Metagenomic comparison of structure and function of microbial community between water, effluent and shrimp intestine of higher place Litopenaeus vannamei ponds

Journal of Applied MicrobiologyVolume 129, Issue 2 p. 243-255 Original Article Metagenomic comparison of structure and function of microbial community between water, effluent and shrimp intestine of higher place Litopenaeus vannamei ponds Z. He, orcid.org/0000-0003-2557-7255 The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorL. Pan, Corresponding Author panlq@ouc.edu.cn The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China Correspondence Luqing Pan, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, China. E-mail: panlq@ouc.edu.cnSearch for more papers by this authorM. Zhang, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorM. Zhang, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorF. Huang, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorS. Gao, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this author Z. He, orcid.org/0000-0003-2557-7255 The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorL. Pan, Corresponding Author panlq@ouc.edu.cn The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China Correspondence Luqing Pan, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, China. E-mail: panlq@ouc.edu.cnSearch for more papers by this authorM. Zhang, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorM. Zhang, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorF. Huang, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this authorS. Gao, The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, ChinaSearch for more papers by this author First published: 11 February 2020 https://doi.org/10.1111/jam.14610Citations: 7Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat Abstract Aims The present study aimed to reveal microbial relationship between shrimp intestine and ambient in higher place shrimp ponds from the aspects of composition and function. Methods and Results Metagenome and 16S rRNA gene sequencing were used to compare microbial compositions and functions of water, effluent and shrimp intestine in higher place Litopenaeus vannamei ponds. Although the three groups had similar dominant phyla, such as Proteobacteria, Bacteroidetes and Tenericutes, their bacterial compositions at the genus level were obviously different. Compared to effluent and intestine, the relative abundance of Vibrio as common opportunistic pathogen for shrimp was significantly higher in water. However, cluster analysis showed that intestinal microbial composition was more similar to that of effluent than water. Metagenomic data showed that the predominant microbial functions in the three groups were mostly related to energy production and biosynthesis, while carbohydrate metabolism was relatively enriched in intestinal microbiota. More importantly, Proteobacteria played a critical role in carbon metabolism and biosynthesis of amino acids in the three habitats, and Vibrio had the most functions related to bacterial virulence and infection. Conclusions Shrimp intestinal microbiota had a close correlation with the ambient microbiota in both structure and function. As the most dominant phylum, Proteobacteria was very important for microbiota communication and nutrient cycling in higher place shrimp ponds. Moreover, due to the pathogenicity, it was necessary to monitor the abundant changes of Vibrio in water to decrease the risk of shrimp disease outbreaks. Significance and Impact of the Study These above results may be helpful to comprehensively understand the characteristics and functions of microbiota in higher place shrimp ponds, thereby providing basic information for developing the management strategies of entire microbiota to sustain shrimp health. Citing Literature Supporting Information Filename Description jam14610-sup-0001-Supinfo.pdfPDF document, 377.6 KB Figure S1. PCA (Principal components analysis) based on the 16S rRNA sequencing profiles. Figure S2a. Relative abundances of top 10 dominant bacterial phyla among water (HW), effluent (HS) and shrimp intestine (HG) based on the metagenome sequencing profiles. Figure S2b. Relative abundances of top 10 dominant bacterial genera among water (HW), effluent (HS) and shrimp intestine (HG) based on the metagenome sequencing profiles. Figure S3. Vibrio harveyi Quorum sensing pathway. The number of Unigenes annotated on genes are reflected by colour legend. Blank colour represents no Unigenes annotated on it. Table S1. 16S rRNA gene sequencing and Alpha diversity metrics results of nine samples. Table S2. The relative abundance of the top 10 dominant bacterial phyla in water (HW), effluent (HS) and shrimp intestine (HG). Table S3. The relative abundance of the top 10 dominant bacterial genera in water (HW), effluent (HS) and shrimp intestine (HG). Table S4. Metadata statistics obtained from metagenome HW, HS and HG. Table S5. Top 10 KEGG pathways annotated by Unigenes of Proteobacteria in HW, HS and HG. Table S6. Top 10 KEGG pathways annotated by Unigenes of Vibrio in HW, HS and HG. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. Volume129, Issue2August 2020Pages 243-255 RelatedInformation