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Bui VN, Nguyen TPT, Nguyen HD, Phi QT, Nguyen TN, Chu HH. Bioactivity responses to changes in mucus-associated bacterial composition between healthy and bleached Porites lobata corals. J Invertebr Pathol 2024; 206:108164. [PMID: 38960029 DOI: 10.1016/j.jip.2024.108164] [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: 03/11/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
This study aims to investigate how bioactivities of the coral surface mucus layer (SML) respond to changes in mucus-associated bacterial communities between bleached and healthy Porites lobata corals in Nha Trang Bay, Vietnam. The findings suggested that significant shifts in the mucus-associated bacterial communities were related to changes in coral health states from bleached to healthy P. lobata colonies (p < 0.05), while bacterial compositions were not significantly different across seasons and locations (p > 0.05). Of which 8 genera, Shewanella, Fusibacter, Halodesulfovibrio, Marinifilum, Endozoicomonas, Litoribacillus, Algicola, and Vibrio were present only in the SML of bleached coral while absent in the SML of the healthy one. As compared with the bleached SML, the healthy SML demonstrated stronger antibacterial activity against a coral bleaching pathogen, V. coralliilyticus, higher antitumor activity against HCT116 cell accompanied with increased induction of cleaved PARP and accelerated cell nucleic apoptosis and cycle arrest at S and G2/M phases exhibiting several typical characteristics, cell shrinkage, lost cell contact, and apoptotic body formation. Moreover, putative compounds detected at 280 nm in the healthy SML were obviously higher than those in the bleached one, probably they could be bioactive molecules responsible for competitively exclusion of pathogens, Algicola and Vibrio, from the healthy SML.
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Affiliation(s)
- Van Ngoc Bui
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Viet Nam; Graduate University of Science and Technology (GUST), VAST, Hanoi, Viet Nam.
| | - Thi Phuong Thao Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Viet Nam; Institute of Biological and Food Technology, Hanoi Open University, Hanoi, Viet Nam
| | - Huy Duong Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Viet Nam
| | - Quyet Tien Phi
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Viet Nam; Graduate University of Science and Technology (GUST), VAST, Hanoi, Viet Nam
| | - Trung Nam Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Viet Nam; Graduate University of Science and Technology (GUST), VAST, Hanoi, Viet Nam
| | - Hoang Ha Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Viet Nam; Graduate University of Science and Technology (GUST), VAST, Hanoi, Viet Nam
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2
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Xiao Z, Feng C, Gao B, Huang Y, Long L, Yang F. Marine macroalgae and their associated bacterial communities affect larval settlement and survivorship of the coral Pocillopora damicornis. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106597. [PMID: 38875898 DOI: 10.1016/j.marenvres.2024.106597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 05/05/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
Macroalgae play crucial roles as major habitat-forming organisms in marine ecosystems, having significant impacts on coral recruitment and reef recovery. However, the interactions between marine macroalgae and coral larvae remain poorly understood. Furthermore, little is known whether differences in bacterial assemblages associated with macroalgae may play roles in this process. Here, we comprehensively investigated the impacts of different macroalgae and their associated microbiomes on larval settlement and survival of coral Pocillopora damicornis. The results revealed significant variations in larval settlement and survival rates when exposed to different macroalgal species. The highest settlement rate, reaching 90%, was observed in the presence of the red alga Hypnea pannosa, followed by green algae Caulerpa serrulata, C. racemosa, and brown algae Turbinaria gracilis, Sargassum polycystum. Correspondingly, similarities in bacterial compositions were observed between H. pannosa and C. racemosa, as well as between T. gracilis and S. polycystum, implying associated bacterial may be related with the algal functions. Furthermore, macroalgae that facilitate larval settlement exhibited higher abundances of amplicon sequence variants (ASVs) associated with the metabolism of dimethylsulfoniopropionate or the antagonism of known coral pathogens. However, the brown alga Padina boryana failed to induce larval settlement with survival rate of zero after 120 h. The algal species harbored more abundances of ASVs related to Rhizobiaceae. These findings highlight the significant impact of macroalgae and their associated microbiomes on coral recruitment, as they influence both larval settlement and survival rates.
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Affiliation(s)
- Zhiliang Xiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Cheng Feng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Bohai Gao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yi Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Lijuan Long
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China.
| | - Fangfang Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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3
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Swaminathan SD, Lafferty KD, Knight NS, Altieri AH. Stony coral tissue loss disease indirectly alters reef communities. SCIENCE ADVANCES 2024; 10:eadk6808. [PMID: 38701216 PMCID: PMC11068009 DOI: 10.1126/sciadv.adk6808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/01/2024] [Indexed: 05/05/2024]
Abstract
Many Caribbean coral reefs are near collapse due to various threats. An emerging threat, stony coral tissue loss disease (SCTLD), is spreading across the Western Atlantic and Caribbean. Data from the U.S. Virgin Islands reveal how SCTLD spread has reduced the abundance of susceptible coral and crustose coralline algae and increased cyanobacteria, fire coral, and macroalgae. A Caribbean-wide structural equation model demonstrates versatility in reef fish and associations with rugosity independent of live coral. Model projections suggest that some reef fishes will decline due to SCTLD, with the largest changes on reefs that lose the most susceptible corals and rugosity. Mapping these projected declines in space indicates how the indirect effects of SCTLD range from undetectable to devastating.
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Affiliation(s)
- Sara D. Swaminathan
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kevin D. Lafferty
- Western Ecological Research Center, US Geological Survey, Santa Barbara, CA 93455, USA
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Nicole S. Knight
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Andrew H. Altieri
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
- Smithsonian Tropical Research Center, Ancon 0843-03092, Republic of Panama
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4
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Becker CC, Weber L, Llopiz JK, Mooney TA, Apprill A. Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs. Environ Microbiol 2024; 26:e16610. [PMID: 38576217 DOI: 10.1111/1462-2920.16610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024]
Abstract
Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water-based disturbance indicators, we conducted a 7-year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation.
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Affiliation(s)
- Cynthia C Becker
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Laura Weber
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Joel K Llopiz
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - T Aran Mooney
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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5
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Howe-Kerr LI, Knochel AM, Meyer MD, Sims JA, Karrick CE, Grupstra CGB, Veglia AJ, Thurber AR, Vega Thurber RL, Correa AMS. Filamentous virus-like particles are present in coral dinoflagellates across genera and ocean basins. THE ISME JOURNAL 2023; 17:2389-2402. [PMID: 37907732 PMCID: PMC10689786 DOI: 10.1038/s41396-023-01526-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023]
Abstract
Filamentous viruses are hypothesized to play a role in stony coral tissue loss disease (SCTLD) through infection of the endosymbiotic dinoflagellates (Family Symbiodiniaceae) of corals. To evaluate this hypothesis, it is critical to understand the global distribution of filamentous virus infections across the genetic diversity of Symbiodiniaceae hosts. Using transmission electron microscopy, we demonstrate that filamentous virus-like particles (VLPs) are present in over 60% of Symbiodiniaceae cells (genus Cladocopium) within Pacific corals (Acropora hyacinthus, Porites c.f. lobata); these VLPs are more prevalent in Symbiodiniaceae of in situ colonies experiencing heat stress. Symbiodiniaceae expelled from A. hyacinthus also contain filamentous VLPs, and these cells are more degraded than their in hospite counterparts. Similar to VLPs reported from SCTLD-affected Caribbean reefs, VLPs range from ~150 to 1500 nm in length and 16-37 nm in diameter and appear to constitute various stages in a replication cycle. Finally, we demonstrate that SCTLD-affected corals containing filamentous VLPs are dominated by diverse Symbiodiniaceae lineages from the genera Breviolum, Cladocopium, and Durusdinium. Although this study cannot definitively confirm or refute the role of filamentous VLPs in SCTLD, it demonstrates that filamentous VLPs are not solely observed in SCTLD-affected corals or reef regions, nor are they solely associated with corals dominated by members of a particular Symbiodiniaceae genus. We hypothesize that filamentous viruses are a widespread, common group that infects Symbiodiniaceae. Genomic characterization of these viruses and empirical tests of the impacts of filamentous virus infection on Symbiodiniaceae and coral colonies should be prioritized.
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Affiliation(s)
| | - Anna M Knochel
- BioSciences Department, Rice University, Houston, TX, USA
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX, USA
| | - Jordan A Sims
- BioSciences Department, Rice University, Houston, TX, USA
- Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | | | - Carsten G B Grupstra
- BioSciences Department, Rice University, Houston, TX, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
- Department of Biology, University of Puerto Rico, Mayagüez, PR, USA
| | - Andrew R Thurber
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
- College of Earth Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | | | - Adrienne M S Correa
- BioSciences Department, Rice University, Houston, TX, USA.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
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6
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Howard RD, Schul MD, Rodriguez Bravo LM, Altieri AH, Meyer JL. Shifts in the coral microbiome in response to in situ experimental deoxygenation. Appl Environ Microbiol 2023; 89:e0057723. [PMID: 37916820 PMCID: PMC10686059 DOI: 10.1128/aem.00577-23] [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: 04/06/2023] [Accepted: 09/12/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels around Siderastrea siderea and Agaricia lamarcki colonies in situ to observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.
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Affiliation(s)
- Rachel D. Howard
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, Florida, USA
| | - Monica D. Schul
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, Florida, USA
| | - Lucia M. Rodriguez Bravo
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andrew H. Altieri
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie L. Meyer
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, Florida, USA
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7
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Becker CC, Weber L, Zgliczynski B, Sullivan C, Sandin S, Muller E, Clark AS, Kido Soule MC, Longnecker K, Kujawinski EB, Apprill A. Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats. PNAS NEXUS 2023; 2:pgad287. [PMID: 37719750 PMCID: PMC10504872 DOI: 10.1093/pnasnexus/pgad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023]
Abstract
As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.
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Affiliation(s)
- Cynthia C Becker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Biological Oceanography, Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering,Cambridge, MA 02139, USA
| | - Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Brian Zgliczynski
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Chris Sullivan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Stuart Sandin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Erinn Muller
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL 33042, USA
- Coral Health and Disease Program, Mote Marine Laboratory, Sarasota, FL 34236, USA
| | - Abigail S Clark
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL 33042, USA
- Marine Science and Technology Department, The College of the Florida Keys, Key West, FL 33040, USA
| | - Melissa C 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
| | - 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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8
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Evans JS, Paul VJ, Ushijima B, Pitts KA, Kellogg CA. Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD). PeerJ 2023; 11:e15836. [PMID: 37637172 PMCID: PMC10460154 DOI: 10.7717/peerj.15836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/11/2023] [Indexed: 08/29/2023] Open
Abstract
Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy "receiver" coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the presence of numerous previously identified SCTLD bioindicators within our mesocosms. The identification in our mesocosms of specific bacterial amplicon sequence variants that also appear across prior studies spanning different collection years, geographic regions, source material, and coral species, suggests that bacteria may play some role in the disease.
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Affiliation(s)
- James S. Evans
- St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, Florida, United States of America
| | - Valerie J. Paul
- Smithsonian Marine Station, Ft. Pierce, Florida, United States of America
| | - Blake Ushijima
- Smithsonian Marine Station, Ft. Pierce, Florida, United States of America
- Department of Biology & Marine Biology, University of North Carolina at Wilmington, Wilmington, North Carolina, United States of America
| | - Kelly A. Pitts
- Smithsonian Marine Station, Ft. Pierce, Florida, United States of America
| | - Christina A. Kellogg
- St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, Florida, United States of America
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9
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Pereira PHF, Fernandes L, Jesus HE, Costa PG, Lacerda CHF, Mies M, Bianchini A, Santos HF. The Impact of Highly Weathered Oil from the Most Extensive Oil Spill in Tropical Oceans (Brazil) on the Microbiome of the Coral Mussismilia harttii. Microorganisms 2023; 11:1935. [PMID: 37630495 PMCID: PMC10458584 DOI: 10.3390/microorganisms11081935] [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: 06/05/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023] Open
Abstract
In 2019, the largest oil spill ever recorded in tropical oceans in terms of extent occurred in Brazil. The oil from the spill was collected directly from the environment and used in an exposure experiment with the endangered reef-building coral Mussismilia harttii. The treatments of the experiment were control (without oil), 1% oil, 2.5% oil, and direct contact of coral with oil. The most abundant hydrocarbon in the seawater of the experiment was phenatrene, which is toxic to corals. However, overall, the concentration of PAHs was not very high. The analysis of the maximum photosynthetic capacity of Symbiodiniaceae dinoflagellates showed a small impact of oil on corals, mainly on the contact treatment. However, coral microbiomes were affected in all oil treatments, with the contact treatment showing the most pronounced impact. A greater number and abundance of stress-indicating and potentially pathogenic bacteria were found in all oil treatments. Finally, this highly weathered oil that had lain in the ocean for a long time was carrying potentially coral-pathogenic bacteria within the Vibrionaceae family and was able to transmit some of these bacteria to corals. Bacteria within Vibrionaceae are the main causes of disease in different species of corals and other marine organisms.
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Affiliation(s)
- Pedro Henrique F. Pereira
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
| | - Luanny Fernandes
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
| | - Hugo E. Jesus
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
| | - Patricia G. Costa
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande—FURG, Av. Itália, s/n, Carreiros, Rio Grande 96203-900, RS, Brazil; (P.G.C.); (A.B.)
| | - Carlos H. F. Lacerda
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
| | - Miguel Mies
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
- Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, São Paulo 05508-120, SP, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande—FURG, Av. Itália, s/n, Carreiros, Rio Grande 96203-900, RS, Brazil; (P.G.C.); (A.B.)
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
| | - Henrique F. Santos
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
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10
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Beavers KM, Van Buren EW, Rossin AM, Emery MA, Veglia AJ, Karrick CE, MacKnight NJ, Dimos BA, Meiling SS, Smith TB, Apprill A, Muller EM, Holstein DM, Correa AMS, Brandt ME, Mydlarz LD. Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae. Nat Commun 2023; 14:2915. [PMID: 37217477 DOI: 10.1038/s41467-023-38612-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Stony coral tissue loss disease (SCTLD), one of the most pervasive and virulent coral diseases on record, affects over 22 species of reef-building coral and is decimating reefs throughout the Caribbean. To understand how different coral species and their algal symbionts (family Symbiodiniaceae) respond to this disease, we examine the gene expression profiles of colonies of five species of coral from a SCTLD transmission experiment. The included species vary in their purported susceptibilities to SCTLD, and we use this to inform gene expression analyses of both the coral animal and their Symbiodiniaceae. We identify orthologous coral genes exhibiting lineage-specific differences in expression that correlate to disease susceptibility, as well as genes that are differentially expressed in all coral species in response to SCTLD infection. We find that SCTLD infection induces increased expression of rab7, an established marker of in situ degradation of dysfunctional Symbiodiniaceae, in all coral species accompanied by genus-level shifts in Symbiodiniaceae photosystem and metabolism gene expression. Overall, our results indicate that SCTLD infection induces symbiophagy across coral species and that the severity of disease is influenced by Symbiodiniaceae identity.
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Affiliation(s)
- Kelsey M Beavers
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Emily W Van Buren
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Ashley M Rossin
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Madison A Emery
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Alex J Veglia
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Carly E Karrick
- Department of BioSciences, Rice University, Houston, TX, USA
| | | | - Bradford A Dimos
- Biology Department, University of Texas at Arlington, Arlington, TX, USA
| | - Sonora S Meiling
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Tyler B Smith
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | - Daniel M Holstein
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, USA
| | | | - Marilyn E Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Laura D Mydlarz
- Biology Department, University of Texas at Arlington, Arlington, TX, USA.
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11
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Wada N, Iguchi A, Urabe Y, Yoshioka Y, Abe N, Takase K, Hayashi S, Kawanabe S, Sato Y, Tang SL, Mano N. Microbial mat compositions and localization patterns explain the virulence of black band disease in corals. NPJ Biofilms Microbiomes 2023; 9:15. [PMID: 37015942 PMCID: PMC10073141 DOI: 10.1038/s41522-023-00381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Black band disease (BBD) in corals is characterized by a distinctive, band-like microbial mat, which spreads across the tissues and often kills infected colonies. The microbial mat is dominated by cyanobacteria but also commonly contains sulfide-oxidizing bacteria (SOB), sulfate-reducing bacteria (SRB), and other microbes. The migration rate in BBD varies across different environmental conditions, including temperature, light, and pH. However, whether variations in the migration rates reflect differences in the microbial consortium within the BBD mat remains unknown. Here, we show that the micro-scale surface structure, bacterial composition, and spatial distribution differed across BBD lesions with different migration rates. The migration rate was positively correlated with the relative abundance of potential SOBs belonging to Arcobacteraceae localized in the middle layer within the mat and negatively correlated with the relative abundance of other potential SOBs belonging to Rhodobacteraceae. Our study highlights the microbial composition in BBD as an important determinant of virulence.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
- Research Laboratory on Environmentally-conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Yuta Urabe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago-City, Okinawa, 905-2192, Japan
| | - Natsumi Abe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Kazuki Takase
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Shuji Hayashi
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Saeko Kawanabe
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan
| | - Yui Sato
- College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No.128, Sec 2, Academia Rd, Nangang, Taipei, 11529, Taiwan.
| | - Nobuhiro Mano
- Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, 252-0813, Japan.
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12
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Apprill A, Girdhar Y, Mooney TA, Hansel CM, Long MH, Liu Y, Zhang WG, Kapit J, Hughen K, Coogan J, Greene A. Toward a New Era of Coral Reef Monitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5117-5124. [PMID: 36930700 PMCID: PMC10077584 DOI: 10.1021/acs.est.2c05369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 06/18/2023]
Abstract
Coral reefs host some of the highest concentrations of biodiversity and economic value in the oceans, yet these ecosystems are under threat due to climate change and other human impacts. Reef monitoring is routinely used to help prioritize reefs for conservation and evaluate the success of intervention efforts. Reef status and health are most frequently characterized using diver-based surveys, but the inherent limitations of these methods mean there is a growing need for advanced, standardized, and automated reef techniques that capture the complex nature of the ecosystem. Here we draw on experiences from our own interdisciplinary research programs to describe advances in in situ diver-based and autonomous reef monitoring. We present our vision for integrating interdisciplinary measurements for select "case-study" reefs worldwide and for learning patterns within the biological, physical, and chemical reef components and their interactions. Ultimately, these efforts could support the development of a scalable and standardized suite of sensors that capture and relay key data to assist in categorizing reef health. This framework has the potential to provide stakeholders with the information necessary to assess reef health during an unprecedented time of reef change as well as restoration and intervention activities.
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Affiliation(s)
- Amy Apprill
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Yogesh Girdhar
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - T. Aran Mooney
- Biology
Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Colleen M. Hansel
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Matthew H. Long
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Yaqin Liu
- Marine
Policy Center, Woods Hole Oceanographic
Institution, Woods Hole, Massachusetts 02543, United States
| | - W. Gordon Zhang
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Jason Kapit
- Department
of Applied Ocean Sciences and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Konrad Hughen
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Jeff Coogan
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Austin Greene
- Department
of Marine Chemistry and Geochemistry, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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13
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Rosales SM, Huebner LK, Evans JS, Apprill A, Baker AC, Becker CC, Bellantuono AJ, Brandt ME, Clark AS, Del Campo J, Dennison CE, Eaton KR, Huntley NE, Kellogg CA, Medina M, Meyer JL, Muller EM, Rodriguez-Lanetty M, Salerno JL, Schill WB, Shilling EN, Stewart JM, Voss JD. A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies. ISME COMMUNICATIONS 2023; 3:19. [PMID: 36894742 PMCID: PMC9998881 DOI: 10.1038/s43705-023-00220-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/24/2023] [Accepted: 02/08/2023] [Indexed: 03/11/2023]
Abstract
Stony coral tissue loss disease (SCTLD) has been causing significant whole colony mortality on reefs in Florida and the Caribbean. The cause of SCTLD remains unknown, with the limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of 16S ribosomal RNA gene datasets generated by 16 field and laboratory SCTLD studies to find consistent bacteria associated with SCTLD across disease zones (vulnerable, endemic, and epidemic), coral species, coral compartments (mucus, tissue, and skeleton), and colony health states (apparently healthy colony tissue (AH), and unaffected (DU) and lesion (DL) tissue from diseased colonies). We also evaluated bacteria in seawater and sediment, which may be sources of SCTLD transmission. Although AH colonies in endemic and epidemic zones harbor bacteria associated with SCTLD lesions, and aquaria and field samples had distinct microbial compositions, there were still clear differences in the microbial composition among AH, DU, and DL in the combined dataset. Alpha-diversity between AH and DL was not different; however, DU showed increased alpha-diversity compared to AH, indicating that, prior to lesion formation, corals may undergo a disturbance to the microbiome. This disturbance may be driven by Flavobacteriales, which were especially enriched in DU. In DL, Rhodobacterales and Peptostreptococcales-Tissierellales were prominent in structuring microbial interactions. We also predict an enrichment of an alpha-toxin in DL samples which is typically found in Clostridia. We provide a consensus of SCTLD-associated bacteria prior to and during lesion formation and identify how these taxa vary across studies, coral species, coral compartments, seawater, and sediment.
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Affiliation(s)
- Stephanie M Rosales
- The University of Miami, Cooperative Institute for Marine and Atmospheric Studies, Miami, FL, USA.
- National Oceanic and Atmospheric Administration, Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA.
| | - Lindsay K Huebner
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, FL, USA
| | - James S Evans
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA, USA
| | - Andrew C Baker
- The University of Miami, Rosenstiel School of Marine, Atmospheric, and Earth Science, Department of Marine Biology and Ecology, Miami, FL, USA
| | - Cynthia C Becker
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA, USA
| | | | - Marilyn E Brandt
- The University of the Virgin Islands, Center for Marine and Environmental Studies, St. Thomas, VI, USA
| | - Abigail S Clark
- The College of the Florida Keys, Marine Science and Technology, Key West, FL, USA
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL, USA
| | - Javier Del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra)-Barcelona, Barcelona, Spain
| | - Caroline E Dennison
- The University of Miami, Rosenstiel School of Marine, Atmospheric, and Earth Science, Department of Marine Biology and Ecology, Miami, FL, USA
| | - Katherine R Eaton
- The University of Miami, Cooperative Institute for Marine and Atmospheric Studies, Miami, FL, USA
- National Oceanic and Atmospheric Administration, Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA
| | - Naomi E Huntley
- The Pennsylvania State University, Biology Department, University Park, PA, USA
| | - Christina A Kellogg
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - Mónica Medina
- The Pennsylvania State University, Biology Department, University Park, PA, USA
| | - Julie L Meyer
- University of Florida, Soil, Water, and Ecosystem Sciences Department, Gainesville, FL, USA
| | - Erinn M Muller
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA
| | | | - Jennifer L Salerno
- George Mason University, Potomac Environmental Research and Education Center, Department of Environmental Science and Policy, Woodbridge, VA, USA
| | - William B Schill
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown, WV, USA
| | - Erin N Shilling
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Julia Marie Stewart
- The Pennsylvania State University, Biology Department, University Park, PA, USA
| | - Joshua D Voss
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
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14
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Sun X, Li Y, Yang Q, Zhang H, Xu N, Tang Z, Wu S, Jiang Y, Mohamed HF, Ou D, Zheng X. Identification of quorum sensing-regulated Vibrio fortis as potential pathogenic bacteria for coral bleaching and the effects on the microbial shift. Front Microbiol 2023; 14:1116737. [PMID: 36819038 PMCID: PMC9935839 DOI: 10.3389/fmicb.2023.1116737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023] Open
Abstract
Coastal pollution, global warming, ocean acidification, and other reasons lead to the imbalance of the coral reef ecosystem, resulting in the increasingly serious problem of coral degradation. Coral bleaching is often accompanied by structural abnormalities of coral symbiotic microbiota, among which Vibrio is highly concerned. In this study, Vibrio fortis S10-1 (MCCC 1H00104), isolated from sea cucumber, was used for the bacterial infection on coral Seriatopora guttatus and Pocillopora damicornis. The infection of S10-1 led to coral bleaching and a significant reduction of photosynthetic function in coral holobiont, and the pathogenicity of V. fortis was regulated by quorum sensing. Meanwhile, Vibrio infection also caused a shift of coral symbiotic microbial community, with significantly increased abundant Proteobacteria and Actinobacteria and significantly reduced abundant Firmicutes; on genus level, the abundance of Bacillus decreased significantly and the abundance of Rhodococcus, Ralstonia, and Burkholderia-Caballeronia-Paraburkholderia increased significantly; S10-1 infection also significantly impacted the water quality in the micro-ecosystem. In contrast, S10-1 infection showed less effect on the microbial community of the live stone, which reflected that the microbes in the epiphytic environment of the live stone might have a stronger ability of self-regulation; the algal symbionts mainly consisted of Cladocopium sp. and showed no significant effect by the Vibrio infection. This study verified that V. fortis is the primary pathogenic bacterium causing coral bleaching, revealed changes in the microbial community caused by its infection, provided strong evidence for the "bacterial bleaching" hypothesis, and provided an experimental experience for the exploration of the interaction mechanism among microbial communities, especially coral-associated Vibrio in the coral ecosystem, and potential probiotic strategy or QS regulation on further coral disease control.
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Affiliation(s)
- Xiaohui Sun
- College of Chemical Engineering, Huaqiao University, Xiamen, China,*Correspondence: Xiaohui Sun,
| | - Yan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Qian Yang
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Han Zhang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Nuo Xu
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Zheng Tang
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Shishi Wu
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Yusheng Jiang
- College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Hala F. Mohamed
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,Botany and Microbiology Department (Girls Branch), Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Danyun Ou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen, China,Danyun Ou,
| | - Xinqing Zheng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen, China,Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Xiamen, China,Xinqing Zheng,
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15
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Bregman G, Lalzar M, Livne L, Bigal E, Zemah-Shamir Z, Morick D, Tchernov D, Scheinin A, Meron D. Preliminary study of shark microbiota at a unique mix-species shark aggregation site, in the Eastern Mediterranean Sea. Front Microbiol 2023; 14:1027804. [PMID: 36910211 PMCID: PMC9996248 DOI: 10.3389/fmicb.2023.1027804] [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: 08/25/2022] [Accepted: 01/16/2023] [Indexed: 02/25/2023] Open
Abstract
Sharks, as apex predators, play an essential ecological role in shaping the marine food web and maintaining healthy and balanced marine ecosystems. Sharks are sensitive to environmental changes and anthropogenic pressure and demonstrate a clear and rapid response. This designates them a "keystone" or "sentinel" group that may describe the structure and function of the ecosystem. As a meta-organism, sharks offer selective niches (organs) for microorganisms that can provide benefits for their hosts. However, changes in the microbiota (due to physiological or environmental changes) can turn the symbiosis into a dysbiosis and may affect the physiology, immunity and ecology of the host. Although the importance of sharks within the ecosystem is well known, relatively few studies have focused on the microbiome aspect, especially with long-term sampling. Our study was conducted at a site of coastal development in Israel where a mixed-species shark aggregation (November-May) is observed. The aggregation includes two shark species, the dusky (Carcharhinus obscurus) and sandbar (Carcharhinus plumbeus) which segregate by sex (females and males, respectively). In order to characterize the bacterial profile and examine the physiological and ecological aspects, microbiome samples were collected from different organs (gills, skin, and cloaca) from both shark species over 3 years (sampling seasons: 2019, 2020, and 2021). The bacterial composition was significantly different between the shark individuals and the surrounding seawater and between the shark species. Additionally, differences were apparent between all the organs and the seawater, and between the skin and gills. The most dominant groups for both shark species were Flavobacteriaceae, Moraxellaceae, and Rhodobacteraceae. However, specific microbial biomarkers were also identified for each shark. An unexpected difference in the microbiome profile and diversity between the 2019-2020 and 2021 sampling seasons, revealed an increase in the potential pathogen Streptococcus. The fluctuations in the relative abundance of Streptococcus between the months of the third sampling season were also reflected in the seawater. Our study provides initial information on shark microbiome in the Eastern Mediterranean Sea. In addition, we demonstrated that these methods were also able to describe environmental episodes and the microbiome is a robust measure for long-term ecological research.
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Affiliation(s)
- Goni Bregman
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Services Unit, University of Haifa, Haifa, Israel
| | - Leigh Livne
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eyal Bigal
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ziv Zemah-Shamir
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Danny Morick
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Aviad Scheinin
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dalit Meron
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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16
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Schaubeck A, Cao D, Cavaleri V, Mun S, Jeon SJ. Carapace microbiota in American lobsters ( Homarus americanus) associated with epizootic shell disease and the green gland. Front Microbiol 2023; 14:1093312. [PMID: 37089549 PMCID: PMC10113626 DOI: 10.3389/fmicb.2023.1093312] [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: 11/14/2022] [Accepted: 03/03/2023] [Indexed: 04/25/2023] Open
Abstract
Epizootic Shell Disease (ESD) has posed a great threat, both ecologically and economically, to the American lobster population of Long Island Sound since its emergence in the late 1990s. Because of the polymicrobial nature of carapace infections, causative agents for ESD remain unclear. In this study, we aimed to identify carapace microbiota associated with ESD and its potential impact on the microbiota of internal organs (green gland, hepatopancreas, intestine, and testis) using high-throughput 16S rRNA gene sequencing. We found that lobsters with ESD harbored specific carapace microbiota characterized by high abundance of Aquimarina, which was significantly different from healthy lobsters. PICRUSt analysis showed that metabolic pathways such as amino acid metabolism were enriched in the carapace microbiota of lobsters with ESD. Aquimarina, Halocynthiibacter, and Tenacibaculum were identified as core carapace bacteria associated with ESD. Particularly, Aquimarina and Halocynthiibacter were detected in the green gland, hepatopancreas, and testis of lobsters with ESD, but were absent from all internal organs tested in healthy lobsters. Hierarchical clustering analysis revealed that the carapace microbiota of lobsters with ESD was closely related to the green gland microbiota, whereas the carapace microbiota of healthy lobsters was more similar to the testis microbiota. Taken together, our findings suggest that ESD is associated with alterations in the structure and function of carapace microbiota, which may facilitate the invasion of bacteria into the green gland.
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Affiliation(s)
- Anna Schaubeck
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
| | - Dianjun Cao
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
| | - Vincent Cavaleri
- Division of Marine Resources, New York State Department of Environmental Conservation, East Setauket, NY, United States
| | - Seyoung Mun
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, Republic of Korea
| | - Soo Jin Jeon
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
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17
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Reshuffling of the Coral Microbiome during Dormancy. Appl Environ Microbiol 2022; 88:e0139122. [PMID: 36383004 PMCID: PMC9746315 DOI: 10.1128/aem.01391-22] [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] [Indexed: 11/17/2022] Open
Abstract
Quiescence, or dormancy, is a response to stressful conditions in which an organism slows or halts physiological functioning. Although most species that undergo dormancy maintain complex microbiomes, there is little known about how dormancy influences and is influenced by the host's microbiome, including in the temperate coral Astrangia poculata. Northern populations of A. poculata undergo winter quiescence. Here, we characterized wild A. poculata microbiomes in a high-resolution sampling time series before, during, and after quiescence using 16S rRNA gene sequencing on active (RNA) and present (DNA) microbiomes. We observed a restructuring of the coral microbiome during quiescence that persisted after reemergence. Upon entering quiescence, corals shed copiotrophic microbes, including putative pathogens, suggesting a removal of these taxa as corals cease normal functioning. During and after quiescence, bacteria and archaea associated with nitrification were enriched, suggesting that the quiescent microbiome may replace essential functions through supplying nitrate to corals and/or microbes. Overall, this study demonstrates that key microbial groups related to quiescence in A. poculata may play a role in the onset or emergence from dormancy and long-term regulation of the microbiome composition. The predictability of dormancy in A. poculata provides an ideal natural manipulation system to further identify factors that regulate host-microbial associations. IMPORTANCE Using a high-resolution sampling time series, this study is the first to demonstrate a persistent microbial community shift with quiescence (dormancy) in a marine organism, the temperate coral Astrangia poculata. Furthermore, during this period of community turnover, there is a shedding of putative pathogens and copiotrophs and an enhancement of the ammonia-oxidizing bacteria (Nitrosococcales) and archaea ("Candidatus Nitrosopumilus"). Our results suggest that quiescence represents an important period during which the coral microbiome can reset, shedding opportunistic microbes and enriching for the reestablishment of beneficial associates, including those that may contribute nitrate while the coral animal is not actively feeding. We suggest that this work provides foundational understanding of the interplay of microbes and the host's dormancy response in marine organisms.
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18
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Selak L, Marković T, Pjevac P, Orlić S. Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157859. [PMID: 35940271 DOI: 10.1016/j.scitotenv.2022.157859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 05/13/2023]
Abstract
Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.
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Affiliation(s)
- Lorena Selak
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Tamara Marković
- Croatian Geological Survey, Milan Sachs 2 Street, 10000 Zagreb, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; University of Vienna, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia.
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19
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Transmission of stony coral tissue loss disease (SCTLD) in simulated ballast water confirms the potential for ship-born spread. Sci Rep 2022; 12:19248. [PMID: 36357458 PMCID: PMC9649619 DOI: 10.1038/s41598-022-21868-z] [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: 06/02/2022] [Accepted: 10/04/2022] [Indexed: 11/12/2022] Open
Abstract
Stony coral tissue loss disease (SCTLD) remains an unprecedented epizootic disease, representing a substantial threat to the persistence and health of coral reef ecosystems in the Tropical Western Atlantic since its first observation near Miami, Florida in 2014. In addition to transport between adjacent reefs indicative of waterborne pathogen(s) dispersing on ocean currents, it has spread throughout the Caribbean to geographically- and oceanographically-isolated reefs, in a manner suggestive of ship and ballast water transmission. Here we evaluate the potential for waterborne transmission of SCTLD including via simulated ballast water, and test the efficacy of commonly-used UV radiation treatment of ballast water. Two species of reef-building corals (Orbicella faveolata and Pseudodiploria strigosa) were subjected to (1) disease-exposed or UV-treated disease-exposed water, and (2) a ballast hold time series of disease-exposed water in two carefully-controlled experiments to evaluate transmission. Our experiments demonstrated transmission of SCTLD through water, rather than direct contact between diseased and healthy corals. While UV treatment of disease-exposed water led to a 50% reduction in the number of corals exhibiting disease signs in both species, the statistical risk of transmission and volume of water needed to elicit SCTLD lesions remained similar to untreated disease-exposed water. The ballast hold time (24 h vs. 120 h) did not have a significant effect on the onset of visible disease signs for either species, though there appeared to be some evidence of a concentration effect for P. strigosa as lesions were only observed after the 120 h ballast hold time. Results from both experiments suggest that the SCTLD pathogens can persist in both untreated and UV-treated ballast water and remain pathogenic. Ballast water may indeed pose a threat to the continued spread and persistence of SCTLD, warranting further investigation of additional ballast water treatments and pathogen detection methods.
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Abstract
Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. However, few studies have explored the diversity of bacteria which can be isolated from a single species. Here, we isolated a total of 395 bacterial strains affiliated with 49 families across nine classes from the coral Pocillopora damicornis. Identification results showed that most of the strains represent potential novel bacterial species or genera. We also sequenced and assembled the genomes of 118 of these isolates, and then the putative functions of these isolates were identified based on genetic signatures derived from the genomes and this information was combined with isolate-specific phenotypic data. Genomic information derived from the isolates identified putative functions including nitrification and denitrification, dimethylsulfoniopropionate transformation, and supply of fixed carbon, amino acids, and B vitamins which may support their eukaryotic partners. Furthermore, the isolates contained genes associated with chemotaxis, biofilm formation, quorum sensing, membrane transport, signal transduction, and eukaryote-like repeat-containing and cell-cell attachment proteins, all of which potentially help the bacterium establish association with the coral host. Our work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates which can be used to refine understanding of the role of bacteria in coral health and are now available to be applied to novel strategies aimed at improving coral resilience through microbiome manipulation. IMPORTANCE Microbes underpin the health of corals which are the building blocks of diverse and productive reef ecosystems. Studying the culturable fraction of coral-associated bacteria has received less attention in recent times than using culture-independent molecular methods. However, the genomic and phenotypic characterization of isolated strains allows assessment of their functional role in underpinning coral health and identification of beneficial microbes for microbiome manipulation. Here, we isolated 395 bacterial strains from tissues of Pocillopora damicornis with many representing potentially novel taxa and therefore providing a significant contribution to coral microbiology through greatly enlarging the existing cultured coral-associated bacterial bank. Through analysis of the genomes obtained in this study for the coral-associated bacteria and coral host, we elucidate putative metabolic linkages and symbiotic establishment. The results of this study will help to elucidate the role of specific isolates in coral health and provide beneficial microbes for efforts aimed at improving coral health.
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Huntley N, Brandt ME, Becker CC, Miller CA, Meiling SS, Correa AMS, Holstein DM, Muller EM, Mydlarz LD, Smith TB, Apprill A. Experimental transmission of Stony Coral Tissue Loss Disease results in differential microbial responses within coral mucus and tissue. ISME COMMUNICATIONS 2022; 2:46. [PMID: 37938315 PMCID: PMC9723713 DOI: 10.1038/s43705-022-00126-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 04/28/2023]
Abstract
Stony coral tissue loss disease (SCTLD) is a widespread and deadly disease that affects nearly half of Caribbean coral species. To understand the microbial community response to this disease, we performed a disease transmission experiment on US Virgin Island (USVI) corals, exposing six species of coral with varying susceptibility to SCTLD. The microbial community of the surface mucus and tissue layers were examined separately using a small subunit ribosomal RNA gene-based sequencing approach, and data were analyzed to identify microbial community shifts following disease acquisition, potential causative pathogens, as well as compare microbiota composition to field-based corals from the USVI and Florida outbreaks. While all species displayed similar microbiome composition with disease acquisition, microbiome similarity patterns differed by both species and mucus or tissue microhabitat. Further, disease exposed but not lesioned corals harbored a mucus microbial community similar to those showing disease signs, suggesting that mucus may serve as an early warning detection for the onset of SCTLD. Like other SCTLD studies in Florida, Rhodobacteraceae, Arcobacteraceae, Desulfovibrionaceae, Peptostreptococcaceae, Fusibacter, Marinifilaceae, and Vibrionaceae dominated diseased corals. This study demonstrates the differential response of the mucus and tissue microorganisms to SCTLD and suggests that mucus microorganisms may be diagnostic for early disease exposure.
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Affiliation(s)
- Naomi Huntley
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Marilyn E Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Cynthia C Becker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA
| | - Carolyn A Miller
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Sonora S Meiling
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | | | - Daniel M Holstein
- Department of Oceanography and Coastal Science, Louisiana State University, Baton Rouge, LA, USA
| | | | - Laura D Mydlarz
- Department of Biology, University of Texas at Austin, Austin, TX, USA
| | - Tyler B Smith
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, USVI, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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22
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Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
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Evans JS, Paul VJ, Ushijima B, Kellogg CA. Combining tangential flow filtration and size fractionation of mesocosm water as a method for the investigation of waterborne coral diseases. Biol Methods Protoc 2022; 7:bpac007. [PMID: 35187265 PMCID: PMC8848328 DOI: 10.1093/biomethods/bpac007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 08/29/2023] Open
Abstract
The causative agents of most coral diseases today remain unknown, complicating disease response and restoration efforts. Pathogen identifications can be hampered by complex microbial communities naturally associated with corals and seawater, which create complicating "background noise" that can potentially obscure a pathogen's signal. Here, we outline an approach to investigate waterborne coral diseases that use a combination of coral mesocosms, tangential flow filtration, and size fractionation to reduce the impact of this background microbial diversity, compensate for unknown infectious dose, and further narrow the suspect pool of potential pathogens. As proof of concept, we use this method to compare the bacterial communities shed into six Montastraea cavernosa coral mesocosms and demonstrate this method effectively detects differences between diseased and healthy coral colonies. We found several amplicon sequence variants (ASVs) in the diseased mesocosms that represented 100% matches with ASVs identified in prior studies of diseased coral tissue, further illustrating the effectiveness of our approach. Our described method is an effective alternative to using coral tissue or mucus to investigate waterborne coral diseases of unknown etiology and can help more quickly narrow the pool of possible pathogens to better aid in disease response efforts. Additionally, this versatile method can be easily adapted to characterize either the entire microbial community associated with a coral or target-specific microbial groups, making it a beneficial approach regardless of whether a causative agent is suspected or is completely unknown.
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Affiliation(s)
- James S Evans
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL 33701, USA
| | | | - Blake Ushijima
- Smithsonian Marine Station, Ft. Pierce, FL 34949, USA
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Christina A Kellogg
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL 33701, USA
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Silva DP, Epstein HE, Vega Thurber RL. Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics. Front Microbiol 2022; 13:1007877. [PMID: 36891260 PMCID: PMC9987214 DOI: 10.3389/fmicb.2022.1007877] [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: 07/31/2022] [Accepted: 12/30/2022] [Indexed: 02/22/2023] Open
Abstract
Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host's responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.
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Affiliation(s)
- Denise P Silva
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Hannah E Epstein
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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Characterization of the Microbiome of Corals with Stony Coral Tissue Loss Disease along Florida's Coral Reef. Microorganisms 2021; 9:microorganisms9112181. [PMID: 34835306 PMCID: PMC8623284 DOI: 10.3390/microorganisms9112181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 01/04/2023] Open
Abstract
Stony coral tissue loss disease (SCTLD) is an emergent and often lethal coral disease that was first reported near Miami, FL (USA) in 2014. Our objective was to determine if coral colonies showing signs of SCTLD possess a specific microbial signature across five susceptible species sampled in Florida’s Coral Reef. Three sample types were collected: lesion tissue and apparently unaffected tissue of diseased colonies, and tissue of apparently healthy colonies. Using 16S rRNA high-throughput gene sequencing, our results show that, for every species, the microbial community composition of lesion tissue was significantly different from healthy colony tissue and from the unaffected tissue of diseased colonies. The lesion tissue of all but one species (Siderastrea siderea) had higher relative abundances of the order Rhodobacterales compared with other types of tissue samples, which may partly explain why S. siderea lesions often differed in appearance compared to other species. The order Clostridiales was also present at relatively high abundances in the lesion tissue of three species compared to healthy and unaffected tissues. Stress often leads to the dysbiosis of coral microbiomes and increases the abundance of opportunistic pathogens. The present study suggests that Rhodobacterales and Clostridiales likely play an important role in SCTLD.
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