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Liu M, Yin F, Zhao W, Tian P, Zhou Y, Jia Z, Huang K, Ding Y, Xiao J, Niu W, Wang X. Diversity of Culturable Bacteria from the Coral Reef Areas in the South China Sea and Their Agar-Degrading Abilities. Microorganisms 2024; 12:187. [PMID: 38258013 PMCID: PMC10818321 DOI: 10.3390/microorganisms12010187] [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: 12/28/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The South China Sea (SCS) is abundant in marine microbial resources with high primary productivity, which is crucial for sustaining the coral reef ecosystem and the carbon cycle. Currently, research on the diversity of culturable bacteria in the SCS is relatively extensive, yet the culturable bacteria in coral reefs has been poorly understood. In this study, we analyzed the bacterial community structure of seawater samples among Daya Bay (Fujian Province), Qionghai (Hainan Province), Xisha Islands, and the southern South China Sea based on culturable methods and detected their abilities for agar degradation. There were 441 bacterial strains, belonging to three phyla, five classes, 43 genera, and 101 species, which were isolated by marine agar 2216E (MA; Becton Dickinson). Strains within Gammaproteobacteria were the dominant group, accounting for 89.6% of the total bacterial isolates. To investigate vibrios, which usually correlated with coral health, 348 isolates were obtained from TCBS agar, and all isolates were identified into three phylum, three classes, 14 orders, 25 families, and 48 genera. Strains belonging to the genus Vibrio had the greatest number (294 strains), indicating the high selectivity of TCBS agar for vibrios. Furthermore, nineteen strains were identified as potentially novel species according to the low 16S rRNA gene similarity (<98.65%), and 28 strains (15 species) had agar-degrading ability. These results indicate a high diversity of culturable bacteria in the SCS and a huge possibility to find novel and agar-degrading species. Our study provides valuable microbial resources to maintain the stability of coral ecosystems and investigate their roles in the marine carbon cycle.
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Affiliation(s)
- Mei Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Fu Yin
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Wenbin Zhao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Peng Tian
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Yi Zhou
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Zhiyu Jia
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Keyi Huang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Yunqi Ding
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Jiaguang Xiao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Wentao Niu
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, China; (P.T.); (Z.J.); (J.X.)
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou 510300, China
| | - Xiaolei Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (M.L.); (F.Y.); (W.Z.); (Y.Z.); (K.H.); (Y.D.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
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Complete genome of Vibrio japonicus strain JCM 31412 T and assessment of the Nereis clade of the genus Vibrio. Antonie Van Leeuwenhoek 2023; 116:129-141. [PMID: 36287289 DOI: 10.1007/s10482-022-01784-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/08/2022] [Indexed: 02/01/2023]
Abstract
Clade-based taxonomy has become a recognised means of classifying members of the family Vibrionaceae. A multilocus sequence analysis (MLSA) approach based on eight housekeeping genes can be used to infer phylogenetic relationships, which then groups species into monophyletic clades. Recent work on the Vibrionaceae clades added newly described species and updated existing relationships; the Nereis clade currently includes Vibrio nereis and Vibrio hepatarius. A publication characterising Vibrio japonicus as a novel species placed it within the Nereis clade, but this strain was not included in a recently published taxonomic update because a genome sequence was not available for phylogenetic assessment. To resolve this discrepancy and assess the taxonomic position of V. japonicus within the updated clades, we sequenced the complete genome of V. japonicus JCM 31412 T and conducted phylogenetic and genomic analyses of this clade. Vibrio japonicus remains within the Nereis clade and phylogenomic, average nucleotide identity (ANI), and average amino acid identity (AAI) analyses confirm this relationship. Additional genomic assessments on all Nereis clade members found gene clusters and inferred functionalities shared among the species. This work represents the first complete genome of a member of the Nereis clade and updates the clade-based taxonomy of the Vibrionaceae family.
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Padovan A, Siboni N, Kaestli M, King WL, Seymour JR, Gibb K. Occurrence and dynamics of potentially pathogenic vibrios in the wet-dry tropics of northern Australia. MARINE ENVIRONMENTAL RESEARCH 2021; 169:105405. [PMID: 34242991 DOI: 10.1016/j.marenvres.2021.105405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
Bacteria from the Vibrio genus are a ubiquitous component of coastal and estuarine ecosystems with several pathogenic Vibrio species displaying preferences for warm tropical waters. We studied the spatial and temporal abundance of three key human potential pathogens V. parahaemolyticus, V. cholerae and V. vulnificus in northern tropical Australia, over the wet and dry seasons, to identify environmental parameters influencing their abundance. Quantitative PCR (qPCR) analysis revealed that V. parahaemolyticus occurred more frequently and in higher abundance than V. cholerae and V. vulnificus across all locations examined. All three species were more abundant during the wet season, with V. parahaemolyticus abundance correlated to temperature and conductivity, whereas nutrient concentrations and turbidity best explained V. vulnificus abundance. In addition to these targeted qPCR analyses, we assessed the composition and dynamics of the entire Vibrio community using hsp60 amplicon sequencing. Using this approach, 42 Vibrio species were identified, including a number of other pathogenic species such as V. alginolyticus, V. mimicus and V. fluvialis. The Vibrio community was more diverse in the wet season, with temperature and dissolved oxygen as the key factors governing community composition. Seasonal differences were primarily driven by a greater abundance of V. parahaemolyticus and V. vulnificus during the wet season, while spatial differences were driven by different abundances of V. harveyi, V. campbellii, V. cholerae and V. navarrensis. When we related the abundance of Vibrio to other bacterial taxa, defined using 16S rRNA gene amplicon sequencing, V. parahaemolyticus was negatively correlated to several taxa, including members of the Rickettsiales and Saccharimonadales, while V. vulnificus was negatively correlated to Rhobacteriaceae and Cyanobiaceae. In contrast, V. alginolyticus, V. harveyi and V. mediterranei were all positively correlated to Cyanobacteria. These observations highlight the dynamic nature of Vibrio communities and expands current understanding of the processes governing the occurrence of potentially pathogenic Vibrio spp. in tropical coastal ecosystems.
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Affiliation(s)
- Anna Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia.
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - William L King
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia; The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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Patterns and drivers of Vibrio isolates phylogenetic diversity in the Beibu Gulf, China. J Microbiol 2020; 58:998-1009. [PMID: 33095386 DOI: 10.1007/s12275-020-0293-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/04/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
Members of the genus Vibrio are ubiquitous in aquatic environments and can be found either in a culturable or a viable but nonculturable (VBNC) state. Despite widespread concerns as to how to define the occurrence and dynamics of Vibrio populations by culture-independent approaches, further physiological research and relevant biotechnological developments will require the isolation and cultivation of the microbes from various environments. The present work provides data and perspectives on our understanding of culturable Vibrio community structure and diversity in the Beibu Gulf. Finally, we isolated 1,037 strains of Vibrio from 45 samples and identified 18 different species. Vibrio alginolyticus, V. cyclitrophicus, V. tasmaniensis, V. brasiliensis, and V. splendidus were the dominant species that had regional distribution characteristics. The correlation between the quantitative distribution and community structure of culturable Vibrio and environmental factors varied with the Vibrio species and geographical locations. Among them, salinity, nitrogen, and phosphorus were the main factors affecting the diversity of culturable Vibrio. These results help to fill a knowledge gap on Vibrio diversity and provide data for predicting and controlling pathogenic Vibrio outbreaks in the Beibu Gulf.
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Vidal LMR, Venas TM, Gonçalves ARP, Mattsson HK, Silva RVP, Nóbrega MS, Azevedo GPR, Garcia GD, Tschoeke DA, Vieira VV, Thompson FL, Thompson CC. Rapid screening of marine bacterial symbionts using MALDI-TOF MS. Arch Microbiol 2020; 202:2329-2336. [PMID: 32529508 DOI: 10.1007/s00203-020-01917-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.
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Affiliation(s)
- Livia M R Vidal
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tainá M Venas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Aline R P Gonçalves
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Hannah K Mattsson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Raphael V P Silva
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Maria S Nóbrega
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gustavo P R Azevedo
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Departamento de Ensino de Graduação, Campus UFRJ - Macaé Professor Aloisio Teixeira, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, RJ, Brazil
| | - Diogo A Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Biomedical Engineer Program - COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Verônica V Vieira
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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6
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Silveira CB, Coutinho FH, Cavalcanti GS, Benler S, Doane MP, Dinsdale EA, Edwards RA, Francini-Filho RB, Thompson CC, Luque A, Rohwer FL, Thompson F. Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. BMC Genomics 2020; 21:126. [PMID: 32024463 PMCID: PMC7003362 DOI: 10.1186/s12864-020-6523-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bacteriophages encode genes that modify bacterial functions during infection. The acquisition of phage-encoded virulence genes is a major mechanism for the rise of bacterial pathogens. In coral reefs, high bacterial density and lysogeny has been proposed to exacerbate reef decline through the transfer of phage-encoded virulence genes. However, the functions and distribution of these genes in phage virions on the reef remain unknown. Results Here, over 28,000 assembled viral genomes from the free viral community in Atlantic and Pacific Ocean coral reefs were queried against a curated database of virulence genes. The diversity of virulence genes encoded in the viral genomes was tested for relationships with host taxonomy and bacterial density in the environment. These analyses showed that bacterial density predicted the profile of virulence genes encoded by phages. The Shannon diversity of virulence-encoding phages was negatively related with bacterial density, leading to dominance of fewer genes at high bacterial abundances. A statistical learning analysis showed that reefs with high microbial density were enriched in viruses encoding genes enabling bacterial recognition and invasion of metazoan epithelium. Over 60% of phages could not have their hosts identified due to limitations of host prediction tools; for those which hosts were identified, host taxonomy was not an indicator of the presence of virulence genes. Conclusions This study described bacterial virulence factors encoded in the genomes of bacteriophages at the community level. The results showed that the increase in microbial densities that occurs during coral reef degradation is associated with a change in the genomic repertoire of bacteriophages, specifically in the diversity and distribution of bacterial virulence genes. This suggests that phages are implicated in the rise of pathogens in disturbed marine ecosystems.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA. .,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA. .,Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, FL, 33146, USA.
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, 03550, San Juan de Alicante, Spain
| | - Giselle S Cavalcanti
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Sean Benler
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Michael P Doane
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Ronaldo B Francini-Filho
- Centro de Biologia Marinha, Universidade de São Paulo, Rodovia Manoel Hypólito do Rego, Km 131,50, São Sebastião, SP, 11600-000, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941- 599, Brazil
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Forest L Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Fabiano Thompson
- SAGE/COPPE, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941- 599, Brazil
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Montánchez I, Kaberdin VR. Vibrio harveyi: A brief survey of general characteristics and recent epidemiological traits associated with climate change. MARINE ENVIRONMENTAL RESEARCH 2020; 154:104850. [PMID: 32056705 DOI: 10.1016/j.marenvres.2019.104850] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/30/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Here we briefly review the major characteristics of the emerging pathogen Vibrio harveyi and discuss survival strategies and adaptation mechanisms underlying the capacity of this marine bacterium to thrive in natural and artificial aquatic settings. Recent studies suggest that some adaptation mechanisms can easily be acquired by V. harveyi and other members of the Vibrionaceae family owing to efficient horizontal gene transfer and elevated mutation rate. While discussing the main factors in charge of the expansion of Vibrio spp. habitats and concomitant spread of Vibrio-associated diseases under climate change, this review highlights the need for future studies able to address the joint impact of environmental and anthropogenic factors on the long-term dynamics and virulence of V. harveyi populations at the global scale.
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Affiliation(s)
- Itxaso Montánchez
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain; IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620, Plentzia, Spain.
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8
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Girard L. Quorum sensing in Vibrio spp.: the complexity of multiple signalling molecules in marine and aquatic environments. Crit Rev Microbiol 2019; 45:451-471. [PMID: 31241379 DOI: 10.1080/1040841x.2019.1624499] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Quorum sensing (QS) is a density-dependent mechanism enabling bacteria to coordinate their actions via the release of small diffusible molecules named autoinducers (AIs). Vibrio spp. are able to adapt to changing environmental conditions by using a wide range of physiological mechanisms and many species pose a threat for human health and diverse marine and estuarine ecosystems worldwide. Cell-to-cell communication controls many of their vital functions such as niche colonization, survival strategies, or virulence. In this review, I summarize (1) the different known QS pathways (2) the diversity of AIs as well as their biological functions, and (3) the QS-mediated interactions between Vibrio and other organisms. However, the current knowledge is limited to a few pathogenic or bioluminescent species and in order to provide a genus-wide view an inventory of QS genes among 87 Vibrio species has been made. The large diversity of signal molecules and their differential effects on a particular physiological function suggest that the complexity of multiple signalling systems within bacterial communities is far from being fully understood. I question here the real level of specificity of such communication in the environment and discuss the different perspectives in order to better apprehend QS in natural habitats.
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Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics , KU Leuven , Belgium
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9
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Díez-Vives C, Nielsen S, Sánchez P, Palenzuela O, Ferrera I, Sebastián M, Pedrós-Alió C, Gasol JM, Acinas SG. Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea. Mol Ecol 2019; 28:2846-2859. [PMID: 30830717 DOI: 10.1111/mec.15068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/13/2019] [Accepted: 02/27/2019] [Indexed: 01/18/2023]
Abstract
Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as Ecologically Significant Taxonomic Units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Department of Life Sciences (Invertebrate Division), The Natural History Museum of London, London, UK
| | - Shaun Nielsen
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, Australia
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Oswaldo Palenzuela
- Department of Biology, Culture and Pathology of Marine Species, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto Español de Oceanografía, Centro Oceanográfico de Málaga, Fuengirola, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Carlos Pedrós-Alió
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Madrid, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
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Shi X, Liu L, Li Y, Xiao Y, Ding G, Lin S, Chen J. Isolation of an algicidal bacterium and its effects against the harmful-algal- bloom dinoflagellate Prorocentrum donghaiense (Dinophyceae). HARMFUL ALGAE 2018; 80:72-79. [PMID: 30502814 DOI: 10.1016/j.hal.2018.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 06/09/2023]
Abstract
The relationship between algicidal bacteria and harmful-algal-bloom-forming dinoflagellates is understudied and their action modes are largely uncharacterized. In this study, an algicidal bacterium (FDHY-03) was isolated from a bloom of Prorocentrum donghaiense and the characteristics of its action against P. donghaiense was investigated at physiological, molecular, biochemical and cytological levels. 16S rDNA sequence analysis placed this strain in the genus of Alteromonas in the subclass of γ-proteobacteria. Algicidal activity was detected in the bacterial filtrate, suggesting a secreted algicidal principle from this bacterium. Strain FDHY-03 showed algicidal activity on a broad range of HAB-forming species, but the greatest effect was found on P. donghaiense, which showed 91.7% mortality in 24 h of challenge. Scanning electron microscopic analysis indicated that the megacytic growth zone of P. donghaiense cells was the major target of the algicidal action of FDHY-03. When treated with FDHY-03 culture filtrate, P. donghaiense cell wall polysaccharides decreased steadily, suggesting that the algicidal activity occurred through the digestion of cell wall polysaccharides. To verify this proposition, the expression profile of beta-glucosidase gene in FDHY-03 cultures with or without P. donghaiense cell addition was investigated using reverse-transcription quantitative PCR. The gene expression level increased in the presence of P. donghaiense cells, indicative of beta-glucosidase induction by P. donghaiense and the enzyme's role in this dinoflagellate's demise. This study has isolated a new bacterial strain with a strong algicidal capability, documented its action mode and biochemical mechanism, providing a potential source of bacterial agent to control P. donghaiense blooms.
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Affiliation(s)
- Xinguo Shi
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Lemian Liu
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Yue Li
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Yuchun Xiao
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Guangmao Ding
- Monitoring Center of Marine Environment and Fishery Resources, Fujian Province, Fuzhou 350003, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, United States
| | - Jianfeng Chen
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China.
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11
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Genetic diversity and phenotypic plasticity of AHL-mediated Quorum sensing in environmental strains of Vibrio mediterranei. ISME JOURNAL 2018; 13:159-169. [PMID: 30116040 DOI: 10.1038/s41396-018-0260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/12/2018] [Accepted: 07/24/2018] [Indexed: 01/28/2023]
Abstract
N-Acyl homoserine lactone (AHL)-mediated Quorum sensing (QS) is one of the most studied social behavior among Proteobacteria. However, despite the current knowledge on QS-associated phenotypes such as bioluminescence, biofilm formation, or pathogenesis, the characterization of environmental factors driving QS in realistic ecological settings remains scarce. We investigated the dynamics of AHL and AHL-producing Vibrio among 840 isolates collected fortnightly from the Salses-Leucate Mediterranean lagoon in spring and summer 2015 and 2016. Vibrio isolates were characterized by gyrB gene sequencing, Enterobacterial repetitive intergenic consensus polymerase chain reaction, and genome sequencing, and AHL production was investigated by a biosensors-based UHPLC-HRMS/MS approach. Our results revealed, for the first time, a succession of V. mediterranei isolates with different AHL production phenotypes over time and this dynamics was observed in a single genotype (average genomic nucleotide identity >99.9). A multivariate DistLM analysis revealed that 83.4% of the temporal variation of V. mediterranei QS phenotypes was explained by environmental variables. Overall, our results suggest that isolates of a single genotype are able to change their QS phenotypes in response to environmental conditions, highlighting the phenotypic plasticity of bacterial communication in the environment.
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12
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Coryell RL, Turnham KE, de Jesus Ayson EG, Lavilla‐Pltogo C, Alcala AC, Sotto F, Gonzales B, Nishiguchi MK. Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid -Vibrio mutualism. Ecol Evol 2018; 8:7421-7435. [PMID: 30151160 PMCID: PMC6106162 DOI: 10.1002/ece3.4266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/05/2022] Open
Abstract
Marine microbes encounter a myriad of biotic and abiotic factors that can impact fitness by limiting their range and capacity to move between habitats. This is especially true for environmentally transmitted bacteria that cycle between their hosts and the surrounding habitat. As geologic history, biogeography, and other factors such as water temperature, salinity, and physical barriers can inhibit bacterial movement to novel environments, we chose to examine the genetic architecture of Euprymna albatrossae (Mollusca: Cephalopoda) and their Vibrio fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach. Eleven separate sites in the Philippine islands were examined using haplotype estimates that were examined via nested clade analysis to determine the relationship between E. albatrossae and V. fischeri populations and their geographic location. Identical analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for host and symbiont genetic data. Host animals demonstrated a significant amount of variation within island groups, while symbiont variation was found within individual populations. Nested clade phylogenetic analysis revealed that hosts and symbionts may have colonized this area at different times, with a sudden change in habitat. Additionally, host data indicate restricted gene flow, whereas symbionts show range expansion, followed by periodic restriction to genetic flow. These differences between host and symbiont networks indicate that factors "outside the squid" influence distribution of Philippine V. fischeri. Our results shed light on how geography and changing environmental factors can impact marine symbiotic associations at both local and global scales.
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Affiliation(s)
- Randy L. Coryell
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico
| | - Kira E. Turnham
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico
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13
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Silveira CB, Cavalcanti GS, Walter JM, Silva-Lima AW, Dinsdale EA, Bourne DG, Thompson CC, Thompson FL. Microbial processes driving coral reef organic carbon flow. FEMS Microbiol Rev 2017; 41:575-595. [PMID: 28486655 DOI: 10.1093/femsre/fux018] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 04/10/2017] [Indexed: 01/13/2023] Open
Abstract
Coral reefs are one of the most productive ecosystems on the planet, with primary production rates compared to that of rain forests. Benthic organisms release 10-50% of their gross organic production as mucus that stimulates heterotrophic microbial metabolism in the water column. As a result, coral reef microbes grow up to 50 times faster than open ocean communities. Anthropogenic disturbances cause once coral-dominated reefs to become dominated by fleshy organisms, with several outcomes for trophic relationships. Here we review microbial processes implicated in organic carbon flux in coral reefs displaying species phase shifts. The first section presents microbial players and interactions within the coral holobiont that contribute to reef carbon flow. In the second section, we identify four ecosystem-level microbial features that directly respond to benthic species phase shifts: community composition, biomass, metabolism and viral predation. The third section discusses the significance of microbial consumption of benthic organic matter to reef trophic relationships. In the fourth section, we propose that the 'microbial phase shifts' discussed here are conducive to lower resilience, facilitating the transition to new degradation states in coral reefs.
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Affiliation(s)
- Cynthia B Silveira
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil.,Biology Department, San Diego State University, 5500 Campanille Dr, San Diego, CA 92182, USA
| | - Giselle S Cavalcanti
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil.,Biology Department, San Diego State University, 5500 Campanille Dr, San Diego, CA 92182, USA
| | - Juline M Walter
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
| | - Arthur W Silva-Lima
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
| | - Elizabeth A Dinsdale
- Biology Department, San Diego State University, 5500 Campanille Dr, San Diego, CA 92182, USA
| | - David G Bourne
- College of Science and Engineering, James Cook University and Australian Institute of Marine Science, Townsville, Queensland 4810, Australia
| | - Cristiane C Thompson
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
| | - Fabiano L Thompson
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
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14
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Characterization of N-Acyl Homoserine Lactones in Vibrio tasmaniensis LGP32 by a Biosensor-Based UHPLC-HRMS/MS Method. SENSORS 2017; 17:s17040906. [PMID: 28425948 PMCID: PMC5426830 DOI: 10.3390/s17040906] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 12/13/2022]
Abstract
Since the discovery of quorum sensing (QS) in the 1970s, many studies have demonstrated that Vibrio species coordinate activities such as biofilm formation, virulence, pathogenesis, and bioluminescence, through a large group of molecules called N-acyl homoserine lactones (AHLs). However, despite the extensive knowledge on the involved molecules and the biological processes controlled by QS in a few selected Vibrio strains, less is known about the overall diversity of AHLs produced by a broader range of environmental strains. To investigate the prevalence of QS capability of Vibrio environmental strains we analyzed 87 Vibrio spp. strains from the Banyuls Bacterial Culture Collection (WDCM911) for their ability to produce AHLs. This screening was based on three biosensors, which cover a large spectrum of AHLs, and revealed that only 9% of the screened isolates produced AHLs in the defined experimental conditions. Among these AHL-producing strains, Vibrio tasmaniensis LGP32 is a well-known pathogen of bivalves. We further analyzed the diversity of AHLs produced by this strain using a sensitive bioguided UHPLC-HRMS/MS approach (Ultra-High-Performance Liquid Chromatography followed by High-Resolution tandem Mass Spectrometry) and we identified C10-HSL, OH-C12-HSL, oxo-C12-HSL and C14:1-HSL as QS molecules. This is the first report that documents the production of AHL by Vibrio tasmaniensis LGP32.
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15
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Kopprio GA, Streitenberger ME, Okuno K, Baldini M, Biancalana F, Fricke A, Martínez A, Neogi SB, Koch BP, Yamasaki S, Lara RJ. Biogeochemical and hydrological drivers of the dynamics of Vibrio species in two Patagonian estuaries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 579:646-656. [PMID: 27871750 DOI: 10.1016/j.scitotenv.2016.11.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
The ecology of the most relevant Vibrio species for human health and their relation to water quality and biogeochemistry were studied in two estuaries in Argentinian Patagonia. Vibrio cholerae and Vibrio parahaemolyticus were reported in >29% of cases at the Río Colorado and Río Negro estuaries. Neither the pandemic serogroups of Vibrio cholerae O1, Vibrio cholerae O139 nor the cholera toxin gene were detected in this study. However, several strains of V. cholerae (not O1 or O139) are able to cause human disease or acquire pathogenic genes by horizontal transfer. Vibrio vulnificus was detected only in three instances in the microplankton fraction of the Río Negro estuary. The higher salinity in the Río Colorado estuary and in marine stations at both estuaries favours an abundance of culturable Vibrio. The extreme peaks for ammonium, heterotrophic bacteria and faecal coliforms in the Río Negro estuary supported a marked impact on sewage discharge. Generally, the more pathogenic strains of Vibrio have a faecal origin. Salinity, pH, ammonium, chlorophyll a, silicate and carbon/nitrogen ratio of suspended organic particulates were the primary factors explaining the distribution of culturable bacteria after distance-based linear models. Several effects of dissolved organic carbon on bacterial distribution are inferred. Global change is expected to increase the trophic state and the salinisation of Patagonian estuaries. Consequently, the distribution and abundance of Vibrio species is projected to increase under future changing baselines. Adaptation strategies should contribute to sustaining good water quality to buffer climate- and anthropogenic- driven impacts.
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Affiliation(s)
- Germán A Kopprio
- Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Sur, Florida 4750, B8000FWB Bahía Blanca, Argentina; Leibniz Center for Tropical Marine Ecology, Fahrenheitstr. 6, 28359 Bremen, Germany.
| | - M Eugenia Streitenberger
- Department of Biology, Biochemistry and Pharmacy, Universidad Nacional del Sur, San Juan 670, 8000 Bahía Blanca, Argentina
| | - Kentaro Okuno
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku orai-kita, Izumisano-shi, Osaka 598-8531, Japan
| | - Mónica Baldini
- Department of Biology, Biochemistry and Pharmacy, Universidad Nacional del Sur, San Juan 670, 8000 Bahía Blanca, Argentina
| | - Florencia Biancalana
- Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Sur, Florida 4750, B8000FWB Bahía Blanca, Argentina
| | - Anna Fricke
- Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Sur, Florida 4750, B8000FWB Bahía Blanca, Argentina; Leibniz Center for Tropical Marine Ecology, Fahrenheitstr. 6, 28359 Bremen, Germany
| | - Ana Martínez
- Department of Chemistry, Universidad Nacional del Sur, Av. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Sucharit B Neogi
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku orai-kita, Izumisano-shi, Osaka 598-8531, Japan
| | - Boris P Koch
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Marine Chemistry, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Shinji Yamasaki
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku orai-kita, Izumisano-shi, Osaka 598-8531, Japan
| | - Rubén J Lara
- Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Sur, Florida 4750, B8000FWB Bahía Blanca, Argentina
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16
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Amin AKMR, Feng G, Al-Saari N, Meirelles PM, Yamazaki Y, Mino S, Thompson FL, Sawabe T, Sawabe T. The First Temporal and Spatial Assessment of Vibrio Diversity of the Surrounding Seawater of Coral Reefs in Ishigaki, Japan. Front Microbiol 2016; 7:1185. [PMID: 27551278 PMCID: PMC4976104 DOI: 10.3389/fmicb.2016.01185] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/18/2016] [Indexed: 01/09/2023] Open
Abstract
Coral reefs perform a major role in regulating marine biodiversity and serve as hotspot for highly dynamic and diverse microbiomes as holobionts. Corals around Ishigaki, however, are at risk due to tremendous stressors including elevation of seawater temperature, eutrophication and so on. However, no information is currently available on how Vibrio diversity fluctuates spatially and temporally due to environmental determinants in Ishigaki coral reef ecosystems. The aim of this study is to elucidate spatiotemporal Vibrio diversity dynamic at both community and population levels and to assess the environmental drivers correlated to Vibrio abundance and diversity. The Vibrio community identified based on pyrH gene phylogeny of 685 isolates from seawater directly connecting to Ishigaki coral holobionts consisted of 22 known and 12 potential novel Vibrionaceae species. The most prominent species were V. hyugaensis, V. owensii and V. harveyi followed by V. maritimus/V. variabillis, V. campbellii, V. coralliilyticus, and Photobacterium rosenbergii. The Vibrio community fluctuations, assessed by PCoA with UniFrac distance and clustering with Euclidiean distance were varied less not only by year but also by site. Interestingly, significant positive correlation was observed between rising seawater temperature and the abundance of V. campbellii (r = 0.62; P < 0.05) whereas the opposite was observed for V. owensii (r = -0.58; P < 0.05) and the C6 group of V. hyugaensis (r = -0.62; P < 0.05). AdaptML-based microhabitat differentiation revealed that V. harveyi, V. campbellii, P. rosenbergii, and V. coralliilyticus populations were less-ecologically distinctive whereas V. astriarenae and V. ishigakensis were ecologically diverse. This knowledge could be important clue for the future actions of coral conservation.
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Affiliation(s)
- A K M R Amin
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate Japan
| | - Gao Feng
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate Japan
| | - Nurhidayu Al-Saari
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate Japan
| | - Pedro M Meirelles
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro Brazil
| | - Yohei Yamazaki
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate Japan
| | - Fabiano L Thompson
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro Brazil
| | - Toko Sawabe
- Department of Nutrition, Hakodate Junior College, Hakodate Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate Japan
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17
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Moreira APB, Meirelles PM, Santos EDO, Amado-Filho GM, Francini-Filho RB, Thompson CC, Thompson FL. Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St. Peter and St. Paul Archipelago, Mid-Atlantic Ridge, Brazil. Front Microbiol 2015; 6:1038. [PMID: 26483769 PMCID: PMC4591530 DOI: 10.3389/fmicb.2015.01038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/11/2015] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to investigate the planktonic and the holobiont Madracis decactis (Scleractinia) microbial diversity along a turbulence-driven upwelling event, in the world's most isolated tropical island, St Peter and St Paul Archipelago (SPSPA, Brazil). Twenty one metagenomes were obtained for seawater (N = 12), healthy and bleached holobionts (N = 9) before, during and after the episode of high seawater turbulence and upwelling. Microbial assemblages differed between low turbulence-low nutrient (LLR) and high-turbulence-high nutrient (HHR) regimes in seawater. During LLR there was a balance between autotrophy and heterotrophy in the bacterioplankton and the ratio cyanobacteria:heterotrophs ~1 (C:H). Prochlorales, unclassified Alphaproteobacteria and Euryarchaeota were the dominant bacteria and archaea, respectively. Basic metabolisms and cyanobacterial phages characterized the LLR. During HHR C:H < < 0.05 and Gammaproteobacteria approximated 50% of the most abundant organisms in seawater. Alteromonadales, Oceanospirillales, and Thaumarchaeota were the dominant bacteria and archaea. Prevailing metabolisms were related to membrane transport, virulence, disease, and defense. Phages targeting heterotrophs and virulence factor genes characterized HHR. Shifts were also observed in coral microbiomes, according to both annotation–indepent and -dependent methods. HHR bleached corals metagenomes were the most dissimilar and could be distinguished by their di- and tetranucleotides frequencies, Iron Acquision metabolism and virulence genes, such as V. cholerae-related virulence factors. The healthy coral holobiont was shown to be less sensitive to transient seawater-related perturbations than the diseased animals. A conceptual model for the turbulence-induced shifts is put forward.
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Affiliation(s)
- Ana Paula B Moreira
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
| | - Pedro M Meirelles
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
| | - Eidy de O Santos
- Fundação Centro Universitário Estadual da Zona Oeste (Uezo) Rio de Janeiro, Brazil
| | - Gilberto M Amado-Filho
- Diretoria de Pesquisa Científica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro Rio de Janeiro, Brazil
| | | | - Cristiane C Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
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