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Xu M, Cai Z, Cheng K, Chen G, Zhou J. Mitigation of Vibrio coralliilyticus-induced coral bleaching through bacterial dysbiosis prevention by Ruegeria profundi. Appl Environ Microbiol 2024; 90:e0227423. [PMID: 38470181 PMCID: PMC11022554 DOI: 10.1128/aem.02274-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
Vibrio species are prevalent in ocean ecosystems, particularly Vibrio coralliilyticus, and pose a threat to corals and other marine organisms under global warming conditions. While microbiota manipulation is considered for coral disease management, understanding the role of commensal bacteria in stress resilience remains limited. Here, a single bacterial species (Ruegeria profundi) rather than a consortium of native was used to combat pathogenic V. coralliilyticus and protect corals from bleaching. R. profundi showed therapeutic activity in vivo, preventing a significant reduction in bacterial diversity in bleached corals. Notably, the structure of the bacterial community differed significantly among all the groups. In addition, compared with the bleached corals caused by V. coralliilyticus, the network analysis revealed that complex interactions and positive correlations in the bacterial community of the R. profundi protected non-bleached corals, indicating R. profundi's role in fostering synergistic associations. Many genera of bacteria significantly increased in abundance during V. coralliilyticus infection, including Vibrio, Alteromonas, Amphritea, and Nautella, contributing to the pathogenicity of the bacterial community. However, R. profundi effectively countered the proliferation of these genera, promoting potential probiotic Endozoicomonas and other taxa, while reducing the abundance of betaine lipids and the type VI section system of the bacterial community. These changes ultimately influenced the interactive relationships among symbionts and demonstrated that probiotic R. profundi intervention can modulate coral-associated bacterial community, alleviate pathogenic-induced dysbiosis, and preserve coral health. These findings elucidated the relationship between the behavior of the coral-associated bacterial community and the occurrence of pathological coral bleaching.IMPORTANCEChanges in the global climate and marine environment can influence coral host and pathogen repartition which refers to an increased likelihood of pathogen infection in hosts. The risk of Vibrio coralliilyticus-induced coral disease is significantly heightened, primarily due to its thermos-dependent expression of virulent and populations. This study investigates how coral-associated bacterial communities respond to bleaching induced by V. coralliilyticus. Our findings demonstrate that Ruegeria profundi exhibits clear evidence of defense against pathogenic bacterial infection, contributing to the maintenance of host health and symbiont homeostasis. This observation suggests that bacterial pathogens could cause dysbiosis in coral holobionts. Probiotic bacteria display an essential capability in restructuring and manipulating coral-associated bacterial communities. This restructuring effectively reduces bacterial community virulence and enhances the pathogenic resistance of holobionts. The study provides valuable insights into the correlation between the health status of corals and how coral-associated bacterial communities may respond to both pathogens and probiotics.
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Affiliation(s)
- Meiting Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Guofu Chen
- School of Environment, Harbin Institute of Technology, Harbin, China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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Modolon F, Schultz J, Duarte G, Vilela CLS, Thomas T, Peixoto RS. In situ devices can culture the microbial dark matter of corals. iScience 2023; 26:108374. [PMID: 38162026 PMCID: PMC10755713 DOI: 10.1016/j.isci.2023.108374] [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: 04/11/2023] [Revised: 09/16/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024] Open
Abstract
Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.
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Affiliation(s)
- Flúvio Modolon
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Júnia Schultz
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Gustavo Duarte
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raquel Silva Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
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Roveta C, Calcinai B, Girolametti F, Fernandes Couceiro J, Puce S, Annibaldi A, Costa R. The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection. ZOOLOGY 2023; 158:126091. [PMID: 37003141 DOI: 10.1016/j.zool.2023.126091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Microbial communities inhabiting sponges are known to take part in many metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of 16S rRNA genes to characterize the prokaryotic communities present in the cortex and choanosome, respectively the external and internal body region of Chondrosia reniformis, and in the surrounding seawater. Furthermore, we estimated the total mercury content (THg) in these body regions of the sponge and in the corresponding microbial cell pellets. Fifteen prokaryotic phyla were detected in association with C. reniformis, 13 belonging to the domain Bacteria and two to the Archaea. No significant differences between the prokaryotic community composition of the two regions were found. Three lineages of ammonium-oxidizing organisms (Cenarchaeum symbiosum, Nitrosopumilus maritimus, and Nitrosococcus sp.) co-dominated the prokaryotic community, suggesting ammonium oxidation/nitrification as a key metabolic pathway within the microbiome of C. reniformis. In the sponge fractions, higher THg levels were found in the choanosome compared to the cortex. In contrast, comparable THg levels found in the microbial pellets obtained from both regions were significantly lower than those observed in the corresponding sponge fractions. Our work provides new insights into the prokaryotic communities and TEs distribution in different body parts of a model organism relevant for marine conservation and biotechnology. In this sense, this study paves the way for scientists to deepen the possible application of sponges not only as bioindicators, but also as bioremediation tools of metal polluted environments.
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Affiliation(s)
- Camilla Roveta
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Barbara Calcinai
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Federico Girolametti
- Department of Industrial Engineering and Mathematical Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Joana Fernandes Couceiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Stefania Puce
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna Annibaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Portugal
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López-Legentil S, Palanisamy SK, Smith KF, McCormack G, Erwin PM. Prokaryotic symbiont communities in three ascidian species introduced in both Ireland and New Zealand. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:6805-6817. [PMID: 36002791 DOI: 10.1007/s11356-022-22652-2] [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: 01/26/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Ascidians or sea squirts are among the marine taxa with the most introduced species worldwide. These animals have a suite of biological characteristics that contribute to their successful establishment, including long reproductive seasons, rapid growth rates, and resistance to pollution. Here, we sequenced a fragment of the 16S ribosomal RNA gene to characterize symbiont diversity and host-specificity in the solitary species Syela clava and Ascidiella aspersa, and the colonial species Didemnum vexillum. Samples were collected from introduced populations in several marinas and mussel facilities around Ireland, and a marina in New Zealand. Two additional colonial species Botrylloides violaceus and Didemnum sp. were collected in Ireland, and ambient seawater was sampled from both countries for comparison. Data revealed a strong effect of host species and location on prokaryote symbiont composition, consistent with recent ascidian microbiome literature. However, a location effect did not manifest in alpha diversity metrics (e.g., the same ascidian species at different locations exhibited similar diversity) but was evident in beta diversity metrics (greater intra-specific differences across locations than within locations). Location effects were stronger than species effects only for the solitary species (i.e., A. aspersa from New Zealand was more similar to S. clava from New Zealand than to A. aspersa from Ireland). D. vexillum and A. aspersa hosted a high abundance of prokaryotic symbionts that were previously found in other ascidian species, while S. clava symbiotic community was more closely related to bacteria common in the marine environment. Further studies should aim to unravel host-microbe coevolutionary patterns and the microbial role in facilitating host establishment in different habitats.
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Affiliation(s)
- Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA.
| | - Satheesh Kumar Palanisamy
- Zoology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Grace McCormack
- Zoology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Patrick M Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
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Almeida JF, Marques M, Oliveira V, Egas C, Mil-Homens D, Viana R, Cleary DFR, Huang YM, Fialho AM, Teixeira MC, Gomes NCM, Costa R, Keller-Costa T. Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens. Mar Drugs 2022; 21:md21010034. [PMID: 36662207 PMCID: PMC9860996 DOI: 10.3390/md21010034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/15/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Marine microbiomes are prolific sources of bioactive natural products of potential pharmaceutical value. This study inspected two culture collections comprising 919 host-associated marine bacteria belonging to 55 genera and several thus-far unclassified lineages to identify isolates with potentially rich secondary metabolism and antimicrobial activities. Seventy representative isolates had their genomes mined for secondary metabolite biosynthetic gene clusters (SM-BGCs) and were screened for antimicrobial activities against four pathogenic bacteria and five pathogenic Candida strains. In total, 466 SM-BGCs were identified, with antimicrobial peptide- and polyketide synthase-related SM-BGCs being frequently detected. Only 38 SM-BGCs had similarities greater than 70% to SM-BGCs encoding known compounds, highlighting the potential biosynthetic novelty encoded by these genomes. Cross-streak assays showed that 33 of the 70 genome-sequenced isolates were active against at least one Candida species, while 44 isolates showed activity against at least one bacterial pathogen. Taxon-specific differences in antimicrobial activity among isolates suggested distinct molecules involved in antagonism against bacterial versus Candida pathogens. The here reported culture collections and genome-sequenced isolates constitute a valuable resource of understudied marine bacteria displaying antimicrobial activities and potential for the biosynthesis of novel secondary metabolites, holding promise for a future sustainable production of marine drug leads.
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Affiliation(s)
- João F. Almeida
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Matilde Marques
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Vanessa Oliveira
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology (CNC), Rua Larga—Faculdade de Medicina, University of Coimbra, 3004-504 Coimbra, Portugal
- Biocant—Transfer Technology Association, BiocantPark, 3060-197 Cantanhede, Portugal
| | - Dalila Mil-Homens
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Romeu Viana
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Daniel F. R. Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Yusheng M. Huang
- Department of Marine Recreation, National Penghu University of Science and Technology, Magong City 880-011, Taiwan
| | - Arsénio M. Fialho
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Miguel C. Teixeira
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Newton C. M. Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rodrigo Costa
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Centre of Marine Sciences (CCMAR/CIMAR LA), University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- Correspondence: (R.C.); (T.K.-C.); Tel.: +351-21-841-7339 (R.C.); +351-21-841-3167 (T.K.-C.)
| | - Tina Keller-Costa
- iBB—Institute for Bioengineering and Biosciences and i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Correspondence: (R.C.); (T.K.-C.); Tel.: +351-21-841-7339 (R.C.); +351-21-841-3167 (T.K.-C.)
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Genome Sequencing Suggests Diverse Secondary Metabolism in Coral-Associated Aquimarina megaterium. Microbiol Resour Announc 2022; 11:e0062022. [PMID: 36259954 PMCID: PMC9670916 DOI: 10.1128/mra.00620-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report here the genome sequences of three Aquimarina megaterium strains isolated from the octocoral Eunicella labiata. We reveal a coding potential for versatile carbon metabolism and biosynthesis of natural products belonging to the polyketide, nonribosomal peptide, and terpene compound classes.
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Abstract
The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
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Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022; 16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
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Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus. Sci Rep 2022; 12:12379. [PMID: 35896693 PMCID: PMC9329357 DOI: 10.1038/s41598-022-16370-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
Missions to detect extraterrestrial life are being designed to visit Europa and Enceladus in the next decades. The contact between the mission payload and the habitable subsurface of these satellites involves significant risk of forward contamination. The standardization of protocols to decontaminate ice cores from planetary field analogs of icy moons, and monitor the contamination in downstream analysis, has a direct application for developing clean approaches crucial to life detection missions in these satellites. Here we developed a comprehensive protocol that can be used to monitor and minimize the contamination of Arctic ice cores in processing and downstream analysis. We physically removed the exterior layers of ice cores to minimize bioburden from sampling. To monitor contamination, we constructed artificial controls and applied culture-dependent and culture-independent techniques such as 16S rRNA amplicon sequencing. We identified 13 bacterial contaminants, including a radioresistant species. This protocol decreases the contamination risk, provides quantitative and qualitative information about contamination agents, and allows validation of the results obtained. This study highlights the importance of decreasing and evaluating prokaryotic contamination in the processing of polar ice cores, including in their use as analogs of Europa and Enceladus.
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Insights into the Antimicrobial Activities and Metabolomes of Aquimarina ( Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere. Mar Drugs 2022; 20:md20070423. [PMID: 35877716 PMCID: PMC9323603 DOI: 10.3390/md20070423] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 12/17/2022] Open
Abstract
Two novel natural products, the polyketide cuniculene and the peptide antibiotic aquimarin, were recently discovered from the marine bacterial genus Aquimarina. However, the diversity of the secondary metabolite biosynthetic gene clusters (SM-BGCs) in Aquimarina genomes indicates a far greater biosynthetic potential. In this study, nine representative Aquimarina strains were tested for antimicrobial activity against diverse human-pathogenic and marine microorganisms and subjected to metabolomic and genomic profiling. We found an inhibitory activity of most Aquimarina strains against Candida glabrata and marine Vibrio and Alphaproteobacteria species. Aquimarina sp. Aq135 and Aquimarina muelleri crude extracts showed particularly promising antimicrobial activities, amongst others against methicillin-resistant Staphylococcus aureus. The metabolomic and functional genomic profiles of Aquimarina spp. followed similar patterns and were shaped by phylogeny. SM-BGC and metabolomics networks suggest the presence of novel polyketides and peptides, including cyclic depsipeptide-related compounds. Moreover, exploration of the ‘Sponge Microbiome Project’ dataset revealed that Aquimarina spp. possess low-abundance distributions worldwide across multiple marine biotopes. Our study emphasizes the relevance of this member of the microbial rare biosphere as a promising source of novel natural products. We predict that future metabologenomics studies of Aquimarina species will expand the spectrum of known secondary metabolites and bioactivities from marine ecosystems.
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Coelho LF, Couceiro JF, Keller-Costa T, Valente SM, Ramalho TP, Carneiro J, Comte J, Blais MA, Vincent WF, Martins Z, Canário J, Costa R. Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154286. [PMID: 35247410 DOI: 10.1016/j.scitotenv.2022.154286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Current knowledge of the processes that shape prokaryotic community assembly in sea ice across polar ecosystems is scarce. Here, we coupled culture-dependent (bacterial isolation on R2A medium) and culture-independent (high-throughput 16S rRNA gene sequencing) approaches to provide the first comprehensive assessment of prokaryotic communities in the late winter ice and its underlying water along a natural salinity gradient in coastal Hudson Bay, an iconic cryo-environment that marks the ecological transition between Canadian Subarctic and Arctic biomes. We found that prokaryotic community assembly processes in the ice were less selective at low salinity since typical freshwater taxa such as Frankiales, Burkholderiales, and Chitinophagales dominated both the ice and its underlying water. In contrast, there were sharp shifts in community structure between the ice and underlying water samples at sites with higher salinity, with the orders Alteromonadales and Flavobacteriales dominating the ice, while the abovementioned freshwater taxa dominated the underlying water communities. Moreover, primary producers including Cyanobium (Cyanobacteria, Synechococcales) may play a role in shaping the ice communities and were accompanied by known Planctomycetes and Verrucomicrobiae taxa. Culture-dependent analyses showed that the ice contained pigment-producing psychrotolerant or psychrophilic bacteria from the phyla Proteobacteria, Actinobacteriota, and Bacteroidota, likely favored by the combination of low temperatures and the seasonal increase in sunlight. Our findings suggest that salinity, photosynthesis and dissolved organic matter are the main drivers of prokaryotic community structure in the late winter ice of coastal Hudson Bay, the ecosystem with the fastest sea ice loss rate in the Canadian North.
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Affiliation(s)
- Lígia Fonseca Coelho
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Joana Fernandes Couceiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sara Martinez Valente
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Tiago Pereirinha Ramalho
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Joana Carneiro
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut National de la Recherche Scientifique, G1K 9A9 Quebec City, QC, Canada; Centre for Northern Studies (CEN), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Marie-Amélie Blais
- Centre for Northern Studies (CEN), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biologie & Takuvik Joint International Laboratory, Université Laval, Quebec City, Québec G1V 0A6, Canada
| | - Warwick F Vincent
- Centre for Northern Studies (CEN), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biologie & Takuvik Joint International Laboratory, Université Laval, Quebec City, Québec G1V 0A6, Canada
| | - Zita Martins
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - João Canário
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal; Department of Energy - Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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12
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Díaz-Almeyda EM, Ryba T, Ohdera AH, Collins SM, Shafer N, Link C, Prado-Zapata M, Ruhnke C, Moore M, González Angel AM, Pollock FJ, Medina M. Thermal Stress Has Minimal Effects on Bacterial Communities of Thermotolerant Symbiodinium Cultures. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.764086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Algae in the dinoflagellate family Symbiodiniaceae are endocellular photosymbionts of corals and other cnidarians. This close relationship is disrupted when seawater temperature increases, causing coral bleaching eventually affecting entire coral reefs. Although the relationship between animal host and photosymbiont has been well-studied, little is known about the bacterial community associated with Symbiodiniaceae in culture. We compared the microbial communities of three isolates from different species of the genus Symbiodinium (formerly known as Symbiodinium clade A) with different ecophysiology, levels of interaction with the animal host, and thermal adaptations. Two species, Symbiodinium microadriaticum and Symbiodinium necroappettens, exhibit intermediate thermotolerance, with a decrease of both growth rate and photochemical efficiency with increased temperature. The third species, Symbiodinium pilosum, has high thermotolerance with no difference in growth rate or photochemical efficiency at 32°C. Microbial communities were characterized after 27 days of growth under control (26°C) and high temperature (32°C). Data shows stronger grouping of bacterial assemblages based on Symbiodinium species than temperature. Microbial communities did not group phylogenetically. We found a shared set of fifteen ASVs belonging to four genera and three families that remained in all three Symbiodiniaceae species. These included Labrenzia, Phycisphaeraceae (SM1A02), Roseovarius, and Muricauda, which are all commonly associated with corals and Symbiodiniaceae cultures. Few ASVs differed significantly by temperature within species. S. pilosum displayed significantly lower levels of microbial diversity and greater individual variability in community composition at 32°C compared to 26°C. These results suggest that bacteria associated or co-cultured with thermotolerant Symbiodinium might play an important role in thermotolerance. Further research on the functional metabolic pathways of these bacteria might hold the key to understanding Symbiodinium’s ability to tolerate thermal stress.
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13
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Haydon TD, Suggett DJ, Siboni N, Kahlke T, Camp EF, Seymour JR. Temporal Variation in the Microbiome of Tropical and Temperate Octocorals. MICROBIAL ECOLOGY 2022; 83:1073-1087. [PMID: 34331071 DOI: 10.1007/s00248-021-01823-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.
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Affiliation(s)
- Trent D Haydon
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Emma F Camp
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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14
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Coral holobionts and biotechnology: from Blue Economy to coral reef conservation. Curr Opin Biotechnol 2021; 74:110-121. [PMID: 34861476 DOI: 10.1016/j.copbio.2021.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/28/2022]
Abstract
Corals are of ecological and economic importance, providing habitat for species and contributing to coastal protection, fisheries, and tourism. Their biotechnological potential is also increasingly recognized. Particularly, the production of pharmaceutically interesting compounds by corals and their microbial associates stimulated natural product-based drug discovery. The efficient light distribution by coral skeletons for optimal photosynthesis by algal symbionts has led to 3D-printed bionic corals that may be used to upscale micro-algal cultivation for bioenergy generation. However, corals are under threat from climate change and pollution, and biotechnological approaches to increase their resilience, like 'probiotics' and 'assisted evolution', are being evaluated. In this review, we summarize the recent biotechnological developments related to corals with an emphasis on coral conservation, drug discovery and bioenergy.
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15
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Barno AR, Villela HDM, Aranda M, Thomas T, Peixoto RS. Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals. Bioessays 2021; 43:e2100068. [PMID: 34463364 DOI: 10.1002/bies.202100068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
Coral reefs have been challenged by the current rate and severity of environmental change that might outpace their ability to adapt and survive. Current research focuses on understanding how microbial communities and epigenetic changes separately affect phenotypes and gene expression of corals. Here, we provide the hypothesis that coral-associated microorganisms may directly or indirectly affect the coral's phenotypic response through the modulation of its epigenome. Homologs of ankyrin-repeat protein A and internalin B, which indirectly cause histone modifications in humans, as well as Rv1988 histone methyltransferase, and the DNA methyltransferases Rv2966c, Mhy1, Mhy2, and Mhy3 found in coral-associated bacteria indicate that there are potential host epigenome-modifying proteins in the coral microbiome. With the ideas presented here, we suggest that microbiome manipulation may be a means to alter a coral's epigenome, which could aid the current efforts to protect coral reefs. Also see the video abstract here: https://youtu.be/CW9GbChjKM4.
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Affiliation(s)
- Adam R Barno
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Helena D M Villela
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Manuel Aranda
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Australia
| | - Raquel S Peixoto
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia.,Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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16
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The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos. Microbiol Resour Announc 2021; 10:e0032021. [PMID: 34435855 PMCID: PMC8388533 DOI: 10.1128/mra.00320-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba) strains that were obtained from the octocoral Eunicella labiata. Genome annotation revealed multiple symbiosis factors common to all genomes, such as eukaryotic-like repeat protein- and multidrug resistance-encoding genes, which likely underpin symbiotic relationships with marine invertebrate hosts.
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17
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Sweet M, Villela H, Keller-Costa T, Costa R, Romano S, Bourne DG, Cárdenas A, Huggett MJ, Kerwin AH, Kuek F, Medina M, Meyer JL, Müller M, Pollock FJ, Rappé MS, Sere M, Sharp KH, Voolstra CR, Zaccardi N, Ziegler M, Peixoto R. Insights into the Cultured Bacterial Fraction of Corals. mSystems 2021; 6:e0124920. [PMID: 34156291 PMCID: PMC8269258 DOI: 10.1128/msystems.01249-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features-not previously described for coral-bacterium symbioses-potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts. IMPORTANCE Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world. This equated to 1,045 individual isolates which had full-length 16S rRNA gene sequences, after filtering of the original 3,055. We also explored which of these had genomes available. Originally, only 36 were available, and as part of this study, we added a further 38-equating to 74 in total. From this, we investigated potential genetic signatures that may facilitate a host-associated lifestyle. Further, such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and potentially applied as a novel strategy in reef restoration and rehabilitation efforts. In the spirit of open access, we have ensured this collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope many scientists across the globe will ask for access to these cultures for future studies.
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Affiliation(s)
- Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Helena Villela
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
- Department of Energy, Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefano Romano
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, Australia
- Australian Institute of Marine Science, Townsville, Australia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Megan J. Huggett
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW, Australia
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | | | - Felicity Kuek
- Australian Institute of Marine Science, Townsville, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Julie L. Meyer
- Soil and Water Sciences Department, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Moritz Müller
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Kuching, Sarawak, Malaysia
| | - F. Joseph Pollock
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Hawaii and Palmyra Programs, The Nature Conservancy, Honolulu, Hawaii, USA
| | - Michael S. Rappé
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
| | - Mathieu Sere
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Koty H. Sharp
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | | | - Nathan Zaccardi
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Raquel Peixoto
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- 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
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18
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Keller-Costa T, Lago-Lestón A, Saraiva JP, Toscan R, Silva SG, Gonçalves J, Cox CJ, Kyrpides N, Nunes da Rocha U, Costa R. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. MICROBIOME 2021; 9:72. [PMID: 33766108 PMCID: PMC7993494 DOI: 10.1186/s40168-021-01031-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/08/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. RESULTS Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system. CONCLUSIONS This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.
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Affiliation(s)
- T. Keller-Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- División de Biología Experimental y Aplicada (DBEA), Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carr. Ensenada-Tijuana 3918, Zona Playitas, C.P 22860 Ensenada, Baja California Mexico
| | - J. P. Saraiva
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Toscan
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - S. G. Silva
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - J. Gonçalves
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - C. J. Cox
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - N. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - U. Nunes da Rocha
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
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19
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Raimundo I, Silva R, Meunier L, Valente SM, Lago-Lestón A, Keller-Costa T, Costa R. Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes. MICROBIOME 2021; 9:43. [PMID: 33583433 PMCID: PMC7883442 DOI: 10.1186/s40168-020-00970-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/18/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater. RESULTS We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates. CONCLUSIONS Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.
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Affiliation(s)
- I. Raimundo
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Silva
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - L. Meunier
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Laboratory of Aquatic Systems Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - S. M. Valente
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- Department of Medical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - T. Keller-Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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20
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Modolon F, Barno AR, Villela HDM, Peixoto RS. Ecological and biotechnological importance of secondary metabolites produced by coral-associated bacteria. J Appl Microbiol 2020; 129:1441-1457. [PMID: 32627318 DOI: 10.1111/jam.14766] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/20/2020] [Accepted: 06/28/2020] [Indexed: 12/16/2022]
Abstract
Symbiotic relationships between corals and their associated micro-organisms are essential to maintain host homeostasis. Coral-associated bacteria (CAB) can have different beneficial roles in the coral metaorganism, such as metabolizing essential nutrients for the coral host and protecting the coral from pathogens. Many CAB exert these functions via secondary metabolites, which include antibacterial, antifouling, antitumour, antiparasitic and antiviral compounds. This review describes how analysis of CAB has led to the discovery of secondary metabolites with potential biotechnological applications. The most commonly found types of secondary metabolites, antimicrobial and antibiofilm compounds, are emphasized and described. Recently developed methods that can be applied to enhance the culturing of CAB from shallow-water reefs and the less-studied deep-sea coral reefs are also discussed. Last, we suggest how the combined use of meta-omics and innovative growth-diffusion techniques can vastly improve the discovery of novel compounds in coral environments.
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Affiliation(s)
- F Modolon
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - A R Barno
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - H D M Villela
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - R S Peixoto
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, RJ, Brazil
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21
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Metagenome-Assembled Genome Sequences of Three Uncultured Planktomarina sp. Strains from the Northeast Atlantic Ocean. Microbiol Resour Announc 2020; 9:9/12/e00127-20. [PMID: 32193237 PMCID: PMC7082456 DOI: 10.1128/mra.00127-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report three metagenome-assembled genomes (MAGs) of Planktomarina strains from coastal seawater (Portugal) to help illuminate the functions of understudied Rhodobacteraceae bacteria in marine environments. The MAGs encode proteins involved in aerobic anoxygenic photosynthesis and a versatile carbohydrate metabolism, strengthening the role of Planktomarina species in oceanic carbon cycling.
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22
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Sang VT, Dat TTH, Vinh LB, Cuong LCV, Oanh PTT, Ha H, Kim YH, Anh HLT, Yang SY. Coral and Coral-Associated Microorganisms: A Prolific Source of Potential Bioactive Natural Products. Mar Drugs 2019; 17. [PMID: 31405226 DOI: 10.3390/md1708046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 05/20/2023] Open
Abstract
Marine invertebrates and their associated microorganisms are rich sources of bioactive compounds. Among them, coral and its associated microorganisms are promising providers of marine bioactive compounds. The present review provides an overview of bioactive compounds that are produced by corals and coral-associated microorganisms, covering the literature from 2010 to March 2019. Accordingly, 245 natural products that possess a wide range of potent bioactivities, such as anti-inflammatory, cytotoxic, antimicrobial, antivirus, and antifouling activities, among others, are described in this review.
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Affiliation(s)
- Vo Thanh Sang
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 5, Ho Chi Minh City 748000, Vietnam
| | - Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Le Ba Vinh
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 100000, Vietnam
| | - Le Canh Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Phung Thi Thuy Oanh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Hoang Ha
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam
| | - Young Ho Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
| | - Hoang Le Tuan Anh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam.
- Graduated University of Science and Technology, VAST, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam.
| | - Seo Young Yang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
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23
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Sang VT, Dat TTH, Vinh LB, Cuong LCV, Oanh PTT, Ha H, Kim YH, Anh HLT, Yang SY. Coral and Coral-Associated Microorganisms: A Prolific Source of Potential Bioactive Natural Products. Mar Drugs 2019; 17:E468. [PMID: 31405226 PMCID: PMC6723858 DOI: 10.3390/md17080468] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Marine invertebrates and their associated microorganisms are rich sources of bioactive compounds. Among them, coral and its associated microorganisms are promising providers of marine bioactive compounds. The present review provides an overview of bioactive compounds that are produced by corals and coral-associated microorganisms, covering the literature from 2010 to March 2019. Accordingly, 245 natural products that possess a wide range of potent bioactivities, such as anti-inflammatory, cytotoxic, antimicrobial, antivirus, and antifouling activities, among others, are described in this review.
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Affiliation(s)
- Vo Thanh Sang
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 5, Ho Chi Minh City 748000, Vietnam
| | - Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Le Ba Vinh
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 100000, Vietnam
| | - Le Canh Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Phung Thi Thuy Oanh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Hoang Ha
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam
| | - Young Ho Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
| | - Hoang Le Tuan Anh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam.
- Graduated University of Science and Technology, VAST, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam.
| | - Seo Young Yang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
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24
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Silva SG, Blom J, Keller‐Costa T, Costa R. Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host‐associated and free‐living
Aquimarina
(
Bacteroidetes, Flavobacteriaceae
) species. Environ Microbiol 2019; 21:4002-4019. [DOI: 10.1111/1462-2920.14747] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 07/12/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Sandra G. Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology Justus‐Liebig‐University Giessen 35392 Giessen Germany
| | - Tina Keller‐Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa Lisbon Portugal
- Centre of Marine Sciences (CCMAR) Algarve University 8005‐139 Faro Portugal
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25
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Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria. Sci Rep 2019; 9:1999. [PMID: 30760820 PMCID: PMC6374434 DOI: 10.1038/s41598-019-38737-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/09/2019] [Indexed: 02/07/2023] Open
Abstract
Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness – were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.
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26
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Raimundo I, Silva SG, Costa R, Keller-Costa T. Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth. Mar Drugs 2018; 16:E485. [PMID: 30518125 PMCID: PMC6316421 DOI: 10.3390/md16120485] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.
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Affiliation(s)
- Inês Raimundo
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Sandra G Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
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27
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Goldsmith DB, Kellogg CA, Morrison CL, Gray MA, Stone RP, Waller RG, Brooke SD, Ross SW. Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype. Sci Rep 2018; 8:12383. [PMID: 30120375 PMCID: PMC6098105 DOI: 10.1038/s41598-018-30901-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 08/08/2018] [Indexed: 12/26/2022] Open
Abstract
Cold-water corals provide critical habitats for a multitude of marine species, but are understudied relative to tropical corals. Primnoa pacifica is a cold-water coral prevalent throughout Alaskan waters, while another species in the genus, Primnoa resedaeformis, is widely distributed in the Atlantic Ocean. This study examined the V4-V5 region of the 16S rRNA gene after amplifying and pyrosequencing bacterial DNA from samples of these species. Key differences between the two species' microbiomes included a robust presence of bacteria belonging to the Chlamydiales order in most of the P. pacifica samples, whereas no more than 2% of any microbial community from P. resedaeformis comprised these bacteria. Microbiomes of P. resedaeformis exhibited higher diversity than those of P. pacifica, and the two species largely clustered separately in a principal coordinate analysis. Comparison of P. resedaeformis microbiomes from samples collected in two submarine canyons revealed a significant difference between locations. This finding mirrored significant genetic differences among the P. resedaeformis from the two canyons based upon population genetic analysis of microsatellite loci. This study presents the first report of microbiomes associated with these two coral species.
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Affiliation(s)
- Dawn B Goldsmith
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, St. Petersburg, FL, United States of America
| | - Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, St. Petersburg, FL, United States of America.
| | - Cheryl L Morrison
- Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of America
| | - Michael A Gray
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, St. Petersburg, FL, United States of America
| | - Robert P Stone
- Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA Fisheries, 17109, Point Lena Loop Road, Juneau, AK, United States of America
| | - Rhian G Waller
- Darling Marine Center, University of Maine, Walpole, ME, United States of America
| | - Sandra D Brooke
- Coastal and Marine Laboratory, Florida State University, St. Teresa, FL, United States of America
| | - Steve W Ross
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, NC, United States of America
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28
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Shelyakin PV, Garushyants SK, Nikitin MA, Mudrova SV, Berumen M, Speksnijder AGCL, Hoeksema BW, Fontaneto D, Gelfand MS, Ivanenko VN. Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea). Sci Rep 2018; 8:11563. [PMID: 30069039 PMCID: PMC6070567 DOI: 10.1038/s41598-018-29953-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
Corals harbor complex and diverse microbial communities that strongly impact host fitness and resistance to diseases, but these microbes themselves can be influenced by stresses, like those caused by the presence of macroscopic symbionts. In addition to directly influencing the host, symbionts may transmit pathogenic microbial communities. We analyzed two coral gall-forming copepod systems by using 16S rRNA gene metagenomic sequencing: (1) the sea fan Gorgonia ventalina with copepods of the genus Sphaerippe from the Caribbean and (2) the scleractinian coral Stylophora pistillata with copepods of the genus Spaniomolgus from the Saudi Arabian part of the Red Sea. We show that bacterial communities in these two systems were substantially different with Actinobacteria, Alphaproteobacteria, and Betaproteobacteria more prevalent in samples from Gorgonia ventalina, and Gammaproteobacteria in Stylophora pistillata. In Stylophora pistillata, normal coral microbiomes were enriched with the common coral symbiont Endozoicomonas and some unclassified bacteria, while copepod and gall-tissue microbiomes were highly enriched with the family ME2 (Oceanospirillales) or Rhodobacteraceae. In Gorgonia ventalina, no bacterial group had significantly different prevalence in the normal coral tissues, copepods, and injured tissues. The total microbiome composition of polyps injured by copepods was different. Contrary to our expectations, the microbial community composition of the injured gall tissues was not directly affected by the microbiome of the gall-forming symbiont copepods.
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Affiliation(s)
- Pavel V Shelyakin
- Kharkevich Institute for Information Transmission Problems RAS, B. Karetny per. 19, Moscow, 127051, Russia.,Vavilov Institute of General Genetics RAS, Gubkina str. 3, Moscow, 119333, Russia
| | - Sofya K Garushyants
- Kharkevich Institute for Information Transmission Problems RAS, B. Karetny per. 19, Moscow, 127051, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Nobel str. 1, Moscow, 121205, Russia
| | - Mikhail A Nikitin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Sofya V Mudrova
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Michael Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | | | - Bert W Hoeksema
- Naturalis Biodiversity Center, Leiden, 2332 AA, The Netherlands
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study, Verbania, 28922, Italy
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems RAS, B. Karetny per. 19, Moscow, 127051, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Nobel str. 1, Moscow, 121205, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.,Faculty of Computer Science, Higher School of Economics, Kochnovsky pr. 3, Moscow, 125319, Russia
| | - Viatcheslav N Ivanenko
- Naturalis Biodiversity Center, Leiden, 2332 AA, The Netherlands. .,Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.
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29
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Hadaidi G, Ziegler M, Shore-Maggio A, Jensen T, Aeby G, Voolstra CR. Ecological and molecular characterization of a coral black band disease outbreak in the Red Sea during a bleaching event. PeerJ 2018; 6:e5169. [PMID: 30013839 PMCID: PMC6046197 DOI: 10.7717/peerj.5169] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/16/2018] [Indexed: 11/20/2022] Open
Abstract
Black Band Disease (BBD) is a widely distributed and destructive coral disease that has been studied on a global scale, but baseline data on coral diseases is missing from many areas of the Arabian Seas. Here we report on the broad distribution and prevalence of BBD in the Red Sea in addition to documenting a bleaching-associated outbreak of BBD with subsequent microbial community characterization of BBD microbial mats at this reef site in the southern central Red Sea. Coral colonies with BBD were found at roughly a third of our 22 survey sites with an overall prevalence of 0.04%. Nine coral genera were infected including Astreopora, Coelastrea, Dipsastraea, Gardineroseris, Goniopora, Montipora, Pavona, Platygyra, and Psammocora. For a southern central Red Sea outbreak site, overall prevalence was 40 times higher than baseline (1.7%). Differential susceptibility to BBD was apparent among coral genera with Dipsastraea (prevalence 6.1%), having more diseased colonies than was expected based on its abundance within transects. Analysis of the microbial community associated with the BBD mat showed that it is dominated by a consortium of cyanobacteria and heterotrophic bacteria. We detected the three main indicators for BBD (filamentous cyanobacteria, sulfate-reducing bacteria (SRB), and sulfide-oxidizing bacteria (SOB)), with high similarity to BBD-associated microbes found worldwide. More specifically, the microbial consortium of BBD-diseased coral colonies in the Red Sea consisted of Oscillatoria sp. (cyanobacteria), Desulfovibrio sp. (SRB), and Arcobacter sp. (SOB). Given the similarity of associated bacteria worldwide, our data suggest that BBD represents a global coral disease with predictable etiology. Furthermore, we provide a baseline assessment of BBD disease prevalence in the Red Sea, a still understudied region.
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Affiliation(s)
- Ghaida Hadaidi
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maren Ziegler
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Amanda Shore-Maggio
- Institute of Marine and Environmental Technology (IMET), University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - Thor Jensen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Greta Aeby
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, United States of America
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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30
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Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong Halogen Degradation Potential. GENOME ANNOUNCEMENTS 2018. [PMID: 29519836 PMCID: PMC5843722 DOI: 10.1128/genomea.00132-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the genome sequence of Labrenzia sp. EL143, an alphaproteobacterium isolated from the gorgonian coral Eunicella labiata that possesses various genes involved in halogen and aromatic compound degradation, as well as polyketide synthesis. The strain also maintains multiple genes that confer resistance to toxic compounds such as heavy metals and antibiotics.
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31
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Draft Genome Sequence of Sphingorhabdus sp. Strain EL138, a Metabolically Versatile Alphaproteobacterium Isolated from the Gorgonian Coral Eunicella labiata. GENOME ANNOUNCEMENTS 2018; 6:6/9/e00142-18. [PMID: 29496842 PMCID: PMC5834330 DOI: 10.1128/genomea.00142-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we report the draft genome sequence of Sphingorhabdus sp. strain EL138, an alphaproteobacterium that shows potential to degrade polycyclic aromatic compounds and to cope with various heavy metals and antibiotics. Moreover, the strain, isolated from the gorgonian coral Eunicella labiata, possesses several genes involved in the biosynthesis of polyphosphates, polyketides, and terpenoids.
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