不同养殖模式下凡纳滨对虾肠道及环境微生物群落结构分析与比较

doi:10.15933/j.cnki.1004-3268.2023.11.015

摘要/Abstract

摘要： 为探究河北省唐山市不同养殖模式下凡纳滨对虾肠道及养殖环境微生物群落结构及差异，采用16S rRNA高通量测序技术和生物信息学方法，分析了淡水精养（Freshwater intensive culture，FI）和混养（Freshwater mixed culture，FM）2种养殖模式不同时期对虾肠道、水体及底泥微生物的多样性、物种组成及差异。结果表明，FI模式所有样品共聚类为6 077个可操作分类单元（OTU），FM模式所有样品共聚类为7 961个OTU。2种模式的底泥微生物多样性均显著高于水体和对虾肠道，且FM模式底泥的多样性更高。在门水平上，变形菌门（Proteobacteria）是所有样品中相对丰度均较高的物种，其次为拟杆菌门（Bacteroidetes）；在属水平上，不同养殖模式下不同样品的优势菌属及相对丰度各不相同。相较于对虾肠道和水体，底泥中微生物的数量和丰富度均为最高；底泥与对虾肠道微生物种类及组成较为相似。研究表明，唐山市2种凡纳滨对虾淡水养殖模式下对虾肠道与环境微生物物种数量随养殖时间的变化基本不变，但物种群落丰富度及多样性均有一定提高；相较于FI模式，FM模式各类型样品微生物群落物种数量更多，且养殖末期时物种相对丰度的变化更加显著，特别是对虾肠道中弧菌属细菌相对丰度显著提高。

关键词: 凡纳滨对虾, 微生物群落结构, 精养, 混养, 高通量测序

Abstract: The present study aimed to explore the microbial community structure in Litopenaeus vannamei intestine and surrounding environment of different culture patterns in Tangshan area of Heibei Province，and to contrast the variations between them.16S rRNA high⁃throughput sequencing technology combined with bioinformatics methods was used to analyze the microbial diversity，community structure composition and variations in L.vannamei intestine，surrounding water and sediment from different culture patterns including freshwater intensive culture（FI）and freshwater mixed culture（FM）.The results showed that sequences of FI and FM patterns were clustered into 6 077 and 7 961 operational taxonomic units（OTUs）respectively.Sediment samples had significantly higher microbial diversity than water and shrimp intestine samples from both patterns.Compared with FI pattern，diversity in sediment samples of FM pattern was higher.Proteobacteria and Bacteroidetes were the most prevalent phyla across all sample types，while all types of samples varied in terms of the dominating genus and its relative abundance.Compared to shrimp intestine and water samples，the microbial species number and richness in the sediment samples were the highest.Cluster analysis showed that the composition of the microbial communities in shrimp intestines resembled sediment samples more than water samples.The research showed that the number of microbial species in L.vannamei intestine and surrounding environment from two kinds of freshwater culture patterns in Tangshan remained constant while the relative abundance and diversity of the microorganisms rose with time.In comparison to the FI pattern，the FM pattern contained a greater number of microbial species in each type of samples，and the relative abundance of species，especially Vibrio，changed more significantly at the final stage of culture.

Key words: Litopenaeus vannamei, Microbial community structure, Intensive culture, Mixed culture, High?throughput sequencing

中图分类号:

S917.1

侯蔷, 周鑫, 张建雄, 马瑞欣, 吴江爱, 崔亚楠, 陈宇, 郑百芹, 张丽芳. 不同养殖模式下凡纳滨对虾肠道及环境微生物群落结构分析与比较[J]. 河南农业科学, 2023, 52(11): 133-145.

HOU Qiang, ZHOU Xin, ZHANG Jianxiong, MA Ruixin, WU Jiang’ai, CUI Ya’nan, CHEN Yu, ZHENG Baiqin, ZHANG Lifang. Comparative Analysis of the Microbial Community Structure in Litopenaeus vannamei Intestine and Surrounding Environment from Different Culture Patterns[J]. Journal of Henan Agricultural Sciences, 2023, 52(11): 133-145.

参考文献

［1］宋盛宪，李色东，陈丹，等.南美白对虾健康养殖技术［M］.2版. 北京：化学工业出版社，2020.
SONG S X，LI S D，CHEN D，et al.Healthy culture technology of Litopenaeus vannamei［M］.2nd ed. Beijing：Chemical Industry Press，2020.
［2］农业农村部渔业渔政管理局. 中国渔业统计年鉴［M］.北京：中国农业出版社，2021.
Fisheries Administration of Ministry of Agriculture and Rural Affairs.China fishery statistical yearbook［M］.Beijing：China Agriculture Press，2021.
［3］THITAMADEE S，PRACHUMWAT A，SRISALA J，et al.Review of current disease threats for cultivated penaeid shrimp in Asia［J］.Aquaculture，2016，452（1）：69⁃87.
［4］高晓华，张海强，伟安.凡纳滨对虾急性肝胰腺坏死病致病菌的分离鉴定、药敏特性及其组织病理学观察［J］.淡水渔业，2022，52（3）：82⁃90.
GAO X H，ZHANG H Q，WEI A.Isolation，identification and antibiotic susceptibility of bacterial pathogen associated with acute hepatopancreatic necrosis disease in Litopenaeus vannamei and its histopathological observations［J］.Freshwater Fisheries，2022，52（3）：82⁃90.
［5］HE Z，PAN L，ZHANG M，et al.Metagenomic comparison of structure and function of microbial community between water，effluent and shrimp intestine of higher place Litopenaeus vannamei ponds［J］.Journal of Applied Microbiology，2020，129（2）：243⁃255.
［6］DAI W，SHENG Z，CHEN J，et al.Shrimp disease progression increases the gut bacterial network complexity and abundances of keystone taxa［J］.Aquaculture，2020，517：734802.
［7］XIONG J，WANG K，WU J，et al.Changes in intestinal bacterial communities are closely associated with shrimp
disease severity［J］.Applied Microbiology and Biotechnology，2015，99（16）：6911⁃6919.
［8］XIONG J，ZHU J，DAI W，et al.Integrating gut microbiota immaturity and disease⁃discriminatory taxa to diagnose the initiation and severity of shrimp disease［J］.Environmental Microbiology，2017，19（4）：1490⁃1501.
［9］赵月季，郭海朋，张德民.不同养殖模式对凡纳滨对虾肠道微生物群落的影响［J］.水产学报，2021，45（2）：221⁃234.
ZHAO Y J，GUO H P，ZHANG D M.Effects of different culture patterns on the intestinal microbiota of Litopenaeus
vannamei［J］.Journal of Fisheries of China，2021，45（2）：221⁃234.
［10］FAN L，WANG Z，CHEN M，et al.Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment［J］.Science of The Total Environment，2019，657：1194⁃1204.
［11］HOU D，HUANG Z，ZENG S，et al.Comparative analysis of the bacterial community compositions of the shrimp intestine，surrounding water and sediment［J］.Journal of Applied Microbiology，2018，125（3）：792⁃799.
［12］金若晨，江敏，孙世玉，等.凡纳滨对虾养殖环境及肠道微生物群落特征分析［J］.水产学报，2020，44（12）：2037⁃2054.
JIN R C，JIANG M，SUN S Y，et al.Microbial community in Litopenaeus vannamei intestine and its aquaculture environment［J］.Journal of Fisheries of China，2020，44（12）：2037⁃2054.
［13］罗同阳，高庆华，董聪，等.白洋淀水域夏季细菌群落结构及与环境因子的关系［J］.淡水渔业，2021，51（1）：96⁃102.
LUO T Y，GAO Q H，DONG C，et al.Bacterial community structure in Baiyangdian lake in summer and its relationship with environmental factors［J］.Freshwater Fisheries，2021，51（1）：96⁃102.
［14］MAGOC T，SALZBERG S L.FLASH：Fast length adjustment of short reads to improve genome assemblies［J］.Bioinformatics， 2011， 27 （21）：2957⁃2963.
［15］EDGAR R C.UPARSE：Highly accurate OTU sequences from microbial amplicon reads［J］.Nature Methods，2013，10：996⁃998.
［16］EDGAR R C，HAAS B J，CLEMENTE J C，et al.UCHIME improves sensitivity and speed of chimera detection［J］.Bioinformatics， 2011， 27 （16）：2194⁃2200.
［17］DESANTIS T Z，HUGENHOLTZ P，LARSEN N，et al.Greengenes，a chimera⁃checked 16S rRNA gene database and workbench compatible with ARB［J］.Applied and Environmental Microbiology，2006，72（7）：5069⁃5072.
［18］SCHLOSS P D，WESTCOTT S L，RYABIN T，et al.Introducing mothur：Open⁃source，platform⁃independent，community⁃supported software for describing and comparing microbial communities［J］.Applied and Environmental Microbiology， 2009， 75 （23）：7537⁃7541.
［19］CAPORASO J G，KUCZYNSKI J，STOMBAUGH J，et al.QIIME allows analysis of high⁃throughput community sequencing data［J］.Nature Methods，2010，7（5）：335⁃336.
［20］WANG J，LI C，NESENGANI L T，et al.Characterization of vaginal microbiota of endometritis and healthy sows using high⁃throughput pyrosequencing of 16S rRNA gene［J］.Microbial Pathogenesis，2017，111：325⁃330.
［21］LI Z，ZHOU J，LIANG H，et al.Differences in alpha diversity of gut microbiota in neurological diseases［J］.Frontiers in Neuroscience，2022，16：879318.
［22］WANG H，JIANG X，HE Y，et al.Spatial and seasonal variations in bacterial communities of the Yellow Sea by T⁃RFLP analysis［J］.Frontiers of Environmental Science & Engineering in China，2009，3（2）：194⁃199.
［23］LIU H，WANG L，LIU M，et al.The intestinal microbial diversity in Chinese shrimp（Fenneropenaeus chinensis）
as determined by PCR⁃DGGE and clone library analyses［J］.Aquaculture，2011，317（1）：32⁃36.
［24］LIU Y，QIN Y，CHEN T，et al.A practical guide to amplicon and metagenomic analysis of microbiome data［J］.Protein & Cell，2021，12（5）：315⁃330.
［25］EILER A，BERTILSSON S.Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes［J］.Environmental Microbiology，2004，6（12）：1228⁃1243.
［26］SHIN N R，WHON T W，BAE J W.Proteobacteria：Microbial signature of dysbiosis in gut microbiota［J］.Trends in Biotechnology，2015，33（9）：496⁃503.
［27］LIU F，LIN G，GAO G，et al.Bacterial and archaeal assemblages in sediments of a large shallow freshwater
lake，Lake Taihu，as revealed by denaturing gradient gel electrophoresis［J］.Journal of Applied Microbiology，2009，106（3）：1022⁃1032.
［28］ZHANG M，PAN L，HUANG F，et al.Metagenomic analysis of composition，function and cycling processes of microbial community in water，sediment and effluent of Litopenaeus vannamei farming environments under different culture modes［J］.Aquaculture，2019，506：280⁃293.
［29］PEI P，LIU X，CHEN Y，et al.Effects of biological water purification grid on microbial community of culture environment and intestine of the shrimp Litopenaeus vannamei［J］.Aquaculture Research，2019，50（4）：1300⁃1312.
［30］BERNAL M G，CAMPA⁃CÓRDOVA Á I，SAUCEDO P E， et al.Isolation and in vitro selection of actinomycetes strains as potential probiotics for aquaculture［J］.Veterinary World，2015，8：170⁃176.
［31］章海鑫，余智杰，张燕萍，等.养殖模式对草鱼池塘底泥微生物群落结构影响的分析［J］.淡水渔业，2021，51（2）：3⁃12.
ZHANG H X，YU Z J，ZHANG Y P，et al.Effect of culture modes on microbial community structure of sediments in grass carp Ctenopharyngodon idellus ponds［J］.Freshwater Fisheries，2021，51（2）：3⁃12.
［32］FAN J，CHEN L，MAI G，et al.Dynamics of the gut microbiota in developmental stages of Litopenaeus vannamei reveal its association with body weight［J］.Scientific Reports，2019，9（1）：734.
［33］袁航，胡乃捷，陈俭，等.养殖密度对凡纳滨对虾生长性能及其肠道消化酶和菌群结构的影响［J］.南方农业学报，2023，54（1）：289⁃302.
YUAN H，HU N J，CHEN J，et al.Effects of stocking density on the growth performance，intestinal digestive
enzyme activities and microflora structure of Litopenaeus vannamei［J］.Journal of Southern Agriculture，2023，54（1）：289⁃302.
［34］ZHANG Z，TANG H，CHEN P，et al.Demystifying the manipulation of host immunity，metabolism，and extraintestinal tumors by the gut microbiome［J］.Signal Transduction and Targeted Therapy，2019，4：41.
［35］朱启飞，贺莹，李云，等.低聚木糖对低盐胁迫下凡纳滨对虾生长、免疫及肠道菌落的影响［J］.南方农业学报，2023，54（2）：618⁃628.
ZHU Q F， HE Y， LI Y， et al.Effects of xylo⁃oligosaccharides on growth，immunity and intestinal flora of Litopenaeus vannamei under low salinity stress［J］.Journal of Southern Agriculture，2023，54（2）：618⁃628.
［36］杨铿，蒋魁，洪敏娜，等.丁酸梭菌拌料投喂对凡纳滨对虾肠道上皮细胞及菌群结构的影响［J］.南方农业学报，2022，53（12）：3576⁃3583.
YANG K，JIANG K，HONG M N，et al.Effects of feedstuff contained Clostridium butyricum on intestinal epithelial cells and bacterial community structure in Litopenaeus vannamei［J］.Journal of Southern Agriculture，2022，53（12）：3576⁃3583.
［37］陈秀梅，王桂芹，单晓枫，等.鱼类肠道屏障损伤与肠道炎症发生发展关系的研究进展［J］.河南农业科学，2022，51（5）：1⁃9.
CHEN X M，WANG G Q，SHAN X F，et al.Research progress on the relationship between intestinal barrier damage and intestinal inflammation development in fish［J］.Journal of Henan Agricultural Sciences，2022，51（5）：1⁃9.
［38］郁维娜，戴文芳，陶震，等.健康与患病凡纳滨对虾肠道菌群结构及功能差异研究［J］.水产学报，2018，42（3）：399⁃409.
YU W N，DAI W F，TAO Z，et al.Characterizing the compositional and functional structures of intestinal microflora between healthy and diseased Litopenaeus vannamei［J］.Journal of Fisheries of China，2018，42（3）：399⁃409.

[1]	李文红, 郭涛, 向立刚, 余知和, 李添群. 3 种抗生素对小菜蛾肠道微生物群落的影响[J]. 河南农业科学, 2023, 52(7): 98-108.
[2]	魏全全, 顾小凤, 芶久兰, 张萌, 饶勇, 肖华贵. 氮肥及有机物料配施对黄壤冬油菜-玉米轮作田土壤微生物群落的影响[J]. 河南农业科学, 2023, 52(6): 41-50.
[3]	任元森, 张海波, 程红艳, 王雨萌, 罗渊, 刘娜. pH值对猪粪与菌糠共发酵产酸特性及微生物群落的影响[J]. 河南农业科学, 2023, 52(5): 110-120.
[4]	杨慧, 路风银, 韩俊豪, 谢永康, 尚朝杰, 李星仪. 高通量测序技术分析鲜食花生贮藏过程中真菌群落的的组成和变化[J]. 河南农业科学, 2023, 52(2): 171-180.
[5]	张涛, 周思旋, 唐远江, 陶小艳, 卢昱希, 杜春林, 王鲁, 齐维金, 郭云勋, 浦同灿. 黔中金荞麦提取物安全性评价及对大鼠肠道菌群的影响[J]. 河南农业科学, 2023, 52(11): 146-156.
[6]	郑天飞, 张倩颖, 李东亮, 张娟, 堵国成. 不同产地雪茄烟叶的风味特征和微生物群落分析[J]. 河南农业科学, 2022, 51(8): 45-54.
[7]	敖金成, 周桂夙, 李永梅. 连作烟田健株与根腐病感病烟株根际土壤微生物多样性研究[J]. 河南农业科学, 2022, 51(2): 86-96.
[8]	姬俊华, 杨瑞先, 刘萍, 王奥一, 李静宜, 孙高峰, 何艳红, 杜凡. 牡丹根腐病病株和健株根内微生物菌群的差异[J]. 河南农业科学, 2022, 51(11): 98-108.
[9]	宋宇. 稻蟹共作稻田根际土壤微生物群落与水稻产量的关联分析[J]. 河南农业科学, 2022, 51(10): 86-95.
[10]	徐佳敏, 王帅丽, 穆心愿, 赵霞, 唐保军, 夏来坤, 赵亚丽, 刘天学. 秸秆附着微生物对土壤养分、小麦根际细菌多样性及产量的影响[J]. 河南农业科学, 2022, 51(1): 60-70.
[11]	吴晓颖, 杨方岩, 李寿如, 贾景丽, 于秀梅, 刘大群, 赵伟全. 菌药协同防治马铃薯疮痂病后蛭石基质微生物菌群的变化[J]. 河南农业科学, 2022, 51(1): 89-96.
[12]	陈则东, 朱建平, 郭书玉, 卢炜, 刘蕾. 植物乳杆菌LR-39对犬的促生长及肠道菌群调节作用[J]. 河南农业科学, 2021, 50(3): 148-156.
[13]	柏秋月, 邓百万, 解修超, 张彩妮, 刘兰兰, 袁敏谦. 天麻病害发生与其真菌群落结构变化关系研究[J]. 河南农业科学, 2021, 50(1): 92-100.
[14]	李桂荣, 陈富凯, 贾胜勇, 王宗硕, 郭泽楠. 茄子秆生物炭联合黑麦草对土壤镉-芘复合污染修复的影响[J]. 河南农业科学, 2020, 49(9): 51-61.
[15]	谢朝, 付天岭, 何腾兵, 成剑波, 符东顺, 罗胜. Cd胁迫对马铃薯根际土壤细菌群落组成及多样性的影响[J]. 河南农业科学, 2020, 49(6): 48-58.