微泡菌属(Microbulbifer)产铁载体海洋细菌的系统发育多样性及相关功能基因簇分析  

Phylogenetic diversity and functional biosynthetic gene clusters of marine siderophore-producing bacteria of Microbulbifer

作　　者：汤倩 陈锦华 邓丽颖 达春瑶 刘祝祥[1] 陈义光[1] TANG Qian;CHEN Jinhua;DENG Liying;DA Chunyao;LIU Zhuxiang;CHEN Yiguang(College of Biology and Environmental Sciences,Jishou University,Jishou,Hunan,China;Yiyang Wanyuan Mingda High School,Yiyang,Hunan,China;School of Medicine,Zhangjiajie College,Zhangjiajie,Hunan,China)

机构地区：[1]吉首大学生物资源与环境科学学院,湖南吉首 [2]益阳万源明达高级中学,湖南益阳 [3]张家界学院医学院,湖南张家界

出　　处：《微生物学报》2025年第4期1616-1634,共19页Acta Microbiologica Sinica

基　　金：国家自然科学基金(31660003,31460004);湖南省自然科学基金(2020JJ4501);湖南省教育厅科技项目(22A0770);湖南省研究生科研创新项目(CX20231081)。

摘　　要：【目的】阐明分离自南海雷州湾硇洲岛潮汐带沉积物的12株产铁载体细菌的系统发育多样性,并探测这些实验菌株及微泡菌属(Microbulbifer)已知物种代表性菌株的铁载体生物合成基因簇的组成、功能、遗传多样性及其演化模式。【方法】采用常规方法观察主要表型特征并进行产铁载体活性验证;利用16S r RNA基因序列分析法了解实验菌株的系统发育多样性(包括类群多样性、物种多样性和遗传多样性);测定代表性实验菌株JSM ZJ756的基因组框架图,通过比较基因组学技术对比分析实验菌株与其系统发育关系密切的典型菌株的G+C含量、平均核苷酸一致性(average nucleotide identity,ANI)和数码DNA-DNA杂交估值(digitalDNA-DNAhybridization,d DDH),以更准确地判定其系统分类地位;采用anti SMASH 7.0、BLASTn、BLASTp和MEGA 11等生物信息学工具,对次级代谢产物合成基因簇(secondary metabolite biosynthetic gene clusters,BGCs)进行快速鉴定、功能注释和序列比对,以探测其产铁载体相关功能基因簇的组成、功能、遗传多样性及其演化模式。【结果】实验菌株均为严格好氧、不产芽孢、具有产铁载体活性的革兰氏阴性杆菌。16S r RNA基因序列和全基因组序列分析结果表明,12株菌均属于微泡菌属,归为6-8个物种,与该属的典型菌株构成4个进化系(clade),其中JSMZJ756为舟山微泡菌(Microbulbifer zhoushanensis)的新成员。通过anti SMASH基因簇分析发现,JSM ZJ756及9个微泡菌属代表性菌株各具有1个铁载体生物合成基因簇(NI-siderophore),其中8个与已知同类型基因簇的相似性在40%及以下。根据与已知基因簇的种类和相似性差异,这10个铁载体基因簇可分为5个功能亚型:JSM ZJ756等3株为Ochrobactin亚型(序列号JYFX01000060.1,相似性28%),M.mangrove DD-13T和M.epialgicus DSM 18651T为Vibrioferrin亚型(AB082123.1,100%;CP005094.1,85%),M.agarilyticusGP101为Putrebactin亚型(NIBS01[Objective]To reveal the phylogenetic diversity of 12 marine siderophore-producing bacteria isolated from intertidal sediment samples of Naozhou Island in Leizhou Bay of South China Sea,and to unravel the components,functions,genetic diversity and genetic evolution of siderophore biosynthetic gene clusters(BGCs)of the isolates as well as representatives of Microbulbifer.[Methods]The phenotypic characteristics as well as the siderophore-producing activity of the strains were observed by conventional methods.The phylogenetic diversity(including taxon,species,and genetic diversity)of the strains was analyzed based on 16S rRNA gene sequences.Then,the exact phylogenetic status of the representative strain JSM ZJ756 was investigated comprehensively by means of comparative genomics analysis based on whole-genome sequences,including comparisons of G+C content,average nucleotide identity(ANI),and digital DNA-DNA hybridization(dDDH)estimated values.We then used multiple bioinformatic stools including antiSMASH 7.0,BLASTn,BLASTp,and MEGA 11 for rapid identification,annotation,and sequence alignment of BGCs,thus exploring the components,functions,genetic diversity,and genetic evolution of siderophore BGCs.[Results]All the 12 isolates were Gram-negative,aerobic,non-sporulating and slightly halophilic rods with siderophore-producing activity.The results of phylogenetic analyses based on 16S rRNA gene sequences as well as whole-genome sequences showed that all the 12 strains belonged to Microbulbifer,representing 6 to 8 species and forming 4 clades with Microbulbifer type strains in the phylogenetic tree.Among them,strain JSM ZJ756 should be a new member of Microbulbifer zhoushanensis.JSM ZJ756 and 9 representative strains of Microbulbifer each carried one copy of NI-siderophore BGCs,and 8 out of the 10 NI-siderophore BGCs shared the similarities≤40%with known BGCs.According to the types and the similarities of known BGCs with the NI-siderophore BGCs identified in this study,the 10 NI-siderophore BGCs could be categorized int

关 键 词：微泡菌属 产铁载体海洋细菌 系统发育多样性 铁载体合成基因簇 遗传演化 新资源微生物 

分 类 号：Q93[生物学—微生物学]