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Selwyn JD, Despard BA, Vollmer MV, Trytten EC, Vollmer SV. Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning. Environ Microbiol 2024; 26:e16700. [PMID: 39289821 DOI: 10.1111/1462-2920.16700] [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: 05/23/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024]
Abstract
Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative pathogens. An example is white band disease (WBD), which has killed up to 95% of the now-endangered Caribbean Acropora corals since 1979, yet the pathogen is still unknown. The 16S rRNA gene surveys have identified hundreds of WBD-associated bacterial amplicon sequencing variants (ASVs) from at least nine bacterial families with little consensus across studies. We conducted a multi-year, multi-site 16S rRNA gene sequencing comparison of 269 healthy and 143 WBD-infected Acropora cervicornis and used machine learning modelling to accurately predict disease outcomes and identify the top ASVs contributing to disease. Our ensemble ML models accurately predicted disease with greater than 97% accuracy and identified 19 disease-associated ASVs and five healthy-associated ASVs that were consistently differentially abundant across sampling periods. Using a tank-based transmission experiment, we tested whether the 19 disease-associated ASVs met the assumption of a pathogen and identified two pathogenic candidate ASVs-ASV25 Cysteiniphilum litorale and ASV8 Vibrio sp. to target for future isolation, cultivation, and confirmation of Henle-Koch's postulate via transmission assays.
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Affiliation(s)
- Jason D Selwyn
- Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Brecia A Despard
- Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Miles V Vollmer
- Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Emily C Trytten
- Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Steven V Vollmer
- Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
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2
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Vohsen SA, Herrera S. Coral microbiomes are structured by environmental gradients in deep waters. ENVIRONMENTAL MICROBIOME 2024; 19:38. [PMID: 38858739 PMCID: PMC11165896 DOI: 10.1186/s40793-024-00579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/02/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53-2224 m) and geographic location (over 680 m) as well as the host coral's genotype using RAD-sequencing. RESULTS Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts' ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location. CONCLUSIONS Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill.
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Affiliation(s)
- Samuel A Vohsen
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
| | - Santiago Herrera
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
- Lehigh Oceans Research Center, Lehigh University, Bethlehem, PA, USA.
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3
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Pogoreutz C, Ziegler M. Frenemies on the reef? Resolving the coral-Endozoicomonas association. Trends Microbiol 2024; 32:422-434. [PMID: 38216372 DOI: 10.1016/j.tim.2023.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 01/14/2024]
Abstract
Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.
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Affiliation(s)
- Claudia Pogoreutz
- EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France.
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany.
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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [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: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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Schul MD, Anastasious DE, Spiers LJ, Meyer JL, Frazer TK, Brown AL. Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis. PeerJ 2023; 11:e15170. [PMID: 37361046 PMCID: PMC10290447 DOI: 10.7717/peerj.15170] [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: 03/17/2021] [Accepted: 03/13/2023] [Indexed: 06/28/2023] Open
Abstract
Background Coral diseases are one of the leading causes of declines in coral populations. In the Caribbean, white band disease (WBD) has led to a substantial loss of Acropora corals. Although the etiologies of this disease have not been well described, characterizing the coral microbiome during the transition from a healthy to diseased state is critical for understanding disease progression. Coral nurseries provide unique opportunities to further understand the microbial changes associated with diseased and healthy corals, because corals are monitored over time. We characterized the microbiomes before and during an outbreak of WBD in Acropora cervicornis reared in an ocean nursery in Little Cayman, CI. We asked (1) do healthy corals show the same microbiome over time (before and during a disease outbreak) and (2) are there disease signatures on both lesioned and apparently healthy tissues on diseased coral colonies? Methods Microbial mucus-tissue slurries were collected from healthy coral colonies in 2017 (before the disease) and 2019 (during the disease onset). Diseased colonies were sampled at two separate locations on an individual coral colony: at the interface of Disease and ∼10 cm away on Apparently Healthy coral tissue. We sequenced the V4 region of the 16S rRNA gene to characterize bacterial and archaeal community composition in nursery-reared A. cervicornis. We assessed alpha diversity, beta diversity, and compositional differences to determine differences in microbial assemblages across health states (2019) and healthy corals between years (2017 and 2019). Results Microbial communities from healthy A. cervicornis from 2017 (before disease) and 2019 (after disease) did not differ significantly. Additionally, microbial communities from Apparently Healthy samples on an otherwise diseased coral colony were more similar to Healthy colonies than to the diseased portion on the same colony for both alpha diversity and community composition. Microbial communities from Diseased tissues had significantly higher alpha diversity than both Healthy and Apparently Healthy tissues but showed no significant difference in beta-diversity dispersion. Our results show that at the population scale, Healthy and Apparently Healthy coral tissues are distinct from microbial communities associated with Diseased tissues. Furthermore, our results suggest stability in Little Cayman nursery coral microbiomes over time. We show healthy Caymanian nursery corals had a stable microbiome over a two-year period, an important benchmark for evaluating coral health via their microbiome.
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Affiliation(s)
- Monica D. Schul
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States of America
| | - Dagny-Elise Anastasious
- Little Cayman Research Center, Central Caribbean Marine Institute, Little Cayman, Cayman Islands
| | - Lindsay J. Spiers
- School of Fisheries, University of Florida, Gainesville, FL, United States of America
- Fish & Wildlife Research Institute, Florida Fish & Wildlife Conservation Commission, Marathon, FL, United States of America
| | - Julie L. Meyer
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States of America
| | - Thomas K. Frazer
- College of Marine Science, University of South Florida, St. Petersburg, FL, United States of America
| | - Anya L. Brown
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, United States of America
- Bodega Marine Lab, Department of Evolution and Ecology, University of California, Davis, Bodega Bay, CA, United States of America
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6
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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Klinges JG, Patel SH, Duke WC, Muller EM, Vega Thurber RL. Microbiomes of a disease-resistant genotype of Acropora cervicornis are resistant to acute, but not chronic, nutrient enrichment. Sci Rep 2023; 13:3617. [PMID: 36869057 PMCID: PMC9984465 DOI: 10.1038/s41598-023-30615-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Chronically high levels of inorganic nutrients have been documented in Florida's coral reefs and are linked to increased prevalence and severity of coral bleaching and disease. Naturally disease-resistant genotypes of the staghorn coral Acropora cervicornis are rare, and it is unknown whether prolonged exposure to acute or chronic high nutrient levels will reduce the disease tolerance of these genotypes. Recently, the relative abundance of the bacterial genus Aquarickettsia was identified as a significant indicator of disease susceptibility in A. cervicornis, and the abundance of this bacterial species was previously found to increase under chronic and acute nutrient enrichment. We therefore examined the impact of common constituents of nutrient pollution (phosphate, nitrate, and ammonium) on microbial community structure in a disease-resistant genotype with naturally low abundances of Aquarickettsia. We found that although this putative parasite responded positively to nutrient enrichment in a disease-resistant host, relative abundances remained low (< 0.5%). Further, while microbial diversity was not altered significantly after 3 weeks of nutrient enrichment, 6 weeks of enrichment was sufficient to shift microbiome diversity and composition. Coral growth rates were also reduced by 6 weeks of nitrate treatment compared to untreated conditions. Together these data suggest that the microbiomes of disease-resistant A. cervicornis may be initially resistant to shifts in microbial community structure, but succumb to compositional and diversity alterations after more sustained environmental pressure. As the maintenance of disease-resistant genotypes is critical for coral population management and restoration, a complete understanding of how these genotypes respond to environmental stressors is necessary to predict their longevity.
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Affiliation(s)
- J Grace Klinges
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA.
- Mote Marine Laboratory International Center for Coral Reef Research and Restoration, 24244 Overseas Hwy, Summerland Key, FL, 33042, USA.
| | - Shalvi H Patel
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - William C Duke
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Erinn M Muller
- Mote Marine Laboratory International Center for Coral Reef Research and Restoration, 24244 Overseas Hwy, Summerland Key, FL, 33042, USA
- Mote Marine Laboratory, 1600 Ken Thompson Pkwy, Sarasota, FL, 34236, USA
| | - Rebecca L Vega Thurber
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
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8
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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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Brown AL, Anastasiou DE, Schul M, MacVittie S, Spiers LJ, Meyer JL, Manfrino C, Frazer TK. Mixtures of genotypes increase disease resistance in a coral nursery. Sci Rep 2022; 12:19286. [PMID: 36369337 PMCID: PMC9652365 DOI: 10.1038/s41598-022-23457-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Marine infectious diseases are a leading cause of population declines globally due, in large part, to challenges in diagnosis and limited treatment options. Mitigating disease spread is particularly important for species targeted for conservation. In some systems, strategic arrangement of organisms in space can constrain disease outbreaks, however, this approach has not been used in marine restoration. Reef building corals have been particularly devastated by disease and continue to experience catastrophic population declines. We show that mixtures of genotypes (i.e., diversity) increased disease resistance in the critically endangered Acropora cervicornis, a species that is frequently targeted for restoration of degraded reefs in the broader Caribbean region. This finding suggests a more generalized relationship between diversity and disease and offers a viable strategy for mitigating the spread of infectious diseases in corals that likely applies to other foundation species targeted for restoration.
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Affiliation(s)
- Anya L. Brown
- grid.15276.370000 0004 1936 8091School of Natural Resources and Environment, University of Florida, Gainesville, FL 32611 USA ,grid.27860.3b0000 0004 1936 9684Present Address: Department of Evolution and Ecology & Bodega Marine Lab, University of California, Davis, Bodega Bay, CA 94923 USA
| | - Dagny-Elise Anastasiou
- Central Caribbean Marine Institute, N Coast Road E, Box 37, Little Cayman, KY3-2501 Cayman Islands
| | - Monica Schul
- grid.15276.370000 0004 1936 8091Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611 USA
| | - Sophia MacVittie
- Central Caribbean Marine Institute, N Coast Road E, Box 37, Little Cayman, KY3-2501 Cayman Islands ,grid.266096.d0000 0001 0049 1282Department of Molecular Cell Biology, University of California, Merced, Merced, CA USA
| | - Lindsay J. Spiers
- grid.15276.370000 0004 1936 8091Department of Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32611 USA ,grid.427218.a0000 0001 0556 4516Florida Fish & Wildlife Conservation Commission, Fish & Wildlife Research Institute, Marathon, FL USA
| | - Julie L. Meyer
- grid.15276.370000 0004 1936 8091Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL 32611 USA
| | - Carrie Manfrino
- Central Caribbean Marine Institute, N Coast Road E, Box 37, Little Cayman, KY3-2501 Cayman Islands
| | - Thomas K. Frazer
- grid.170693.a0000 0001 2353 285XCollege of Marine Science, University of South Florida, St. Petersburg, FL 33701 USA
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10
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Vega Thurber R, Schmeltzer ER, Grottoli AG, van Woesik R, Toonen RJ, Warner M, Dobson KL, McLachlan RH, Barott K, Barshis DJ, Baumann J, Chapron L, Combosch DJ, Correa AMS, DeCarlo TM, Hagedorn M, Hédouin L, Hoadley K, Felis T, Ferrier-Pagès C, Kenkel C, Kuffner IB, Matthews J, Medina M, Meyer C, Oster C, Price J, Putnam HM, Sawall Y. Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration. PeerJ 2022; 10:e14176. [PMID: 36345483 PMCID: PMC9636870 DOI: 10.7717/peerj.14176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/13/2022] [Indexed: 12/15/2022] Open
Abstract
Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at -80 °C to -20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses.
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Affiliation(s)
- Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Emily R. Schmeltzer
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Andréa G. Grottoli
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Robert van Woesik
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, Fl, United States
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kāne’ohe, HI, United States
| | - Mark Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Kerri L. Dobson
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Rowan H. McLachlan
- Department of Microbiology, Oregon State University, Corvallis, OR, United States,School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Katie Barott
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Daniel J. Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States
| | - Justin Baumann
- Biology Department, Bowdoin College, Brunswick, ME, United States
| | - Leila Chapron
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | | | | | - Thomas M. DeCarlo
- College of Natural and Computational Sciences, Hawai’i Pacific University, Honolulu, HI, United States
| | - Mary Hagedorn
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kāne’ohe, HI, United States,Conservation Biology Institute, Smithsonian, Kāne’ohe, HI, United States
| | - Laetitia Hédouin
- Centre de Recherches Insulaires et Observatoire de l’Environnement, Chargée de Recherches CNRS, Papetō’ai, Moorea, French Polynesia
| | - Kenneth Hoadley
- Department of Biological Sciences, University of Alabama – Tuscaloosa, Tuscaloosa, AL, United States
| | - Thomas Felis
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | | - Carly Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | | | - Jennifer Matthews
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian, Washington DC, United States
| | - Corinna Oster
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - James Price
- School of Earth Sciences, Ohio State University, Columbus, OH, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Yvonne Sawall
- Bermuda Institute of Ocean Sciences, St. George’s, St. George’s, Bermuda
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11
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Williams SD, Klinges JG, Zinman S, Clark AS, Bartels E, Villoch Diaz Maurino M, Muller EM. Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida's Coral Reef. PeerJ 2022; 10:e13574. [PMID: 35729906 PMCID: PMC9206844 DOI: 10.7717/peerj.13574] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/22/2022] [Indexed: 01/17/2023] Open
Abstract
Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida's Coral Reef and sampled after residing within Mote Marine Laboratory's in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.
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Affiliation(s)
| | - J. Grace Klinges
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America
| | - Samara Zinman
- Nova Southeastern University, Dania Beach, FL, United States of America
| | - Abigail S. Clark
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America,The College of the Florida Keys, Key West, FL, United States of America
| | - Erich Bartels
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America
| | - Marina Villoch Diaz Maurino
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, United States of America
| | - Erinn M. Muller
- Mote Marine Laboratory, Sarasota, FL, United States of America
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The 'other' Rickettsiales: an overview of the family ' Candidatus Midichloriaceae'. Appl Environ Microbiol 2022; 88:e0243221. [PMID: 35108076 DOI: 10.1128/aem.02432-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The family 'Candidatus Midichloriaceae' constitutes the most diverse but least studied lineage within the important order of intracellular bacteria Rickettsiales. Midichloriaceae endosymbionts are found in many hosts, including terrestrial arthropods, aquatic invertebrates, and protists. Representatives of the family are not documented to be pathogenic, but some are associated with diseased fish or corals. Different genera display a range of unusual features, such as full sets of flagellar genes without visible flagella, or the ability to invade host mitochondria. Since studies on 'Ca. Midichloriaceae' tend to focus on the host, the family is rarely addressed as a unit and we therefore lack a coherent picture of its diversity. Here we provide four new midichloriaceae genomes and we survey molecular and ecological data from the entire family. Features like genome size, ecological context, and host transitions vary considerably even among closely related midichloriaceae, suggesting a high frequency of such shifts, incomplete sampling, or both. Important functional traits involved in energy metabolism, flagella and secretion systems were independently reduced multiple times with no obvious correspondence to host or habitat, corroborating the idea that many features of these 'professional symbionts' are largely independent of host identity. Finally, despite 'Ca. Midichloriaceae' being predominantly studied in ticks, our analyses show that the clade is mainly aquatic, with a few terrestrial offshoots. This highlights the importance of considering aquatic hosts, and protists in particular, when reconstructing the evolution of these endosymbionts and by extension all Rickettsiales. Importance Among endosymbiotic bacterial lineages, few are as intensely studied as Rickettsiales, which include the causative agents of spotted fever, typhus, and anaplasmosis. And yet, an important subgroup called 'Candidatus Midichloriaceae' receives little attention despite accounting for a third of the diversity of Rickettsiales and harbouring a wide range of bacteria with unique features, like the ability to infect mitochondria. Midichloriaceae are found in many hosts, from ticks to corals to unicellular protozoa, and studies on them tend to focus on the host groups. Here, for the first time since the establishment of this clade, we address the genomics, evolution, and ecology of 'Ca. Midichloriaceae' as a whole, highlighting trends and patterns, the remaining gaps in our knowledge, and its importance for the understanding of symbiotic processes in intracellular bacteria.
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Baker LJ, Reich HG, Kitchen SA, Grace Klinges J, Koch HR, Baums IB, Muller EM, Thurber RV. The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally. THE ISME JOURNAL 2022; 16:400-411. [PMID: 34363004 PMCID: PMC8776821 DOI: 10.1038/s41396-021-01077-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/28/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
The symbiont "Candidatus Aquarickettsia rohweri" infects a diversity of aquatic hosts. In the threatened Caribbean coral, Acropora cervicornis, Aquarickettsia proliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality of coral. This study evaluated the extent, as well as the ecology and evolution of Aquarickettsia infecting threatened corals, Ac. cervicornis, and Ac. palmata and their hybrid ("Ac. prolifera"). Aquarickettsia was found in all acroporids, with coral host and geographic location impacting the infection magnitude. Phylogenomic and genome-wide single-nucleotide variant analysis of Aquarickettsia found phylogenetic clustering by geographic region, not by coral taxon. Analysis of Aquarickettsia fixation indices suggests multiple sequential infections of the same coral colony are unlikely. Furthermore, relative to other Rickettsiales species, Aquarickettsia is undergoing positive selection, with Florida populations experiencing greater positive selection relative to other Caribbean locations. This may be due in part to Aquarickettsia proliferating in response to greater nutrient stress in Florida, as indicated by greater in situ replication rates in these corals. Aquarickettsia was not found to significantly codiversify with either the coral animal or the coral's algal symbiont (Symbiodinium "fitti"). Quantitative PCR analysis showed that gametes, larvae, recruits, and juveniles from susceptible, captive-reared coral genets were not infected with Aquarickettsia. Thus, horizontal transmission of Aquarickettsia via coral mucocytes or an unidentified host is more likely. The prevalence of Aquarickettsia in Ac. cervicornis and its high abundance in the Florida coral population suggests that coral disease mitigation efforts focus on preventing early infection via horizontal transmission.
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Affiliation(s)
- Lydia J Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.
| | - Hannah G Reich
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sheila A Kitchen
- Division of Biology and Biological Engineering, California Institute of Science and Technology, Pasadena, CA, USA
| | - J Grace Klinges
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Hanna R Koch
- Coral Restoration Program, Mote Marine Laboratory, Summerland Key, FL, USA
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Erinn M Muller
- Coral Restoration Program, Mote Marine Laboratory, Summerland Key, FL, USA
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Klinges JG, Patel SH, Duke WC, Muller EM, Vega Thurber RL. OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6528370. [PMID: 35157069 PMCID: PMC8902694 DOI: 10.1093/femsec/fiac013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
Nutrient pollution is linked to coral disease susceptibility and severity, but the mechanism behind this effect remains underexplored. A recently identified bacterial species, ‘Ca. Aquarickettsia rohweri,’ is hypothesized to parasitize the Caribbean staghorn coral, Acropora cervicornis, leading to reduced coral growth and increased disease susceptibility. Aquarickettsia rohweri is hypothesized to assimilate host metabolites and ATP and was previously demonstrated to be highly nutrient-responsive. As nutrient enrichment is a pervasive issue in the Caribbean, this study examined the effects of common nutrient pollutants (nitrate, ammonium, and phosphate) on a disease-susceptible genotype of A. cervicornis. Microbial diversity was found to decline over the course of the experiment in phosphate-, nitrate-, and combined-treated samples, and quantitative PCR indicated that Aquarickettsia abundance increased significantly across all treatments. Only treatments amended with phosphate, however, exhibited a significant shift in Aquarickettsia abundance relative to other taxa. Furthermore, corals exposed to phosphate had significantly lower linear extension than untreated or nitrate-treated corals after 3 weeks of nutrient exposure. Together these data suggest that while experimental tank conditions, with an elevated nutrient regime associated with coastal waters, increased total bacterial abundance, only the addition of phosphate significantly altered the ratios of Aquarickettsia compared to other members of the microbiome.
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Affiliation(s)
- J Grace Klinges
- Corresponding author: Mote Marine Laboratory International Center for Coral Reef Research and Restoration, 24244 Overseas Hwy, Summerland Key, FL 33042, USA. Tel: +(941) 504-3801; E-mail:
| | - Shalvi H Patel
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331, USA
| | - William C Duke
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331, USA
| | - Erinn M Muller
- Mote Marine Laboratory International Center for Coral Reef Research and Restoration, 24244 Overseas Hwy, Summerland Key, FL 33042, USA
- Mote Marine Laboratory, 1600 Ken Thompson Pkwy, Sarasota, FL 34236, USA
| | - Rebecca L Vega Thurber
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331, USA
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Maire J, Blackall LL, van Oppen MJH. Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions. Microorganisms 2021; 9:2209. [PMID: 34835335 PMCID: PMC8619543 DOI: 10.3390/microorganisms9112209] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 02/07/2023] Open
Abstract
Corals are the main primary producers of coral reefs and build the three-dimensional reef structure that provides habitat to more than 25% of all marine eukaryotes. They harbor a complex consortium of microorganisms, including bacteria, archaea, fungi, viruses, and protists, which they rely on for their survival. The symbiosis between corals and bacteria is poorly studied, and their symbiotic relationships with intracellular bacteria are only just beginning to be acknowledged. In this review, we emphasize the importance of characterizing intracellular bacteria associated with corals and explore how successful approaches used to study such microorganisms in other systems could be adapted for research on corals. We propose a framework for the description, identification, and functional characterization of coral-associated intracellular bacterial symbionts. Finally, we highlight the possible value of intracellular bacteria in microbiome manipulation and mitigating coral bleaching.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Linda L. Blackall
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
| | - Madeleine J. H. van Oppen
- School of Biosciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.L.B.); (M.J.H.v.O.)
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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Vega Thurber R, Mydlarz LD, Brandt M, Harvell D, Weil E, Raymundo L, Willis BL, Langevin S, Tracy AM, Littman R, Kemp KM, Dawkins P, Prager KC, Garren M, Lamb J. Deciphering Coral Disease Dynamics: Integrating Host, Microbiome, and the Changing Environment. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.575927] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Diseases of tropical reef organisms is an intensive area of study, but despite significant advances in methodology and the global knowledge base, identifying the proximate causes of disease outbreaks remains difficult. The dynamics of infectious wildlife diseases are known to be influenced by shifting interactions among the host, pathogen, and other members of the microbiome, and a collective body of work clearly demonstrates that this is also the case for the main foundation species on reefs, corals. Yet, among wildlife, outbreaks of coral diseases stand out as being driven largely by a changing environment. These outbreaks contributed not only to significant losses of coral species but also to whole ecosystem regime shifts. Here we suggest that to better decipher the disease dynamics of corals, we must integrate more holistic and modern paradigms that consider multiple and variable interactions among the three major players in epizootics: the host, its associated microbiome, and the environment. In this perspective, we discuss how expanding the pathogen component of the classic host-pathogen-environment disease triad to incorporate shifts in the microbiome leading to dysbiosis provides a better model for understanding coral disease dynamics. We outline and discuss issues arising when evaluating each component of this trio and make suggestions for bridging gaps between them. We further suggest that to best tackle these challenges, researchers must adjust standard paradigms, like the classic one pathogen-one disease model, that, to date, have been ineffectual at uncovering many of the emergent properties of coral reef disease dynamics. Lastly, we make recommendations for ways forward in the fields of marine disease ecology and the future of coral reef conservation and restoration given these observations.
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