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Lee CY, Lee SY. Contribution of Aerobic Cellulolytic Gut Bacteria to Cellulose Digestion in Fifteen Coastal Grapsoid Crabs Underpins Potential for Mineralization of Mangrove Production. Curr Microbiol 2024; 81:224. [PMID: 38874676 PMCID: PMC11178586 DOI: 10.1007/s00284-024-03718-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/26/2024] [Indexed: 06/15/2024]
Abstract
Grapsoid crabs (Decapoda: Grapsoidea) inhabiting along the land-sea transition provided various amounts and quality of vascular plant carbon (e.g., fresh mangrove leaf, leaf litter, and mangrove-derived organic carbon) and perform differing levels of herbivory. Other than endogenous cellulase, symbiotic cellulolytic bacteria could also contribute to the crabs' vascular plant carbon assimilation and mineralization. In this study, we isolated culturable cellulolytic bacteria from three gut regions (i.e., stomach, midgut, and hindgut) of 15 species of grapsoid crabs that inhabit in various coastal habitats (i.e., land margin, mangrove forest, tidal flat, and subtidal area). Bacillus, which was isolated from 11 out of the 15 grapsoid crabs, was the most common genus of culturable prominently cellulolytic bacteria among the target species. Seventy to ninety nine percent of culturable cellulolytic bacteria were removed, and the endoglucanase activity of five species was significantly reduced by 14.4-27.7% after antibiotic treatment. These results suggest that cellulolytic bacteria play a role in assisting mangrove carbon utilization in coastal grapsoid crabs, especially those inhabiting mangrove, mudflat, and subtidal areas. The significantly higher abundance of cellulolytic bacteria and the generally higher hydrolytic capacity of the bacteria in mangrove crab species suggest that they receive more contribution from symbionts for mangrove carbon utilization, while semi-terrestrial crabs seem to depend little on symbiotic cellulase due to the lower abundances.
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Affiliation(s)
- Cheuk Yan Lee
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shing Yip Lee
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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2
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Jia C, Wang Y, Zheng B, Wang Y, He L, Xu Q, Gao F. Comparative Analysis of Gut Bacterial Community Composition in Two Tropical Economic Sea Cucumbers under Different Seasons of Artificial Environment. Int J Mol Sci 2024; 25:4573. [PMID: 38674158 PMCID: PMC11049810 DOI: 10.3390/ijms25084573] [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: 03/14/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
With the continuous rise of the sea cucumber aquaculture industry in China, the tropical sea cucumber aquaculture industry is also improving. However, research on the gut microorganisms of tropical sea cucumbers in captivity is scarce. In this study, high-throughput sequencing methods were used to analyze the gut microbial composition of Stichopus monotuberculatus and Holothuria scabra in the dry season and wet season of artificial environments. The results showed that 66 phyla were obtained in all samples, of which 59 phyla were obtained in the dry season, and 45 phyla were obtained in the wet season. The Tax4Fun analysis showed that certain gut bacterial communities affect the daily metabolism of two sea cucumber species and are involved in maintaining gut microecological balance in the gut of two sea cucumber species. In addition, compared with differences between species, PCoA and UPGMA clustering analysis showed the gut prokaryotes of the same sea cucumber species varied more in different seasons, indicating that the influence of environment was higher than the feeding choices of sea cucumbers under relatively closed conditions. These results revealed the gut bacterial community composition of S. monotuberculatus and H. scabra and the differences in gut bacterial structure between two sea cucumber species in different seasons were compared, which would provide the foundation for tropical sea cucumber aquaculture in the future.
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Affiliation(s)
- Chenghao Jia
- School of Ecology and Environment, Hainan University, Haikou 570228, China;
| | - Yuanhang Wang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (Y.W.); (B.Z.); (Y.W.); (L.H.); (Q.X.)
| | - Bojun Zheng
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (Y.W.); (B.Z.); (Y.W.); (L.H.); (Q.X.)
| | - Yanan Wang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (Y.W.); (B.Z.); (Y.W.); (L.H.); (Q.X.)
| | - Linwen He
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (Y.W.); (B.Z.); (Y.W.); (L.H.); (Q.X.)
| | - Qiang Xu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (Y.W.); (B.Z.); (Y.W.); (L.H.); (Q.X.)
| | - Fei Gao
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (Y.W.); (B.Z.); (Y.W.); (L.H.); (Q.X.)
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Sanches-Fernandes GMM, Sá-Correia I, Costa R. Vibriosis Outbreaks in Aquaculture: Addressing Environmental and Public Health Concerns and Preventive Therapies Using Gilthead Seabream Farming as a Model System. Front Microbiol 2022; 13:904815. [PMID: 35898915 PMCID: PMC9309886 DOI: 10.3389/fmicb.2022.904815] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022] Open
Abstract
Bacterial and viral diseases in aquaculture result in severe production and economic losses. Among pathogenic bacteria, species belonging to the Vibrio genus are one of the most common and widespread disease-causing agents. Vibrio infections play a leading role in constraining the sustainable growth of the aquaculture sector worldwide and, consequently, are the target of manifold disease prevention strategies. During the early, larval stages of development, Vibrio species are a common cause of high mortality rates in reared fish and shellfish, circumstances under which the host organisms might be highly susceptible to disease preventive or treatment strategies such as vaccines and antibiotics use, respectively. Regardless of host developmental stage, Vibrio infections may occur suddenly and can lead to the loss of the entire population reared in a given aquaculture system. Furthermore, the frequency of Vibrio-associated diseases in humans is increasing globally and has been linked to anthropic activities, in particular human-driven climate change and intensive livestock production. In this context, here we cover the current knowledge of Vibrio infections in fish aquaculture, with a focus on the model species gilthead seabream (Sparus aurata), a highly valuable reared fish in the Mediterranean climatic zone. Molecular methods currently used for fast detection and identification of Vibrio pathogens and their antibiotic resistance profiles are addressed. Targeted therapeutic approaches are critically examined. They include vaccination, phage therapy and probiotics supplementation, which bear promise in supressing vibriosis in land-based fish rearing and in mitigating possible threats to human health and the environment. This literature review suggests that antibiotic resistance is increasing among Vibrio species, with the use of probiotics constituting a promising, sustainable approach to prevent Vibrio infections in aquaculture.
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Affiliation(s)
- Gracinda M. M. Sanches-Fernandes
- Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
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Stratev D, Stoyanchev T, Bangieva D. Occurrence of Vibrio parahaemolyticus and Staphylococcus aureus in seafood. Ital J Food Saf 2021; 10:10027. [PMID: 35018291 PMCID: PMC8672316 DOI: 10.4081/ijfs.2021.10027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022] Open
Abstract
The objective of this study was to establish the occurrence of Vibrio parahaemolyticus and Staphylococcus aureus in several species of sea fish and mussels (Mytilus galloprovincialis). The study included a total of 33 samples of frozen sea fish and 64 samples of fresh wild and farmed mussels purchased from the stores. V. parahaemolyticus was isolated and confirmed via PCR in 2 (6%) fish samples (Atlantic cod and Alaska pollock) and 20 (31%) mussel samples. S. aureus was also isolated and confirmed via PCR in 2 (6%) fish samples (Argentine hake and Atlantic cod). Significant differences were found in the total bacterial contamination between wild mussels (6.54 log cfu/g) and farmed mussels (6.69 log cfu/g). Total V. parahaemolyticus count did not show significant differences either between wild (4.45 log cfu/g) and farmed mussels (4.99 log cfu/g). In wild mussels the S. aureus count was found to be 4.50 log cfu/g, while in farmed mussels it was 3.14 log cfu/g. The occurrence of V. parahaemolyticus and S. aureus in fish and mussels presents a risk to the consumer's health.
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Affiliation(s)
- Deyan Stratev
- Department of Food Quality and Safety and Veterinary Legislation, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Todor Stoyanchev
- Department of Food Quality and Safety and Veterinary Legislation, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Desislava Bangieva
- Department of Food Quality and Safety and Veterinary Legislation, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
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Heyse J, Props R, Kongnuan P, De Schryver P, Rombaut G, Defoirdt T, Boon N. Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products. Environ Microbiol 2020; 23:281-298. [PMID: 33169932 DOI: 10.1111/1462-2920.15310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/21/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023]
Abstract
The development of effective management strategies to reduce the occurrence of diseases in aquaculture is hampered by the limited knowledge on the microbial ecology of these systems. In this study, the dynamics and dominant community assembly processes in the rearing water of Litopenaeus vannamei larviculture tanks were determined. Additionally, the contribution of peripheral microbiomes, such as those of live and dry feeds, to the rearing water microbiome were quantified. The community assembly in the hatchery rearing water over time was dominated by stochasticity, which explains the observed heterogeneity between replicate cultivations. The community undergoes two shifts that match with the dynamics of the algal abundances in the rearing water. Source tracking analysis revealed that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds. Our findings provide fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of these peripheral microbiomes in maintaining health-promoting rearing water microbiomes.
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Affiliation(s)
- Jasmine Heyse
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | | | | | - Geert Rombaut
- INVE Technologies NV, Hoogveld 93, Dendermonde, 9200, Belgium
| | - Tom Defoirdt
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
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Arab S, Nalbone L, Giarratana F, Berbar A. Occurrence of Vibrio spp. along the Algerian Mediterranean coast in wild and farmed Sparus aurata and Dicentrarchus labrax. Vet World 2020; 13:1199-1208. [PMID: 32801574 PMCID: PMC7396341 DOI: 10.14202/vetworld.2020.1199-1208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023] Open
Abstract
Background and Aim: Vibrio bacteria are autochthonous inhabitants of aquatic and marine environments. Certain strains are responsible for important seafood-borne outbreaks in developed nations. The aim of this study was to investigate the occurrence of Vibrio spp. along the Algerian Mediterranean coast in several samples of two prominent wild and farmed marine fishes, Sparus aurata and Dicentrarchus labrax. Materials and Methods: A total of 350 S. aurata (n=280 farmed and n=70 wild) and 340 D. labrax (n=250 farmed and n=90 wild) were sampled among three different locations along the Algerian Mediterranean coastal area. The samples were processed for Vibrio research according to the ISO methods. Isolated colonies were identified utilizing biochemical tests and consecutively confirmed with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry, combined with polymerase chain reaction (PCR) analysis when appropriate, or confirmed with PCR analysis alone. Results: A total of 42 Vibrio spp. were detected only among the farmed fishes. Taking into account, all 690 fishes sampled, the incidence of Vibrio spp. was 6.08% (with peaks up to 7.92%) among the total number of farmed fishes. Overall, 25 strains were isolated from S. aurata and 17 strains were isolated from D. labrax. The isolated strains belonged to four different species and were represented as follows: Vibrio alginolyticus (n=20), Vibrio cholerae (n=15), Vibrio fluvialis (n=5), and Vibrio hollisae (n=2). The incidence of Vibrio was higher in places characterized by greater levels of anthropogenic contamination of seawater. Conclusion: Considering the growing production and consequent rising consumption of farmed fish in Algeria, the reported incidence of Vibrio and the presence of potentially pathogenic strains of Vibrio such as V. cholerae cause particular concern for food safety matters. Even if innovative and natural techniques are desired in aquaculture, proper hygiene and manufacturing practices are essential for the correct management of Vibrio infection risk in farmed fishes at both industrial and domestic levels.
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Affiliation(s)
- Sonia Arab
- Institut des Sciences Vétérinaires, Laboratoire de Recherche de Biotechnologies liées à la Reproduction Animale, University of Saad Dahlab - Blida, route de Soumâa BP 270, Blida, 09000, Algeria
| | - Luca Nalbone
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Filippo Giarratana
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Ali Berbar
- Institut des Sciences Vétérinaires, Laboratoire de Recherche de Biotechnologies liées à la Reproduction Animale, University of Saad Dahlab - Blida, route de Soumâa BP 270, Blida, 09000, Algeria
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Machado H, Cardoso J, Giubergia S, Rapacki K, Gram L. FurIOS: A Web-Based Tool for Identification of Vibrionaceae Species Using the fur Gene. Front Microbiol 2017; 8:414. [PMID: 28348552 PMCID: PMC5346536 DOI: 10.3389/fmicb.2017.00414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Gene based methods for identification of species from the Vibrionaceae family have been developed during the last decades to address the limitations of the commonly used 16S rRNA gene phylogeny. Recently, we found that the ferric-uptake regulator gene (fur) can be used as a single identification marker providing species discrimination, consistent with multi-locus sequencing analyses and whole genome phylogenies. To allow for broader and easy use of this marker, we have developed an online prediction service that allows the identification of Vibrionaceae species based on their fur-sequence. The input is a DNA sequence that can be uploaded on the web service; the output is a table containing the strain identifier, e-value, and percentage of identity for each of the matches with rows colored in green for hits with high probability of being the same species. The service is available on the web at: http://www.cbs.dtu.dk/services/furIOS-1.0/. The fur-sequences can be derived either from genome sequences or from PCR-amplification of the genomic region encoding the fur gene. We have used 191 strains identified as Vibrionaceae based on 16S rRNA gene sequence to test the PCR method and the web service on a large dataset. We were able to classify 171 of 191 strains at the species level and 20 strains remained unclassified. Furthermore, the fur phylogenetics and subsequent in silico DNA-DNA hybridization demonstrated that two strains (ATCC 33789 and ZS-139) previously identified as Vibrio splendidus are more closely related to V. tasmaniensis and V. cyclitrophicus, respectively. FurIOS is an easy-to-use online service that allows the identification of bacteria from the Vibrionaceae family at the species level using the fur gene as a single marker. Its simplistic design and straightforward pipeline makes it suitable for any research environment, from academia to industry.
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Affiliation(s)
- Henrique Machado
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark
| | - João Cardoso
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark
| | - Sonia Giubergia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kongens LyngbyDenmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark
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Rahmani R, Zarrini G, Aein F, Hosseingholi EZ. Identification of extremely halophilic archaea associated with adult Artemia urmiana. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716030127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Zhong ZP, Liu Y, Liu HC, Wang F, Zhou YG, Liu ZP. Vibrio salilacus sp. nov., a new member of the Anguillarum clade with six alleles of the 16S rRNA gene from a saline lake. Int J Syst Evol Microbiol 2015; 65:2653-2660. [DOI: 10.1099/ijs.0.000316] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A Gram-stain-negative, catalase- and oxidase-positive, facultatively aerobic bacterium, strain DSG-S6T, was isolated from Dasugan Lake (salinity 3.1 %, w/w), China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S6T were non-spore-forming, slightly bent rods, and motile by means of a single polar flagellum. Growth occurred in the presence of 0–7.0 % (w/v) NaCl (optimum, 2.0 %), at 4–35 °C (optimum, 30 °C) and at pH 6.0–10.5 (optimum, pH 8.0–8.5). C16 : 0, C18 : 1ω7c and C16 : 1ω7c and/or C16 : 1ω6c were the major fatty acids. Six alleles of the 16S rRNA gene sharing 98.9–99.9 % similarity were detected in strain DSG-S6T, which showed highest 16S rRNA gene sequence similarity to Vibrio aestuarianus ATCC 35048T (97.7 %), then to Vibrio pacinii LMG 19999T (97.6 %) and Vibrio metschnikovii CIP 69.14T (96.8 %). Multilocus sequence analysis of four housekeeping genes and 16S rRNA genes clearly clustered it as a member of the Anguillarum clade. Mean DNA–DNA relatedness between strain DSG-S6T and V. aestuarianus NBRC 15629T, V. pacinii CGMCC 1.12557T and V. metschnikovii JCM 21189T was 20.6 ± 2.3, 38.1 ± 3.5 and 24.2 ± 2.8 %, respectively. The DNA G+C content was 46.8 mol% (T
m). Based on the data, it is concluded that strain DSG-S6T represents a novel species of the genus Vibrio, for which the name Vibrio salilacus sp. nov. is proposed. The type strain is DSG-S6T ( = CGMCC 1.12427T = JCM 19265T).
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Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100089, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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The fur gene as a new phylogenetic marker for Vibrionaceae species identification. Appl Environ Microbiol 2015; 81:2745-52. [PMID: 25662978 DOI: 10.1128/aem.00058-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family Vibrionaceae, where other molecular techniques allow better interspecies resolution. Although multilocus sequence analysis (MLSA) has been used successfully in the identification of Vibrio species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an in silico approach based on genomes from 103 Vibrionaceae strains, we demonstrate here the high resolution of the fur gene in the identification of Vibrionaceae species and its usefulness as a phylogenetic marker. The fur gene showed within-species similarity higher than 95%, and the relationships inferred from its use were in agreement with those observed for 16S rRNA analysis and MLSA. Furthermore, we developed a fur PCR sequencing-based method that allowed identification of Vibrio species. The discovery of the phylogenetic power of the fur gene and the development of a PCR method that can be used in amplification and sequencing of the gene are of general interest whether for use alone or together with the previously suggested loci in an MLSA.
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11
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Romalde JL, Dieguez AL, Lasa A, Balboa S. New Vibrio species associated to molluscan microbiota: a review. Front Microbiol 2014; 4:413. [PMID: 24427157 PMCID: PMC3877837 DOI: 10.3389/fmicb.2013.00413] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 12/16/2013] [Indexed: 01/22/2023] Open
Abstract
The genus Vibrio consists of more than 100 species grouped in 14 clades that are widely distributed in aquatic environments such as estuarine, coastal waters, and sediments. A large number of species of this genus are associated with marine organisms like fish, molluscs and crustaceans, in commensal or pathogenic relations. In the last decade, more than 50 new species have been described in the genus Vibrio, due to the introduction of new molecular techniques in bacterial taxonomy, such as multilocus sequence analysis or fluorescent amplified fragment length polymorphism. On the other hand, the increasing number of environmental studies has contributed to improve the knowledge about the family Vibrionaceae and its phylogeny. Vibrio crassostreae, V. breoganii, V. celticus are some of the new Vibrio species described as forming part of the molluscan microbiota. Some of them have been associated with mortalities of different molluscan species, seriously affecting their culture and causing high losses in hatcheries as well as in natural beds. For other species, ecological importance has been demonstrated being highly abundant in different marine habitats and geographical regions. The present work provides an updated overview of the recently characterized Vibrio species isolated from molluscs. In addition, their pathogenic potential and/or environmental importance is discussed.
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Affiliation(s)
- Jesús L. Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Santiago de CompostelaSpain
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12
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Riddle MR, Baxter BK, Avery BJ. Molecular identification of microorganisms associated with the brine shrimp Artemia franciscana. AQUATIC BIOSYSTEMS 2013; 9:7. [PMID: 23497541 PMCID: PMC3599907 DOI: 10.1186/2046-9063-9-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 02/21/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Prior research on the microorganisms associated with the brine shrimp, Artemia franciscana, has mainly been limited to culture-based identification techniques or feeding studies for aquaculture. Our objective was to identify bacteria and archaea associated with Artemia adults and encysted embryos to understand the role of microbes in the Artemia life cycle and, therefore, their importance in a hypersaline food chain. RESULTS We used small subunit (SSU) 16S ribosomal RNA gene sequencing to identify bacteria and archaea associated with adults and encysted Artemia embryos from one of their natural environments - Great Salt Lake (GSL), Utah, USA. We found that bacterial sequences most closely related to the genera Halomonas and Vibrio were commonly extracted from GSL adult Artemia, while bacterial sequences most similar to the genera Halomonas, Psychroflexus and Alkalilimnicola dominate in GSL water. Encysted embryos (cysts) yielded bacterial sequences from the genera Idiomarina and Salinivibrio, which were absent from adults and water. Common archaeal sequences in adults were most closely related to the genera Haloterrigena and Haloarcula, while all of the archaeal sequences from GSL water were most similar to the genus Halogeometricum. Cyst derived archaeal sequences were most closely related to the genera Halorubrum and Haloarcula. CONCLUSIONS In addition to identifying microbial rRNA sequences that are specific to different stages of the Artemia life cycle, we observed striking differences in the sequences associated with the adult Artemia population in samples collected from GSL at different times and locations. While our study was limited in scope and the sample was small, our findings provide a foundation for future research into how the bacteria and archaea associated with Artemia influence the Artemia life cycle, and GSL food web.
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Affiliation(s)
- Misty R Riddle
- Department of Biology and Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, UT 84105, USA
- Present address: Department of Molecular, Cellular and Developmental Biology, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Bonnie K Baxter
- Department of Biology and Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, UT 84105, USA
| | - Brian J Avery
- Department of Biology and Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, UT 84105, USA
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Moreira APB, Pereira N, Thompson FL. Usefulness of a real-time PCR platform for G+C content and DNA–DNA hybridization estimations in vibrios. Int J Syst Evol Microbiol 2011; 61:2379-2383. [DOI: 10.1099/ijs.0.023606-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to evaluate the utility of a real-time PCR platform to estimate the DNA G+C content (mol%) and DNA–DNA hybridization (DDH) values in the genus Vibrio. In total, nine vibrio strains were used to determine the relationship between genomic DNA G+C content and T
m (°C). The T
m and HPLC datasets fit a linear regression curve with a significant correlation coefficient, corroborating that this methodology has a high correlation with the standard methodology based on HPLC (R2 = 0.94). Analysis of 31 pairs of vibrios provided a wide range of ΔT
m values, varying between 0.72 and 12.5 °C. Pairs corresponding to strains of the same species or strains from sister species showed the lowest ΔT
m values. For instance, the ΔT
m of the sister species Vibrio harveyi LMG 4044T and Vibrio campbellii LMG 11216T was 5.2 °C, whereas the ΔT
m of Vibrio coralliilyticus LMG 20984T and Vibrio neptunius LMG 20536T was 8.75 °C. The mean ΔT
m values corresponding to pairs of strains with DDH values lower than 60 % or higher than 80 % were, respectively, 8.29 and 2.21 °C (significant difference, P<0.01). The high correlation between DDH values obtained in previous studies and the ΔT
m values (R2 = 0.7344) indicates that the fluorimetric methodology is a reliable alternative for the estimation of both DNA G+C content and ΔT
m in vibrios. We suggest that strains of the same Vibrio species will have less than 4 °C ΔT
m. The use of a real-time PCR platform represents a valuable alternative for the development of the taxonomy of vibrios.
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Affiliation(s)
- Ana Paula B. Moreira
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Brazil
| | - Nei Pereira
- Laboratory of Bioprocesses, School of Chemistry, Federal University of Rio de Janeiro (UFRJ), Brazil
| | - Fabiano L. Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Brazil
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Tkavc R, Ausec L, Oren A, Gunde-Cimerman N. Bacteria associated with Artemia spp. along the salinity gradient of the solar salterns at Eilat (Israel). FEMS Microbiol Ecol 2011; 77:310-21. [PMID: 21492196 DOI: 10.1111/j.1574-6941.2011.01112.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The crustacean genus Artemia naturally inhabits various saline and hypersaline environments and is the most frequently laboratory-hatched animal for live feed in mari- and aquaculture. Because of its high economic importance, Artemia-bacteria interactions were so far studied mostly in laboratory strains. In this study, we focused our attention on the Artemia-associated microbiota in its natural environment in the solar salterns of Eilat, Israel. We applied a culture-independent method (clone libraries) to investigate the bacterial community structure associated with Artemia in five evaporation ponds with salinities from slightly above seawater (5%) to the point of saturation (32%), in two different developmental stages: in nauplii and in the intestine of adult animals. Bacteria found in naupliar and adult stages were classified within the Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Cyanobacteria. The halophilic proteobacterial genera Halomonas spp. and Salinivibrio spp. dominated the Artemia microbiota in both stages in all ponds. We also analysed a clone library of entire adult animals, revealing a novel bacterial phylogenetic lineage. This is the first molecular study of bacteria associated with two developmental stages of Artemia along a salinity gradient.
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Affiliation(s)
- Rok Tkavc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Dikow RB. Systematic relationships within the Vibrionaceae (Bacteria: Gammaproteobacteria): steps toward a phylogenetic taxonomy. Cladistics 2011; 27:9-28. [DOI: 10.1111/j.1096-0031.2010.00312.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Hoffmann M, Brown EW, Feng PCH, Keys CE, Fischer M, Monday SR. PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species. BMC Microbiol 2010; 10:90. [PMID: 20331883 PMCID: PMC2856557 DOI: 10.1186/1471-2180-10-90] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 03/23/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Vibrio is a diverse group of Gram-negative bacteria comprised of 74 species. Furthermore, the genus has and is expected to continue expanding with the addition of several new species annually. Consequently, it is of paramount importance to have a method which is able to reliably and efficiently differentiate the numerous Vibrio species. RESULTS In this study, a novel and rapid polymerase chain reaction (PCR)-based intergenic spacer (IGS)-typing system for vibrios was developed that is based on the well-known IGS regions located between the 16S and 23S rRNA genes on the bacterial chromosome. The system was optimized to resolve heteroduplex formation as well as to take advantage of capillary gel electrophoresis technology such that reproducible analyses could be achieved in a rapid manner. System validation was achieved through testing of 69 archetypal Vibrio strains, representing 48 Vibrio species, from which an 'IGS-type' profile database was generated. These data, presented here in several cluster analyses, demonstrated successful differentiation of the 69 type strains showing that this PCR-based fingerprinting method easily discriminates bacterial strains at the species level among Vibrio. Furthermore, testing 36 strains each of V. parahaemolyticus and V. vulnificus, important food borne pathogens, isolated from a variety of geographical locations with the IGS-typing method demonstrated distinct IGS-typing patterns indicative of subspecies divergence in both populations making this technique equally useful for intraspecies differentiation, as well. CONCLUSION This rapid, reliable and efficient IGS-typing system, especially in combination with 16S rRNA gene sequencing, has the capacity to not only discern and identify vibrios at the species level but, in some cases, at the sub-species level, as well. This procedure is particularly well-suited for preliminary species identification and, lends itself nicely to epidemiological investigations providing information more quickly than other time-honoured methods traditionally used in these types of analyses.
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Affiliation(s)
- Maria Hoffmann
- Division of Microbiology, Office of Regulatory Science Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD 20740, USA.
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Beaz Hidalgo R, Cleenwerck I, Balboa S, De Wachter M, Thompson FL, Swings J, De Vos P, Romalde JL. Diversity of Vibrios associated with reared clams in Galicia (NW Spain). Syst Appl Microbiol 2008; 31:215-22. [PMID: 18482814 DOI: 10.1016/j.syapm.2008.04.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The aim of the present study was to characterize and identify vibrios isolated from cultured clams in Galicia (NW Spain). A total of 759 isolates were obtained, phenotypically characterized, grouped and assigned to the genus Vibrio. Subsequently, the genomic diversity of 145 representative strains was analyzed by means of amplified fragment length polymorphism (AFLP), which revealed a high genetic diversity amongst these isolates. Only 57 out of 145 strains could be identified to the species level, and they were distributed in 13 AFLP clusters. V. cyclitrophicus, V. splendidus and V. alginolyticus were the most abundantly represented species. Eighty-eight isolates remained unidentified, 59 were distributed over 16 clusters, while 29 were unclustered. Sequencing of the 16S rRNA and two house-keeping genes (rpoA and recA) from representative strains belonging to eight unidentified clusters with the highest number of isolates confirmed their assignation to the Vibrionaceae family, and some of these probably represent new species within the genus. The present study confirmed that the phenotypic characterization of vibrios is not sufficient to identify them at the species level. A wide diversity of vibrios was found in cultured clams from all four geographic locations analyzed. In total, more than 12 Vibrio species and at least three potential new species in this genus were identified.
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Affiliation(s)
- Roxana Beaz Hidalgo
- Departamento de Microbiología y Parasitología, Facultad de Biología e Instituto de Acuicultura, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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Kita-Tsukamoto K, Wada M, Yao K, Kamiya A, Yoshizawa S, Uchiyama N, Kogure K. Rapid identification of marine bioluminescent bacteria by amplified 16S ribosomal RNA gene restriction analysis. FEMS Microbiol Lett 2006; 256:298-303. [PMID: 16499620 DOI: 10.1111/j.1574-6968.2006.00129.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To rapidly identify natural isolates of marine bioluminescent bacteria, we developed amplified ribosomal DNA restriction analysis (ARDRA) methods. ARDRA, which is based on the restriction patterns of 16S rRNA gene digested with five enzymes (EcoRI, DdeI, HhaI, HinfI, RsaI), clearly distinguished the 14 species of marine bioluminescent bacteria currently known, which belong to the genera Vibrio, Photobacterium, and Shewanella. When we applied ARDRA to 129 natural isolates from two cruises in Sagami Bay, Japan, 127 were grouped into six ARDRA types with distinctive restriction patterns; these isolates represented the bioluminescent species, P. angustum, P. leiognathi, P. phosphoreum, S. woodyi, V. fischeri, and V. harveyi. The other two isolates showing unexpected ARDRA patterns turned out to have 16S rRNA gene sequences similar to P. leiognathi and P. phosphoreum. Nevertheless, ARDRA provides a simple and fairly robust means for rapid identification of the natural isolates of marine bioluminescent bacteria, and is therefore useful in studying their diversity.
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Austin B, Austin D, Sutherland R, Thompson F, Swings J. Pathogenicity of vibrios to rainbow trout (Oncorhynchus mykiss, Walbaum) and Artemia nauplii. Environ Microbiol 2005; 7:1488-95. [PMID: 16104871 DOI: 10.1111/j.1462-2920.2005.00847.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The taxonomy of marine vibrios has changed rapidly over the last two decades, and a wealth of new species have been identified. Many Vibrio species are pathogenic to fish and crustaceans; however, little is known about the virulence of many of the novel species. The purpose of this study was to determine the ability of various recent isolates of vibrios to cause disease in rainbow trout (Oncorhynchus mykiss, Walbaum) and crustacea, i.e. Artemia nauplii. Of 56 isolates, representing 26 species of Enterovibrio, Photobacterium and Vibrio, obtained from a diversity of healthy and diseased aquatic animal hosts and water samples from many geographical locations, Vibrio brasiliensis, V. coralliilyticus, V. ezurae, V. fortis, V. kanaloaei, V. neptunius, V. rotiferianus and V. tubiashii were pathogenic to rainbow trout and Artemia nauplii with mortalities of up to 100%. The extracellular products of these pathogenic isolates were harmful to the animal models. In contrast, cultures of Enterovibrio norvegicus, E. coralii, Photobacterium rosenbergii, Vibrio campbellii, V. chagasii, V. cyclitrophicus, V. gallicus, V. gigasii, V. hepatarius, V. hispanicus, V. lentus, V. nereis, V. pacini, V. pomeroyi, V. shilonii, V. superstes, V. tasmaniensis and V. xuii demonstrated either non- or low virulence in the animal models.
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Affiliation(s)
- Brian Austin
- School of Life Sciences, John Muir Building, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS, Scotland, UK.
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Affiliation(s)
- X-H Zhang
- Department of Marine Biology, Ocean University of China, Qingdao, China
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Abstract
Vibrios are ubiquitous and abundant in the aquatic environment. A high abundance of vibrios is also detected in tissues and/or organs of various marine algae and animals, e.g., abalones, bivalves, corals, fish, shrimp, sponges, squid, and zooplankton. Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing. The 74 species of this group are distributed among four different families, i.e., Enterovibrionaceae, Photobacteriaceae, Salinivibrionaceae, and Vibrionaceae. Two new genera, i.e., Enterovibrio norvegicus and Grimontia hollisae, and 20 novel species, i.e., Enterovibrio coralii, Photobacterium eurosenbergii, V. brasiliensis, V. chagasii, V. coralliillyticus, V. crassostreae, V. fortis, V. gallicus, V. hepatarius, V. hispanicus, V. kanaloaei, V. neonatus, V. neptunius, V. pomeroyi, V. pacinii, V. rotiferianus, V. superstes, V. tasmaniensis, V. ezurae, and V. xuii, have been described in the last few years. Comparative genome analyses have already revealed a variety of genomic events, including mutations, chromosomal rearrangements, loss of genes by decay or deletion, and gene acquisitions through duplication or horizontal transfer (e.g., in the acquisition of bacteriophages, pathogenicity islands, and super-integrons), that are probably important driving forces in the evolution and speciation of vibrios. Whole-genome sequencing and comparative genomics through the application of, e.g., microarrays will facilitate the investigation of the gene repertoire at the species level. Based on such new genomic information, the taxonomy and the species concept for vibrios will be reviewed in the next years.
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Affiliation(s)
- Fabiano L Thompson
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium.
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