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Han S, Cheng X, Wang T, Li X, Cai Z, Zheng H, Xiao B, Zhou J. AI-2 quorum sensing signal disrupts coral symbiotic homeostasis and induces host bleaching. ENVIRONMENT INTERNATIONAL 2024; 188:108768. [PMID: 38788416 DOI: 10.1016/j.envint.2024.108768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Symbiotic microorganisms play critical ecophysiological roles that facilitate the maintenance of coral health. Currently, information on the gene and protein pathways contributing to bleaching responses is lacking, including the role of autoinducers. Although the autoinducer AI-1 is well understood, information on AI-2 is insufficient. Here, we observed a 3.7-4.0 times higher abundance of the AI-2 synthesis gene luxS in bleached individuals relative to their healthy counterparts among reef-building coral samples from the natural environment. Laboratory tests further revealed that AI-2 contributed significantly to an increase in coral bleaching, altered the ratio of potential probiotic and pathogenic bacteria, and suppressed the antiviral activity of specific pathogenic bacteria while enhancing their functional potential, such as energy metabolism, chemotaxis, biofilm formation and virulence release. Structural equation modeling indicated that AI-2 influences the microbial composition, network structure, and pathogenic features, which collectively contribute to the coral bleaching status. Collectively, our results offer novel potential strategies for coral conservation based on a signal manipulation approach.
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Affiliation(s)
- Shuo Han
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Xueyu Cheng
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Tao Wang
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Xinyang Li
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Huina Zheng
- Guangdong Ocean University Shenzhen Research Institute, Shenzhen 518055, PR China
| | - Baohua Xiao
- Guangdong Ocean University Shenzhen Research Institute, Shenzhen 518055, PR China
| | - Jin Zhou
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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2
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Mohammed V, Arockiaraj J. Unveiling the trifecta of cyanobacterial quorum sensing: LuxI, LuxR and LuxS as the intricate machinery for harmful algal bloom formation in freshwater ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171644. [PMID: 38471587 DOI: 10.1016/j.scitotenv.2024.171644] [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: 06/28/2023] [Revised: 02/22/2024] [Accepted: 03/09/2024] [Indexed: 03/14/2024]
Abstract
Harmful algal blooms (HABs) are causing significant disruptions in freshwater ecosystems, primarily due to the proliferation of cyanobacteria. These blooms have a widespread impact on various lakes globally, leading to profound environmental and health consequences. Cyanobacteria, with their ability to produce diverse toxins, pose a particular concern as they negatively affect the well-being of humans and animals, exacerbating the situation. Notably, cyanobacteria utilize quorum sensing (QS) as a complex communication mechanism that facilitates coordinated growth and toxin production. QS plays a critical role in regulating the dynamics of HABs. However, recent advances in control and mitigation strategies have shown promising results in effectively managing and reducing the occurrence of HABs. This comprehensive review explores the intricate aspects of cyanobacteria development in freshwater ecosystems, explicitly focusing on deciphering the signaling molecules associated with QS and their corresponding genes. Furthermore, a concise overview of diverse measures implemented to efficiently control and mitigate the spread of these bacteria will be provided, shedding light on the ongoing global efforts to address this urgent environmental issue. By deepening our understanding of the mechanisms driving cyanobacteria growth and developing targeted control strategies, we hope to safeguard freshwater ecosystems and protect the health of humans and animals from the detrimental impacts of HABs.
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Affiliation(s)
- Vajagathali Mohammed
- Department of Forensic Science, Yenepoya Institute of Arts, Science, Commerce, and Management, Yenepoya (Deemed to be University), Mangaluru 575013, Karnataka, India
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603203, Chengalpattu District, Tamil Nadu, India.
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3
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Swaminathan SD, Lafferty KD, Knight NS, Altieri AH. Stony coral tissue loss disease indirectly alters reef communities. SCIENCE ADVANCES 2024; 10:eadk6808. [PMID: 38701216 PMCID: PMC11068009 DOI: 10.1126/sciadv.adk6808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/01/2024] [Indexed: 05/05/2024]
Abstract
Many Caribbean coral reefs are near collapse due to various threats. An emerging threat, stony coral tissue loss disease (SCTLD), is spreading across the Western Atlantic and Caribbean. Data from the U.S. Virgin Islands reveal how SCTLD spread has reduced the abundance of susceptible coral and crustose coralline algae and increased cyanobacteria, fire coral, and macroalgae. A Caribbean-wide structural equation model demonstrates versatility in reef fish and associations with rugosity independent of live coral. Model projections suggest that some reef fishes will decline due to SCTLD, with the largest changes on reefs that lose the most susceptible corals and rugosity. Mapping these projected declines in space indicates how the indirect effects of SCTLD range from undetectable to devastating.
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Affiliation(s)
- Sara D. Swaminathan
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kevin D. Lafferty
- Western Ecological Research Center, US Geological Survey, Santa Barbara, CA 93455, USA
- Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Nicole S. Knight
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Andrew H. Altieri
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
- Smithsonian Tropical Research Center, Ancon 0843-03092, Republic of Panama
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4
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Zhai X, Zhang Y, Zhou J, Li H, Wang A, Liu L. Physiological and microbiome adaptation of coral Turbinaria peltata in response to marine heatwaves. Ecol Evol 2024; 14:e10869. [PMID: 38322002 PMCID: PMC10844694 DOI: 10.1002/ece3.10869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 02/08/2024] Open
Abstract
Against the backdrop of global warming, marine heatwaves are projected to become increasingly intense and frequent. This trend poses a potential threat to the survival of corals and the maintenance of entire coral reef ecosystems. Despite extensive evidence for the resilience of corals to heat stress, their ability to withstand repeated heatwave events has not been determined. In this study, we examined the responses and resilience of Turbinaria peltata to repeated exposure to marine heatwaves, with a focus on physiological parameters and symbiotic microorganisms. In the first heatwave, from a physiological perspective, T. peltata showed decreases in the Chl a content and endosymbiont density and significant increases in GST, caspase-3, CAT, and SOD levels (p < .05), while the effects of repeated exposure on heatwaves were weaker than those of the initial exposure. In terms of bacteria, the abundance of Leptospira, with the potential for pathogenicity and intracellular parasitism, increased significantly during the initial exposure. Beneficial bacteria, such as Achromobacter arsenitoxydans and Halomonas desiderata increased significantly during re-exposure to the heatwave. Overall, these results indicate that T. peltata might adapt to marine heatwaves through physiological regulation and microbial community alterations.
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Affiliation(s)
- Xin Zhai
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
| | - YanPing Zhang
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
- Guangdong Laboratory of Southern Ocean Science and EngineeringZhanjiangChina
| | - Jie Zhou
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
| | - Hao Li
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
| | - Ao Wang
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
| | - Li Liu
- College of FisheriesGuangdong Ocean UniversityZhanjiangChina
- Guangdong Laboratory of Southern Ocean Science and EngineeringZhanjiangChina
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5
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Liu Z, Tang K, Zhou Y, Liu T, Guo Y, Wu D, Wang X. Active prophages in coral-associated Halomonas capable of lateral transduction. THE ISME JOURNAL 2024; 18:wrae085. [PMID: 38739683 PMCID: PMC11131426 DOI: 10.1093/ismejo/wrae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.
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Affiliation(s)
- Ziyao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yiqing Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Duoting Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
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6
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Wang Y, Berthold DE, Hu J, Lefler FW, Huang IS, Laughinghouse HD. Novel diversity within Roseofilum (Desertifilaceae, Cyanobacteria) from marine benthic mats with description of four new species. JOURNAL OF PHYCOLOGY 2023; 59:1147-1165. [PMID: 37824435 DOI: 10.1111/jpy.13392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/09/2023] [Accepted: 09/07/2023] [Indexed: 10/14/2023]
Abstract
Benthic cyanobacterial mats (BCMs) are natural phenomena in marine environments. Reports of BCMs occurring across coastal marine environments have increased, partly driven by nutrient loading and climate change; thus, there is a need to understand the diversity involved in the proliferations and potential toxicity of the BCMs. Furthermore, marine cyanobacterial mats are observed growing on and affecting the health of corals with one specific cyanobacterial genus, Roseofilum, dominating the microbial mats associated with black band disease (BBD), a destructive polymicrobial disease that affects corals. To explore the diversity of Roseofilum, cyanobacterial mats from various marine habitats were sampled, and individual isolates were identified based on morphology, 16S rRNA gene phylogenies, 16S-23S ITS rRNA region sequence dissimilarities, and phylogenomics. Four novel species of Roseofilum were isolated from benthic marine mats, three from the coasts of Florida, United States (R. capinflatum sp. nov., R. casamattae sp. nov., and R. acuticapitatum sp. nov.) and one from the coast of France (R. halophilum sp. nov.). Our analyses revealed that Roseofilum associated with coral BBD and those not associated with corals but rather from coastal benthic mats are systematically distinct based on both phylogenetic and phylogenomic analyses. Enzyme-linked immunosorbent assay (ELISA) and LC-MS data indicated that microcystin production was found in one of the four species.
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Affiliation(s)
- Yi Wang
- Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
| | - David E Berthold
- Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
| | - Jing Hu
- Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Forrest W Lefler
- Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
| | - I-Shuo Huang
- Office of Regulatory Science, United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland, USA
| | - H Dail Laughinghouse
- Fort Lauderdale Research and Education Center, University of Florida - IFAS, Davie, Florida, USA
- Department of Botany, National Musuem of Natural History, Smithsonian Institution, Washington, DC, USA
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7
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Rose C, Lund MB, Schramm A, Bilde T, Bechsgaard J. Does ecological drift explain variation in microbiome composition among groups in a social host species? J Evol Biol 2023; 36:1684-1694. [PMID: 37776090 DOI: 10.1111/jeb.14228] [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: 12/30/2022] [Revised: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 10/01/2023]
Abstract
Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless divergence in microbiome composition among related groups arise. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider Stegodyphus dumicola. We simulated the initiation of new groups by splitting field-collected nests into groups of 1, 3, and 10 individuals respectively, and compared variation in microbiome composition among and within groups after 6 weeks using 16S rRNA gene sequencing. Theory predicts that ecological drift increases with decreasing group size. We found that microbiome composition among single founders was more dissimilar than among individuals kept in groups, supporting this prediction. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Individual founders appear to harbour higher relative abundances of non-core symbionts compared with founders in small groups, some of which are possible pathogens. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.
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Affiliation(s)
- Clémence Rose
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Marie Braad Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Trine Bilde
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jesper Bechsgaard
- Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark
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8
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Connelly MT, Snyder G, Palacio-Castro AM, Gillette PR, Baker AC, Traylor-Knowles N. Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression. Mol Ecol 2023; 32:4677-4694. [PMID: 37317893 DOI: 10.1111/mec.17049] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
Corals are important models for understanding invertebrate host-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral-bacteria associations are needed. Coral-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-building corals Pocillopora meandrina and P. verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-associated bacteria.
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Affiliation(s)
- Michael T Connelly
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Grace Snyder
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Ana M Palacio-Castro
- University of Miami Cooperative Institute for Marine and Atmospheric Studies, Miami, Florida, USA
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
| | - Phillip R Gillette
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Andrew C Baker
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
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9
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Maitre A, Wu-Chuang A, Mateos-Hernández L, Piloto-Sardiñas E, Foucault-Simonin A, Cicculli V, Moutailler S, Paoli JC, Falchi A, Obregón D, Cabezas-Cruz A. Rickettsial pathogens drive microbiota assembly in Hyalomma marginatum and Rhipicephalus bursa ticks. Mol Ecol 2023; 32:4660-4676. [PMID: 37366236 DOI: 10.1111/mec.17058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023]
Abstract
Most tick-borne pathogens (TBPs) are secondarily acquired by ticks during feeding on infected hosts, which imposes 'priority effect' constraints, as arrival order influences the establishment of new species in a microbial community. Here we tested whether once acquired, TBPs contribute to bacterial microbiota functioning by increasing community stability. For this, we used Hyalomma marginatum and Rhipicephalus bursa ticks collected from cattle in different locations of Corsica and combined 16S rRNA amplicon sequencing and co-occurrence network analysis, with high-throughput pathogen detection, and in silico removal of nodes to test for impact of rickettsial pathogens on network properties. Despite its low centrality, Rickettsia showed preferential connections in the networks, notably with a keystone taxon in H. marginatum, suggesting facilitation of Rickettsia colonisation by the keystone taxon. In addition, conserved patterns of community assembly in both tick species were affected by Rickettsia removal, suggesting that privileged connections of Rickettsia in the networks make this taxon a driver of community assembly. However, Rickettsia removal had minor impact on the conserved 'core bacterial microbiota' of H. marginatum and R. bursa. Interestingly, networks of the two tick species with Rickettsia have similar node centrality distribution, a property that is lost after Rickettsia removal, suggesting that this taxon drives specific hierarchical interactions between bacterial microbes in the microbiota. The study indicates that tick-borne Rickettsia play a significant role in the tick bacterial microbiota, despite their low centrality. These bacteria are influential and contribute to the conservation of the 'core bacterial microbiota' while also promoting community stability.
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Affiliation(s)
- Apolline Maitre
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Lourdes Mateos-Hernández
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Elianne Piloto-Sardiñas
- Direction of Animal Health, National Center for Animal and Plant Health, Carretera de Tapaste y Autopista Nacional, San José de las Lajas, Cuba
| | - Angélique Foucault-Simonin
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Vincent Cicculli
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Sara Moutailler
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Jean-Christophe Paoli
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), Corte, France
| | - Alessandra Falchi
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Dasiel Obregón
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
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10
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Lima LFO, Alker AT, Papudeshi B, Morris MM, Edwards RA, de Putron SJ, Dinsdale EA. Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale. MICROBIAL ECOLOGY 2023; 86:392-407. [PMID: 35965269 PMCID: PMC10293411 DOI: 10.1007/s00248-022-02094-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.
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Affiliation(s)
- Laís F. O. Lima
- Department of Biology, San Diego State University, San Diego, CA USA
- College of Biological Sciences, University of California Davis, Davis, CA USA
| | - Amanda T. Alker
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Bhavya Papudeshi
- College of Science and Engineering, Flinders University, Adelaide, South Australia Australia
| | | | - Robert A. Edwards
- Department of Biology, San Diego State University, San Diego, CA USA
- College of Science and Engineering, Flinders University, Adelaide, South Australia Australia
| | | | - Elizabeth A. Dinsdale
- Department of Biology, San Diego State University, San Diego, CA USA
- College of Science and Engineering, Flinders University, Adelaide, South Australia Australia
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Schul MD, Anastasious DE, Spiers LJ, Meyer JL, Frazer TK, Brown AL. Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis. PeerJ 2023; 11:e15170. [PMID: 37361046 PMCID: PMC10290447 DOI: 10.7717/peerj.15170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 03/13/2023] [Indexed: 06/28/2023] Open
Abstract
Background Coral diseases are one of the leading causes of declines in coral populations. In the Caribbean, white band disease (WBD) has led to a substantial loss of Acropora corals. Although the etiologies of this disease have not been well described, characterizing the coral microbiome during the transition from a healthy to diseased state is critical for understanding disease progression. Coral nurseries provide unique opportunities to further understand the microbial changes associated with diseased and healthy corals, because corals are monitored over time. We characterized the microbiomes before and during an outbreak of WBD in Acropora cervicornis reared in an ocean nursery in Little Cayman, CI. We asked (1) do healthy corals show the same microbiome over time (before and during a disease outbreak) and (2) are there disease signatures on both lesioned and apparently healthy tissues on diseased coral colonies? Methods Microbial mucus-tissue slurries were collected from healthy coral colonies in 2017 (before the disease) and 2019 (during the disease onset). Diseased colonies were sampled at two separate locations on an individual coral colony: at the interface of Disease and ∼10 cm away on Apparently Healthy coral tissue. We sequenced the V4 region of the 16S rRNA gene to characterize bacterial and archaeal community composition in nursery-reared A. cervicornis. We assessed alpha diversity, beta diversity, and compositional differences to determine differences in microbial assemblages across health states (2019) and healthy corals between years (2017 and 2019). Results Microbial communities from healthy A. cervicornis from 2017 (before disease) and 2019 (after disease) did not differ significantly. Additionally, microbial communities from Apparently Healthy samples on an otherwise diseased coral colony were more similar to Healthy colonies than to the diseased portion on the same colony for both alpha diversity and community composition. Microbial communities from Diseased tissues had significantly higher alpha diversity than both Healthy and Apparently Healthy tissues but showed no significant difference in beta-diversity dispersion. Our results show that at the population scale, Healthy and Apparently Healthy coral tissues are distinct from microbial communities associated with Diseased tissues. Furthermore, our results suggest stability in Little Cayman nursery coral microbiomes over time. We show healthy Caymanian nursery corals had a stable microbiome over a two-year period, an important benchmark for evaluating coral health via their microbiome.
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Affiliation(s)
- Monica D. Schul
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States of America
| | - Dagny-Elise Anastasious
- Little Cayman Research Center, Central Caribbean Marine Institute, Little Cayman, Cayman Islands
| | - Lindsay J. Spiers
- School of Fisheries, University of Florida, Gainesville, FL, United States of America
- Fish & Wildlife Research Institute, Florida Fish & Wildlife Conservation Commission, Marathon, FL, United States of America
| | - Julie L. Meyer
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States of America
| | - Thomas K. Frazer
- College of Marine Science, University of South Florida, St. Petersburg, FL, United States of America
| | - Anya L. Brown
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, United States of America
- Bodega Marine Lab, Department of Evolution and Ecology, University of California, Davis, Bodega Bay, CA, United States of America
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Xu M, Cheng K, Xiao B, Tong M, Cai Z, Jong MC, Chen G, Zhou J. Bacterial Communities Vary from Different Scleractinian Coral Species and between Bleached and Non-Bleached Corals. Microbiol Spectr 2023; 11:e0491022. [PMID: 37191552 PMCID: PMC10269541 DOI: 10.1128/spectrum.04910-22] [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: 11/30/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Bleaching is one of the most relevant factors implicated in the integrity of coral reef ecosystems, with the increasing frequency and intensity of damaging events representing a serious threat to reef biodiversity. Here, we analyzed changes in coral-associated bacteria from three types of non-bleached and bleached scleractinian corals (Acropora digitifera, Galaxea fascicularis, and Porites pukoensis) in Hainan Luhuitou peninsula coastal areas. The community structure of symbiotic bacteria differed significantly among the three apparently healthy corals. The bleached corals had higher bacterial alpha diversity and some specific bacteria genera, including Ruegeria, Methyloceanibacter, Filomicrobium, Halioglobus, Rubripirellula, Rhodopirellula, Silicimonas, Blastopirellula, Sva0996 marine group, Woeseia, and unclassified_c_Gammaproteobacteria, were consistently increased in bleached groups. Network analysis revealed significantly different degrees of modularity between bleached and non-bleached groups at the bacterial genus level, and a higher proportion of links was dominated by positive co-occurrences. Functional prediction analysis illustrated that coral-associated bacteria remained relatively consistent in the bleached and non-bleached groups. Structure equation modeling revealed that the bacterial community diversity and function were directly influenced by host and environment factors. These findings suggested that coral-associated bacterial responses to bleaching occur in a host-dependent manner, informing novel strategies for restoring coral and aiding adaption to bleaching stress. IMPORTANCE Accumulating evidence indicates that coral-associated bacteria play an important role in the health of holobionts. However, the variability of the symbiotic bacterial community structure among coral species with different coral health statuses remains largely unknown. Here, we investigated three apparent non-bleached (healthy) and bleached coral species (sampled in situ), involving related symbiotic bacterial profiles, including composition, alpha diversity, network relationship, and potential function. Structural equation modeling analysis was used to analyze the relationship between coral status and abiotic and biotic factors. The bacterial community structure of different groups was shown to exhibit host-specific traits. Both host and environmental impacts had primary effects on coral-associated microbial communities. Future studies are needed to identify the mechanisms that mediate divergent microbial consortia.
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Affiliation(s)
- Meiting Xu
- School of Environment, Harbin Institute of Technology, Harbin, People’s Republic of China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, Shandong Province, People’s Republic of 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, People’s Republic of China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, People’s Republic of China
| | - Mengmeng Tong
- Ocean College, Zhejiang University, Zhoushan, People’s Republic of 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, People’s Republic of China
| | - Mui-Choo Jong
- Institute of Environment and Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| | - Guofu Chen
- School of Environment, Harbin Institute of Technology, Harbin, People’s Republic of China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, Shandong Province, People’s Republic of 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, People’s Republic of China
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13
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Salleh NF, Wang J, Kundukad B, Oluwabusola ET, Goh DXY, Phyo MY, Tong JJL, Kjelleberg S, Tan LT. Cyclopropane-Containing Specialized Metabolites from the Marine Cyanobacterium cf. Lyngbya sp. Molecules 2023; 28:molecules28093965. [PMID: 37175374 PMCID: PMC10180397 DOI: 10.3390/molecules28093965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/28/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023] Open
Abstract
Marine cyanobacteria are known to produce structurally diverse bioactive specialized metabolites during bloom occurrence. These ecologically active allelochemicals confer chemical defense for the microalgae from competing microbes and herbivores. From a collection of a marine cyanobacterium, cf. Lyngbya sp., a small quantity of a new cyclopropane-containing molecule, benderadiene (2), and lyngbyoic acid (1) were purified and characterized using spectroscopic methods. Using live reporter quorum-sensing (QS) inhibitory assays, based on P. aeruginosa PAO1 lasB-gfp and rhlA-gfp strains, both compounds were found to inhibit QS-regulated gene expression in a dose-dependent manner. In addition to lyngbyoic acid being more active in the PAO1 lasB-gfp biosensor strain (IC50 of 20.4 µM), it displayed anti-biofilm activity when incubated with wild-type P. aeruginosa. The discovery of lyngbyoic acid in relatively high amounts provided insights into its ecological significance as a defensive allelochemical in targeting competing microbes through interference with their QS systems and starting material to produce other related analogs. Similar strategies could be adopted by other marine cyanobacterial strains where the high production of other lipid acids has been reported. Preliminary evidence is provided from the virtual molecular docking of these cyanobacterial free acids at the ligand-binding site of the P. aeruginosa LasR transcriptional protein.
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Affiliation(s)
- Nurul Farhana Salleh
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
| | - Jiale Wang
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
| | - Binu Kundukad
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Emmanuel T Oluwabusola
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Delia Xin Yin Goh
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
| | - Ma Yadanar Phyo
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
| | - Jasmine Jie Lin Tong
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW 2033, Australia
| | - Lik Tong Tan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
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Cryptic Diversity of Black Band Disease Cyanobacteria in Siderastrea siderea Corals Revealed by Chemical Ecology and Comparative Genome-Resolved Metagenomics. Mar Drugs 2023; 21:md21020076. [PMID: 36827117 PMCID: PMC9967302 DOI: 10.3390/md21020076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Black band disease is a globally distributed and easily recognizable coral disease. Despite years of study, the etiology of this coral disease, which impacts dozens of stony coral species, is not completely understood. Although black band disease mats are predominantly composed of the cyanobacterial species Roseofilum reptotaenium, other filamentous cyanobacterial strains and bacterial heterotrophs are readily detected. Through chemical ecology and metagenomic sequencing, we uncovered cryptic strains of Roseofilum species from Siderastrea siderea corals that differ from those on other corals in the Caribbean and Pacific. Isolation of metabolites from Siderastrea-derived Roseofilum revealed the prevalence of unique forms of looekeyolides, distinct from previously characterized Roseofilum reptotaenium strains. In addition, comparative genomics of Roseofilum strains showed that only Siderastrea-based Roseofilum strains have the genetic capacity to produce lasso peptides, a family of compounds with diverse biological activity. All nine Roseofilum strains examined here shared the genetic capacity to produce looekeyolides and malyngamides, suggesting these compounds support the ecology of this genus. Similar biosynthetic gene clusters are not found in other cyanobacterial genera associated with black band disease, which may suggest that looekeyolides and malyngamides contribute to disease etiology through yet unknown mechanisms.
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15
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Wang JT, Wang YT, Chen CA, Meng PJ, Tew KS, Chiang PW, Tang SL. Extra high superoxide dismutase in host tissue is associated with improving bleaching resistance in "thermal adapted" and Durusdinium trenchii-associating coral. PeerJ 2022; 10:e12746. [PMID: 35070504 PMCID: PMC8760857 DOI: 10.7717/peerj.12746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023] Open
Abstract
Global warming threatens reef-building corals with large-scale bleaching events; therefore, it is important to discover potential adaptive capabilities for increasing their temperature resistance before it is too late. This study presents two coral species (Platygyra verweyi and Isopora palifera) surviving on a reef having regular hot water influxes via a nearby nuclear power plant that exhibited completely different bleaching susceptibilities to thermal stress, even though both species shared several so-called "winner" characteristics (e.g., containing Durusdinium trenchii, thick tissue, etc.). During acute heating treatment, algal density did not decline in P. verweyi corals within three days of being directly transferred from 25 to 31 °C; however, the same treatment caused I. palifera to lose < 70% of its algal symbionts within 24 h. The most distinctive feature between the two coral species was an overwhelmingly higher constitutive superoxide dismutase (ca. 10-fold) and catalase (ca. 3-fold) in P. verweyi over I. palifera. Moreover, P. verweyi also contained significantly higher saturated and lower mono-unsaturated fatty acids, especially a long-chain saturated fatty acid (C22:0), than I. palifera, and was consistently associated with the symbiotic bacteria Endozoicomonas, which was not found in I. palifera. However, antibiotic treatment and inoculation tests did not support Endozoicomonas having a direct contribution to thermal resistance. This study highlights that, besides its association with a thermally tolerable algal symbiont, a high level of constitutive antioxidant enzymes in the coral host is crucial for coral survivorship in the more fluctuating and higher temperature environments.
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Affiliation(s)
- Jih-Terng Wang
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Yi-Ting Wang
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | | | - Pei-Jei Meng
- General Education Center, National Dong Hwa University, Hualien, Taiwan,National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Kwee Siong Tew
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan,Institute of Marine Biodiversity and Evolution, National Dong Hwa University, Pingtung, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Pathirana E, Whittington RJ, Hick PM. Impact of seawater temperature on the Pacific oyster (Crassostrea gigas) microbiome and susceptibility to disease associated with Ostreid herpesvirus-1 (OsHV-1). ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Influence of temperature changes on symbiotic Symbiodiniaceae and bacterial communities’ structure: an experimental study on soft coral Sarcophyton trocheliophorum (Anthozoa: Alcyoniidae). JOURNAL OF TROPICAL ECOLOGY 2021. [DOI: 10.1017/s0266467421000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractIt is well concluded that microbial composition and diversity of coral species can be affected under temperature alterations. However, the interaction of environmental accumulation of corals and temperature stress on symbiotic Symbiodiniaceae and bacterial communities are rarely studied. In this study, two groups of soft coral Sarcophyton trocheliophorum were cultured under constant (26 °C) and inconstant (22 °C to 26 °C) temperature conditions for 30 days as control treatments. After that, water was cooled rapidly to decrease to 20 °C in 24 h. The results of diversity analysis showed that symbiotic Symbiodiniaceae and bacterial communities had a significant difference between the two accumulated groups. The principal coordinate analyses confirmed that symbiotic Symbiodiniaceae and bacterial communities of both control treatments were clustered into two groups. Our results evidenced that rapid cooling stress could not change symbiotic Symbiodiniaceae and bacterial communities’ composition. On the other hand, cooling stress could alter only bacterial communities in constant group. In conclusion, our study represents a clear relationship between environmental accumulation and the impact of short-term cooling stress in which microbial composition structure can be affected by early adaptation conditions.
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Mikryukov VS, Dulya OV, Likhodeevskii GA, Vorobeichik EL. Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors. RUSS J ECOL+ 2021. [DOI: 10.1134/s1067413621030085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Microbial dysbiosis reflects disease resistance in diverse coral species. Commun Biol 2021; 4:679. [PMID: 34083722 PMCID: PMC8175568 DOI: 10.1038/s42003-021-02163-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/28/2021] [Indexed: 01/28/2023] Open
Abstract
Disease outbreaks have caused significant declines of keystone coral species. While forecasting disease outbreaks based on environmental factors has progressed, we still lack a comparative understanding of susceptibility among coral species that would help predict disease impacts on coral communities. The present study compared the phenotypic and microbial responses of seven Caribbean coral species with diverse life-history strategies after exposure to white plague disease. Disease incidence and lesion progression rates were evaluated over a seven-day exposure. Coral microbiomes were sampled after lesion appearance or at the end of the experiment if no disease signs appeared. A spectrum of disease susceptibility was observed among the coral species that corresponded to microbial dysbiosis. This dysbiosis promotes greater disease susceptiblity in coral perhaps through different tolerant thresholds for change in the microbiome. The different disease susceptibility can affect coral’s ecological function and ultimately shape reef ecosystems. MacKnight et al. compared the phenotypic and microbial responses of seven Caribbean coral species with diverse life-history strategies after exposure to white plague disease. The different species exhibited a spectrum of disease susceptibility and associated mortality that corresponded with their tolerances to microbial change, indicating that coral disease and microbial dysbiosis may ultimately shape reef ecosystems.
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20
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Lu L, Li M, Yi G, Liao L, Cheng Q, Zhu J, Zhang B, Wang Y, Chen Y, Zeng M. Screening strategies for quorum sensing inhibitors in combating bacterial infections. J Pharm Anal 2021; 12:1-14. [PMID: 35573879 PMCID: PMC9073242 DOI: 10.1016/j.jpha.2021.03.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/04/2021] [Accepted: 03/25/2021] [Indexed: 01/20/2023] Open
Abstract
Interference with quorum sensing (QS) represents an antivirulence strategy with a significant promise for the treatment of bacterial infections and a new approach to restoring antibiotic tolerance. Over the past two decades, a novel series of studies have reported that quorum quenching approaches and the discovery of quorum sensing inhibitors (QSIs) have a strong impact on the discovery of anti-infective drugs against various types of bacteria. The discovery of QSI was demonstrated to be an appropriate strategy to expand the anti-infective therapeutic approaches to complement classical antibiotics and antimicrobial agents. For the discovery of QSIs, diverse approaches exist and develop in-step with the scale of screening as well as specific QS systems. This review highlights the latest findings in strategies and methodologies for QSI screening, involving activity-based screening with bioassays, chemical methods to seek bacterial QS pathways for QSI discovery, virtual screening for QSI screening, and other potential tools for interpreting QS signaling, which are innovative routes for future efforts to discover additional QSIs to combat bacterial infections. Interference with QSrepresents a promising antivirulence strategy for the treatment of bacterial infections. The discovery ofQSIs was demonstrated as an appropriate strategy to expand the anti-infective therapeutic arsenal to complement classical antibiotics and antimicrobial agents. For the discovery of QSIs, diverse approaches exist and develop in-step with the scale of screening and targeted QS systems. Few previous reviews have summarized the strategies and approaches of QSI screening, whereas this review highlights the recent findings in QSI screening strategies and methodologies.
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Affiliation(s)
- Lan Lu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
- Corresponding author.
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Guojuan Yi
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Li Liao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Qiang Cheng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Jie Zhu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Bin Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Yingying Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Yong Chen
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Ming Zeng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
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Thome PE, Rivera-Ortega J, Rodríguez-Villalobos JC, Cerqueda-García D, Guzmán-Urieta EO, García-Maldonado JQ, Carabantes N, Jordán-Dahlgren E. Local dynamics of a white syndrome outbreak and changes in the microbial community associated with colonies of the scleractinian brain coral Pseudodiploria strigosa. PeerJ 2021; 9:e10695. [PMID: 33604172 PMCID: PMC7863780 DOI: 10.7717/peerj.10695] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 12/12/2020] [Indexed: 01/04/2023] Open
Abstract
Reef corals in the Mexican Reef System have been severely affected by the emergence of a white syndrome that resembles both White Plague II and SCTLD descriptions. Meandroid scleractinian coral species are among the most severely affected. To gain insight into this affliction we conducted a broad study in the brain coral Pseudodiploria strigosa at a rear reef site in the NE Mexican Caribbean. We describe macro and microscopical signals of the disease, characterize the outbreak dynamics, the tissue histopathology, explore immunological responses in the individuals, and compare microbial assemblages associated with the surface mucus layer of healthy and unhealthy colonies. At the study site, the white syndrome outbreak on P. strigosa showed a high incidence rate in summer-fall and a low one in winter, as well as low survival expectation of diseased colonies at the end of the study. After 306 days of observation, out of 96 tracked colonies, eight remained apparently healthy and seven were diseased. No effective resistance to colony disease progression was observed once white syndrome signs developed. Tissue loss rate during the study varied among colonies (mean = 10.8 cm2, s.d. = 7.8 cm2) suggesting a complex relation between causal agents and colony resistance. The deterioration of tissues was evidenced from the basal to the surface body wall of polyps (up to 66% hypertrophy and liquefactive necrosis in unhealthy colonies), implying that microscopic alterations begin before macroscopic signals develop, suggesting this may be a systemic disease. We measured high levels of phenoloxidase (two orders of magnitude higher PO activity than P. strigosa affected by BBD) and antibacterial activity without significant reduction in unhealthy samples from the mucus layer, indicative of an enhanced immunological response. Results showed that opportunistic bacteria dominated damaged colonies, where six genera of the Bacteroidia class were found with significant changes in unhealthy colonies after DeSeq2 analysis. Nevertheless, histological observations did not support infection of the tissues. The opportunistic overload seems to be contained within the mucus layer but may be associated with the mortality of tissues in a yet unclear way. Future research should focus on experimental infections, the tracking of natural infections, and the immunocompetence of corals in the face of environmental pressures due to local, regional, and global impacts. If environmental deterioration is the primary cause of the continuing emergence and re-emergence of lethal coral diseases, as has been proposed by many authors, the only true option to effectively help preserve the coral reef biodiversity and services, is to restore the environmental quality of reef waters at the local scale and reduce greenhouse gases at the global scale.
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Affiliation(s)
- Patricia E Thome
- Instituto de Ciencias Del Mar y Limnología, Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, Mexico
| | - Jacqueline Rivera-Ortega
- Instituto de Ciencias Del Mar y Limnología, Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, Mexico
| | - Jenny C Rodríguez-Villalobos
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, La Paz, Baja California Sur, Mexico.,Ecosistemas y Conservación, ProAzul Terrestre A.C., La Paz, Baja California Sur, Mexico
| | - Daniel Cerqueda-García
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Mérida, Departamento de Recursos del Mar, Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | - Edgar O Guzmán-Urieta
- Instituto de Ciencias Del Mar y Limnología, Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, Mexico
| | - José Q García-Maldonado
- CONACyT, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Mérida, Mérida, Yucatán, Mexico
| | - Natalia Carabantes
- Instituto de Ciencias Del Mar y Limnología, Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, Mexico
| | - Eric Jordán-Dahlgren
- Instituto de Ciencias Del Mar y Limnología, Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, Mexico
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22
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Neu AT, Hughes IV, Allen EE, Roy K. Decade-scale stability and change in a marine bivalve microbiome. Mol Ecol 2021; 30:1237-1250. [PMID: 33432685 DOI: 10.1111/mec.15796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, is lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition of its microbiome over a decadal timescale. Site-level measurements of temperature, salinity and chlorophyll a allowed us to test how the microbiome of this species responded to two natural experiments: a seasonal increase in temperature and a phytoplankton bloom. Our results show that ethanol-preserved tissue can provide high-resolution information about temporal trends in compositions of host-associated microbial communities. Specifically, we found that the richness of amplicon sequence variants (ASVs) associated with D.gouldii did not change significantly over time despite increases in water temperature (+1.6°C due to seasonal change) and chlorophyll a concentration (more than ninefold). The phylogenetic composition of the communities, on the other hand, varied significantly between all collection years, with only six ASVs persisting over our sampling period. Overall, these results suggest that the diversity of microbial taxa associated with D.gouldii has remained stable over time and in response to seasonal environmental change over the course of more than a decade, but such stability is underlain by substantial turnover in the composition of the microbiome.
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Affiliation(s)
- Alexander T Neu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ian V Hughes
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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23
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Chen J, Lu Y, Ye X, Emam M, Zhang H, Wang H. Current advances in Vibrio harveyi quorum sensing as drug discovery targets. Eur J Med Chem 2020; 207:112741. [PMID: 32871343 DOI: 10.1016/j.ejmech.2020.112741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 07/16/2020] [Accepted: 07/26/2020] [Indexed: 12/25/2022]
Abstract
Vibrio harveyi is a marine bacterial pathogen which infects a wide range of marine organisms and results in severe loss. Antibiotics have been used for prophylaxis and treatment of V. harveyi infection. However, antibiotic resistance is a major public health threat to both human and animals. Therefore, there is an urgent need for novel antimicrobial agents with new modes of action. In V. harveyi, many virulence factors production and bioluminescence formation depend on its quorum sensing (QS) network. Therefore, the QS system has been widely investigated as an effective potential target for the treatment of V. harveyi infection. This perspective focuses on the quorum sensing inhibitors (QSIs) of V. harveyi QS systems (LuxM/N, LuxS/PQ, and CqsA/S) and evaluates medicinal chemistry strategies.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yaojia Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xinyi Ye
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mahmoud Emam
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China; Phytochemistry and Plant Systematics Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, 12622, Egypt
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China.
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24
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Stephens K, Bentley WE. Synthetic Biology for Manipulating Quorum Sensing in Microbial Consortia. Trends Microbiol 2020; 28:633-643. [DOI: 10.1016/j.tim.2020.03.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022]
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25
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Zhou J, Lin ZJ, Cai ZH, Zeng YH, Zhu JM, Du XP. Opportunistic bacteria use quorum sensing to disturb coral symbiotic communities and mediate the occurrence of coral bleaching. Environ Microbiol 2020; 22:1944-1962. [PMID: 32249540 DOI: 10.1111/1462-2920.15009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022]
Abstract
Coral associated microorganisms, especially some opportunistic pathogens can utilize quorum-sensing (QS) signals to affect population structure and host health. However, direct evidence about the link between coral bleaching and dysbiotic microbiomes under QS regulation was lacking. Here, using 11 opportunistic bacteria and their QS products (AHLs, acyl-homoserine-lactones), we exposed Pocillopora damicornis to three different treatments: test groups (A and B: mixture of AHLs-producing bacteria and cocktail of AHLs signals respectively); control groups (C and D: group A and B with furanone added respectively); and a blank control (group E: only seawater) for 21 days. The results showed that remarkable bleaching phenomenon was observed in groups A and B. The operational taxonomic units-sequencing analysis shown that the bacterial network interactions and communities composition were significantly changed, becoming especially enhanced in the relative abundances of Vibrio, Edwardsiella, Enterobacter, Pseudomonas, and Aeromonas. Interestingly, the control groups (C and D) were found to have a limited influence upon host microbial composition and reduced bleaching susceptibility of P. damicornis. These results indicate bleaching's initiation and progression may be caused by opportunistic bacteria of resident microbes in a process under regulation by AHLs. These findings add a new dimension to our understanding of the complexity of bleaching mechanisms from a chemoecological perspective.
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Affiliation(s)
- Jin Zhou
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Zi-Jun Lin
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.,Department of Earth System Science, Tsinghua University of Education Key Laboratory for Earth System Modeling, Beijing, 100084, People's Republic of China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Yan-Hua Zeng
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Jian-Ming Zhu
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.,School of Environment, Harbin Institute of Technology, Harbin, 150001, People's Republic of China
| | - Xiao-Peng Du
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
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26
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Clerissi C, de Lorgeril J, Petton B, Lucasson A, Escoubas JM, Gueguen Y, Dégremont L, Mitta G, Toulza E. Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome. Front Microbiol 2020; 11:311. [PMID: 32174904 PMCID: PMC7056673 DOI: 10.3389/fmicb.2020.00311] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/12/2020] [Indexed: 01/01/2023] Open
Abstract
Pacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and causes important economic losses. Disease dynamic was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 μVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to protect oysters against POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favor of POMS. After 5 days of transplantation, oysters from each family were either sampled for individual microbiota analyses using 16S rRNA gene-metabarcoding or transferred into facilities to record their survival using controlled condition. As expected, all oysters from susceptible families died, and all oysters from the resistant family survived. Quantification of OsHV-1 and bacteria showed that 5 days of transplantation were long enough to contaminate oysters by POMS, but not for entering the pathogenesis process. Thus, it was possible to compare microbiota characteristics between resistant and susceptible oysters families at the early steps of infection. Strikingly, we found that microbiota evenness and abundances of Cyanobacteria (Subsection III, family I), Mycoplasmataceae, Rhodobacteraceae, and Rhodospirillaceae were significantly different between resistant and susceptible oyster families. We concluded that these microbiota characteristics might predict oyster mortalities.
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Affiliation(s)
- Camille Clerissi
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France.,PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Julien de Lorgeril
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Bruno Petton
- Ifremer, LEMAR UMR 6539 (Université de Bretagne Occidentale, CNRS, IRD, Ifremer), Argenton-en-Landunvez, France
| | - Aude Lucasson
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Jean-Michel Escoubas
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Yannick Gueguen
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | | | - Guillaume Mitta
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
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27
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Mhuantong W, Nuryadi H, Trianto A, Sabdono A, Tangphatsornruang S, Eurwilaichitr L, Kanokratana P, Champreda V. Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea. PeerJ 2019; 7:e8137. [PMID: 31875145 PMCID: PMC6925950 DOI: 10.7717/peerj.8137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/01/2019] [Indexed: 01/22/2023] Open
Abstract
Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.
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Affiliation(s)
- Wuttichai Mhuantong
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Handung Nuryadi
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Agus Trianto
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Agus Sabdono
- Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | | | - Lily Eurwilaichitr
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Pattanop Kanokratana
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Verawat Champreda
- Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
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28
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Hewson I. Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson. DISEASES OF AQUATIC ORGANISMS 2019; 137:109-124. [PMID: 31854329 DOI: 10.3354/dao03432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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29
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Montilla LM, Ascanio A, Verde A, Croquer A. Systematic review and meta-analysis of 50 years of coral disease research visualized through the scope of network theory. PeerJ 2019; 7:e7041. [PMID: 31198644 PMCID: PMC6555395 DOI: 10.7717/peerj.7041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/29/2019] [Indexed: 11/20/2022] Open
Abstract
Coral disease research encompasses five decades of undeniable progress. Since the first descriptions of anomalous signs, we have come to understand multiple processes and environmental drivers that interact with coral pathologies. In order to gain a better insight into the knowledge we already have, we explored how key topics in coral disease research have been related to each other using network analysis. We reviewed 719 papers and conference proceedings published from 1965 to 2017. From each study, four elements determined our network nodes: (1) studied disease(s); (2) host genus; (3) marine ecoregion(s) associated with the study site; and (4) research objectives. Basic properties of this network confirmed that there is a set of specific topics comprising the majority of research. The top five diseases, genera, and ecoregions studied accounted for over 48% of the research effort in all cases. The community structure analysis identified 15 clusters of topics with different degrees of overlap among them. These clusters represent the typical sets of elements that appear together for a given study. Our results show that while some coral diseases have been studied considering multiple aspects, the overall trend is for most diseases to be understood under a limited range of approaches, e.g., bacterial assemblages have been considerably studied in Yellow and Black band diseases while immune response has been better examined for the aspergillosis-Gorgonia system. Thus, our challenge in the near future is to identify and resolve potential gaps in order to achieve a more comprehensive progress on coral disease research.
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30
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Zhao J, Li X, Hou X, Quan C, Chen M. Widespread Existence of Quorum Sensing Inhibitors in Marine Bacteria: Potential Drugs to Combat Pathogens with Novel Strategies. Mar Drugs 2019; 17:md17050275. [PMID: 31072008 PMCID: PMC6562741 DOI: 10.3390/md17050275] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022] Open
Abstract
Quorum sensing (QS) is a phenomenon of intercellular communication discovered mainly in bacteria. A QS system consisting of QS signal molecules and regulatory protein components could control physiological behaviors and virulence gene expression of bacterial pathogens. Therefore, QS inhibition could be a novel strategy to combat pathogens and related diseases. QS inhibitors (QSIs), mainly categorized into small chemical molecules and quorum quenching enzymes, could be extracted from diverse sources in marine environment and terrestrial environment. With the focus on the exploitation of marine resources in recent years, more and more QSIs from the marine environment have been investigated. In this article, we present a comprehensive review of QSIs from marine bacteria. Firstly, screening work of marine bacteria with potential QSIs was concluded and these marine bacteria were classified. Afterwards, two categories of marine bacteria-derived QSIs were summarized from the aspects of sources, structures, QS inhibition mechanisms, environmental tolerance, effects/applications, etc. Next, structural modification of natural small molecule QSIs for future drug development was discussed. Finally, potential applications of QSIs from marine bacteria in human healthcare, aquaculture, crop cultivation, etc. were elucidated, indicating promising and extensive application perspectives of QS disruption as a novel antimicrobial strategy.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Xinyun Li
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Xiyan Hou
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Chunshan Quan
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Ming Chen
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116600, China.
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31
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Gunasekera S, Meyer JL, Ding Y, Abboud KA, Luo D, Campbell JE, Angerhofer A, Goodsell JL, Raymundo LJ, Liu J, Ye T, Luesch H, Teplitski M, Paul VJ. Chemical and Metagenomic Studies of the Lethal Black Band Disease of Corals Reveal Two Broadly Distributed, Redox-Sensitive Mixed Polyketide/Peptide Macrocycles. JOURNAL OF NATURAL PRODUCTS 2019; 82:111-121. [PMID: 30636420 PMCID: PMC6350197 DOI: 10.1021/acs.jnatprod.8b00804] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Indexed: 05/14/2023]
Abstract
Black band disease (BBD), a lethal, polymicrobial disease consortium dominated by the cyanobacterium Roseofilum reptotaenium, kills many species of corals worldwide. To uncover chemical signals or cytotoxins that could be important in proliferation of Roseofilum and the BBD layer, we examined the secondary metabolites present in geographically diverse collections of BBD from Caribbean and Pacific coral reefs. Looekeyolide A (1), a 20-membered macrocyclic compound formed by a 16-carbon polyketide chain, 2-deamino-2-hydroxymethionine, and d-leucine, and its autoxidation product looekeyolide B (2) were extracted as major compounds (∼1 mg g-1 dry wt) from more than a dozen field-collected BBD samples. Looekeyolides A and B were also produced by a nonaxenic R. reptotaenium culture under laboratory conditions at similar concentrations. R. reptotaenium genomes that were constructed from four different metagenomic data sets contained a unique nonribosomal peptide/polyketide biosynthetic cluster that is likely responsible for the biosynthesis of the looekeyolides. Looekeyolide A, which readily oxidizes to looekeyolide B, may play a biological role in reducing H2O2 and other reactive oxygen species that could occur in the BBD layer as it overgrows and destroys coral tissue.
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Affiliation(s)
| | - Julie L. Meyer
- Soil
and Water Sciences Department, University
of Florida−Institute of Food and Agricultural Sciences, Gainesville, Florida 32611, United States
| | - Yousong Ding
- Department
of Medicinal Chemistry and Center for Natural Products, Drug Discovery
and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Khalil A. Abboud
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Danmeng Luo
- Department
of Medicinal Chemistry and Center for Natural Products, Drug Discovery
and Development, University of Florida, Gainesville, Florida 32610, United States
| | | | - Alexander Angerhofer
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Justin L. Goodsell
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | | | - Junyang Liu
- State Key
Laboratory of Chemical Oncogenomics, School of Chemical Biology and
Biotechnology, Peking University Shenzhen
Graduate School, Xili, Nanshan
District, Shenzhen, 518055, People’s Republic of China
| | - Tao Ye
- State Key
Laboratory of Chemical Oncogenomics, School of Chemical Biology and
Biotechnology, Peking University Shenzhen
Graduate School, Xili, Nanshan
District, Shenzhen, 518055, People’s Republic of China
| | - Hendrik Luesch
- Department
of Medicinal Chemistry and Center for Natural Products, Drug Discovery
and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Max Teplitski
- Smithsonian
Marine Station, Ft. Pierce, Florida 34949, United States
- Soil
and Water Sciences Department, University
of Florida−Institute of Food and Agricultural Sciences, Gainesville, Florida 32611, United States
| | - Valerie J. Paul
- Smithsonian
Marine Station, Ft. Pierce, Florida 34949, United States
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32
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Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME JOURNAL 2018; 13:921-936. [PMID: 30518818 PMCID: PMC6461899 DOI: 10.1038/s41396-018-0323-6] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 11/03/2018] [Accepted: 11/17/2018] [Indexed: 12/29/2022]
Abstract
Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora damicornis and surrounding seawater) putatively beneficial microorganisms for corals (pBMCs), including five Pseudoalteromonas sp., a Halomonas taeanensis and a Cobetia marina-related species strains. The results from a controlled aquarium experiment in two temperature regimes (26 °C and 30 °C) and four treatments (pBMC; pBMC with pathogen challenge - Vibrio coralliilyticus, VC; pathogen challenge, VC; and control) revealed the ability of the pBMC consortium to partially mitigate coral bleaching. Significantly reduced coral-bleaching metrics were observed in pBMC-inoculated corals, in contrast to controls without pBMC addition, especially challenged corals, which displayed strong bleaching signs as indicated by significantly lower photopigment contents and Fv/Fm ratios. The structure of the coral microbiome community also differed between treatments and specific bioindicators were correlated with corals inoculated with pBMC (e.g., Cobetia sp.) or VC (e.g., Ruegeria sp.). Our results indicate that the microbiome in corals can be manipulated to lessen the effect of bleaching, thus helping to alleviate pathogen and temperature stresses, with the addition of BMCs representing a promising novel approach for minimizing coral mortality in the face of increasing environmental impacts.
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33
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Kalia VC, Patel SKS, Kang YC, Lee JK. Quorum sensing inhibitors as antipathogens: biotechnological applications. Biotechnol Adv 2018; 37:68-90. [PMID: 30471318 DOI: 10.1016/j.biotechadv.2018.11.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/19/2018] [Accepted: 11/18/2018] [Indexed: 12/20/2022]
Abstract
The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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See-Too WS, Convey P, Pearce DA, Chan KG. Characterization of a novel N-acylhomoserine lactonase, AidP, from Antarctic Planococcus sp. Microb Cell Fact 2018; 17:179. [PMID: 30445965 PMCID: PMC6240239 DOI: 10.1186/s12934-018-1024-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 11/07/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND N-acylhomoserine lactones (AHLs) are well-studied signalling molecules produced by some Gram-negative Proteobacteria for bacterial cell-to-cell communication or quorum sensing. We have previously demonstrated the degradation of AHLs by an Antarctic bacterium, Planococcus versutus L10.15T, at low temperature through the production of an AHL lactonase. In this study, we cloned the AHL lactonase gene and characterized the purified novel enzyme. RESULTS Rapid resolution liquid chromatography analysis indicated that purified AidP possesses high AHL-degrading activity on unsubstituted, and 3-oxo substituted homoserine lactones. Liquid chromatography-mass spectrometry analysis confirmed that AidP functions as an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs. Multiple sequence alignment analysis and phylogenetic analysis suggested that the aidP gene encodes a novel AHL lactonase enzyme. The amino acid composition analysis of aidP and the homologous genes suggested that it might be a cold-adapted enzyme, however, the optimum temperature is 28 °C, even though the thermal stability is low (reduced drastically above 32 °C). Branch-site analysis of several aidP genes of Planococcus sp. branch on the phylogenetic trees also showed evidence of episodic positive selection of the gene in cold environments. Furthermore, we demonstrated the effects of covalent and ionic bonding, showing that Zn2+ is important for activity of AidP in vivo. The pectinolytic inhibition assay confirmed that this enzyme attenuated the pathogenicity of the plant pathogen Pectobacterium carotovorum in Chinese cabbage. CONCLUSION We demonstrated that AidP is effective in attenuating the pathogenicity of P. carotovorum, a plant pathogen that causes soft-rot disease. This anti-quorum sensing agent is an enzyme with low thermal stability that degrades the bacterial signalling molecules (AHLs) that are produced by many pathogens. Since the enzyme is most active below human body temperature (below 28 °C), and lose its activity drastically above 32 °C, the results of a pectinolytic inhibition assay using Chinese cabbage indicated the potential of this anti-quorum sensing agent to be safely applied in the field trials.
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Affiliation(s)
- Wah Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- National Antarctic Research Centre, IPS Building, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre, IPS Building, University Malaya, 50603, Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - David A Pearce
- National Antarctic Research Centre, IPS Building, University Malaya, 50603, Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 OET, UK
- Applied Sciences, University of Northumbria at Newcastle, Newcastle-upon-Tyne, NE1 8ST, UK
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- International Genome Centre, Jiangsu University, Zhenjiang, China.
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Ochsenkühn MA, Schmitt-Kopplin P, Harir M, Amin SA. Coral metabolite gradients affect microbial community structures and act as a disease cue. Commun Biol 2018; 1:184. [PMID: 30417121 PMCID: PMC6218554 DOI: 10.1038/s42003-018-0189-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
Corals are threatened worldwide due to prevalence of disease and bleaching. Recent studies suggest the ability of corals to resist disease is dependent on maintaining healthy microbiomes that span coral tissues and surfaces, the holobiont. Although our understanding of the role endosymbiotic microbes play in coral health has advanced, the role surface-associated microbes and their chemical signatures play in coral health is limited. Using minimally invasive water sampling, we show that the corals Acropora and Platygyra harbor unique bacteria and metabolites at their surface, distinctly different from surrounding seawater. The surface metabolites released by the holobiont create concentration gradients at 0–5 cm away from the coral surface. These molecules are identified as chemo-attractants, antibacterials, and infochemicals, suggesting they may structure coral surface-associated microbes. Further, we detect surface-associated metabolites characteristic of healthy or white syndrome disease infected corals, a finding which may aid in describing effects of diseases. Michael Ochsenkühn et al. look at the microbial and metabolic composition of coral surfaces and the surrounding seawater. They find that the metabolites found on the surface of the coral create a concentration gradient that influences the surrounding microbiome.
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Affiliation(s)
- Michael A Ochsenkühn
- Biology Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,Lehrstuhl für Analytische Lebensmittelchemie, Technische Universität München, Alte Akademie 10, 85354, Freising, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Shady A Amin
- Biology Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates. .,Chemistry Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates.
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36
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Röttjers L, Faust K. From hairballs to hypotheses-biological insights from microbial networks. FEMS Microbiol Rev 2018; 42:761-780. [PMID: 30085090 PMCID: PMC6199531 DOI: 10.1093/femsre/fuy030] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022] Open
Abstract
Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these networks is not straightforward, and the biological implications of network properties are unclear. Analysis of microbial networks allows researchers to predict hub species and species interactions. Additionally, such analyses can help identify alternative community states and niches. Here, we review factors that can result in spurious predictions and address emergent properties that may be meaningful in the context of the microbiome. We also give an overview of studies that analyse microbial networks to identify new hypotheses. Moreover, we show in a simulation how network properties are affected by tool choice and environmental factors. For example, hub species are not consistent across tools, and environmental heterogeneity induces modularity. We highlight the need for robust microbial network inference and suggest strategies to infer networks more reliably.
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Affiliation(s)
- Lisa Röttjers
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Karoline Faust
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
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37
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Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease. Sci Rep 2018; 8:14636. [PMID: 30279438 PMCID: PMC6168572 DOI: 10.1038/s41598-018-33007-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 09/17/2018] [Indexed: 01/22/2023] Open
Abstract
Microbiome disruptions triggering disease outbreaks are increasingly threatening corals worldwide. In the Tropical Eastern Pacific, a necrotic-patch disease affecting gorgonian corals (sea fans, Pacifigorgia spp.) has been observed in recent years. However, the composition of the microbiome and its disease-related disruptions remain unknown in these gorgonian corals. Therefore, we analysed 16S rRNA gene amplicons from tissues of healthy colonies (n = 19) and from symptomatic-asymptomatic tissues of diseased colonies (n = 19) of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) in order to test for disease-related changes in the bacterial microbiome. We found that potential endosymbionts (mostly Endozoicomonas spp.) dominate the core microbiome in healthy colonies. Moreover, healthy tissues differed in community composition and functional profile from those of the symptomatic tissues but did not show differences to asymptomatic tissues of the diseased colonies. A more diverse set of bacteria was observed in symptomatic tissues, together with the decline in abundance of the potential endosymbionts from the healthy core microbiome. Furthermore, according to a comparative taxonomy-based functional profiling, these symptomatic tissues were characterized by the increase in heterotrophic, ammonia oxidizer and dehalogenating bacteria and by the depletion of nitrite and sulphate reducers. Overall, our results suggest that the bacterial microbiome associated with the disease behaves opportunistically and is likely in a state of microbial dysbiosis. We also conclude that the confinement of the disease-related consortium to symptomatic tissues may facilitate colony recovery.
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38
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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: 7] [Impact Index Per Article: 1.2] [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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Engene N, Tronholm A, Paul VJ. Uncovering cryptic diversity of Lyngbya: the new tropical marine cyanobacterial genus Dapis (Oscillatoriales). JOURNAL OF PHYCOLOGY 2018; 54:435-446. [PMID: 29791035 DOI: 10.1111/jpy.12752] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria comprise an extraordinarily diverse group of microorganisms and, as revealed by increasing molecular information, this biodiversity is even more extensive than previously estimated. In this sense, the cyanobacterial genus Lyngbya is a highly polyphyletic group composed of many unrelated taxa with morphological similarities. In this study, the new genus Dapis was erected from the genus Lyngbya, based on a combined molecular, chemical, and morphological approach. Herein, two new species of cyanobacteria are described: D. pleousa and D. pnigousa. Our analyses found these species to be widely distributed and abundant in tropical and subtropical marine habitats. Seasonally, both species have the ability to form extensive algal blooms in marine habitats: D. pleousa in shallow-water, soft bottom habitats and D. pnigousa on coral reefs below depths of 10 m. Electron microscopy showed that D. pleousa contains gas vesicles, a character not previously reported in Lyngbya. These gas vesicles, in conjunction with a mesh-like network of filaments that trap oxygen released from photosynthesis, provide this species with an unusual mechanism to disperse in coastal marine waters, allowing D. pleousa to be present in both benthic and planktonic forms. In addition, both D. pleousa and D. pnigousa contained nitrogen-fixing genes as well as bioactive secondary metabolites. Several specimens of D. pnigousa biosynthesized the secondary metabolite lyngbic acid, a molecule that has also been isolated from many other marine cyanobacteria. Dapis pleousa consistently produced the secondary metabolite malyngolide, which may provide a promising chemotaxonomic marker for this species.
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Affiliation(s)
- Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, USA
| | - Ana Tronholm
- Southeast Environmental Research Center, Florida International University, Miami, Florida, 33199, USA
| | - Valerie J Paul
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA
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40
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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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41
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Haque S, Ahmad F, Dar SA, Jawed A, Mandal RK, Wahid M, Lohani M, Khan S, Singh V, Akhter N. Developments in strategies for Quorum Sensing virulence factor inhibition to combat bacterial drug resistance. Microb Pathog 2018; 121:293-302. [PMID: 29857121 DOI: 10.1016/j.micpath.2018.05.046] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022]
Abstract
Quorum sensing (QS) is a complex bacterial intercellular communication system. It is mediated by molecules called auto-inducers (AIs) and allows coordinated responses to a variety of environmental signals by inducing alterations in gene expression. Communication through QS can tremendously stimulate the pathogenicity and virulence via multiple mechanisms in pathogenic bacteria. The present review explores the major types of multitudinous QS systems known in Gram-positive and Gram-negative bacteria and their roles in bacterial pathogenesis and drug resistance. Because bacterial resistance to antibiotics is increasingly becoming a significant clinical challenge to human health; alternate strategies to combat drug resistance are warranted. Targeting bacterial pathogenicity by interruptions in QS using natural QS inhibitors and synthetic quorum-quenching analogs are being increasingly considered for development of next generation antimicrobials. The review highlights the recent advancements in discovery of promising new QS modulators and their efficiency in controlling infections caused by multidrug-resistant bacterial pathogens.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia.
| | - Faraz Ahmad
- Department of Public Health, College of Public Health, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Sajad A Dar
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Saif Khan
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Ha'il, 2440, Saudi Arabia
| | - Vineeta Singh
- Department of Biotechnology, Institute of Engineering & Technology, Lucknow, 226021, Uttar Pradesh, India
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha, 65431, Saudi Arabia
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Pogoreutz C, Rädecker N, Cárdenas A, Gärdes A, Wild C, Voolstra CR. Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome. Ecol Evol 2018; 8:2240-2252. [PMID: 29468040 PMCID: PMC5817147 DOI: 10.1002/ece3.3830] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/11/2017] [Accepted: 12/17/2017] [Indexed: 01/04/2023] Open
Abstract
The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora-associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.
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Affiliation(s)
- Claudia Pogoreutz
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Marine Ecology GroupFaculty of Biology and ChemistryUniversity of BremenBremenGermany
- Coral Reef Ecology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Nils Rädecker
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Anny Cárdenas
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Tropical Marine Microbiology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Astrid Gärdes
- Tropical Marine Microbiology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Christian Wild
- Marine Ecology GroupFaculty of Biology and ChemistryUniversity of BremenBremenGermany
- Coral Reef Ecology GroupLeibniz Center for Tropical Marine Research (ZMT)BremenGermany
| | - Christian R. Voolstra
- Red Sea Research Center, Biological and Environment Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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43
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Mera H, Bourne DG. Disentangling causation: complex roles of coral-associated microorganisms in disease. Environ Microbiol 2017; 20:431-449. [DOI: 10.1111/1462-2920.13958] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hanaka Mera
- College of Science and Engineering; James Cook University; Townsville Queensland 4811, Australia
| | - David G. Bourne
- College of Science and Engineering; James Cook University; Townsville Queensland 4811, Australia
- Australian Institute of Marine Science; PMB 3, Townsville, Queensland 4810 Australia
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44
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Lee JY, Sim TB, Lee JE, Na HK. Chemopreventive and Chemotherapeutic Effects of Fish Oil derived Omega-3 Polyunsaturated Fatty Acids on Colon Carcinogenesis. Clin Nutr Res 2017; 6:147-160. [PMID: 28770178 PMCID: PMC5539209 DOI: 10.7762/cnr.2017.6.3.147] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is the third most common cause of cancer related death in the world. Multiple lines of evidence suggest that there is an association between consumption of dietary fat and colon cancer risk. Not only the amount but also the type and the ratio of fatty acids comprising dietary fats consumed have been implicated in the etiology and pathogenesis of colon cancer. Omega-3 (n-3) polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have been known to inhibit development of colon cancer by downregulating the expression of genes involved in colon carcinogenesis and also by altering the membrane lipid composition. Data from laboratory, epidemiological, and clinical studies substantiate the beneficial role of n-3 PUFAs in preventing colitis and subsequent development of colon cancer. In addition, recent studies suggest that some n-3 PUFAs can be effective as an adjuvant with chemotherapeutic agents and other natural anticancer compounds in the management of colon cancer. In this review, we discuss chemopreventive and therapeutic effects of fish oil derived long chain n-3 PUFAs, particularly EPA and DHA, with focus on synergetic effects of which they exert when combined with chemotherapeutic agents and other natural compounds.
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Affiliation(s)
- Ja Young Lee
- Department of Food and Nutrition, College of Health and Wellness, Sungshin Women's University, Seoul 01133, Korea
| | - Tae-Bu Sim
- Department of Food and Nutrition, College of Health and Wellness, Sungshin Women's University, Seoul 01133, Korea
| | - Jeong-Eun Lee
- Department of Food and Nutrition, College of Health and Wellness, Sungshin Women's University, Seoul 01133, Korea
| | - Hye-Kyung Na
- Department of Food and Nutrition, College of Health and Wellness, Sungshin Women's University, Seoul 01133, Korea.,Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul 01133, Korea
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Meyer JL, Paul VJ, Raymundo LJ, Teplitski M. Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals. Front Microbiol 2017; 8:618. [PMID: 28458657 PMCID: PMC5394123 DOI: 10.3389/fmicb.2017.00618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/27/2017] [Indexed: 12/16/2022] Open
Abstract
Black Band Disease (BBD), the destructive microbial consortium dominated by the cyanobacterium Roseofilum reptotaenium, affects corals worldwide. While the taxonomic composition of BBD consortia has been well-characterized, substantially less is known about its functional repertoire. We sequenced the metagenomes of Caribbean and Pacific black band mats and cultured Roseofilum and obtained five metagenome-assembled genomes (MAGs) of Roseofilum, nine of Proteobacteria, and 12 of Bacteroidetes. Genomic content analysis suggests that Roseofilum is a source of organic carbon and nitrogen, as well as natural products that may influence interactions between microbes. Proteobacteria and Bacteroidetes members of the disease consortium are suited to the degradation of amino acids, proteins, and carbohydrates. The accumulation of sulfide underneath the black band mat, in part due to a lack of sulfur oxidizers, contributes to the lethality of the disease. The presence of sulfide:quinone oxidoreductase genes in all five Roseofilum MAGs and in the MAGs of several heterotrophs demonstrates that resistance to sulfide is an important characteristic for members of the BBD consortium.
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Affiliation(s)
- Julie L Meyer
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural SciencesGainesville, FL, USA
| | | | | | - Max Teplitski
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural SciencesGainesville, FL, USA.,Smithsonian Marine StationFort Pierce, FL, USA
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Peixoto RS, Rosado PM, Leite DCDA, Rosado AS, Bourne DG. Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience. Front Microbiol 2017; 8:341. [PMID: 28326066 PMCID: PMC5339234 DOI: 10.3389/fmicb.2017.00341] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental "probiotics" to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.
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Affiliation(s)
- Raquel S. Peixoto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - Phillipe M. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | | | - Alexandre S. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - David G. Bourne
- College of Science and Engineering, James Cook University, TownsvilleQLD, Australia
- Australian Institute of Marine Science, TownsvilleQLD, Australia
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Saurav K, Costantino V, Venturi V, Steindler L. Quorum Sensing Inhibitors from the Sea Discovered Using Bacterial N-acyl-homoserine Lactone-Based Biosensors. Mar Drugs 2017; 15:md15030053. [PMID: 28241461 PMCID: PMC5367010 DOI: 10.3390/md15030053] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/17/2022] Open
Abstract
Marine natural products with antibiotic activity have been a rich source of drug discovery; however, the emergence of antibiotic-resistant bacterial strains has turned attention towards the discovery of alternative innovative strategies to combat pathogens. In many pathogenic bacteria, the expression of virulence factors is under the regulation of quorum sensing (QS). QS inhibitors (QSIs) present a promising alternative or potential synergistic treatment since they disrupt the signaling pathway used for intra- and interspecies coordination of expression of virulence factors. This review covers the set of molecules showing QSI activity that were isolated from marine organisms, including plants (algae), animals (sponges, cnidarians, and bryozoans), and microorganisms (bacteria, fungi, and cyanobacteria). The compounds found and the methods used for their isolation are the emphasis of this review.
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Affiliation(s)
- Kumar Saurav
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, 31905 Haifa, Israel.
| | - Valeria Costantino
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Vittorio Venturi
- Bacteriology Group, International Centre for Genetic Engineering & Biotechnology, Padriciano 99, 34149 Trieste, Italy.
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, 31905 Haifa, Israel.
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48
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Unraveling the microbial processes of black band disease in corals through integrated genomics. Sci Rep 2017; 7:40455. [PMID: 28094312 PMCID: PMC5240343 DOI: 10.1038/srep40455] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/29/2016] [Indexed: 11/08/2022] Open
Abstract
Coral disease outbreaks contribute to the ongoing degradation of reef ecosystems, however, microbial mechanisms underlying the onset and progression of most coral diseases are poorly understood. Black band disease (BBD) manifests as a cyanobacterial-dominated microbial mat that destroys coral tissues as it rapidly spreads over coral colonies. To elucidate BBD pathogenesis, we apply a comparative metagenomic and metatranscriptomic approach to identify taxonomic and functional changes within microbial lesions during in-situ development of BBD from a comparatively benign stage termed cyanobacterial patches. Results suggest that photosynthetic CO2-fixation in Cyanobacteria substantially enhances productivity of organic matter within the lesion during disease development. Photosynthates appear to subsequently promote sulfide-production by Deltaproteobacteria, facilitating the major virulence factor of BBD. Interestingly, our metagenome-enabled transcriptomic analysis reveals that BBD-associated cyanobacteria have a putative mechanism that enables them to adapt to higher levels of hydrogen sulfide within lesions, underpinning the pivotal roles of the dominant cyanobacterium within the polymicrobial lesions during the onset of BBD. The current study presents sequence-based evidence derived from whole microbial communities that unravel the mechanism of development and progression of BBD.
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Abstract
Quorum sensing (QS) is a form of chemical communication used by certain bacteria that regulates a wide range of biogeochemically important bacterial behaviors. Although QS was first observed in a marine bacterium nearly four decades ago, only in the past decade has there been a rise in interest in the role that QS plays in the ocean. It has become clear that QS, regulated by signals such as acylated homoserine lactones (AHLs) or furanosyl-borate diesters [autoinducer-2 (AI-2) molecules], is involved in important processes within the marine carbon cycle, in the health of coral reef ecosystems, and in trophic interactions between a range of eukaryotes and their bacterial associates. The most well-studied QS systems in the ocean occur in surface-attached (biofilm) communities and rely on AHL signaling. AHL-QS is highly sensitive to the chemical and biological makeup of the environment and may respond to anthropogenic change, including ocean acidification and rising sea surface temperatures.
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Affiliation(s)
- Laura R Hmelo
- School of Oceanography, University of Washington, Seattle, Washington 98195;
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50
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Henao J, Pérez H, Abril D, Ospina K, Piza A, Botero K, Rincón C, Donato J, Hurtado A, García E, Otero V, Del Risco A, Guerra B, Cifuentes Y, Ordoñez A, Rojas D, Suarez K, Osorio D, Pinzón A. Genome sequencing of three bacteria associated to black band disease from a Colombian reef-building coral. GENOMICS DATA 2016; 11:73-74. [PMID: 28018855 PMCID: PMC5176132 DOI: 10.1016/j.gdata.2016.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/02/2016] [Accepted: 12/07/2016] [Indexed: 01/09/2023]
Abstract
We announce the draft genome sequence of three Gram-negative bacteria isolated from coral tissues affected with the black band disease (BBD), identified with the NCBI's Assembly Database accession numbers: MBQF, MAYB and MBQE. These genome drafts constitute an useful tool for the characterisation of these bacteria and for the understanding of the relationship between the microbial consortia associated with the disease and the onset and progression of the pathology.
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Affiliation(s)
- Juan Henao
- Bioinformatics and Systems Biology Group, National University of Colombia, Bogotá, Colombia
| | - Hermes Pérez
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Deisy Abril
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Katterine Ospina
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Adriana Piza
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Kelly Botero
- Bioinformatics and Systems Biology Group, National University of Colombia, Bogotá, Colombia
| | - Cristhian Rincón
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Jhon Donato
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Andrea Hurtado
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Erika García
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Vanessa Otero
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Alexander Del Risco
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Brenda Guerra
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Yina Cifuentes
- Bioinformatics and Systems Biology Group, National University of Colombia, Bogotá, Colombia
| | - Alvaro Ordoñez
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Daniel Rojas
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Karen Suarez
- Bioinformatics for Omics, Postgraduate Class, National University of Colombia, Bogotá, Colombia
| | - Daniel Osorio
- Bioinformatics and Systems Biology Group, National University of Colombia, Bogotá, Colombia
| | - Andrés Pinzón
- Bioinformatics and Systems Biology Group, National University of Colombia, Bogotá, Colombia
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