Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre.
Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre.
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DOI：
10.3389/fmicb.2017.01122
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发表时间：
2017
影响因子：
5.2
通讯作者：
White AE
中科院分区：
文献类型：
--
作者：
Gradoville MR;Crump BC;Letelier RM;Church MJ;White AE
毛霉属的丝状重氮营养蓝藻通常以殖民地形式存在，为热带和亚热带海洋生态系统提供了新的氮源。菌落由几个木霉分支组成，与不同的细菌和真核表面生物群落相关联。我们使用高通量的16S rRNA和nifH基因测序，碳(C)和氮(N_2)固定分析，以及元基因组学来描述北太平洋亚热带环流(NPSG)中与木霉菌落相关的微生物群的多样性和功能潜力。从人工挑选的菌落中获得的16S rRNA和nifH基因序列主要(>；99%)来自支链霉菌(Trichodesum Clade I)，即蒂包毛霉(Trichodesum Thiebautii)，与大多数实验室研究中使用的支链霉菌III IMS101分离株在系统发育和生态上是不同的。表层细菌群落主要由拟杆菌属、α蛋白细菌和伽马蛋白细菌组成，包括几个已知的表面附着的类群，而在NPSG地表水中占主导地位的单细胞蓝藻和小型光异养细菌相对贫乏。对nifH基因(编码固氮酶的一个亚组分)进行测序后，发现了非毛霉重氮菌，它们主要聚集在簇III nifH序列类型中，其中包括假定的厌氧重氮菌。毛霉菌落可能是这些III类重氮菌的重要栖息地，这些重氮菌在周围海水中相对罕见。对nifH基因转录本的序列分析显示，与这些菌落相关的几个蓝藻群体，包括异晶黎塞氏菌。16S rRNA和nifH数据集都表明周围海水中的毛霉表生物和微浮游生物之间，以及生活在毛霉泡状和簇状菌落形态中的表生生物之间存在着显著的差异。元基因组和16S rRNA基因序列分析表明，通常与共营养生活方式相关的谱系包括很大一部分群体相关的表生生物，而不是这些少营养水域中浮游细菌典型的流线型基因组。此外，表观生物超基因组还富含与表层海水超基因组有关的磷酸盐和铁的获取和反硝化途径的特定基因。我们认为，栖息在群体中的独特微生物群落对远洋环境中木霉群体的生物地球化学功能有重要影响。
Filamentous diazotrophic Cyanobacteria of the genus Trichodesmium, often found in colonial form, provide an important source of new nitrogen to tropical and subtropical marine ecosystems. Colonies are composed of several clades of Trichodesmium in association with a diverse community of bacterial and eukaryotic epibionts. We used high-throughput 16S rRNA and nifH gene sequencing, carbon (C) and dinitrogen (N2) fixation assays, and metagenomics to describe the diversity and functional potential of the microbiome associated with Trichodesmium colonies collected from the North Pacific Subtropical Gyre (NPSG). The 16S rRNA and nifH gene sequences from hand-picked colonies were predominantly (>99%) from Trichodesmium Clade I (i.e., T. thiebautii), which is phylogenetically and ecologically distinct from the Clade III IMS101 isolate used in most laboratory studies. The bacterial epibiont communities were dominated by Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria, including several taxa with a known preference for surface attachment, and were relatively depleted in the unicellular Cyanobacteria and small photoheterotrophic bacteria that dominate NPSG surface waters. Sequencing the nifH gene (encoding a subcomponent of the nitrogenase enzyme) identified non-Trichodesmium diazotrophs that clustered predominantly among the Cluster III nifH sequence-types that includes putative anaerobic diazotrophs. Trichodesmium colonies may represent an important habitat for these Cluster III diazotrophs, which were relatively rare in the surrounding seawater. Sequence analyses of nifH gene transcripts revealed several cyanobacterial groups, including heterocystous Richelia, associated with the colonies. Both the 16S rRNA and nifH datasets indicated strong differences between Trichodesmium epibionts and picoplankton in the surrounding seawater, and also between the epibionts inhabiting Trichodesmium puff and tuft colony morphologies. Metagenomic and 16S rRNA gene sequence analyses suggested that lineages typically associated with a copiotrophic lifestyle comprised a large fraction of colony-associated epibionts, in contrast to the streamlined genomes typical of bacterioplankton in these oligotrophic waters. Additionally, epibiont metagenomes were enriched in specific genes involved in phosphate and iron acquisition and denitrification pathways relative to surface seawater metagenomes. We propose that the unique microbial consortium inhabiting colonies has a significant impact on the biogeochemical functioning of Trichodesmium colonies in pelagic environments.