Article(id=1241376207107838021, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1241376204247331313, articleNumber=null, orderNo=null, doi=10.13343/j.cnki.wsxb.20230674, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1698854400000, receivedDateStr=2023-11-02, revisedDate=null, revisedDateStr=null, acceptedDate=1709136000000, acceptedDateStr=2024-02-29, onlineDate=1773896751429, onlineDateStr=2026-03-19, pubDate=1714752000000, pubDateStr=2024-05-04, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1773896751429, onlineIssueDateStr=2026-03-19, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1773896751429, creator=13701087609, updateTime=1773896751429, updator=13701087609, issue=Issue{id=1241376204247331313, tenantId=1146029695717560320, journalId=1192105938417971205, year='2024', volume='64', issue='5', pageStart='1331', pageEnd='1682', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=0, createTime=1773896750747, creator=13701087609, updateTime=1773897643611, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1241379949253284790, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1241376204247331313, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1241379949253284791, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1241376204247331313, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=1455, endPage=1468, ext={EN=ArticleExt(id=1241376208953331786, articleId=1241376207107838021, tenantId=1146029695717560320, journalId=1192105938417971205, language=EN, title=Characteristics of bacterial communities in different habitats of the biofloc-based culture system ofPenaeus vannamei, columnId=1241045257748533520, journalTitle=Acta Microbiologica Sinica, columnName=Research Articles, runingTitle=null, highlight=null, articleAbstract=

[Objective] The biofloc-based culture system (BFS) ofPenaeus vannamei is a new ecological shrimp production mode based on the concept of cultivating and regulating the microbial community in the aquaculture system. However, the characteristics and assembly processes of microbial communities in different habitats of the BFS remain unclear. [Methods] The 16S rRNA gene sequencing was employed to explore the bacterial community composition in three different habitats (water, bioflocs, and shrimp gut) of the BFS. SourceTracker and the neutral model were adopted to explore the characteristics and assembly processes of bacterial communities in different habitats. [Results] The bacterial community diversity and composition varied significantly in the three habitats, and the structures and composition of bacterial communities were similar between bioflocs and shrimp gut. SourceTracker results showed that 98.76% of bacterial taxa in the shrimp gut were sourced from bioflocs, and only 0.83% were derived from water.Ruegeria existed in all the three habitats, with the relative abundance of 1.72%, 7.34%, and 6.00% in water, bioflocs, and shrimp gut, respectively. The unique amplicon sequence variants (ASVs) showed the maximal number of 89 in water, mainly belonging toMariculis andOwenweeksia. Bioflocs contained 56 ASVs, which were mainlyRheinheimera. Only 10 ASVs were present in the shrimp gut, mainly belonging toRoseobacter. The bacterial communities in water, bioflocs, and shrimp gut were all fit to the neutral model, which indicated that the bacterial communities in the three habitats were dominated by the neutral process. [Conclusion] The microbial communities in different habitats of the BFS were significantly different, and the intestinal bacteria of shrimp mainly came from bioflocs. The assembly processes in the three habitats were dominated by neutral processes. The results provide a theoretical basis for regulating the microbial community in the BFS.

, correspAuthors=Haipeng GUO, authorNote=null, correspAuthorsNote=
*GUO Haipeng, E-mail:
, copyrightStatement=Copyright ©2024 Acta Microbiologica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Nan LUO, Guimeng LU, Fan GAO, Chen CHEN, Demin ZHANG, Haipeng GUO), CN=ArticleExt(id=1241376213890027668, articleId=1241376207107838021, tenantId=1146029695717560320, journalId=1192105938417971205, language=CN, title=凡纳滨对虾生物絮团养殖系统中不同生境细菌群落特征, columnId=1192149544164012138, journalTitle=微生物学报, columnName=研究报告, runingTitle=null, highlight=null, articleAbstract=

【目的】凡纳滨对虾生物絮团养殖系统(biofloc-based culture system, BFS)是一种基于培育和调控微生物群落的新型生态养殖模式。然而,目前对于BFS在不同生境中的微生物群落特征及其构建过程还不清楚。【方法】采用16S rRNA基因测序技术探究BFS在3种不同生境(水体、絮团和对虾肠道)的细菌群落组成;通过溯源分析和中性模型等方法,探究不同生境细菌群落的特征及其构建过程。【结果】3种生境的微生物群落多样性和组成具有显著性差异,絮团和对虾肠道的群落结构和组成最为相似,溯源结果显示对虾肠道有98.76%的细菌类群来自絮团,仅有0.83%的细菌类群来自水体;3种生境共有的细菌主要为鲁杰氏菌(Ruegeria),在水体、絮团和对虾肠道中的丰度分别为1.72%、7.34%和6.00%,水体中特有的扩增子变异序列(amplicon sequence variants, ASV)数量为89个,主要属于海茎状菌(Maricaulis)和欧文威克斯菌(Owenweeksia),絮团中有56个,主要为莱茵海默氏菌(Rheinheimera),而对虾肠道中仅有10个,主要属于玫瑰杆菌(Roseobacter);中性模型结果表明,水体、絮团和对虾肠道细菌群落构建均符合中性模型,表明3种生境中细菌群落构建均受中性过程主导。【结论】在BFS系统中,不同生境的微生物群落具有显著差异,对虾肠道细菌主要来自生物絮团,而3种生境的细菌群落构建过程由中性过程主导。这些结果为调控生物絮团养殖系统中微生物群落提供了理论依据。

, correspAuthors=郭海朋, authorNote=null, correspAuthorsNote=null, copyrightStatement=版权所有©《微生物学报》编辑部2024, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=MqHymBirbqCP+8s7wi0zbg==, magXml=PdL87mPY/Oa0hOaLCpe+qg==, pdfUrl=null, pdf=7rLRv/jMU1BryCyAvHfTpQ==, pdfFileSize=1287874, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=YcfvvLg4LtATiWRPEdOw5Q==, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=cjfpOfEti7rPAzskzjGsjQ==, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=罗楠, 卢贵盟, 高繁, 陈琛, 张德民, 郭海朋)}, authors=[Author(id=1241446115619435005, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, orderNo=0, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1241446115783012869, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, authorId=1241446115619435005, language=EN, stringName=Nan LUO, firstName=Nan, middleName=null, lastName=LUO, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, 2, address=1 State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China
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tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=EN, label=Figure 1, caption=Biofloc culture system and bioflocs. A: Biological floc culture barrels and aquaculture water bodies. B: Inhofer conical barrels for biofloc sedimentation. C: The color and shape of the bioflocs., figureFileSmall=cyW9YhfUm6OFUnLfwnTF8g==, figureFileBig=eaykX6Pai7EpUoVLeV5/RQ==, tableContent=null), ArticleFig(id=1241446122477122311, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=CN, label=图1, caption=生物絮团养殖系统及生物絮团

A:生物絮团养殖桶及养殖水体. B:英霍夫锥形桶进行生物絮团沉降. C:生物絮团颜色及形状

, figureFileSmall=cyW9YhfUm6OFUnLfwnTF8g==, figureFileBig=eaykX6Pai7EpUoVLeV5/RQ==, tableContent=null), ArticleFig(id=1241446122623922962, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=EN, label=Figure 2, caption=Bacterial communities alpha diversity indices in different habitats. A: Richness. B: Shannon index. C: Chao1 index. D: PD_whole_tree index. Different letters indicate a significant difference between groups at theP<0.05 level., figureFileSmall=0QpUKc/XJfTjWk1kU8cBsw==, figureFileBig=aF1IIaF29cjMJq61G1ABZQ==, tableContent=null), ArticleFig(id=1241446122753946396, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=CN, label=图2, caption=不同生境细菌群落α多样性指数

A:Richness. B:Shannon指数. C:Chao1指数. D:PD_whole_tree指数. 不同字母表示各组之间在P<0.05水平上有显著性差异

, figureFileSmall=0QpUKc/XJfTjWk1kU8cBsw==, figureFileBig=aF1IIaF29cjMJq61G1ABZQ==, tableContent=null), ArticleFig(id=1241446122900747041, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=EN, label=Figure 3, caption=Analysis of the β diversity of bacterial communities in different habitats. A: PCoA cluster analysis between different habitats. B: Distances within sample groups in different habitats. C: Distances between different habitats. * indicates significant differences at different levels (*:P<0.05; **:P<0.01; ***:P<0.001)., figureFileSmall=Pl8KDVMpfDcqWfGxK0x/HA==, figureFileBig=SFCZt31HnGnGaRvQlEd8Rg==, tableContent=null), ArticleFig(id=1241446123022381863, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=CN, label=图3, caption=不同生境细菌群落的β多样性分析

A:不同生境间的PCoA聚类分析. B:不同生境样本组内距离. C:不同生境之间两两比较的距离. *表示在不同水平上有显著性差异(*:P<0.05;**:P<0.01;***:P<0.001)

, figureFileSmall=Pl8KDVMpfDcqWfGxK0x/HA==, figureFileBig=SFCZt31HnGnGaRvQlEd8Rg==, tableContent=null), ArticleFig(id=1241446123139822379, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=EN, label=Figure 4, caption=Mean relative abundance of dominant bacterial genera (average relative abundance>1% in at least one sample) in different habitats., figureFileSmall=oqnndeoSDyt4BV7i2YqV9A==, figureFileBig=0RoYyb2E2JphBz+a7/3S9g==, tableContent=null), ArticleFig(id=1241446123248874291, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=CN, label=图4, caption=不同生境中优势细菌属(至少在一个样品中平均相对丰度>1%)的平均相对丰度, figureFileSmall=oqnndeoSDyt4BV7i2YqV9A==, figureFileBig=0RoYyb2E2JphBz+a7/3S9g==, tableContent=null), ArticleFig(id=1241446123387286331, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=EN, label=Figure 5, caption=Analysis of core microorganisms and their sources in the intestinal bacterial communities of water biofloc and gut. A: Venn analysis of bacterial communities at ASV levels in different habitats. B: Relative abundance of genus-level bacterial taxa common to water, biofloc, and gut. C: Analysis of the percentage of contribution of bacterial sources in different habitats based on SourceTracker., figureFileSmall=JMDQgNaROmuNgVs0pixBYw==, figureFileBig=IoNMMiZ1F+hz225jzEjZqA==, tableContent=null), ArticleFig(id=1241446123496338243, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=CN, label=图5, caption=水体、生物絮团和对虾肠道细菌群落核心微生物及其来源分析

A:不同生境ASV水平的细菌群落的Venn分析. B:水体、生物絮团、对虾肠道所共有的属水平细菌类群的相对丰度. C:基于SourceTracker分析不同生境中细菌来源的贡献百分比

, figureFileSmall=JMDQgNaROmuNgVs0pixBYw==, figureFileBig=IoNMMiZ1F+hz225jzEjZqA==, tableContent=null), ArticleFig(id=1241446123588612939, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=EN, label=Figure 6, caption=Specificity-occupancy of species in the intestinal bacterial communities of water, biofloc, and gut (SPEC-OCCU figure). A: SPEC-OCCU plots of ASVs in three habitats, with thex-axis representing the occupancy rate, the distribution of ASV in all samples; They-axis represents specificity, whether these ASVs are present in other samples. B: Pie plots showing the number of ASVs specific to the three habitats. C: Taxonomic composition at the level of specific species of the three habitats., figureFileSmall=SjnChj2p0Ipf+yee35xSgQ==, figureFileBig=HUT9btLwSY44JpfnUOlowA==, tableContent=null), ArticleFig(id=1241446123706053460, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=CN, label=图6, caption=水体、生物絮团和对虾肠道细菌群落物种的特异性-占有率(SPEC-OCCU图)

A:3种生境ASV的SPEC-OCCU图,x轴代表占用率,即ASV在所有样本中的分布情况;y轴代表特异性,即这些ASV是否存在于其他样本中. B:饼状图显示3种生境特异性ASV数量. C:3种生境的特异种属水平的类群组成

, figureFileSmall=SjnChj2p0Ipf+yee35xSgQ==, figureFileBig=HUT9btLwSY44JpfnUOlowA==, tableContent=null), ArticleFig(id=1241446123810911066, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=EN, label=Figure 7, caption=Neutral model of the construction process of intestinal bacterial communities in water, biofloc, and gut. Nm represents the product of metacommunity and migration rate., figureFileSmall=T2UxcFJKtLOv22dLtcxUuw==, figureFileBig=qXj4j2KrT1zHInCvJuPw8Q==, tableContent=null), ArticleFig(id=1241446123924157280, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1241376207107838021, language=CN, label=图7, caption=水体、生物絮团和对虾肠道细菌群落构建过程的中性模型

Nm表示元群落与迁移率的乘积

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凡纳滨对虾生物絮团养殖系统中不同生境细菌群落特征
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罗楠 1, 2 , 卢贵盟 1, 2 , 高繁 1, 2 , 陈琛 3 , 张德民 1, 2 , 郭海朋 1, 2, *
微生物学报 | 研究报告 2024,64(5): 1455-1468
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微生物学报 | 研究报告 2024, 64(5): 1455-1468
凡纳滨对虾生物絮团养殖系统中不同生境细菌群落特征
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罗楠1, 2, 卢贵盟1, 2, 高繁1, 2, 陈琛3, 张德民1, 2, 郭海朋1, 2, *
作者信息
  • 1 宁波大学 农产品质量安全危害因子与风险防控国家重点实验室, 浙江 宁波 315211
  • 2 宁波大学海洋学院, 浙江 宁波 315211
  • 3 浙江省海洋水产研究所, 浙江 温州 325005
Characteristics of bacterial communities in different habitats of the biofloc-based culture system ofPenaeus vannamei
Nan LUO1, 2, Guimeng LU1, 2, Fan GAO1, 2, Chen CHEN3, Demin ZHANG1, 2, Haipeng GUO1, 2, *
Affiliations
  • 1 State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, Zhejiang, China
  • 2 School of Marine Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
  • 3 Zhejiang Marine Fisheries Research Institute, Wenzhou 325005, Zhejiang, China
出版时间: 2024-05-04 doi: 10.13343/j.cnki.wsxb.20230674
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【目的】凡纳滨对虾生物絮团养殖系统(biofloc-based culture system, BFS)是一种基于培育和调控微生物群落的新型生态养殖模式。然而,目前对于BFS在不同生境中的微生物群落特征及其构建过程还不清楚。【方法】采用16S rRNA基因测序技术探究BFS在3种不同生境(水体、絮团和对虾肠道)的细菌群落组成;通过溯源分析和中性模型等方法,探究不同生境细菌群落的特征及其构建过程。【结果】3种生境的微生物群落多样性和组成具有显著性差异,絮团和对虾肠道的群落结构和组成最为相似,溯源结果显示对虾肠道有98.76%的细菌类群来自絮团,仅有0.83%的细菌类群来自水体;3种生境共有的细菌主要为鲁杰氏菌(Ruegeria),在水体、絮团和对虾肠道中的丰度分别为1.72%、7.34%和6.00%,水体中特有的扩增子变异序列(amplicon sequence variants, ASV)数量为89个,主要属于海茎状菌(Maricaulis)和欧文威克斯菌(Owenweeksia),絮团中有56个,主要为莱茵海默氏菌(Rheinheimera),而对虾肠道中仅有10个,主要属于玫瑰杆菌(Roseobacter);中性模型结果表明,水体、絮团和对虾肠道细菌群落构建均符合中性模型,表明3种生境中细菌群落构建均受中性过程主导。【结论】在BFS系统中,不同生境的微生物群落具有显著差异,对虾肠道细菌主要来自生物絮团,而3种生境的细菌群落构建过程由中性过程主导。这些结果为调控生物絮团养殖系统中微生物群落提供了理论依据。

凡纳滨对虾  /  生物絮团养殖系统  /  不同生境  /  细菌群落  /  构建过程

[Objective] The biofloc-based culture system (BFS) ofPenaeus vannamei is a new ecological shrimp production mode based on the concept of cultivating and regulating the microbial community in the aquaculture system. However, the characteristics and assembly processes of microbial communities in different habitats of the BFS remain unclear. [Methods] The 16S rRNA gene sequencing was employed to explore the bacterial community composition in three different habitats (water, bioflocs, and shrimp gut) of the BFS. SourceTracker and the neutral model were adopted to explore the characteristics and assembly processes of bacterial communities in different habitats. [Results] The bacterial community diversity and composition varied significantly in the three habitats, and the structures and composition of bacterial communities were similar between bioflocs and shrimp gut. SourceTracker results showed that 98.76% of bacterial taxa in the shrimp gut were sourced from bioflocs, and only 0.83% were derived from water.Ruegeria existed in all the three habitats, with the relative abundance of 1.72%, 7.34%, and 6.00% in water, bioflocs, and shrimp gut, respectively. The unique amplicon sequence variants (ASVs) showed the maximal number of 89 in water, mainly belonging toMariculis andOwenweeksia. Bioflocs contained 56 ASVs, which were mainlyRheinheimera. Only 10 ASVs were present in the shrimp gut, mainly belonging toRoseobacter. The bacterial communities in water, bioflocs, and shrimp gut were all fit to the neutral model, which indicated that the bacterial communities in the three habitats were dominated by the neutral process. [Conclusion] The microbial communities in different habitats of the BFS were significantly different, and the intestinal bacteria of shrimp mainly came from bioflocs. The assembly processes in the three habitats were dominated by neutral processes. The results provide a theoretical basis for regulating the microbial community in the BFS.

Penaeus vannamei  /  biofloc-based culture system  /  different habitats  /  bacterial community  /  assembly process
罗楠, 卢贵盟, 高繁, 陈琛, 张德民, 郭海朋. 凡纳滨对虾生物絮团养殖系统中不同生境细菌群落特征. 微生物学报, 2024 , 64 (5) : 1455 -1468 . DOI: 10.13343/j.cnki.wsxb.20230674
Nan LUO, Guimeng LU, Fan GAO, Chen CHEN, Demin ZHANG, Haipeng GUO. Characteristics of bacterial communities in different habitats of the biofloc-based culture system ofPenaeus vannamei[J]. Acta Microbiologica Sinica, 2024 , 64 (5) : 1455 -1468 . DOI: 10.13343/j.cnki.wsxb.20230674
凡纳滨对虾(Penaeus vannamei)是我国重要的水产养殖经济物种,2021年中国凡纳滨对虾养殖产量达197.74万t[1]。然而随着对虾高密度、集约化、工厂化的养殖[2],以高产为目的的高密度养殖模式弊端逐渐呈现。集约化、高密度养殖极易引起水质恶化,导致病害频发,严重制约了我国对虾养殖业的可持续发展。生物絮团技术通过在水体中添加额外的碳源,促使水体中形成絮团悬浮物,已被广泛地用于降低集约化养殖系统中对虾病害的发生[3-4]。该养殖系统有利于维持环境的可持续性和生态系统的稳定性,在很大程度上依赖于系统中的微生物群落,特别是高碳氮比刺激下的异养细菌[5]
生物絮团养殖系统(biofloc-based culture system, BFS)中异养细菌的积累,不仅有效地将氨或有机氮废物转化为细菌的蛋白质,形成的絮团悬浮物还可以被对虾摄食,进而降低饲料成本[6-7]。水体环境的改善又对养殖系统微生物菌群的稳定性产生了积极的影响,从而为对虾提供了有利的生存环境。此外,水体和絮团中的微生物群落可以通过摄食进入对虾肠道,进而显著影响对虾肠道的微生物群落结构[8]。之前研究表明,对虾肠道菌群与环境微生物密切相关,尤其是在BFS中[9]。然而,更深层次地理解环境微生物如何影响肠道菌群,以及对虾肠道与环境微生物的相互作用仍很缺乏。
基于此,本研究通过向对虾养殖系统中添加葡萄糖进行生物絮团养殖,系统地分析了葡萄糖添加对水体、絮团和肠道细菌群落结构和组成的差异,以及不同生境中微生物群落的互作特征及构建过程,以期为BFS中微生物群落的定向调控提供理论依据。
本实验在宁波市咸祥镇(121°48′34″E, 29°40′18″N)某水产养殖场进行。采用规范一致的对虾养殖体系(600 L),该体系为经简易改装的圆形养殖桶,均配备增氧、排污和补水装置。葡萄糖按商品饲料添加量的64.5%添加葡萄糖(C含量为40.0%),以维持输入碳氮比约为10[10],设置6个重复。养殖第10天开始产生生物絮团(图1),至第24天,生物絮团量趋于稳定,维持在30 mL/L左右。在养殖第32天时,分别采集BFS水环境(水体和絮团)和对虾肠道微生物样品。具体方法如下:每桶采集1 000 mL表层水,水样先用100 μm筛绢过滤,收集筛绢上的絮状物,即为絮团样品。收集100 μm筛绢过滤后的滤液,再用孔径为0.22 μm的碳酸纤维素酯滤膜(Millipore公司)过滤,滤膜收集的为水体微生物样品。每桶采集15只对虾,用灭菌牙签挑取对虾肠道,每5只对虾肠道混为一个样品,装入灭菌EP管中,即为对虾肠道样品。所有采集样品置于−80 ℃冰箱中保存。
按照试剂盒说明书,使用PowerSoil DNA (MOBIO公司)提取水体和絮团样品的核酸DNA,使用QIAamp DNA (QIAGEN公司)试剂盒提取对虾肠道样品核酸DNA。用分光光度计(NanoDrop公司)测定DNA浓度和纯度。选用带barcode的通用引物338F (5′-ACTCCTACGGAG GCAGCAG-3′)和806R (5′-GGACTACHVGGGT WTCTAAT-3′)扩增细菌16S rRNA基因的V4区[11]。PCR扩增体系:上、下游引物(10 mmol/L)各0.5 µL,2×Mix 12.5 µL,DNA模板2 µL,ddH2O 9.5 µL,每个样品设置3个重复。PCR扩增条件:95 ℃预变性3 min;95 ℃变性30 s,55 ℃退火30 s,72 ℃延伸45 s,27个循环;72 ℃延伸10 min。扩增产物使用试剂盒(TaKaRa公司)进行纯化,用Agilent 2100生物测定仪(Agilent公司)检测片段大小,然后用Qubit 2.0荧光光度计(Life Technologies公司)定量。最后,对PCR产物进行等摩尔量混合,在Illumina MiSeq平台上进行测序。
利用QIIME 2平台对测序数据进行处理,使用DADA2方法鉴定和去除序列中的嵌合体。将相似性为100%的序列归为同一扩增子变异序列(amplicon sequence variants, ASV)[12]。与SILVA138数据库进行比对,以获取物种分类信息,去除古菌(archaea)、叶绿体(chloroplast)、线粒体(mitochondria)及不能分类到的细菌界的序列,并生成各个分类水平的物种组成信息,随后每个样品随机选取35 860条序列进行分析。
使用R语言“Vegan”函数计算各样品中细菌群落的α多样性指数,并使用IBM SPSS Statistics 27进行方差分析(one-way analysis of variance, one-way ANOVA)检验水体、絮团及肠道微生物群落的差异;利用“Vegan”函数对不同组别的细菌用基于Bray-Curtis非相似性的主坐标分析(primary coordinate analysis, PCoA)对水体、絮团及肠道微生物群落组成的整体变化进行可视化,并通过聚类分析进一步展现各组间群落Bray-Curtis距离;在细菌属水平(至少在一个样品中平均相对丰度>1%)水平分析优势细菌群落组成;使用Venn图分析水体、絮团和对虾肠道菌群的差异和联系;利用SourceTracker分析不同生境中总细菌群落的来源[13];根据Dufrene和Legendre[14]计算特异性和占有率,特异性(公式1)定义为生境(H)样本中物种的平均丰度(S);占有率(公式2)定义为S在H的样本中出现的相对频率。
公式1中,NindividualsS, H为生境H所有样本中ASV个体的平均数量,而NindividualsS是所有栖息地的平均个体数S的总和;公式2中,NsitesS, H为H中存在S的样本数,而NsitesH为H中样本总数。这两个指标随后被用作SPEC-OCCU图中的轴。为了评估不同养殖生境微生物群落组装的生态过程,使用Burns等[15]的R包构建中性模型。
三种生境的细菌群落α多样性指数(Richness、Shannon指数、Chao1指数、PD_whole_tree指数)显著不同。水体细菌群落的Richness和Chao1指数显著高于絮团和对虾肠道,对虾肠道细菌群落最低,絮团细菌群落的Shannon指数显著高于水体和对虾肠道(P<0.05) (图2)。PCoA结果表明不同生境细菌群落结构明显分离,水体细菌群落显著偏离絮团和对虾肠道,而絮团和对虾肠道细菌群落联系较为紧密(图3A)。相较于絮团和对虾肠道,水体的细菌类群波动性更大,稳定性较差,组内变异更大(图3B)。水体微生物群落与絮团、对虾肠道微生物距离较远且具有显著性差异,絮团和对虾肠道的距离更为接近(图3C)。
BFS不同生境的细菌优势类群在属水平上显著不同(图4)。水体中最丰富的类群为海生杆菌(Marivita, 35.14%)、潮滩杆状菌(Aestuariibacter, 11.39%)、海胞菌(Marinicella, 4.20%)和鲁杰氏菌(Ruegeria, 3.11%);絮团中最丰富的类群为弧菌(Vibrio, 22.14%)、Ruegeria (12.75%),假交替单胞菌(Pseudoalteromonas, 6.68%)、运动单胞菌(Motilimonas, 6.06%)、Marinicella (5.31%)和黏着杆菌(Tenacibaculum, 4.59%);在对虾肠道生境中最丰富的类群为Vibrio (32.46%)、Pseudoalteromonas (16.35%)、Ruegeria (15.33%)和Roseobacter_clade_CHAB-I-5_ lineage (6.24%)。以上结果表明,絮团和对虾肠道的细菌组成更相似,主要优势类群为弧菌、假交替单胞菌和鲁杰氏菌,而它们与水体微生物群落组成差异较大。
在ASV水平上,水体、絮团和对虾肠道3种生境共享的ASV数为223个,特有的ASV数分别为792、418和159个(图5A)。共享223个ASV的相对丰度在水体、絮团和对虾肠道中分别为74.38%、94.93%和99.77%,其中水体中的优势类群主要为Marivita (23.50%)、Marinicella (1.92%)、Ruegeria (1.72%)和小海员杆菌(Nautella, 1.43%);絮团中主要为Vibrio (12.52%)、Ruegeria (7.34%)、Pseudoalteromonas (4.10%)、Motilimonas (3.59%)和Marinicella (3.42%);对虾肠道中主要为Vibrio (12.74%)、Pseudoalteromonas (6.76%)、Ruegeria (6.00%)、Motilimonas (2.90%)和Roseobacter_clade_ CHAB-I-5_lineage (2.47%) (图5B)。SourceTracker分析结果表明对虾肠道中的98.76%的细菌类群来自于生物絮团,仅有0.83%的细菌群落来自于水体。此外,75.07%絮团细菌类群来自于对虾肠道,7.56%的来自于水体(图5C)。
细菌类群特异性和占有率结果表明,不同生境间的ASV都具有均匀的占有率,即在所有样点的ASV数量都相似。为了找到归属于每种生境的特殊物种,选择了特异性和占用率大于或等于0.7的ASV (图6A中的点框)。这些特异性ASV的数量在水体、絮团和对虾肠道3个生境间差异显著,分别为89、56和10个(图6B)。在属水平对这些特异性ASV组成进行分析发现,在水体中海茎状菌(Maricaulis, 6.16%)、欧文威克斯菌(Owenweeksia, 3.83%)、斯塔普氏菌(Stappiaceae, 2.21%)的相对丰度较高;在生物絮团中Rheinheimera (1.96%)的相对丰度较高;对虾肠道中Roseobacter_clade_CHAB-I-5_lineage (2.47%)、Vibrio (1.23%)、Pseudoalteromonas (1.20%)的相对丰度较高(图6C)。该结果表明,在不同生境之间其特异性ASV数量不同,特异性微生物类群组成也不同,凸显了不同生境之间的独特性。
三种生境的细菌群落构建过程均符合中性模型(R2>0),表明BFS不同生境的细菌群落的构建主要由中性过程主导(图7)。中性群落模型成功地估计了ASV的出现频率与其相对丰度变化之间的大部分关系,在水体、絮团中均有很高的解释率,分别为0.630和0.694,而肠道解释率最低,为0.340。此外,细菌类群在水体的Nm值(Nm=2 599)高于絮团(Nm=1 343)和对虾肠道(Nm=327),表明细菌的物种扩散在水体中高于絮团和对虾肠道。在高于中性预测部分中絮团和对虾肠道的组成更为相似,水体中占相对丰度较高的为TenacibaculumMarinicella,絮团和对虾肠道中主要为VibrioRuegeria;低于中性预测部分中各生境之间的组成差异较大,水体中主要为MarivitaAestuariibacter,絮团为VibrioMarinicella,对虾肠道大部分都为Vibrio;在符合中性预测的部分中,絮团和对虾肠道更为相似,水体主要为MarivitaAestuariibacter,絮团和对虾肠道丰度较高的为VibrioRuegeriaPseudoalteromonas (图8)。
凡纳滨对虾的健康生长与养殖环境的微生物群落变化密切相关[16],细菌群落在养殖中起着关键作用,在许多生态系统中微生物作为关键的驱动因素,在养分循环、有机物分解、水生动物的共生和致病中发挥着重要作用[17-18],尤其是在BFS中,通过添加碳源调节碳氮比(C/N)可以有效地改善养殖环境,减少养殖水体中有机物的积累,降低有毒氮素对养殖动物产生的胁迫[6]。本研究发现,BFS三种生境的α多样性显著不同,养殖水体微生物群落结构发生明显改变,絮团与对虾肠道的微生物群落结构更为相似。现有的研究表明,在养殖系统中添加葡萄糖、淀粉和木薯渣等碳源,可以显著改变对虾养殖系统的细菌群落结构和组成[19]。在水体中添加碳源会显著富集某些特异性细菌类群,从而使养殖水体的细菌群落产生较大差异[20]。葡萄糖添加使絮团与对虾肠道的多样性更加相似,这可能与养殖过程中对虾会摄食絮团有关。这与之前的研究结果相似,絮团可以被对虾摄食,因此改变对虾肠道微生物群落,这种现象在自然养殖系统也同样存在,肠道的细菌群落更接近于沉积物而不是养殖水体[21-22]。在属水平群落组成中发现,养殖水体与絮团和对虾肠道明显不同,在水体中海滨海命菌、潮滩杆状菌和鲁杰氏菌属为优势类群,而絮团和对虾肠道中的优势类群为弧菌、鲁杰氏菌和假交替单胞菌。絮团和对虾肠道的优势类群更为相似,这与前面不同生境多样性的结果一致。溯源分析也进一步证明了对虾肠道细菌主要来自于生物絮团,极少部分来自于养殖水体。絮团作为对虾的天然饵料,其排泄物和生物絮团中的各种微生物可能会增加肠道细菌群落与絮团的相互作用,使肠道细菌群落与絮团的关系更为密切。此外,先前的研究也发现,商业饲料与生物膜的结合可以塑造虾的肠道微生物类群[23]。对虾养殖系统中的絮团包括许多产生物膜的细菌,这些细菌可能在形成肠道微生物群中起重要作用[24]
在对虾养殖系统中,由于养殖水体、絮团和对虾处于同一环境中,因此各生境之间的微生物类群具有较大的交换机会。然而,各生境也具有其不同的环境特征,因此推测不同生境会聚集其生境特异性的类群,以此来适应不同生境的营养物质或环境[25-26]。Grossart[27]研究也发现,许多水生细菌可以经常在水体和固着物之间交替生活,这是由于水环境中有机物的高度复杂性和时空变异性,促进了细菌对环境的适应进化。在本研究中,部分ASV高度特定于一种生境类型,在养殖水体中特异性ASV最多有89个,其次是生物絮56个,对虾肠道中最少仅有10种特异性ASV。不同生境的特异性ASV在属水平上所占丰度也具有较大差异,在养殖水体中特异性ASV所占丰度为70.01%,絮团为10.78%,对虾肠道为5.55%,养殖水体的特异性ASV显著高于絮团和对虾肠道,这可能与养殖水体环境波动大且复杂,可以积极地选择特异性的类群有关,而絮团和对虾肠道其环境相对稳定,因此对特异性的类群选择力较小[28-29]
微生物多样性是养殖系统中生物多样性的重要组成部分,揭示养殖系统不同生境微生物群落的构建过程是解析生物多样性产生和维持的关键[30]。本研究发现,BFS不同生境细菌群落中类群的发生频率总体上符合中性模型,表明各生境的细菌群落构建主要由中性过程主导。在斑马鱼的实验中发现,中性过程的相对重要性随斑马鱼的发育降低,中性过程足以在斑马鱼发育期间产生肠道微生物群落的实质性变化[31-33]。而在成虾养殖体系中发现,中性过程随对虾发育变得更为重要[34]。在本研究中,不同生境的大多数ASV的分布都遵循相同的基本趋势,即丰富的分类群普遍存在。但在不同生境中仍然有许多偏离中性预测分布的类群,在水体中有33.83%的细菌类群偏离中性过程,絮团中有33.80%,对虾肠道中有36.17%。这些类群并非随机分布在整个群落中,这可能意味着这些细菌群落的功能是截然不同的,可能包括与群落中其他成员以及宿主强烈相互作用的类群。高于中性模型预测且比预期更频繁出现的类群,可能是适合于宿主环境并由宿主积极选择的类群,这些ASV具有更大的竞争优势,相对于其他细菌类群具有更强的扩散能力[35],偏离中性模型的类群可能具有更强的宿主内增殖和生境间扩散的能力,这些ASV可能是潜在的益生菌。由Sloan等[36]提出的中性群落模型在量化随机过程重要性方面发挥了重要作用,但是由于中性模型假设本地群落(单个样本)中所有物种均来自整个群落(所有样本)的扩散与定殖,这可能导致其在量化养殖系统微生物群落构建有局限性。尽管每一个养殖系统都是相互独立,连通性不好,但每一个养殖系统都采用统一的管理,投入品和进水基本一致,不同养殖系统中微生物群落相似,可以理解为整体群落一致。此外,中性模型在预测群落构建过程时主要关注物种丰度,忽略了不同类群之间的进化关系,在预测微生物群落构建过程中有一定的局限性,可能需要更多的预测模型解析养殖系统中微生物群落的构建过程。
BFS三种生境的细菌群落多样性存在显著差异,养殖水体细菌群落显著偏离絮团和对虾肠道,絮团和对虾肠道的相似性更高。在属水平上,不同生境的细菌群落组成也存在显著差异,絮团和对虾肠道的优势类群更为相似,3种生境的共享微生物类群也具有相同的现象。溯源分析表明,对虾肠道的微生物类群主要来自于生物絮团。不同生境的特异性ASV数量差异显著,养殖水体最高,对虾肠道最低,丰富度整体上呈现丰富度下降趋势。此外,中性模型也表明不同生境的群落构建主要受中性过程主导,部分偏离中性预测分布的ASV (如MarinicellaRguegeriaVibrioTenacibaculum等)可能是宿主积极选择的类群。该研究为BFS细菌群落的定向调控提供了科学依据。
  • 宁波市农业重大专项(2021Z105)
  • 温州市重大科技创新攻关(ZN2021001)
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doi: 10.13343/j.cnki.wsxb.20230674
  • 接收时间:2023-11-02
  • 首发时间:2026-03-19
  • 出版时间:2024-05-04
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  • 收稿日期:2023-11-02
  • 录用日期:2024-02-29
基金
Ningbo Major Agricultural Project(2021Z105)
宁波市农业重大专项(2021Z105)
Wenzhou Major Scientific and Technological Innovation Project(ZN2021001)
温州市重大科技创新攻关(ZN2021001)
作者信息
    1 宁波大学 农产品质量安全危害因子与风险防控国家重点实验室, 浙江 宁波 315211
    2 宁波大学海洋学院, 浙江 宁波 315211
    3 浙江省海洋水产研究所, 浙江 温州 325005

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2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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