Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, SAR, China.
Appl Microbiol Biotechnol. 2014 Aug;98(15):6885-95. doi: 10.1007/s00253-014-5756-x. Epub 2014 Apr 26.
Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC 1.12.99.6) catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO2-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.
在这里，通过 shotgun 宏基因组测序揭示了富营养化的 Thauera 主导的菌胶团中的氢氧化自养反硝化代谢。通过覆盖度定义的 binning 方法，从 3.5 Gb 配对末端 Illumina 读取数据中，我们获得了一个超过 90%完整性（3.8 Mb）的草案基因组，命名为 Thauera R4。我们鉴定了 1263 个基因（占已完成的 Thauera aminoaromatica MZ1T 基因组总基因的 33%），它们与 Thauera R4 和 T. aminoaromatica MZ1T 之间的平均核苷酸同一性为 87.6%。尽管 Thauera R4 和 T. aminoaromatica 在氮代谢和 16S 核糖体 RNA 基因方面具有非常相似的核苷酸相似性（98.8%），但它们在几个重要的与环境相关的过程中表现出不同的功能潜力。与 T. aminoaromatica MZ1T 不同，Thauera R4 携带一个[NiFe]-氢化酶（EC 1.12.99.6）操纵子，能够在富含硝酸盐的溶液中催化分子氢的氧化。此外，Thauera R4 是一种混合营养细菌，具有自养 CO2 固定和异养乙酸同化代谢的关键酶。这个 Thauera R4 菌 bin 为更好地理解 Thauera 的生态位提供了另一个遗传参考，并展示了一种从环境研究中的简化混合培养物中揭示功能谱和重建新型和主导基因组的模型管道。
