刺参肠道及养殖环境菌群结构与功能
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摘要
基于Mi Seq高通量测序技术,分析了黄、渤海秋季池塘养殖刺参(Apostichopus japonicus)肠道及养殖环境菌落结构、α-多样性指数和菌群功能。结果表明:黄海和渤海养殖池塘底泥菌群Chao1指数、ACE的指数均较高,表明养殖池塘底泥菌群较为丰富;黄海和渤海养殖刺参肠道及养殖环境中优势菌门均为变形菌门(比例>43.25%);两个海域中刺参肠道中优势菌属相同,均为Halioglobus(比例>12.67%);养殖环境中的优势菌属则存在差异,黄海养殖水体的优势菌属为Roseibacillus(13.59%);渤海养殖水体优势菌属为海命菌属(Marivita)(21. 33%);黄海养殖底泥样品DN-1和DN-2中优势菌属为Desulfopila(>9.26%),DN-3中优势菌属为Halioglobus(3.67%);渤海养殖底泥中优势菌属为硫深海菌属(Thioprofundum)(3.79%);在渤海海域中还发现了特有菌属海命菌属(Marivita)、Ascidiaceihabitans、别弧菌属(Aliivibrio),且所占比例较大;黄海和渤海各样品中菌群经COG及KEGG数据库分析,共注释到24组COG功能分类,主要集中在氨基酸转运与代谢; 41条KEGG信号通路,主要集中在氨基酸转运与代谢、碳水化合物代谢、膜转运。研究结果为合理进行刺参养殖、疾病防控提供了理论依据。
Based on the Mi Seq high-throughput sequencing technology,we investigated the structure,α-diversity and function of bacterial community in the intestinal tracts and culture environment of the sea cucumbers( Apostichopus japonicus) in autumn. The sea cucumbers were cultured in the ponds of the Yellow Sea and Bohai Sea. The results showed that the Chao1 and ACE indices of bacterial community in the bottom sediments of the Yellow Sea and the Bohai Sea were relatively high,indicating that the bacterial community in the bottom sediments of the culture ponds was abundant. The dominant bacterial phylum was Proteobacteria( with a proportion of>43.25%) in the intestine of sea cucumbers,pond sediments,and seawater of the Yellow Sea and Bohai Sea. Halioglobus( with a proportion of >12.67%) was the dominant bacterial genus in the intestine of the sea cucumbers in both sea areas. There were differences in the dominant genera in the culture environment. The dominant genus was Roseibacillus( 13. 59%) in the aquaculture water of the Yellow Sea and Marivita( 21.33%) in that of the Bohai Sea. In the aquaculture sediments,the dominant genus was Desulfopila( > 9. 26%) in Yellow Sea and Thioprofundum( 3.79%) in Bohai Sea. In addition,special species belonging to genera Marivita,Ascidiaceihabitans and Aliivibrio were found in the Bohai Sea and accounted for a large proportion. COG and KEGG annotation analysis revealed 24 COG functional groups( primarily serving functions such as amino acid transport and metabolism),and 41 KEGG pathways( mainly representing amino acid transport and metabolism,carbohydrate metabolism,and membrane transport). Our results provide scientific basis for healthy aquaculture of sea cucumber and disease prevention.
Based on the Mi Seq high-throughput sequencing technology,we investigated the structure,α-diversity and function of bacterial community in the intestinal tracts and culture environment of the sea cucumbers( Apostichopus japonicus) in autumn. The sea cucumbers were cultured in the ponds of the Yellow Sea and Bohai Sea. The results showed that the Chao1 and ACE indices of bacterial community in the bottom sediments of the Yellow Sea and the Bohai Sea were relatively high,indicating that the bacterial community in the bottom sediments of the culture ponds was abundant. The dominant bacterial phylum was Proteobacteria( with a proportion of>43.25%) in the intestine of sea cucumbers,pond sediments,and seawater of the Yellow Sea and Bohai Sea. Halioglobus( with a proportion of >12.67%) was the dominant bacterial genus in the intestine of the sea cucumbers in both sea areas. There were differences in the dominant genera in the culture environment. The dominant genus was Roseibacillus( 13. 59%) in the aquaculture water of the Yellow Sea and Marivita( 21.33%) in that of the Bohai Sea. In the aquaculture sediments,the dominant genus was Desulfopila( > 9. 26%) in Yellow Sea and Thioprofundum( 3.79%) in Bohai Sea. In addition,special species belonging to genera Marivita,Ascidiaceihabitans and Aliivibrio were found in the Bohai Sea and accounted for a large proportion. COG and KEGG annotation analysis revealed 24 COG functional groups( primarily serving functions such as amino acid transport and metabolism),and 41 KEGG pathways( mainly representing amino acid transport and metabolism,carbohydrate metabolism,and membrane transport). Our results provide scientific basis for healthy aquaculture of sea cucumber and disease prevention.
引文
白洁,李海艳,赵阳国.2009.黄海北部不同站位海洋细菌群落分布特征.微生物学报,49(3):343-350.
常亚青,丁君,宋坚,等.2004.海参、海胆生物学研究与养殖.北京:海洋出版社.
陈琼,李贵阳,罗坤,等.2017.凡纳滨对虾(Litopenaeus vannamei)亲虾繁殖期水体微生物多样性.海洋与湖沼,48(1):130-138.
陈孝煊,吴志新,周文豪.2006.鱼类消化道菌群的作用与影响因素研究进展.养殖与饲料,24(3):523-528.
窦妍,丁君,曲凌云,等.2015.秋、冬季刺参养殖池塘菌群的多样性分析.大连海洋大学学报,30(2):143-148.
窦妍,赵晓伟,丁君,等.2016.基于高通量测序技术分析患病与健康虾夷扇贝(Patinopecten yessoensis)闭壳肌菌群多样性.生态学杂志,35(4):1019-1025.
黄佩蓓,焦念志,冯洁,等.2014.海洋浮霉状菌多样性与生态学功能研究进展.微生物学通报,41(9):1891-1902.
姜成林,徐丽华.1997.微生物资源学.北京:科学出版社.
李彬,廖梅杰,荣小军,等.2016.池塘养殖仿刺参(Apostichopus japonicus)肠含物、附着基和底泥中的菌群结构及其相关性.渔业科学进展,37(5):127-132.
廖玉膦.1997.中国动物志:棘皮动物门.海参纲.北京:科学出版社.
陆振,杨求华,黄瑞芳,等.2017.池塘养殖和海上吊笼养殖仿刺参肠道菌群结构对比分析.应用海洋学学报,36(2):187-194.
王蓉,何晓娜,刘维,等.2013.海洋放线菌作为益生菌在水产养殖中的潜在应用.安徽农业科学,41(24):10007-10009.
王轶南,朱世伟,常亚青.2010.刺参肠道及养殖池塘菌群组成的PCR-DGGE指纹图谱分析.渔业科学进展,31(3):119-122.
于东祥.2010.海参健康养殖技术.北京:海洋出版社.
Amann RI,Ludwig W,Schleifer KH.1995.Phylogenetic identification and in situ detection of individual microbial cells without cultivation.Microbiological Reviews,59:143-169.
Atkinson S,Williams P.2009.Quorum sensing and social networking in the microbial world.Journal of the Royal Society Interface,6:959-978.
Auguet JC,Barberan A,Casamayor EO.2010.Global ecological patterns in uncultured Archaea.ISME Journal,4:182-190.
Beaz-Hidalgo R,Doce A,Balboa S,et al.2010.Aliivibrio finisterrensis sp.nov.isolated from Manila clam,Ruditapes philippinarum and emended description of the Aliivibrio.International Journal of Systematic and Evolutionary Microbiology,60:223-228.
Bordbar S,Anwar F,Saari N,et al.2011.High-value components and bio-actives from sea cucumbers for functional foods:A review.Marine Drugs,9:1761-1805.
Cao R,Zhao L,Sun H,et al.2018.Characterization of microbial community in high-pressure treated oysters by highthroughput sequencing technology.Innovative Food Science&Emerging Technologies,45:241-248.
Caporaso JG,Lauber CL,Walters WA,et al.2011.Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.Proceedings of the National Academy of Sciences of the United States of America,108:4516-4522.
Clifford C,Walsh J,Reidy N,et al.1982.Digestive enzymes and subcellular localization of disaccharidases in some echinoderms.Comparative Biochemistry&Physiology Part B:Comparative Biochemistry,71:105-110.
Colquhoun DJ,Sorum H.2001.Temperature dependent siderophore production in Vibrio salmonicida.Microbial Pathogenesis,31:213-219.
Cottrell MT,Kirchman DL.2000.Natural assemblages of marine proteobacteria and members of the cytophaga-flavobacter cluster consuming low and high-molecular-weight dissolved organic matter.Applied&Environmental Microbiology,66:1692-1697.
Erickson AR,Cantarel BL,Lamendella R,et al.2012.Integrated metagenomics/metaproteomics reveals human hostmicrobiota signatures of Crohn’s disease.PLo S One,7:e49138.
Fidopiastis PM,Von BS,Ruby EG.1998.A new niche for Vibrio logei,the predominant light organ symbiont of squids in the genus sepiola.Journal of Bacteriology,180:59-64.
Gao F,Li F,Tan J,et al.2014.Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.PLo S One,9:e100092.
Henryk U,Ast JC,Higgins MJ,et al.2007.Reclassification of Vibrio fischeri,Vibrio logei,Vibrio salmonicida and Vibri owodanis as Aliivibrio fischergen nov.comb.nov.Aliivibrio logei com.nov.Aliivibrio salmonicida comb.nov.and Aliivibrio wodanis comb.nov.Iranian Journal of Systematic and Evolutionary Microbiology,57:2823-2829.
Hugenholtz P,Hooper SD,Kyrpides NC.2010.Focus:Synergistetes.Environmental Microbiology,11:1327-1329.
Hughes DT,Sperandio V.2008.Inter-kingdom signalling:Communication between bacteria and their hosts.Nature Reviews Microbiology,6:111-120.
Koh EY,Atamnaismaeel N,Martin A,et al.2010.Proteorhodopsin-bearing bacteria in Antarctic sea ice.Applied&Environmental Microbiology,76:5918.
Lamendella R,Santo Domingo JW,Ghosh S,et al.2011.Comparative fecal metagenomics unveils unique functional capacity of the swine gut.BMC Microbiology,11:103.
Lunder T,Eversen,Holstad G,et al.1995.‘Winter ulcer’in the Atlantic salmon Salmo salar.Pathological and bacteriological investigations and transmission experiments.Diseases of Aquatic Organisms,23:39-49.
Margulies M,Egholm M,Altman WE,et al.2005.Genome sequencing in microfabricated high-density picolitre reactors.Nature,437:376-380.
O’Sullivan LA,Weightman AJ,Fry JC.2002.New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon.Applied&Environmental Microbiology,68:201-10.
Pujalte MJ,Lucena T,Ruvira MA,et al.2014.The Family Rhodobacteraceae.Berlin:Springer.
Rossellómora R,Amann R.2001.The species concept for prokaryotes.FEMS Microbiology Reviews,25:39-67.
Sha Y,Liu M,Wang B,et al.2016.Gut bacterial diversity of farmed sea cucumbers Apostichopus japonicus,with different growth rates.Microbiology,85:109-115.
Stevens H,Stübner M,Simon M,et al.2010.Phylogeny of proteobacteria and bacteroidetes from oxic habitats of a tidal flat ecosystem.FEMS Microbiology Ecology,54:351-365.
Youssef N,Sheik CS,Krumholz LR,et al.2009.Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys.Applied&Environmental Microbiology,75:5227.
Zhou M,Hernandez-Sanabria E,Guan ALL.2009.Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies.Applied&Environmental Microbiology,75:6524-6533.
常亚青,丁君,宋坚,等.2004.海参、海胆生物学研究与养殖.北京:海洋出版社.
陈琼,李贵阳,罗坤,等.2017.凡纳滨对虾(Litopenaeus vannamei)亲虾繁殖期水体微生物多样性.海洋与湖沼,48(1):130-138.
陈孝煊,吴志新,周文豪.2006.鱼类消化道菌群的作用与影响因素研究进展.养殖与饲料,24(3):523-528.
窦妍,丁君,曲凌云,等.2015.秋、冬季刺参养殖池塘菌群的多样性分析.大连海洋大学学报,30(2):143-148.
窦妍,赵晓伟,丁君,等.2016.基于高通量测序技术分析患病与健康虾夷扇贝(Patinopecten yessoensis)闭壳肌菌群多样性.生态学杂志,35(4):1019-1025.
黄佩蓓,焦念志,冯洁,等.2014.海洋浮霉状菌多样性与生态学功能研究进展.微生物学通报,41(9):1891-1902.
姜成林,徐丽华.1997.微生物资源学.北京:科学出版社.
李彬,廖梅杰,荣小军,等.2016.池塘养殖仿刺参(Apostichopus japonicus)肠含物、附着基和底泥中的菌群结构及其相关性.渔业科学进展,37(5):127-132.
廖玉膦.1997.中国动物志:棘皮动物门.海参纲.北京:科学出版社.
陆振,杨求华,黄瑞芳,等.2017.池塘养殖和海上吊笼养殖仿刺参肠道菌群结构对比分析.应用海洋学学报,36(2):187-194.
王蓉,何晓娜,刘维,等.2013.海洋放线菌作为益生菌在水产养殖中的潜在应用.安徽农业科学,41(24):10007-10009.
王轶南,朱世伟,常亚青.2010.刺参肠道及养殖池塘菌群组成的PCR-DGGE指纹图谱分析.渔业科学进展,31(3):119-122.
于东祥.2010.海参健康养殖技术.北京:海洋出版社.
Amann RI,Ludwig W,Schleifer KH.1995.Phylogenetic identification and in situ detection of individual microbial cells without cultivation.Microbiological Reviews,59:143-169.
Atkinson S,Williams P.2009.Quorum sensing and social networking in the microbial world.Journal of the Royal Society Interface,6:959-978.
Auguet JC,Barberan A,Casamayor EO.2010.Global ecological patterns in uncultured Archaea.ISME Journal,4:182-190.
Beaz-Hidalgo R,Doce A,Balboa S,et al.2010.Aliivibrio finisterrensis sp.nov.isolated from Manila clam,Ruditapes philippinarum and emended description of the Aliivibrio.International Journal of Systematic and Evolutionary Microbiology,60:223-228.
Bordbar S,Anwar F,Saari N,et al.2011.High-value components and bio-actives from sea cucumbers for functional foods:A review.Marine Drugs,9:1761-1805.
Cao R,Zhao L,Sun H,et al.2018.Characterization of microbial community in high-pressure treated oysters by highthroughput sequencing technology.Innovative Food Science&Emerging Technologies,45:241-248.
Caporaso JG,Lauber CL,Walters WA,et al.2011.Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.Proceedings of the National Academy of Sciences of the United States of America,108:4516-4522.
Clifford C,Walsh J,Reidy N,et al.1982.Digestive enzymes and subcellular localization of disaccharidases in some echinoderms.Comparative Biochemistry&Physiology Part B:Comparative Biochemistry,71:105-110.
Colquhoun DJ,Sorum H.2001.Temperature dependent siderophore production in Vibrio salmonicida.Microbial Pathogenesis,31:213-219.
Cottrell MT,Kirchman DL.2000.Natural assemblages of marine proteobacteria and members of the cytophaga-flavobacter cluster consuming low and high-molecular-weight dissolved organic matter.Applied&Environmental Microbiology,66:1692-1697.
Erickson AR,Cantarel BL,Lamendella R,et al.2012.Integrated metagenomics/metaproteomics reveals human hostmicrobiota signatures of Crohn’s disease.PLo S One,7:e49138.
Fidopiastis PM,Von BS,Ruby EG.1998.A new niche for Vibrio logei,the predominant light organ symbiont of squids in the genus sepiola.Journal of Bacteriology,180:59-64.
Gao F,Li F,Tan J,et al.2014.Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.PLo S One,9:e100092.
Henryk U,Ast JC,Higgins MJ,et al.2007.Reclassification of Vibrio fischeri,Vibrio logei,Vibrio salmonicida and Vibri owodanis as Aliivibrio fischergen nov.comb.nov.Aliivibrio logei com.nov.Aliivibrio salmonicida comb.nov.and Aliivibrio wodanis comb.nov.Iranian Journal of Systematic and Evolutionary Microbiology,57:2823-2829.
Hugenholtz P,Hooper SD,Kyrpides NC.2010.Focus:Synergistetes.Environmental Microbiology,11:1327-1329.
Hughes DT,Sperandio V.2008.Inter-kingdom signalling:Communication between bacteria and their hosts.Nature Reviews Microbiology,6:111-120.
Koh EY,Atamnaismaeel N,Martin A,et al.2010.Proteorhodopsin-bearing bacteria in Antarctic sea ice.Applied&Environmental Microbiology,76:5918.
Lamendella R,Santo Domingo JW,Ghosh S,et al.2011.Comparative fecal metagenomics unveils unique functional capacity of the swine gut.BMC Microbiology,11:103.
Lunder T,Eversen,Holstad G,et al.1995.‘Winter ulcer’in the Atlantic salmon Salmo salar.Pathological and bacteriological investigations and transmission experiments.Diseases of Aquatic Organisms,23:39-49.
Margulies M,Egholm M,Altman WE,et al.2005.Genome sequencing in microfabricated high-density picolitre reactors.Nature,437:376-380.
O’Sullivan LA,Weightman AJ,Fry JC.2002.New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon.Applied&Environmental Microbiology,68:201-10.
Pujalte MJ,Lucena T,Ruvira MA,et al.2014.The Family Rhodobacteraceae.Berlin:Springer.
Rossellómora R,Amann R.2001.The species concept for prokaryotes.FEMS Microbiology Reviews,25:39-67.
Sha Y,Liu M,Wang B,et al.2016.Gut bacterial diversity of farmed sea cucumbers Apostichopus japonicus,with different growth rates.Microbiology,85:109-115.
Stevens H,Stübner M,Simon M,et al.2010.Phylogeny of proteobacteria and bacteroidetes from oxic habitats of a tidal flat ecosystem.FEMS Microbiology Ecology,54:351-365.
Youssef N,Sheik CS,Krumholz LR,et al.2009.Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys.Applied&Environmental Microbiology,75:5227.
Zhou M,Hernandez-Sanabria E,Guan ALL.2009.Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies.Applied&Environmental Microbiology,75:6524-6533.