Stagars Marion H, Ruff S Emil, Amann Rudolf, Knittel Katrin
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany.
Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany.
Front Microbiol. 2016 Jan 7;6:1511. doi: 10.3389/fmicb.2015.01511. eCollection 2015.
Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. These environments are typically anoxic and host diverse microbial communities that grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well as to identify factors structuring the alkane-degrading community. Using next generation sequencing we obtained a total of 420 MasD species-level operational taxonomic units (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD community structure is clearly driven by the hydrocarbon source available at the various seeps. Two of the detected OTU0.96 were cosmopolitan and abundant while 75% were locally restricted, suggesting the presence of few abundant and globally distributed alkane degraders as well as specialized variants that have developed under specific conditions at the diverse seep environments. Of the three MasD clades identified, the most diverse was affiliated with Deltaproteobacteria. A second clade was affiliated with both Deltaproteobacteria and Firmicutes likely indicating lateral gene transfer events. The third clade was only distantly related to known alkane-degrading organisms and comprises new divergent lineages of MasD homologs, which might belong to an overlooked phylum of alkane-degrading bacteria. In addition, masD geneFISH allowed for the in situ identification and quantification of the target guild in alkane-degrading enrichment cultures. Altogether, these findings suggest an unexpectedly high number of yet unknown groups of anaerobic alkane degraders and underline the need for comprehensive surveys of microbial diversity based on metabolic genes in addition to ribosomal genes.
烷烃占原油的很大一部分，并且在海洋渗漏处普遍存在。这些环境通常是缺氧的，并且存在以烷烃为食的多样微生物群落。厌氧烷烃活化最广泛分布的机制是通过（1-甲基烷基）琥珀酸合酶（Mas）将烷烃添加到富马酸酯中。在这里，我们研究了在七个渗漏处采集的12个海洋沉积物中该酶的催化亚基MasD的多样性。我们旨在识别世界性物种以及确定构建烷烃降解群落的因素。使用下一代测序技术，我们在96%的氨基酸同一性水平上共获得了420个MasD物种水平的操作分类单元（OTU0.96）。多样性分析表明烷烃降解细菌具有很高的丰富度和均匀度。基于MasD基因，具有相似烃类组成的地点拥有相似的烷烃降解群落；MasD群落结构显然由各个渗漏处可用的烃源驱动。检测到的OTU0.96中有两个是世界性的且数量丰富，而75%是局部受限的，这表明存在少数丰富且全球分布的烷烃降解菌以及在不同渗漏环境的特定条件下形成发展的特化变体。在鉴定出的三个MasD进化枝中，最多样化的与δ-变形菌纲相关。第二个进化枝与δ-变形菌纲和厚壁菌门都相关，这可能表明发生了横向基因转移事件。第三个进化枝与已知的烷烃降解生物只有远缘关系，并且包含MasD同源物的新的分化谱系，这些谱系可能属于一个被忽视的烷烃降解细菌门。此外，masD基因荧光原位杂交技术能够在原位鉴定和定量烷烃降解富集培养物中的目标菌群。总之，这些发现表明厌氧烷烃降解菌中未知群体的数量出乎意料地多，并强调除了核糖体基因外，还需要基于代谢基因对微生物多样性进行全面调查。
