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Jefferson T, Henley EM, Erwin PM, Lager C, Perry R, Chernikhova D, Powell-Palm MJ, Ushijima B, Hagedorn M. Evaluating the coral microbiome during cryopreservation. Cryobiology 2024; 117:104960. [PMID: 39187231 DOI: 10.1016/j.cryobiol.2024.104960] [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: 12/07/2023] [Revised: 08/01/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
Abstract
Coral reefs are threatened by various local and global stressors, including elevated ocean temperatures due to anthropogenic climate change. Coral cryopreservation could help secure the diversity of threatened corals. Recently, isochoric vitrification was used to demonstrate that coral fragments lived to 24 hr post-thaw; however, in this study, they were stressed post-thaw. The microbial portion of the coral holobiont has been shown to affect host fitness and the impact of cryopreservation treatment on coral microbiomes is unknown. Therefore, we examined the coral-associated bacterial communities pre- and post-cryopreservation treatments, with a view towards informing potential future stress reduction strategies. We characterized the microbiome of the Hawaiian finger coral, Porites compressa in the wild and at seven steps during the isochoric vitrification process. We observed significant changes in microbiome composition, including: 1) the natural wild microbiomes of P. compressa were dominated by Endozoicomonadaceae (76.5 % relative abundance) and consistent between samples, independent of collection location across Kāne'ohe Bay; 2) Endozoicomonadaceae were reduced to <6.9 % in captivity, and further reduced to <0.5 % relative abundance after isochoric vitrification; and 3) Vibrionaceae dominated communities post-thaw (58.5-74.7 % abundance). Thus, the capture and cryopreservation processes, are implicated as possible causal agents of dysbiosis characterized by the loss of putatively beneficial symbionts (Endozoicomonadaceae) and overgrowth of potential pathogens (Vibrionaceae). Offsetting these changes with probiotic restoration treatments may alleviate cryopreservation stress and improve post-thaw husbandry.
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Affiliation(s)
- Tori Jefferson
- University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC, 28403, USA
| | - E Michael Henley
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22360, USA; Hawaii Institute of Marine Biology, Kāne'ohe, HI, 96744, USA
| | - Patrick M Erwin
- University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC, 28403, USA; Center for Marine Science, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Claire Lager
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22360, USA; Hawaii Institute of Marine Biology, Kāne'ohe, HI, 96744, USA
| | - Riley Perry
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22360, USA; Hawaii Institute of Marine Biology, Kāne'ohe, HI, 96744, USA
| | - Darya Chernikhova
- Environment and Natural Resources Program, Faculty of Life Sciences, University of Iceland, Reykjavík, Iceland
| | - Matthew J Powell-Palm
- J. Mike Walker '66 Department of Mechanical Engineering, Texas A&M University, College Station, TX, 77843, USA; Department of Materials Science and Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Blake Ushijima
- University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC, 28403, USA
| | - Mary Hagedorn
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22360, USA; Hawaii Institute of Marine Biology, Kāne'ohe, HI, 96744, USA.
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2
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Wang J, Li P, Di X, Lu H, Wei H, Zhi S, Fewer DP, He S, Liu L. Phylogenomic analysis uncovers an unexpected capacity for the biosynthesis of secondary metabolites in Pseudoalteromonas. Eur J Med Chem 2024; 279:116840. [PMID: 39244863 DOI: 10.1016/j.ejmech.2024.116840] [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: 05/22/2024] [Revised: 08/07/2024] [Accepted: 08/24/2024] [Indexed: 09/10/2024]
Abstract
Pseudoalteromonas is a genus of marine bacteria and a promising source of natural products with antibacterial, antifungal, and antifouling bioactivities. To accelerate the exploration of new compounds from this genus, we applied the gene-first approach to study 632 public Pseudoalteromonas genomes. We identified 3968 biosynthetic gene clusters (BGCs) involved in the biosynthesis of secondary metabolites and classified them into 995 gene cluster families (GCFs). Surprisingly, only 9 GCFs (0.9 %) included an experimentally identified reference biosynthetic gene cluster from the Minimum Information about a Biosynthetic Gene cluster database (MIBiG), suggesting a striking novelty of secondary metabolites in Pseudoalteromonas. Bioinformatic analysis of the biosynthetic diversity encoded in the identified BGCs uncovered six dominant species of this genus, P. citrea, P. flavipulchra, P. luteoviolacea, P. maricaloris, P. piscicida, and P. rubra, that encoded more than 17 BGCs on average. Moreover, each species exhibited a species-specific distribution of BGC. However, a deep analysis revealed two BGCs conserved across five of the six dominant species. These BGCS encoded an unknown lanthipeptide and the siderophore myxochelin B implying an essential role of antibiotics for Pseudoalteromonas. We chemically profiled 11 strains from the 6 dominant species and identified four new antibiotics, korormicins L-O (1-4), from P. citrea WJX-3. Our results highlight the unexplored biosynthetic potential for bioactive compounds in Pseudoalteromonas and provide an important guideline for targeting exploration.
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Affiliation(s)
- Jingxuan Wang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Peng Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xue Di
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hongmei Lu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huamao Wei
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Shuai Zhi
- School of Public Health, Ningbo University, Ningbo, Zhejiang, 315000, China
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Pienaari 9, FI-00014 Helsinki, Finland
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo, Zhejiang 315800, China
| | - Liwei Liu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China.
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3
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Voolstra CR, Raina JB, Dörr M, Cárdenas A, Pogoreutz C, Silveira CB, Mohamed AR, Bourne DG, Luo H, Amin SA, Peixoto RS. The coral microbiome in sickness, in health and in a changing world. Nat Rev Microbiol 2024; 22:460-475. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/06/2024]
Abstract
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
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Affiliation(s)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Melanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, American University, Washington, DC, USA
| | - Claudia Pogoreutz
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | | | - Amin R Mohamed
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Haiwei Luo
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC) and Computational Biology Research Center (CBRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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4
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Videau P, Shlafstein MD, Oline DK, Givan SA, Chapman LF, Strangman WK, Hahnke RL, Saw JH, Ushijima B. Genome-based taxonomic analysis of the genus Pseudoalteromonas reveals heterotypic synonyms. Environ Microbiol 2024; 26:e16672. [PMID: 39040020 DOI: 10.1111/1462-2920.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/31/2024] [Indexed: 07/24/2024]
Abstract
The Pseudoalteromonas genus comprises members that have been demonstrated to play significant ecological roles and produce enzymes, natural products, and activities that are beneficial to the environment and economy. A comprehensive evaluation of the genus revealed that the genomes of several Pseudoalteromonas species are highly similar to each other, exceeding species cutoff values. This evaluation involved determining and comparing the average nucleotide identity, in silico DNA-DNA hybridization, average amino acid identity, and the difference in G + C% between Pseudoalteromonas type strains with publicly available genomes. The genome of the Pseudoalteromonas elyakovii type strain was further assessed through additional sequencing and genomic comparisons to historical sequences. These findings suggest that six Pseudoalteromonas species, namely P. mariniglutinosa, P. donghaensis, P. maricaloris, P. elyakovii, P. profundi, and P. issachenkonii, should be reclassified as later heterotypic synonyms of the following validly published species: P. haloplanktis, P. lipolytica, P. flavipulchra, P. distincta, P. gelatinilytica, and P. tetraodonis. Furthermore, two names without valid standing, 'P. telluritireducens' and 'P. spiralis', should be associated with the validly published Pseudoalteromonas species P. agarivorans and P. tetraodonis, respectively.
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Affiliation(s)
- Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | | | - David K Oline
- Department of Biology, Southern Oregon University, Ashland, Oregon, USA
| | - Scott A Givan
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Linda Fleet Chapman
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Wendy K Strangman
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Richard L Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jimmy H Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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5
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Garcia B, Becker CC, Weber L, Swarr GJ, Kido Soule MC, Apprill A, Kujawinski EB. Benzoyl Chloride Derivatization Advances the Quantification of Dissolved Polar Metabolites on Coral Reefs. J Proteome Res 2024; 23:2041-2053. [PMID: 38782401 PMCID: PMC11166142 DOI: 10.1021/acs.jproteome.4c00049] [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: 01/22/2024] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Extracellular chemical cues constitute much of the language of life among marine organisms, from microbes to mammals. Changes in this chemical pool serve as invisible signals of overall ecosystem health and disruption to this finely tuned equilibrium. In coral reefs, the scope and magnitude of the chemicals involved in maintaining reef equilibria are largely unknown. Processes involving small, polar molecules, which form the majority components of labile dissolved organic carbon, are often poorly captured using traditional techniques. We employed chemical derivatization with mass spectrometry-based targeted exometabolomics to quantify polar dissolved phase metabolites on five coral reefs in the U.S. Virgin Islands. We quantified 45 polar exometabolites, demonstrated their spatial variability, and contextualized these findings in terms of geographic and benthic cover differences. By comparing our results to previously published coral reef exometabolomes, we show the novel quantification of 23 metabolites, including central carbon metabolism compounds (e.g., glutamate) and novel metabolites such as homoserine betaine. We highlight the immense potential of chemical derivatization-based exometabolomics for quantifying labile chemical cues on coral reefs and measuring molecular level responses to environmental stressors. Overall, improving our understanding of the composition and dynamics of reef exometabolites is vital for effective ecosystem monitoring and management strategies.
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Affiliation(s)
- Brianna
M. Garcia
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | | | - Laura Weber
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Gretchen J. Swarr
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Melissa C. Kido Soule
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Amy Apprill
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
| | - Elizabeth B. Kujawinski
- Department of Marine Chemistry
and Geochemistry, Woods Hole Oceanographic
Institution, Woods
Hole, Massachusetts 02543, United States
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6
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Cardoso PM, Hill LJ, Villela HDM, Vilela CLS, Assis JM, Rosado PM, Rosado JG, Chacon MA, Majzoub ME, Duarte GAS, Thomas T, Peixoto RS. Localization and symbiotic status of probiotics in the coral holobiont. mSystems 2024; 9:e0026124. [PMID: 38606974 PMCID: PMC11097643 DOI: 10.1128/msystems.00261-24] [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: 02/26/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome. IMPORTANCE Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.
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Affiliation(s)
- P. M. Cardoso
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - L. J. Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - H. D. M. Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - C. L. S. Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - J. M. Assis
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - P. M. Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - J. G. Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - M. A. Chacon
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M. E. Majzoub
- Center for Marine Science and Innovation; School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - G. A. S. Duarte
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - T. Thomas
- Center for Marine Science and Innovation; School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - R. S. Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Biology Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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7
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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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8
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Hill LJ, Messias CSMDA, Vilela CLS, Garritano AN, Villela HDM, do Carmo FL, Thomas T, Peixoto RS. Bacteria associated with the in hospite Symbiodiniaceae's phycosphere. iScience 2024; 27:109531. [PMID: 38585661 PMCID: PMC10995889 DOI: 10.1016/j.isci.2024.109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/23/2023] [Accepted: 03/16/2024] [Indexed: 04/09/2024] Open
Abstract
Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.
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Affiliation(s)
- Lilian Jorge Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Helena Dias Muller Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Flavia Lima do Carmo
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Raquel S. Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
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9
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Delgadillo-Ordoñez N, Garcias-Bonet N, Raimundo I, García FC, Villela H, Osman EO, Santoro EP, Curdia J, Rosado JGD, Cardoso P, Alsaggaf A, Barno A, Antony CP, Bocanegra C, Berumen ML, Voolstra CR, Benzoni F, Carvalho S, Peixoto RS. Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment. Commun Biol 2024; 7:434. [PMID: 38594357 PMCID: PMC11004148 DOI: 10.1038/s42003-024-06135-3] [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: 10/19/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Neus Garcias-Bonet
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Inês Raimundo
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Francisca C García
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Eslam O Osman
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Erika P Santoro
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao Curdia
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao G D Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pedro Cardoso
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Alsaggaf
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Adam Barno
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Chakkiath Paul Antony
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carolina Bocanegra
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Francesca Benzoni
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Raquel S Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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10
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Zhang Q, Su H, Lu C, Huang Q, Wang S, He X, Zou J, Chen Q, Liu Y, Zeng L. Ammonia removal mitigates white plague type II in the coral Pocillopora damicornis. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106403. [PMID: 38335857 DOI: 10.1016/j.marenvres.2024.106403] [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: 10/05/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
White Plague Type II (WPL II) is a disease increasingly affecting scleractinian coral species and progresses rapidly. However, the etiological pathogen and remedy remain elusive. In this study, transmission experiments demonstrated that Aureimonas altamirensis and Aurantimonas coralicida, representing the WPL II pathogens, could infect Pocillopora damicorni. The infection produced selected pathological symptoms, including bleaching, tissue loss, and decolorization. Furthermore, ammonia degradation significantly reduced the severity of infection by these pathogens, indicating that ammonia may be a virulence factor for WPL II. Coral microbiome analysis suggested that ammonia degradation mediates the anti-white plague effect by maintaining the density of Symbiodiniaceae and stabilizing the core and symbiotic bacteria. Aureimonas altamirensis and Aurantimonas coralicida have been shown to cause diseases of P. damicornis, with ammonia acting as a virulence factor, and ammoniac degradation may be a promising and innovative approach to mitigate coral mortality suffering from increasing diseases.
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Affiliation(s)
- Qi Zhang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Hongfei Su
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China.
| | - Chunrong Lu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Qinyu Huang
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Shuying Wang
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
| | - Xucong He
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Jie Zou
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
| | - Qiqi Chen
- School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
| | - Yuan Liu
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Lujia Zeng
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
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11
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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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12
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Wang L, Bin Q, Liu H, Zhang Y, Wang S, Luo S, Chen Z, Zhang M, Yu K. New insights into the on-site monitoring of probiotics eDNA using biosensing technology for heat-stress relieving in coral reefs. Biosens Bioelectron 2024; 243:115790. [PMID: 37906999 DOI: 10.1016/j.bios.2023.115790] [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: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023]
Abstract
Coral probiotics can improve the tolerance of corals to heat stress, thus mitigating the process of coral thermal bleaching. Sensitive and specific detection of coral probiotics at low abundances is highly desirable but remains challenging, especially for rapid and on-site detection of coral probiotics. Since the electrochemical biosensor has been recently used in the field of environmental DNA (eDNA) detection, herein, an efficient electrochemical biosensor was developed based on CoS2/CoSe2-NC HNCs electrode material with a specific DNA probe for the C. marina detection. After optimization, the lower limit of detection (LOD) values of such biosensors for the target DNA and genomic DNA were 1.58 fM and 6.5 pM, respectively. On this basis, a portable device was constructed for the practical detection of C. marina eDNA, and its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). For each analysis, the average cost was only ∼ $1.08 and could be completed within 100 min with reliable sensitivity and specificity. Overall, the biosensor could reflect the protective effect of probiotics on coral heat stress, and the proposed technique will put new insights into the rapid and on-site detection of coral probiotics to assist corals against global warming.
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Affiliation(s)
- Liwei Wang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China; Guangxi, Key Laboratory of Processing for Non-ferrous Metallic and Featured Materials, Nanning, 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qi Bin
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Hongjie Liu
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yibo Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Shaopeng Wang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Songlin Luo
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Zhenghua Chen
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China
| | - Man Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China.
| | - Kefu Yu
- School of Marine Sciences, School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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13
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Lewbart GA, Zachariah TT. Aquatic and Terrestrial Invertebrate Welfare. Animals (Basel) 2023; 13:3375. [PMID: 37958134 PMCID: PMC10649180 DOI: 10.3390/ani13213375] [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: 09/11/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Invertebrates are a diverse group of animals that make up the majority of the animal kingdom and encompass a wide array of species with varying adaptations and characteristics. Invertebrates are found in nearly all of the world's habitats, including aquatic, marine, and terrestrial environments. There are many misconceptions about invertebrate sentience, welfare requirements, the need for environmental enrichment, and overall care and husbandry for this amazing group of animals. This review addresses these topics and more for a select group of invertebrates with biomedical, economical, display, and human companionship importance.
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Affiliation(s)
- Gregory A. Lewbart
- College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA
| | - Trevor T. Zachariah
- Brevard Zoo|Sea Turtle Healing Center, 8225 North Wickham Road, Melbourne, FL 32940, USA;
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14
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Alker AT, Farrell MV, Demko AM, Purdy TN, Adak S, Moore BS, Sneed JM, Paul VJ, Shikuma NJ. Linking bacterial tetrabromopyrrole biosynthesis to coral metamorphosis. ISME COMMUNICATIONS 2023; 3:98. [PMID: 37726481 PMCID: PMC10509201 DOI: 10.1038/s43705-023-00309-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
An important factor dictating coral fitness is the quality of bacteria associated with corals and coral reefs. One way that bacteria benefit corals is by stimulating the larval to juvenile life cycle transition of settlement and metamorphosis. Tetrabromopyrrole (TBP) is a small molecule produced by bacteria that stimulates metamorphosis with and without attachment in a range of coral species. A standing debate remains, however, about whether TBP biosynthesis from live Pseudoalteromonas bacteria is the primary stimulant of coral metamorphosis. In this study, we create a Pseudoalteromonas sp. PS5 mutant lacking the TBP brominase gene, bmp2. Using this mutant, we confirm that the bmp2 gene is critical for TBP biosynthesis in Pseudoalteromonas sp. PS5. Mutation of this gene ablates the bacterium's ability in live cultures to stimulate the metamorphosis of the stony coral Porites astreoides. We further demonstrate that expression of TBP biosynthesis genes is strongest in stationary and biofilm modes of growth, where Pseudoalteromonas sp. PS5 might exist within surface-attached biofilms on the sea floor. Finally, we create a modular transposon plasmid for genomic integration and fluorescent labeling of Pseudoalteromonas sp. PS5 cells. Our results functionally link a TBP biosynthesis gene from live bacteria to a morphogenic effect in corals. The genetic techniques established here provide new tools to explore coral-bacteria interactions and could help to inform future decisions about utilizing marine bacteria or their products for coral restoration.
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Affiliation(s)
- Amanda T Alker
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
| | - Morgan V Farrell
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
| | | | - Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | | | - Nicholas J Shikuma
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA.
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15
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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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16
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Powell-Palm MJ, Henley EM, Consiglio AN, Lager C, Chang B, Perry R, Fitzgerald K, Daly J, Rubinsky B, Hagedorn M. Cryopreservation and revival of Hawaiian stony corals using isochoric vitrification. Nat Commun 2023; 14:4859. [PMID: 37612315 PMCID: PMC10447501 DOI: 10.1038/s41467-023-40500-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
Corals are under siege by both local and global threats, creating a worldwide reef crisis. Cryopreservation is an important intervention measure and a vital component of the modern coral conservation toolkit, but preservation techniques are currently limited to sensitive reproductive materials that can only be obtained a few nights per year during spawning. Here, we report the successful cryopreservation and revival of cm-scale coral fragments via mL-scale isochoric vitrification. We demonstrate coral viability at 24 h post-thaw using a calibrated oxygen-uptake respirometry technique, and further show that the method can be applied in a passive, electronics-free configuration. Finally, we detail a complete prototype coral cryopreservation pipeline, which provides a platform for essential next steps in modulating post-thaw stress and initiating long-term growth. These findings pave the way towards an approach that can be rapidly deployed around the world to secure the biological genetic diversity of our vanishing coral reefs.
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Affiliation(s)
- Matthew J Powell-Palm
- J. Mike Walker '66 Department of Mechanical Engineering, Texas A&M University, College Station, TX, USA.
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, USA.
| | - E Michael Henley
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA.
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA.
| | - Anthony N Consiglio
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Claire Lager
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Brooke Chang
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Riley Perry
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Kendall Fitzgerald
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
| | - Jonathan Daly
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, NSW, 2088, Australia
- Centre for Ecosystem Science and Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Boris Rubinsky
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Mary Hagedorn
- Smithsonian National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
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17
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Doering T, Tandon K, Topa SH, Pidot SJ, Blackall LL, van Oppen MJH. Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis. MICROBIOME 2023; 11:185. [PMID: 37596630 PMCID: PMC10439622 DOI: 10.1186/s40168-023-01622-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
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Affiliation(s)
- Talisa Doering
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sanjida H. Topa
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
- Australian Institute of Marine Science, Townsville, QLD Australia
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Pérez-Llano Y, Yarzábal Rodríguez LA, Martínez-Romero E, Dobson ADW, Gunde-Cimerman N, Vasconcelos V, Batista-García RA. From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios. Front Microbiol 2023; 14:1213340. [PMID: 37670990 PMCID: PMC10476623 DOI: 10.3389/fmicb.2023.1213340] [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: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
Global change, experienced in the form of ocean warming and pollution by man-made goods and xenobiotics, is rapidly affecting reef ecosystems and could have devastating consequences for marine ecology. Due to their critical role in regulating marine food webs and trophic connections, sponges are an essential model for studying and forecasting the impact of global change on reef ecosystems. Microbes are regarded as major contributors to the health and survival of sponges in marine environments. While most culture-independent studies on sponge microbiome composition to date have focused on prokaryotic diversity, the importance of fungi in holobiont behavior has been largely overlooked. Studies focusing on the biology of sponge fungi are uncommon. Thus, our current understanding is quite limited regarding the interactions and “crosstalk” between sponges and their associated fungi. Anthropogenic activities and climate change may reveal sponge-associated fungi as novel emerging pathogens. Global change scenarios could trigger the expression of fungal virulence genes and unearth new opportunistic pathogens, posing a risk to the health of sponges and severely damaging reef ecosystems. Although ambitious, this hypothesis has not yet been proven. Here we also postulate as a pioneering hypothesis that manipulating sponge-associated fungal communities may be a new strategy to cope with the threats posed to sponge health by pathogens and pollutants. Additionally, we anticipate that sponge-derived fungi might be used as novel sponge health promoters and beneficial members of the resident sponge microbiome in order to increase the sponge's resistance to opportunistic fungal infections under a scenario of global change.
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Affiliation(s)
- Yordanis Pérez-Llano
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Center for Genomic Sciences, Autonomous National University of Mexico (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Esperanza Martínez-Romero
- Center for Genomic Sciences, Autonomous National University of Mexico (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty. University of Ljubljana, Ljubljana, Slovenia
| | - Vitor Vasconcelos
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
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Villela H, Modolon F, Schultz J, Delgadillo-Ordoñez N, Carvalho S, Soriano AU, Peixoto RS. Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Sci Rep 2023; 13:12273. [PMID: 37507453 PMCID: PMC10382565 DOI: 10.1038/s41598-023-38512-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
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Affiliation(s)
- Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Flúvio Modolon
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Júnia Schultz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Raquel Silva Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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