中华绒螯蟹生态育苗池塘细菌群落分析
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摘要
为探究江苏省射阳地区沿海滩涂中华绒螯蟹(Eriocheir sinensis)生态育苗池塘细菌群落结构,分别对养殖池塘水体(S7,S8,S9)和池塘底泥(N7,N8,N9)细菌群落16SrDNA的V3、V4、V5可变区进行扩增,检测合格的文库进行高通量测序;利用Qiime(v1.7)软件,对序列阈值97%相似性水平进行聚类分析;分别以门、纲、目、科和属的分类水平对样本进行α-多样性指数分析;以Chaol指数和Shannon指数评估菌种丰富度和多样性。结果表明,3个生态育苗池塘得到OTU分别为8 881、7 406、8 566个。S7微生物归属于16门、29纲、58目、97科、191属;S8为9门、18纲、38目、68科、132属;S9为17门、32纲、60目、111科、227属。N7为41门、103纲、198目、325科、572属;N8为42门、103纲、203目、318科、534属;N9为40门、99纲、196目、323科、578属。养殖水体优势菌群以变形菌门(Proteobacteria)为主,其次是拟杆菌门(Bacteroidetes);池塘底泥优势菌群以变形菌门为主,其次为拟杆菌门、绿弯菌门(Chloroflexi)和浮霉菌门(Planctomycetes)。养殖池塘底泥中细菌群落的丰富度和物种多样性明显高于养殖水体,水体中细菌群落的丰富度S9>S7>S8,物种的多样性S7>S9>S8。池塘底泥中细菌群落的丰富度N7>N9>N8,物种的多样性N7> N9>N8。
Microbial community composition plays an important role in aquaculture systems,affecting the nutrition and immune response of aquaculture organisms.In this study,we investigated the microbial community structure and diversity in the water and sediment of Chinese mitten crab ecological breeding ponds in Sheyang,Jiangsu Province,aiming to provide a reference for environmental protection and healthy breeding of the crab.Water and sediment samples(labeled as S7,S8,S9 and N7,N8,N9)were collected from three breeding ponds in the aquatic seedling farm of Sheyang County.The V3-V5 hypervariable region of the 16 SrRNA gene from bacteria in water and sediment samples was sequenced using highthroughput sequencing technology and expressed in operational taxonomic units(OTUs)using MOTHUR software.The resulting sequences with no less than 97% sequence similarity were clustered using Qiime(v1.7)software and the richness and diversity of the microbial community were evaluated based on the Chaol index and Shannon index.Ponds 7,8,and 9displayed,respectively,8 881,7 406 and 8 566 OTUs.The microbial community of water sample S7 included 191genera,97 families,58orders,29 classes and16phyla;for S8,132 genera,68families,38 orders,18classes and 9phyla;and for S9,227 genera,111families,60 orders,32classes and 17 phyla.The microbial community of sediment sample N7 included 572genera,325 families,198orders,103 classes and 41phyla;for N8,534 genera,318families,203 orders,103classes and 42phyla;and for N9,578 genera,323families,196 orders,99classes and 40 phyla.Proteobacteria was the dominant taxa detected in the water and sediment samples,followed by Bacteroidetes.The abundance and diversity of microbes in the sediment were much higher than in the water.The information provided by this study will be helpful in rearing Chinese mitten crab larvae.
Microbial community composition plays an important role in aquaculture systems,affecting the nutrition and immune response of aquaculture organisms.In this study,we investigated the microbial community structure and diversity in the water and sediment of Chinese mitten crab ecological breeding ponds in Sheyang,Jiangsu Province,aiming to provide a reference for environmental protection and healthy breeding of the crab.Water and sediment samples(labeled as S7,S8,S9 and N7,N8,N9)were collected from three breeding ponds in the aquatic seedling farm of Sheyang County.The V3-V5 hypervariable region of the 16 SrRNA gene from bacteria in water and sediment samples was sequenced using highthroughput sequencing technology and expressed in operational taxonomic units(OTUs)using MOTHUR software.The resulting sequences with no less than 97% sequence similarity were clustered using Qiime(v1.7)software and the richness and diversity of the microbial community were evaluated based on the Chaol index and Shannon index.Ponds 7,8,and 9displayed,respectively,8 881,7 406 and 8 566 OTUs.The microbial community of water sample S7 included 191genera,97 families,58orders,29 classes and16phyla;for S8,132 genera,68families,38 orders,18classes and 9phyla;and for S9,227 genera,111families,60 orders,32classes and 17 phyla.The microbial community of sediment sample N7 included 572genera,325 families,198orders,103 classes and 41phyla;for N8,534 genera,318families,203 orders,103classes and 42phyla;and for N9,578 genera,323families,196 orders,99classes and 40 phyla.Proteobacteria was the dominant taxa detected in the water and sediment samples,followed by Bacteroidetes.The abundance and diversity of microbes in the sediment were much higher than in the water.The information provided by this study will be helpful in rearing Chinese mitten crab larvae.
引文
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Ivanova E P,Sawabe T,Zhukova N V,et al,2003.Occurrence and Diversity of Mesophilic Shewanella Strains I-solated from the North-West Pacific Ocean[J].Systematic and Applied Microbiology,26(2):293-301.
Payne M S,Hall M R,Bannister R,et al,2006.Microbial diversity within the water column of a larval rearing system for the ornate rock lobster(Panulirus ornatus)[J].Aquaculture,258(1):80-90.
Sogin M L,Morrison H G,Huber J A,et al,2006.Microbial Diversity in the Deep Sea and the Underexplored“Rare Biosphere”[J].Proceedings of the National Academy of Sciences of the United States of America,103(32):12115-12120.
Stenholm A R,Dalsgaard I,Middelboe M,2008.Isolation and characterization of bacteriophages infecting the fish pathogen Flavobacterium psychrophilum[J].Appl Environ Microbiol,74(13):4070-4078.
黄志涛,宋协法,李勋,等,2016.基于高通量测序的石斑鱼循环水养殖生物滤池微生物群落分析[J].农业工程学报,32(S1):242-247.
裘钱玲琳,徐如卫,朱建林,等,2015.凡纳滨虾土塘养殖与循环养殖系统细菌菌落结构比较研究[J].生物学杂志,32(6):45-49.
孙欣,高莹,杨云峰,2013.环境微生物的宏基因组学研究新进展[J].生物多样性,21(4):393-400.
王武,李应森,2010.河蟹生态养殖[M].北京:中国农业出版社.
Amann R I,Ludwig W,Schleifer K H,1995.Phylogenetic identification and in situ detection of individual microbial cells without cultivation[J].Microbiological Reviews,59(1):143-169.
Auguet J C,Barberan A,Casamayor E O,2009.Global ecological patterns in uncultured Archaea[J].The Interational Society for Microbial Ecology Journal,59(1):143-169.
Bakunina I,Shevchenko L S,Nedashkovskaia O I,1999.Screening of marine bacteria for fucoidan hydrolases[J].Mikrobiologiia,69(3):370-376.
Cottrell M T,Kirchman D L,2000.Natural assemblages of marine proteobactria and members of the Cytophaga Flavobacter cluster consuming low and high-molecularweight dissolved organic matter[J].Applied and Environmental Microbiology,66(4):1692-1697.
Huber I,Spanggaard B,Appel K F,et al,2004.Phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout(Oncorhynchus mykiss Walbaum)[J].Joural of Applied Microbiology,96(1):117-132.
Hugenholtz P,Hooper S D,Kyrpides N C,2009.Focus:Synergistetes[J].Environmental Microbiology,11(6):1327-1329.
Ivanova E P,Sawabe T,Zhukova N V,et al,2003.Occurrence and Diversity of Mesophilic Shewanella Strains I-solated from the North-West Pacific Ocean[J].Systematic and Applied Microbiology,26(2):293-301.
Payne M S,Hall M R,Bannister R,et al,2006.Microbial diversity within the water column of a larval rearing system for the ornate rock lobster(Panulirus ornatus)[J].Aquaculture,258(1):80-90.
Sogin M L,Morrison H G,Huber J A,et al,2006.Microbial Diversity in the Deep Sea and the Underexplored“Rare Biosphere”[J].Proceedings of the National Academy of Sciences of the United States of America,103(32):12115-12120.
Stenholm A R,Dalsgaard I,Middelboe M,2008.Isolation and characterization of bacteriophages infecting the fish pathogen Flavobacterium psychrophilum[J].Appl Environ Microbiol,74(13):4070-4078.