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浙江大学学报（农业与生命科学版）
Journal of Zhejiang University (Agriculture and Life Sciences)  2024, Vol. 50 Issue (1): 123-136    DOI: 10.3785/j.issn.1008-9209.2023.03.281
Animal Sciences & Veterinary Medicines     
Characteristics of microbial communities and their association with immunity and metabolism at the early developmental stage of Protosalanx chinensis
Yifan ZHOU1(),Xizhao ZHANG1,2(),Yanfeng ZHOU1,2,Dongpo XU1,2,Chenhe WANG1,Shiyue GUO1,Shulun JIANG2,Yang YOU1,2()
1.Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, Jiangsu, China
2.Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, Jiangsu, China
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Abstract  

In order to understand the changes and characteristics of microbial communities during early development of Protosalanx chinensis, samples were collected at five developmental periods, which are the embryonic period (heartbeat stage, XT), the endogenous nutrition period (the first day after hatching, H1), the mixed nutrition period (the fourth day after hatching, H4), the open feeding period (the seventh day after hatching, H7), and the exogenous nutrition period (the tenth day after hatching, H10). Microbial community succession during early development was observed by 16S rRNA gene sequencing technology, especially the characteristics and key microbial genera before and after feeding. Combined with the transcriptome data of the same batch of samples, the microbial genera related to immunity and metabolism were analyzed based on the association network method. The results showed that there were significant differences in β diversity among the different periods at the early developmental stage (P＜0.001). The dominant bacteria in the XT period were Flavobacterium and Chryseobacterium, and the dominant bacterium in the H1 period was Pseudomonas. The main bacteria in the H4 period were Flavobacterium and Pseudomonas. The main bacteria in H7 and H10 periods were Flectobacillus and Pseudomonas. The abundance of Pseudomonas was stable at all developmental periods. Node bacteria such as Flectobacillus were significantly associated with the expression of various immune and metabolic genes. This study has obtained the microbial succession information of the early developmental stage of P. chinensis for the first time, and screened out the dominant bacteria and node bacteria, which will provide references and ideas for the scaled cultivation of P. chinensis fry.

Key words： Protosalanx chinensis      early development      microbiota      16S rRNA      transcriptome     
Received: 28 March 2023      Published: 01 March 2024
CLC:  S917.4  
Corresponding Authors: Xizhao ZHANG,Yang YOU     E-mail: 18203889079@163.com;zhangxizhao@ffrc.cn;youy@ffrc.cn
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Yifan ZHOU
Xizhao ZHANG
Yanfeng ZHOU
Dongpo XU
Chenhe WANG
Shiyue GUO
Shulun JIANG
Yang YOU
Cite this article:

Yifan ZHOU,Xizhao ZHANG,Yanfeng ZHOU,Dongpo XU,Chenhe WANG,Shiyue GUO,Shulun JIANG,Yang YOU. Characteristics of microbial communities and their association with immunity and metabolism at the early developmental stage of Protosalanx chinensis. Journal of Zhejiang University (Agriculture and Life Sciences), 2024, 50(1): 123-136.

URL:

https://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2023.03.281     OR     https://www.zjujournals.com/agr/Y2024/V50/I1/123


大银鱼早期发育阶段微生物群落特征及其与免疫和代谢的关联

为了解大银鱼早期发育过程中的微生物群落变化规律与特征，采集大银鱼胚胎期（心跳期，XT）、内源性营养期（采样时间为孵化后第1天，记为H1）、混合性营养期（孵化后第4天，H4）、开口摄食期（孵化后第7天，H7）和外源性营养期（孵化后第10天，H10）5个发育时期的样本。通过16S rRNA基因测序技术观察大银鱼早期发育过程中的微生物群落演替，尤其是摄食前后的微生物群落特征和关键菌属；并结合同批次样品的转录组数据，基于关联网络方法重点分析了与免疫和代谢相关的菌属。结果显示：大银鱼早期发育阶段各时期的β多样性存在显著差异（P＜0.001），其中，XT的优势菌群为黄杆菌属（Flavobacterium）和金黄杆菌属（Chryseobacterium）；胚后H1时期的优势菌群为假单胞菌属（Pseudomonas）；H4时期的主要菌群为黄杆菌属和假单胞菌属；H7和H10时期的主要菌群为弯曲杆菌属（Flectobacillus）和假单胞菌属。假单胞菌属在各时期中稳定存在。与多种免疫和代谢基因表达显著相关的是弯曲杆菌属等节点菌属。本研究首次获得了大银鱼早期发育阶段的微生物演替信息，同时，筛选到的优势菌属与节点菌属将为大银鱼苗种的规模化培育提供思路和参考。


关键词： 大银鱼,  早期发育,  微生物,  16S rRNA,  转录组 
时期 Period

采样时间

Sampling time

肠道内食物

Intestinal food

卵黄囊

Yolk sac

XT心跳期无
H1孵化后第1天无约占鱼体积的3/4
H4孵化后第4天零星出现约占鱼体积的1/2
H7孵化后第7天轮虫约占鱼体积的1/4
H10孵化后第10天轮虫及桡足类卵黄囊消失
Table 1 Details of samples
Fig. 1 Schematic diagrams of five periods at the early developmental stage of P. chinensis
Fig. 2 α and β diversity analyses of microbial communities of five periodsA. Box plots of α diversity analysis (the Kruskal-Wallis method was used to test the significant differences between periods); B. β diversity analysis of NMDS based on Bray-Curtis distance.
Fig. 3 Microbial compositions of five periods (phylum level)1-3 represent three replicate samples under the same period. The same as Fig. 4.
Fig. 4 Microbial compositions of five periods (genus level)
Fig. 5 KEGG functional analysis of microbial communities of five periodsEach heat map represents a KEGG pathway secondary classification. Each color block represents the mean value of functional abundance of each period and is centered and scaled by row. Red represents a high abundance, and blue represents a low abundance.
Fig. 6 Microbial association networks of five periodsA. Microbial modular networks (each node represents an ASV, and the node size represents the average relative abundance of ASV. The red line segment indicates a negative correlation between the nodes, and the blue line segment indicates a positive correlation between the nodes); B. Analysis for Hub nodes of the modular network (the higher the Hub score, the higher the degree of association with other nodes).
Fig. 7 KEGG annotation and classification results of genes in microbial communities of five periods
Fig. 8 Association networks of microbial community and immune pathway related genesEach node represents an ASV or a gene, and the node’s size represents the igraph degree. Node label indicates the genus name to which the ASV belongs. The red line segment indicates a negative correlation between the nodes, and the blue line segment indicates a positive correlation between the nodes.
Fig. 9 Association networks of microbial community and metabolic pathway related genesA. Venn diagram about genes belonging to carbohydrate metabolism, amino acid metabolism, and lipid metabolism; B. Association network of microbial community and metabolic pathway related genes (each node represents an ASV or a gene, and the node’s size represents the igraph degree. Node label indicates genus name or gene name. The red line segment indicates a negative correlation between the nodes, and the blue line segment indicates a positive correlation between the nodes); C. Heat map of ASV nodes with igraph degree greater than 5; D. Heat map for gene nodes with igraph degree greater than 5. ANPR: Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium.
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