Hilton Jason A, Satinsky Brandon M, Doherty Mary, Zielinski Brian, Zehr Jonathan P
Department of Ocean Sciences, University of California, Santa Cruz, CA, USA.
Department of Microbiology, University of Georgia, Athens, GA, USA.
ISME J. 2015 Jul;9(7):1557-69. doi: 10.1038/ismej.2014.240. Epub 2014 Dec 16.
Biological N2 fixation is an important nitrogen source for surface ocean microbial communities. However, nearly all information on the diversity and gene expression of organisms responsible for oceanic N2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. Using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from the Amazon River plume, an area characterized by salinity and nutrient gradients. Diazotroph genome and transcript sequences were most abundant in the transitional waters compared with lower salinity or oceanic water masses. We were able to distinguish two genetically divergent phylotypes within the Hemiaulus-associated Richelia sequences, which were the most abundant diazotroph sequences in the data set. Photosystem (PS)-II transcripts in Richelia populations were much less abundant than those in Trichodesmium, and transcripts from several Richelia PS-II genes were absent, indicating a prominent role for cyclic electron transport in Richelia. In addition, there were several abundant regulatory transcripts, including one that targets a gene involved in PS-I cyclic electron transport in Richelia. High sequence coverage of the Richelia transcripts, as well as those from Trichodesmium populations, allowed us to identify expressed regions of the genomes that had been overlooked by genome annotations. High-coverage genomic and transcription analysis enabled the characterization of distinct phylotypes within diazotrophic populations, revealed a distinction in a core process between dominant populations and provided evidence for a prominent role for noncoding RNAs in microbial communities.
生物固氮是海洋表层微生物群落的重要氮源。然而，几乎所有关于环境中负责海洋固氮的生物多样性和基因表达的信息都来自于仅检测少数基因和生物的靶向方法。利用固氮蓝细菌的基因组从大量宏基因组和转录组文库中提取 reads，我们研究了亚马逊河羽流中固氮生物的多样性和基因表达，该区域以盐度和营养梯度为特征。与低盐度或大洋水体相比，固氮生物的基因组和转录序列在过渡水体中最为丰富。我们能够在与半管藻相关的里氏藻序列中区分出两种遗传上不同的系统型，它们是数据集中最丰富的固氮生物序列。里氏藻群体中的光系统（PS）-II 转录本比束毛藻中的要少得多，并且几个里氏藻 PS-II 基因的转录本缺失，这表明循环电子传递在里氏藻中起重要作用。此外，还有几个丰富的调控转录本，包括一个靶向里氏藻中参与 PS-I 循环电子传递的基因的转录本。里氏藻转录本以及束毛藻群体转录本的高序列覆盖率使我们能够识别基因组注释中被忽视的基因组表达区域。高覆盖率的基因组和转录分析能够对固氮生物群体中的不同系统型进行表征，揭示了优势群体之间核心过程的差异，并为非编码 RNA 在微生物群落中的重要作用提供了证据。
