we explore the impacts of changing sponge dominance on coral reefs. Qualitative modelling of reef futures suggests that changing sponge dominance due to increased sponge abundance will have different outcomes for other trophic levels compared with increased sponge dominance as a result of declining coral abundance. By exploring uncertainty in the model outcomes we identify the need to (1) quantify changes in carbon flow through sponges, (2) determine the importance of food limitation for sponges, (3) assess the ubiquity of the recently described "sponge loop," (4) determine the competitive relationships between sponges and other benthic taxa, particularly algae, and (5) understand how changing dominance of other organisms alters trophic pathways and energy flows through ecosystems. Addressing these knowledge gaps will facilitate development of more complex models that assess functional attributes of sponge-dominated reef ecosystems.
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Affiliation(s)
- James J Bell
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Alberto Rovellini
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Michael W Taylor
- School of Biological Sciences & Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Elizabeth A Fulton
- CSIRO Oceans & Atmosphere, G.P.O. Box 1538, Hobart, Tasmania, 7001, Australia.,Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania, Australia
| | - Matthew R Dunn
- National Institute of Water and Atmospheric Research Ltd., 301 Evans Bay Parade, Wellington, 6021, New Zealand
| | - Holly M Bennett
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Nora M Kandler
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Heidi M Luter
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand.,Australian Institute of Marine Science, PMB 3, Townsville Mail Centre, Townsville, Queensland, 4810, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, PMB 3, Townsville Mail Centre, Townsville, Queensland, 4810, Australia.,Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, 4072, Australia
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33
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Coutinho FH, Gregoracci GB, Walter JM, Thompson CC, Thompson FL. Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses. Trends Microbiol 2018; 26:955-965. [PMID: 29937307 DOI: 10.1016/j.tim.2018.05.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 01/31/2023]
Abstract
Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
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Affiliation(s)
- Felipe Hernandes Coutinho
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Evolutionary Genomics Group, Departamento de Produccíon Vegetal y Microbiología, Universidad Miguel Hernández (UMH), Alicante, Spain
| | | | - Juline Marta Walter
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Carneiro Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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34
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Frommlet JC, Wangpraseurt D, Sousa ML, Guimarães B, Medeiros da Silva M, Kühl M, Serôdio J. Symbiodinium-Induced Formation of Microbialites: Mechanistic Insights From in Vitro Experiments and the Prospect of Its Occurrence in Nature. Front Microbiol 2018; 9:998. [PMID: 29892272 PMCID: PMC5966549 DOI: 10.3389/fmicb.2018.00998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/27/2018] [Indexed: 12/21/2022] Open
Abstract
Dinoflagellates in the genus Symbiodinium exhibit a variety of life styles, ranging from mutualistic endosymbioses with animal and protist hosts to free-living life styles. In culture, Symbiodinium spp. and naturally associated bacteria are known to form calcifying biofilms that produce so-called symbiolites, i.e., aragonitic microbialites that incorporate Symbiodinium as endolithic cells. In this study, we investigated (i) how algal growth and the combined physiological activity of these bacterial-algal associations affect the physicochemical macroenvironment in culture and the microenvironment within bacterial-algal biofilms, and (ii) how these interactions induce the formation of symbiolites. In batch culture, calcification typically commenced when Symbiodinium spp. growth approached stationary phase and when photosynthetic activity and its influence on pH and the carbonate system of the culture medium had already subsided, indicating that symbiolite formation is not simply a function of photosynthetic activity in the bulk medium. Physical disturbance of bacteria-algal biofilms, via repeated detaching and dispersing of the developing biofilm, generally impeded symbiolite formation, suggesting that the structural integrity of biofilms plays an important role in generating conditions conducive to calcification. Microsensor measurements of pH and O2 revealed a biofilm microenvironment characterized by high photosynthetic rates and by dynamic changes in photosynthesis and respiration with light intensity and culture age. Ca2+ microsensor measurements confirmed the significance of the biofilm microenvironment in inducing calcification, as photosynthesis within the biofilm induced calcification without the influence of batch culture medium and under environmentally relevant flow conditions. Furthermore, first quantitative data on calcification from 26 calcifying cultures enabled a first broad comparison of Symbiodinium-induced bacterial-algal calcification with other calcification processes. Our findings support the idea that symbiolite formation is a typical, photosynthesis-induced, bacterial-algal calcification process that is likely to occur under natural conditions.
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Affiliation(s)
- Jörg C Frommlet
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Daniel Wangpraseurt
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.,Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maria L Sousa
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Bárbara Guimarães
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Mariana Medeiros da Silva
- Coral Reef and Global Changes Research Group (RECOR), Department of Oceanography, Institute of Geosciences, Federal University of Bahia (UFBA), Salvador, Brazil
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.,Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - João Serôdio
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
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35
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Abstract
Tropical scleractinian corals are dependent to varying degrees on their photosymbiotic partners. Under normal levels of temperature and irradiance, they can provide most, but not all, of the host's nutritional requirements. Heterotrophy is required to adequately supply critical nutrients, especially nitrogen and phosphorus. Scleractinian corals are known as mesozooplankton predators, and most employ tentacle capture. The ability to trap nano- and picoplankton has been demonstrated by several coral species and appears to fulfill a substantial proportion of their daily metabolic requirements. The mechanism of capture likely involves mucociliary activity or extracoelenteric digestion, but the relative contribution of these avenues have not been evaluated. Many corals employ mesenterial filaments to procure food in various forms, but the functional morphology and chemical activities of these structures have been poorly documented. Corals are capable of acquiring nutrition from particulate and dissolved organic matter, although the degree of reliance on these sources generally has not been established. Corals, including tropical, deep- and cold-water species, are known as a major source of carbon and other nutrients for benthic communities through the secretion of mucus, despite wide variation in chemical composition. Mucus is cycled through the planktonic microbial loop, the benthos, and the microbial community within the sediments. The consensus indicates that the dissolved organic fraction of mucus usually exceeds the insoluble portion, and both serve as sources for the growth of nano- and picoplankton. As many corals employ mucus to trap food, a portion is taken back during feeding. The net gain or loss has not been evaluated, although production is generally thought to exceed consumption. The same is true for the net uptake and loss of dissolved organic matter by mucus secretion. Octocorals are thought not to employ mucus capture or mesenterial filaments during feeding and generally rely on tentacular filtration of weakly swimming mesozooplankton, particulates, dissolved organic matter, and picoplankton. Nonsymbiotic species in the tropics favor phytoplankton and weakly swimming zooplankton. Azooxanthellate soft corals are opportunistic feeders and shift their diet according to the season from phyto- and nanoplankton in summer to primarily particulate organic matter (POM) in winter. Cold-water species favor POM, phytodetritus, microplankton, and larger zooplankton when available. Antipatharians apparently feed on mesozooplankton but also use mucus nets, possibly for capture of POM. Feeding modes in this group are poorly known.
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Affiliation(s)
- Walter M Goldberg
- Department of Biological Sciences, Florida International University, Miami, FL, USA.
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36
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Unlocking Marine Biotechnology in the Developing World. Trends Biotechnol 2017; 35:1119-1121. [PMID: 28890138 DOI: 10.1016/j.tibtech.2017.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 12/12/2022]
Abstract
Fulfilling the promise of marine biotechnology as a source for environmental and biomedical applications remains challenging. New technologies will be necessary to harness marine biodiversity, and collaboration across government, academic, and private sectors will be crucial to create mechanisms of technology transfer and promote the development of new marine biotechnology companies.
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