He Shaomei, Tominski Claudia, Kappler Andreas, Behrens Sebastian, Roden Eric E
Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Appl Environ Microbiol. 2016 Apr 18;82(9):2656-2668. doi: 10.1128/AEM.03493-15. Print 2016 May.
Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458-1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochromec system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochromecand multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.
硝酸盐依赖的亚铁[Fe(II)]氧化作用（NDFO）是缺氧沉积物中一种广为人知的化能无机营养途径。最初从淡水沉积物中获得的嗜中性化能无机自养富集培养物KS（K. L. 施特劳布、M. 本茨、B. 欣克和F. 维德尔，《应用与环境微生物学》62:1458 - 1460，1996）已被用作研究NDFO的模型系统。然而，尽管为此付出了巨大努力，该培养物中的主要Fe(II)氧化菌仍未被分离出来。在此，我们对这种富集培养物进行了宏基因组分析，以便深入了解电子传递途径以及培养物中不同细菌的作用。我们获得了主要Fe(II)氧化菌（Gallionellaceae科的一个物种）的近乎完整的基因组，以及其相邻群落成员的草图基因组。对这些基因组中假定的细胞外电子传递途径进行搜索，在Gallionellaceae菌属中鉴定出了MtoAB复合物的一个同源物（在嗜中性微需氧Fe(II)氧化的嗜铁氧化菌Sideroxydans lithotrophicus ES - 1中鉴定出的一种孔蛋白 - 多血红素细胞色素c系统），并发现了其他涉及细胞色素c和多铜氧化酶的假定基因，如Cyc2和OmpB。基于基因组的代谢重建表明，这种Gallionellaceae菌属缺乏一氧化氮和一氧化二氮还原酶基因，可能与能够进行完全反硝化作用的相邻菌群合作，以避免有毒代谢产物的积累，这可能解释了其在纯培养中生长的抗性。这种以及其他揭示的氮和碳代谢中的种间相互作用和代谢相互依存关系，可能使这些生物体能够有效合作，以实现强大的化能无机自养NDFO。总体而言，这些结果显著扩展了我们对NDFO的认识，并提出了一系列有待进一步探索的遗传靶点。
