凡纳滨对虾肠道及其养殖环境的细菌群落结构研究

doi:10.3969/j.issn.1000-5641.2025.04.011

摘要/Abstract

摘要：

为探究温室大棚池塘养殖条件下凡纳滨对虾 (Litopenaeus vannamei) 肠道与养殖环境中细菌群落之间的关系, 采用Illumina Miseq高通量测序方法, 对凡纳滨对虾肠道、养殖水体及底泥细菌的16S rRNA基因2个高变区 (V3—V4) 进行测序分析. 结果显示, 凡纳滨对虾肠道与养殖环境中的细菌分布于62门175纲381目631科1141属2035种. 根据测序结果, 对虾肠道中变形菌门 (Proteobacteria)、放线菌门 (Actinobacteriota) 和绿弯菌门 (Chloroflexi) 为优势菌门, 平均占比分别为33.67%, 25.33%和12.77%; 养殖水体中的优势菌门为放线菌门、蓝细菌门 (Cyanobacteria) 和变形菌门, 平均占比分别为29.33%, 27.0%和21.33%; 底泥中的优势菌门为变形菌门、绿弯菌门和厚壁菌门 (Firmicutes), 平均占比分别为28.33%, 17.33%和11.13%. 对虾肠道、水体和底泥的细菌群落在部分指标上存在明显差异, 如底泥菌群的ACE (Abundance-based Coverage Estimator) 指数和Chao指数最高, 对虾肠道菌群次之, 水体菌群最低; 对虾肠道菌群的丰富度与水体菌群相似, 均高于底泥菌群; Shannon指数上, 对虾肠道菌群高于水体菌群, 但低于底泥菌群; Simpson指数上, 对虾肠道菌群高于底泥菌群, 但低于水体菌群. 在操作分类单元水平上, 对虾肠道和底泥中检测到1492个相同单元, 对虾肠道和水体中检测到588个相同单元. 系统聚类分析和主坐标分析结果显示, 对虾肠道和底泥的细菌群落结构较为相似. 本研究揭示了凡纳滨对虾肠道细菌生态结构与养殖环境的相关性, 为其科学养殖提供了数据支撑.

关键词: 凡纳滨对虾, 高通量测序, 细菌群落, 16S rRNA

Abstract:

The aim of this study was to compare the bacterial community structure of Litopenaeus vannamei in different cultivation environments. An Illumina MiSeq high-throughput sequencing-based method was used for detecting the 16S rRNA gene of the bacterial community in the intestine of L. vannamei and water and sediment samples from cultivation ponds. The results showed that the bacterial community in the intestine of L. vannamei and in the cultivation environment included 62 phyla, 175 classes, 381 orders, 631 families, 1141 genera, and 2035 species. Proteobacteria, Actinobacteriota, and Chloroflexi were the dominant bacterial phyla in the intestine of L. vannamei, with average percentages of 33.67%, 25.33%, and 12.77%, respectively. Proteobacteria, Chloroflexi, and Firmicutes were the dominant bacteria in the sediments, accounting for 28.33%, 17.33%, and 11.13%, respectively. The dominant bacteria in the water were Actinobacteria, Cyanobacteria, and Proteobacteria, with average percentages of 29.33%, 27.0%, and 21.33%, respectively. The abundance-based coverage estimator (ACE) and Chao diversity index of bacterial community in the intestine of L. vannamei were higher than those in the water, while lower than those in the sediments. The bacterial community richness in the intestine of L. vannamei was similar to that in water, but higher than that in the sediments. The Shannon index of the bacterial community in the intestine of L. vannamei was higher than that in the sediments, but lower than that in water. The Simpson index of the bacterial community in the intestine of L. vannamei was higher than that in the sediments but lower than that in the water. Nevertheless, some dominant bacterial species were similar in the intestine of L. vannamei and in the cultivation environment. At the operational taxonomic unit (OTU) level, 1492 identical units were detected in the intestines of L. vannamei and sediments, and 588 identical units were detected in the intestine of L. vannamei and water. Both cluster and principal coordinate analyses showed that the bacterial community in the intestine of L. vannamei was relatively similar to that in the sediments. This study explored the relationship between the bacterial community in the intestine of L. vannamei and its cultivation environment, providing valuable data for the scientific use of environmental probiotics, quality and production, and disease and epidemic prevention.

Key words: Litopenaeus vannamei, high-throughput sequencing, bacterial community structure, 16S rRNA

中图分类号:

S966
S917.4

金沁, 邱楚雯, 袁新程. 凡纳滨对虾肠道及其养殖环境的细菌群落结构研究[J]. 华东师范大学学报（自然科学版）, 2025, 2025(4): 104-113.

Qin JIN, Chuwen QIU, Xincheng YUAN. Study on bacterial community structure in the intestine of Litopenaeus vannamei and its cultivation environment[J]. J* E* C* N* U* N* S*, 2025, 2025(4): 104-113.

图/表 8

表1

图1

表2

表3

图2

图3

图4

图5

参考文献 38

1	MORIARTY D J W.. The role of microorganisms in aquaculture ponds. Aquaculture, 1997, 151 (1/2/3/4): 333- 349.
2	ABRAHAM T J, GHOSH S, NAGESH T S, et al.. Distribution of bacteria involved in nitrogen and sulphur cycles in shrimp culture systems of West Bengal, India. Aquaculture, 2004, 239 (1/2/3/4): 275- 288.
3	林国荣, 王春忠, 孙富林, 等.. 海水混养池塘虾蛤肠道与养殖环境的微生物多样性. 微生物学通报, 2018, 45 (9): 1989- 1999.
4	杨彬彬, 邵庆均.. 鱼类肠道微生物的研究进展. 中国饲料, 2013, (23): 1- 4.
5	ORCUTT B N, SYLVAN J B, KNAB N J, et al.. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiology and Molecular Biology Reviews, 2011, 75 (2): 361- 422.
6	冯丹, 高小迪, 李云凯.. 海洋鱼类肠道微生物研究进展及应用前景. 生态学杂志, 2021, 40 (1): 255- 265.
7	ROH S W, ABELL G C J, KIM K H, et al.. Comparing microarrays and next- generation sequencing technologies for microbial ecology research. Trends in Biotechnology, 2010, 28 (6): 291- 299.
8	EISENSTEIN M.. The hunt for a healthy microbiome. Nature, 2020, 577 (7792): S6- S8.
9	ECKBURG P B, BIK E M, BERNSTEIN C N, et al.. Diversity of the human intestinal microbial flora. Science, 2005, 308 (5728): 1635- 1638.
10	GAJARDO K, RODILES A, KORTNER T M, et al.. A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research. Scientific Reports, 2016, (6): 30893.
11	CLEMENTS K D, ANGERT E R, LINN MONTGOMERY W, et al.. Intestinal microbiota in fishes: What’s known and what’s not. Molecular Ecology, 2014, 23 (8): 1891- 1898.
12	油九菊, 柳敏海, 殷小龙, 等.. 基于高通量测序的东海带鱼肠道菌群结构分析. 渔业研究, 2018, 40 (6): 434- 440.
13	DEVARAJA T N, YUSOFF F M, SHARIFF M.. Changes in bacterial populations and shrimp production in ponds treated with commercial microbial products. Aquaculture, 2002, 206 (13/14): 245- 256.
14	VERSCUHERE L, ROMBAUT G, SORGELOOS P, et al.. Probiotic bacteria as biological control agents in aquaculture. Microbiology and Molecular Biology Reviews, 2000, 64 (4): 655- 671.
15	宛立, 王吉桥, 高峰, 等.. 南美白对虾肠道细菌菌群分析. 水产科学, 2006, 25 (1): 13- 15.
16	李可, 郑天凌, 田蕴, 等.. 南美白对虾肠道微生物群落的分子分析. 微生物学报, 2007, 47 (4): 649- 653.
17	孙振丽, 宣引明, 张皓, 等.. 南美白对虾养殖环境及其肠道细菌多样性分析. 中国水产科学, 2016, 23 (3): 594- 605.
18	张海耿, 吴小茜, 姜世豪, 等.. 不同养殖模式对南美白对虾生长性能及肠道菌群的影响. 渔业现代化, 2023, 50 (3): 27- 35.
19	邱楚雯, 袁新程, 施永海, 等.. 池塘鱼菜立体种养系统的微生物群落结构分析. 大连海洋大学学报, 2021, 36 (3): 454- 461.
20	翟万营, 郭安宁.. 鱼类肠道微生物研究进展. 河南水产, 2016, (4): 18- 21.
21	SPANGGAARD B, HUBER I, NIELSEN J, et al.. The microflora of rainbow trout intestine: A comparison of traditional and molecular identification. Aquaculture, 2000, 182 (1/2): 1- 15.
22	MIYAKE S, NGUGI D K, STINGL U.. Diet strongly influences the gut microbiota of surgeonfishes. Molecular Ecology, 2015, 24 (3): 656- 672.
23	钟蕾, 向建国, 曾丹, 等.. 饵料对鳡肠道微生物多样性的影响. 水生生物学报, 2016, 40 (4): 830- 835.
24	王姣姣, 李丹, 宋坚, 等.. 不同时期刺参养殖池塘海水菌群结构分析. 中国农业科技导报, 2015, 17 (2): 134- 140.
25	AULENTA F, DIONISI D, MAJONE, et al.. Effect of periodic feeding in sequencing batch reactor on substrate uptake and storage rates by a pure culture of Amaricoccus kaplicensis. Water Research, 2003, 37 (11): 2764- 2772.
26	金若晨. 凡纳滨对虾养殖池塘水质及养殖环境和虾肠道微生物群落结构研究 [D]. 上海: 上海海洋大学, 2020.
27	吴金凤, 熊金波, 王欣, 等.. 肠道菌群对凡纳滨对虾健康的指示作用. 应用生态学报, 2016, 27 (2): 611- 621.
28	尹军霞, 沈文英, 郦萍.. 水温对南美白对虾肠道菌群影响的研究. 海洋科学, 2004, 28 (5): 33- 36.
29	GATESOUPE F J.. The use of probiotics in aquaculture. Aquaculture, 1999, 180 (1/2): 147- 165.
30	SUN Z, LI G P, WANG C W, et al.. Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir. Scientific Reports, 2014, (4): 6966.
31	BOUTIN S, BERNATCHEZ L, AUDET C, et al.. Network analysis highlights complex interactions between pathogen, host and commensal microbiota. PLoS One, 2013, 8 (12): e84772.
32	LAVILLA-PITOGO C R, LEAÑO E M, PANER M G.. Mortalities of pond-cultured juvenile shrimp, Penaeus monodon, associated with dominance of luminescent vibrios in the rearing environment. Aquaculture, 1998, 164 (1/2/3/4): 337- 349.
33	ALONGE S, AIUDI G G, LACALANDRA G M, et al.. Pre- and probiotics to increase the immune power of colostrum in dogs. Frontiers in Veterinary Science, 2020, 7, 570414.
34	ABID R, WASEEM H, ALI J, et al.. Probiotic yeast Saccharomyces: Back to nature to improve human health. Journal of Fungi, 2022, 8 (5): 444.
35	STAROSILA D, RYBALKO S, VARBANETZ L, et al.. Anti-influenza activity of a Bacillus subtilis probiotic strain. Antimicrobial Agents and Chemotherapy, 2017, 61 (7): e00539.
36	LIANG Q, LIU Z, LI Z, et al.. Bacillus licheniformis affects the bacterial community in the zero-water exchange aquaculture system of Penaeus vannamei. Acta Microbiologica Sinica, 2023, 63 (10): 3923- 3938.
37	李鹏飞. 丁酸梭菌对南美白对虾肠道菌群和抗溶藻弧菌感染的影响 [D]. 山东泰安: 山东农业大学, 2023.
38	曾思源, 饶从稳, 韩坤煌, 等.. 饲料中添加乳酸菌对南美白对虾虾苗生长的影响. 水产养殖, 2022, 43 (8): 35- 39.

样品	序列数	碱基数	平均长度/bp	最短序列长度/bp	最长序列长度/bp
PB1	40277	16689501	414.37	201	472
PB2	50228	20835647	414.368	328	443
PB3	43770	18048962	414.821	360	444
SS1	47205	19738081	412.359	338	464
SS2	50414	21086018	418.135	337	481
SS3	50648	21160339	418.257	212	478
WS1	51628	21298860	417.792	247	476
WS2	50991	21033750	412.545	202	453
WS3	48464	19965823	412.499	247	441

成对样本	t 值	自由度(df)	p 值
PB1 vs. PB2	0.030	9	0.977
PB1 vs. PB3	–0.052	9	0.960
PB2 vs. PB3	–0.052	9	0.960
SS1 vs. SS2	–0.484	9	0.640
SS1 vs. SS3	–0.238	9	0.818
SS2 vs. SS3	0.368	9	0.722
WS1 vs. WS2	0.037	9	0.971
WS1 vs. WS3	0.292	9	0.777
WS2 vs. WS3	0.146	9	0.887
PB vs. WS	–2.856	9	0.019
PB vs. SS	0.538	9	0.603
SS vs. WS	2.067	9	0.069

样品	分类单元(OTU)	ACE 指数	Chao 指数	Shannon 指数	Simpson 指数
PB1	23622	1826.092	1702.357	5.318	0.022
PB2	23622	1753.956	1608.848	5.014	0.028
PB3	23622	1734.755	1666.508	5.420	0.013
SS1	23622	3150.131	2946.270	6.543	0.008
SS2	23622	3362.110	3133.345	6.380	0.014
SS3	23622	3218.741	2999.246	6.354	0.011
WS1	23622	1171.201	1125.484	4.775	0.025
WS2	23622	1421.824	1319.099	4.795	0.026
WS3	23622	1280.454	1185.641	4.699	0.027

[1]	蒋德明，马海龙，古丽斯坦·努尔艾合麦提，买尔丹·帕力合提. 华东师范大学在校生皮肤上葡萄球菌类型及其抗药性分析[J]. 华东师范大学学报(自然科学版), 20120, 2012(6): 122-130,138.
[2]	龚俊, 刘玉配, 李媛媛. 烟叶表面微生物类群两种检测方法的比较研究[J]. 华东师范大学学报(自然科学版), 2016, 2016(3): 92-101.
[3]	高云航, 王巍, 刘萌, 勾长龙, 娄玉杰, 马红霞. 白蚁肠道木质素分解菌PY12的分离鉴定及 lip基因的克隆[J]. 华东师范大学学报(自然科学版), 2014, 2014(4): 113-121, 179.