The diversity of microbial communities associated with oysters within a commercial mariculture system wasexamined using molecular analysis of 16S rRNA Illumina sequencing. The aim of the study is to identify microbialdiversity using molecular-based techniques, and compare the results obtained using three sampling points. Results showed,the microbial diversity associated with farmed oysters was dominated by Vibrio spp., Photobacterium spp., andPseudoalteromons spp., while Psychrilyobacter spp., Prolixibacter spp., Cytophaga spp., Planococcus spp., andExiguobacterium spp. were minor in abundance. These findings provide valuable information on the microbial community,demonstrating the microbial diversity in oysters and its major abundant species.
___
Anderson, M.J., Connell, S.D., Gillanders, B.M., Diebel, C.E., Blom, W.M., Saunders, J.E., & Landers, T.J. (2005). Relationships between taxonomic resolution and spatial scales of multivariate variation. Journal of Animal Ecology, 74, 636-646. http://dx.doi.org/10.1111/j.1365- 2656.2005.00959.x
Austin, B. (2006). The bacterial microflora of fish, revised. The Scientific World Journal, 6, 931- 945. http://dx.doi.org/10.1100/tsw.2002.137
Austin, B., & Zhang, X.H. (2006). Vibrio harveyi: a significant pathogen of marine vertebrates and invertebrates. Letters in Applied Microbiology, 43, 119-124. http://dx.doi.org/10.1111/j.1472-765X.2006.01989.x
Cao, R., Xue, C.H., Liu, Q., & Xue, Y. (2009). Microbiological, Chemical, and Sensory Assessment of Pacific Oysters (Crassostrea gigas) Stored at Different Temperatures. Czech Journal Food Science, 27, 102-108. ISSN: 1212- 1800.
Colwell, R.R., & Liston, J. (1960). Microbiology of shellfish. Bacteriological study of the natural flora of Pacific oysters (Crassostrea gigas). Applied Microbiology, 8, 104–109.
Deepanjali, A., Kumar, H.S., & Karunasagar, I. (2005). Seasonal variation in abundance of total and pathogenic Vibrio parahaemolyticus bacteria in oysters along the southwest coast of India. Applied and Environmental Microbiology, 71, 3575-3580. http://dx.doi.org/10.1128/AEM.71.7.3575- 3580.2005
De Hoon, M.J., Imoto, S., Nolan, J., & Miyano, S. (2004). Open source clustering software. Bioinformatics, 20, 1453-1454. http://dx.doi.org/10.1093/bioinformatics/bth078
DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G.L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72, 5069-5072. http://dx.doi.org/10.1128/AEM.03006-05
Dupont, J., Jehl-Pietri, C., & Mnard, D. (1992). Comparative study of bacterial and viral faecal contamination in shellfish: demonstration of seasonal variations. Biomedical Letters, 47, 329– 335.
Edgar, R.C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996-998. http://dx.doi.org/10.1038/nmeth.2604
Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200. http://dx.doi.org/10.1093/bioinformatics/btr381
Edgar, R.C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113. http://dx.doi.org/10.1186/1471-2105-5-113
Fulton, S. (2009). Cyanobacterial blooms in Tasmania. Cyanobacterial Bloom Management, Current and Future Options, 18.
Garland, C., Nash, G., Summer, C. & McMeekin, T. (1983). Bacterial pathogens of oyster larvae (Crassostrea gigas) in a Tasmanian hatchery. Marine and Freshwater Research, 34, 483-487. http://dx.doi.org/10.1071/MF9830483
Garnier, M., Labreuche, Y., Garcia, C., Robert, M., & Nicolas, J.L. (2007). Evidence for the involvement of pathogenic bacteria in summer mortalities of the Pacific oyster Crassostrea gigas. Microbial Ecology, 53, 187-196. http://dx.doi.org/10.1007/s00248-006-9061-9
Green, T.J., & Barnes, A.C. (2010). Bacterial diversity of the digestive gland of Sydney rock oysters, Saccostrea glomerata infected with the paramyxean parasite, Marteilia sydneyi. Journal of Applied Microbiology, 109, 613–622. http://dx.doi.org/10.1111/j.1365- 2672.2010.04687.x
Hara-Kudo, Y., Nishina, T., Nakagawa, H., Konuma, H., Hasegawa, J., & Kumagai, S. (2001). Improved method for detection of Vibrio parahaemolyticus in seafood. Applied and Environmental Microbiology, 67, 5819-5823. http://dx.doi.org/10.1128/AEM.67.12.5819- 5823.2001
Hatje, E., Neuman, C., Stevenson, H., Bowman, J.P., & Katouli, M. (2014). Population Dynamics of Vibrio and Pseudomonas Species Isolated from Farmed Tasmanian Atlantic Salmon (Salmo salar L.): A Seasonal Study. Microbial Ecology, 68, 679-687. http://dx.doi.org/10.1007/s00248-014-0462-x
Holben, W., Williams, P., Saarinen, M., Särkilahti, L., & Apajalahti, J. (2002). Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon. Microbial Ecology, 44, 175-185. http://dx.doi.org/10.1007/s00248-002-1011-6
Hovda, M.B., Lunestad, B.T., Fontanillas, R., & Rosnes, J.T. (2007). Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.). Aquaculture, 272, 581- 588. http://dx.doi.org/10.1016/j.aquaculture.2007.08. 045
Lorca, T.A. (2000). An Evaluation of the Role of Storage Temperature on the Safety and Quality of Raw Shellstock Oysters and Bluefish. Blackburg, Virginia Polytechnic Institute and State University.
Lyons, P.P., Turnbull, J.F., Dawson, K.A., & Crumlish, M. (2016). Phylogenetic and functional characterization of the distal intestinal microbiome of rainbow trout Oncorhynchus mykiss from both farm and aquarium settings. Journal of Applied Microbiology, 122, 347–363. http://dx.doi.org/10.1111/jam.13347
Neuman, C., Hatje, E., Zarkasi, K.Z., Smullen, R., Bowman, J.P., & Katouli, M. (2016). The effect of diet and environmental temperature on the faecal microbiota of farmed Tasmanian Atlantic salmon (Salmo salar L.). Aquaculture Research, 47, 660-672. http://dx.doi.org/10.1111/are.12522
Olafsen, J.A. (2001). Interactions between fish larvae and bacteria in marine aquaculture. Aquaculture, 200, 223-247. http://dx.doi.org/10.1016/S0044- 8486(01)00702-5
Piquer, J.F. (2010). Protecting the Safety and Quality of Australian Oysters with Integrated Predictive Tools Hobart, University of Tasmania. Price, M.N., Dehal, P.S., & Arkin, A.P. (2010). FastTree 2–approximately maximum-likelihood trees for large alignments. PLOS ONE, 5, e9490. http://dx.doi.org/10.1371/journal.pone.0009490
Pujalte, M.J., Ortigosa, M., Macián, M.C., & Garay, E. (1999). Aerobic and facultative anaerobic heterotrophic bacteria associated to Mediterranean oysters and seawater. International Microbiology, 2, 259-266.
Reilly, A., & Kaeferstein, F. (1998). Food safety and products from aquaculture. Journal of Applied Microbiology, 85, 249S–257S. http://dx.doi.org/10.1111/j.1365- 2672.1998.tb05305.x
Ringø, E., Strøm, E., & Tabachek, J. (1995). Intestinal microflora of salmonids: a review. Aquaculture Research, 26, 773-789. http://dx.doi.org/10.1111/j.1365- 2109.1995.tb00870.x
Ringø, E., & Birkbeck, T. (1999). Intestinal microflora of fish larvae and fry. Aquaculture Research, 30, 73-93.
Ringø, E., Sperstad, S., Myklebust, R., Refstie, S., & Krogdahl, Å. (2006). Characterisation of the microbiota associated with intestine of Atlantic cod (Gadus morhua L.): The effect of fish meal, standard soybean meal and a bioprocessed soybean meal. Aquaculture, 261, 829-841. http://dx.doi.org/10.1016/j.aquaculture.2006.06. 030
Romero, J., Garcia-Varela, M., Laclette, J., & Espejo, R. (2002). Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis). Microbial Ecology, 44, 365-371. http://dx.doi.org/10.1007/s00248-002-1063-7
Romero, J., Gonzalez, N., & Espejo, R.T. (2002). Marine Pseudoalteromonas sp. Composes Most of the Bacterial Population Developed in Oysters (Tiostrea chilensis) Spoiled During Storage. Journal of Food Science, 67, 2300–2303. http://dx.doi.org/10.1111/j.1365- 2621.2002.tb09544.x
Saldanha, A.J. (2004). Java Treeview—extensible visualization of microarray data. Bioinformatics, 20, 3246-3248. http://dx.doi.org/10.1093/bioinformatics/bth349
Sellner, K.G. (1997). Physiology, ecology and toxic properties of marine cyanobacteria blooms. Limnology and Oceanography, 42, 1089-1104.
Tarnecki, A.M., Burgos, F.A., Ray, C.L., & Arias, C.R. (2017). Fish Intestinal Microbiome: Diversity and Symbiosis Unraveled by Metagenomics. Journal of Applied Microbiology. http://dx.doi.org/10.1111/jam.13415
Urbanczyk, H., Ast, C.J., Higgins, M.J., Carson, J., & Dunlap, P.V. (2007). Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov. International Journal of Systematic and Evolutionary Microbiology, 57, 2823-2829. http://dx.doi.org/10.1099/ijs.0.65081-0
Wang, Q., Garrity, G.M., Tiedje, J.M., & Cole, J.R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267. http://dx.doi.org/10.1128/AEM.00062-07
Wu, S., Wang, G., Angert, E.R., Wang, W., Li, W., & Zou, H. (2012). Composition, diversity, and origin of the bacterial community in grass carp intestine. PLOS ONE, 7, e30440. http://dx.doi.org/10.1371/journal.pone.0030440
Yoon, J.H., Weiss, N., Kang, K.H., Oh, T.K., & Park, Y.H. (2003). Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea. International Journal of Systematic and Evolutionary Microbiology, 53, 2013-2017. http://dx.doi.org/10.1099/ijs.0.02557-0
Zarkasi, K.Z., Abell, G.C.J., Taylor, R.S., Neuman, C., Hatje, E., Tamplin, M.L., Katouli, M., & Bowman, J.P. (2014). Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system. Journal of Applied Microbiology, 117, 18-27. http://dx.doi.org/10.1111/jam.12514
Zarkasi, K.Z., Taylor, R.S., Abell, G.C.J., Tamplin, M.L., Glencross, B.D., & Bowman, J.P. (2016). Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet. Microbial Ecology, 71, 589–603. http://dx.doi.org/10.1007/s00248-015-0728-y
Zhang, J., Zhang, Y., Liu, S.N., Han, Y., & Zhou, Z.J. (2012). Modelling growth and bacteriocin production by Pediococcus acidilactici PA003 as a function of temperature and pH value. Applied Biochemistry and Biotechnology, 166, 1388-1400. http://dx.doi.org/10.1007/s12010-011-9532-4
Zhao, J.S., Manno, D., & Hawari, J. (2009). Psychrilyobacter atlanticus gen. nov., sp. nov., a marine member of the phylum Fusobacteria that produces H2 and degrades nitramine explosives under low temperature conditions. International Journal of Systematic and Evolutionary Microbiology, 59, 491-497. http://dx.doi.org/10.1099/ijs.0.65263-0