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Howe-Kerr LI, Grupstra CGB, Rabbitt KM, Conetta D, Coy SR, Klinges JG, Maher RL, McConnell KM, Meiling SS, Messyasz A, Schmeltzer ER, Seabrook S, Sims JA, Veglia AJ, Thurber AR, Thurber RLV, Correa AMS. Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape. ISME Commun 2023; 3:27. [PMID: 37009785 PMCID: PMC10068613 DOI: 10.1038/s43705-023-00227-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 02/17/2023] [Accepted: 03/01/2023] [Indexed: 05/31/2023]
Abstract
Viruses can affect coral health by infecting their symbiotic dinoflagellate partners (Symbiodiniaceae). Yet, viral dynamics in coral colonies exposed to environmental stress have not been studied at the reef scale, particularly within individual viral lineages. We sequenced the viral major capsid protein (mcp) gene of positive-sense single-stranded RNA viruses known to infect symbiotic dinoflagellates ('dinoRNAVs') to analyze their dynamics in the reef-building coral, Porites lobata. We repeatedly sampled 54 colonies harboring Cladocopium C15 dinoflagellates, across three environmentally distinct reef zones (fringing reef, back reef, and forereef) around the island of Moorea, French Polynesia over a 3-year period and spanning a reef-wide thermal stress event. By the end of the sampling period, 28% (5/18) of corals in the fringing reef experienced partial mortality versus 78% (14/18) of corals in the forereef. Over 90% (50/54) of colonies had detectable dinoRNAV infections. Reef zone influenced the composition and richness of viral mcp amino acid types ('aminotypes'), with the fringing reef containing the highest aminotype richness. The reef-wide thermal stress event significantly increased aminotype dispersion, and this pattern was strongest in the colonies that experienced partial mortality. These findings demonstrate that dinoRNAV infections respond to environmental fluctuations experienced in situ on reefs. Further, viral productivity will likely increase as ocean temperatures continue to rise, potentially impacting the foundational symbiosis underpinning coral reef ecosystems.
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Affiliation(s)
| | - Carsten G B Grupstra
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Kristen M Rabbitt
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA, USA
| | - Dennis Conetta
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Samantha R Coy
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Oceanography, Texas A & M University, College Station, TX, USA
| | - J Grace Klinges
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, USA
| | - Rebecca L Maher
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | | - Sonora S Meiling
- University of the Virgin Islands, St. Thomas, US Virgin Islands, USA
| | - Adriana Messyasz
- Rutgers School of Environmental and Biological Sciences, New Brunswick, NJ, USA
| | | | - Sarah Seabrook
- Oregon State University, Corvallis, OR, USA
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Jordan A Sims
- Department of BioSciences, Rice University, Houston, TX, USA
- Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Alex J Veglia
- Department of BioSciences, Rice University, Houston, TX, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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. ISME J 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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Akob DM, Mumford AC, Orem W, Engle MA, Klinges JG, Kent DB, Cozzarelli IM. Wastewater Disposal from Unconventional Oil and Gas Development Degrades Stream Quality at a West Virginia Injection Facility. Environ Sci Technol 2016; 50:5517-25. [PMID: 27158829 DOI: 10.1021/acs.est.6b00428] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The development of unconventional oil and gas (UOG) resources has rapidly increased in recent years; however, the environmental impacts and risks are poorly understood. A single well can generate millions of liters of wastewater, representing a mixture of formation brine and injected hydraulic fracturing fluids. One of the most common methods for wastewater disposal is underground injection; we are assessing potential risks of this method through an intensive, interdisciplinary study at an injection disposal facility in West Virginia. In June 2014, waters collected downstream from the site had elevated specific conductance (416 μS/cm) and Na, Cl, Ba, Br, Sr, and Li concentrations, compared to upstream, background waters (conductivity, 74 μS/cm). Elevated TDS, a marker of UOG wastewater, provided an early indication of impacts in the stream. Wastewater inputs are also evident by changes in (87)Sr/(86)Sr in streamwater adjacent to the disposal facility. Sediments downstream from the facility were enriched in Ra and had high bioavailable Fe(III) concentrations relative to upstream sediments. Microbial communities in downstream sediments had lower diversity and shifts in composition. Although the hydrologic pathways were not able to be assessed, these data provide evidence demonstrating that activities at the disposal facility are impacting a nearby stream and altering the biogeochemistry of nearby ecosystems.
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Affiliation(s)
- Denise M Akob
- U.S. Geological Survey , National Research Program, Reston, Virginia 20192, United States
| | - Adam C Mumford
- U.S. Geological Survey , National Research Program, Reston, Virginia 20192, United States
| | - William Orem
- U.S. Geological Survey , Eastern Energy Resources Science Center, Reston, Virginia 20192, United States
| | - Mark A Engle
- U.S. Geological Survey , Eastern Energy Resources Science Center, Reston, Virginia 20192, United States
| | - J Grace Klinges
- U.S. Geological Survey , National Research Program, Reston, Virginia 20192, United States
| | - Douglas B Kent
- U.S. Geological Survey , National Research Program, Menlo Park, California 94025, United States
| | - Isabelle M Cozzarelli
- U.S. Geological Survey , National Research Program, Reston, Virginia 20192, United States
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