Table_4_Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean.XLSX

Despite being the world’s third largest ocean, the Indian Ocean is one of the least studied and understood with respect to microbial diversity as well as biogeochemical and ecological functions. In this study, we investigated the microbial community and its metabolic potential for nitrogen (N) acquisition in the oligotrophic surface waters of the Indian Ocean using a metagenomic approach. Proteobacteria and Cyanobacteria dominated the microbial community with an average 37.85 and 23.56% of relative abundance, respectively, followed by Bacteroidetes (3.73%), Actinobacteria (1.69%), Firmicutes (0.76%), Verrucomicrobia (0.36%), and Planctomycetes (0.31%). Overall, only 24.3% of functional genes were common among all sampling stations indicating a high level of gene diversity. However, the presence of 82.6% common KEGG Orthology (KOs) in all samples showed high functional redundancy across the Indian Ocean. Temperature, phosphate, silicate and pH were important environmental factors regulating the microbial distribution in the Indian Ocean. The cyanobacterial genus Prochlorococcus was abundant with an average 17.4% of relative abundance in the surface waters, and while 54 Prochlorococcus genomes were detected, 53 were grouped mainly within HLII clade. In total, 179 of 234 Prochlorococcus sequences extracted from the global ocean dataset were clustered into HL clades and exhibited less divergence, but 55 sequences of LL clades presented more divergence exhibiting different branch length. The genes encoding enzymes related to ammonia metabolism, such as urease, glutamate dehydrogenase, ammonia transporter, and nitrilase presented higher abundances than the genes involved in inorganic N assimilation in both microbial community and metagenomic Prochlorococcus population. Furthermore, genes associated with dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification and anammox were absent in metagenome Prochlorococcus population, i.e., nitrogenase and nitrate reductase. Notably, the de novo biosynthesis pathways of six different amino acids were incomplete in the metagenomic Prochlorococcus population and Prochlorococcus genomes, suggesting compensatory uptake of these amino acids from the environment. These results reveal the features of the taxonomic and functional structure of the Indian Ocean microbiome and their adaptive strategies to ambient N deficiency in the oligotrophic ocean.

作为全球第三大洋，印度洋在微生物多样性、生物地球化学与生态功能相关研究方面，是受关注最少、认知程度最低的海域之一。本研究采用宏基因组学方法，对印度洋寡营养表层海域的微生物群落及其氮（N）获取代谢潜力展开了调查。微生物群落以变形菌门（Proteobacteria）和蓝细菌门（Cyanobacteria）为主，平均相对丰度分别为37.85%和23.56%；其次依次为拟杆菌门（Bacteroidetes，3.73%）、放线菌门（Actinobacteria，1.69%）、厚壁菌门（Firmicutes，0.76%）、疣微菌门（Verrucomicrobia，0.36%）以及浮霉菌门（Planctomycetes，0.31%）。总体而言，所有采样站位中共有的功能基因仅占24.3%，表明基因多样性水平较高。但所有样本中共有82.6%的KEGG直系同源簇（KEGG Orthology，KOs）被检出，说明印度洋海域微生物群落存在较高的功能冗余性。温度、磷酸盐、硅酸盐以及pH值是调控印度洋微生物分布的关键环境因子。表层海域中，蓝细菌原球菌属（Prochlorococcus）的相对丰度平均达17.4%；本次研究共检出54个原球菌属基因组，其中53个主要归属于HLII演化支（HLII clade）。从全球海洋数据集中共提取得到234条原球菌属序列，其中179条被聚类为高光适应型演化支（HL clades），序列分化程度较低；剩余55条属于低光适应型演化支（LL clades），序列分化程度更高且分支长度存在差异。在微生物群落和宏基因组原球菌种群中，参与氨代谢的编码酶类基因（如脲酶、谷氨酸脱氢酶、氨转运蛋白及腈水解酶）的丰度均高于参与无机氮同化的相关基因。此外，宏基因组原球菌种群中未检出与异化硝酸盐还原、反硝化、固氮、硝化作用及厌氧氨氧化相关的基因，例如固氮酶与硝酸还原酶的编码基因。值得注意的是，宏基因组原球菌种群及原球菌属基因组中，6种氨基酸的从头生物合成通路均不完整，提示其需从环境中补偿性摄取这些氨基酸。本研究结果揭示了印度洋微生物组的分类与功能结构特征，以及其对寡营养海洋环境中氮素匮乏的适应策略。