Data from: Nitrous oxide emission by the non-denitrifying, nitrite ammonifier Bacillus licheniformis

Background: Firmicutes have the capacity to remove excess nitrate from the environment via either denitrification, dissimilatory nitrate reduction to ammonium or both. The recent renewed interest in their nitrogen metabolism has revealed many interesting features, the most striking being their wide variety of dissimilatory nitrate reduction pathways. In the present study, nitrous oxide production from Bacillus licheniformis, a ubiquitous Gram-positive, spore-forming species with many industrial applications, is investigated. Results: B. licheniformis has long been considered a denitrifier but physiological experiments on three different strains demonstrated that nitrous oxide is not produced from nitrate in stoichiometric amounts, rather ammonium is the most important end-product, produced during fermentation. Significant strain dependency in end-product ratios, attributed to nitrite and ammonium, and medium dependency in nitrous oxide production were also observed. Genome analyses confirmed the lack of a nitrite reductase to nitric oxide, the key enzyme of denitrification. Based on the gene inventory and building on knowledge from other non-denitrifying nitrous oxide emitters, hypothetical pathways for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are proposed. In addition, all publically available genomes of B. licheniformis demonstrated similar gene inventories, with specific duplications of the nar operon, narK and hmp genes as well as NarG phylogeny supporting the evolutionary separation of previously described distinct BALI1 and BALI2 lineages. Conclusions: Using physiological and genomic data we have demonstrated that the common soil bacterium B. licheniformis does not denitrify but is capable of fermentative dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with concomitant production of N2O. Considering its ubiquitous nature and non-fastidious growth in the lab, B. licheniformis is a suitable candidate for further exploration of the actual mechanism of N2O production in DNRA bacteria and its relevance in situ.

研究背景：厚壁菌门（Firmicutes）可通过反硝化作用、异化硝酸盐还原为铵（dissimilatory nitrate reduction to ammonium, DNRA）或二者结合的方式去除环境中过量硝酸盐。近年来，学界对其氮代谢的再度关注揭示了诸多有趣特性，其中最突出的是其异化硝酸盐还原途径的多样性。本研究针对一种广泛存在、具有多种工业应用价值的革兰氏阳性产芽孢菌种——地衣芽孢杆菌（Bacillus licheniformis）的一氧化二氮（nitrous oxide, N₂O）生成情况展开探究。

研究结果：长期以来，地衣芽孢杆菌被认为是反硝化菌，但针对3株不同菌株的生理学实验表明，其无法通过硝酸盐以化学计量比生成一氧化二氮，反而铵是发酵过程中产生的最主要终产物。研究还观察到，亚硝酸盐与铵的终产物比例存在显著的菌株依赖性，而一氧化二氮的生成则具有培养基依赖性。基因组分析证实，地衣芽孢杆菌缺乏介导亚硝酸盐还原为一氧化氮的关键酶——亚硝酸盐还原酶。基于基因组成，并结合其他非反硝化型一氧化二氮产生菌的研究知识，本研究提出了涉及NarG、NirB、qNor及Hmp基因的一氧化二氮生成假想途径。此外，所有公开可用的地衣芽孢杆菌基因组均具有相似的基因组成，其中nar操纵子、narK与hmp基因的特异性复制，以及NarG的系统发育分析结果，均支持此前报道的BALI1与BALI2两个不同谱系的进化分离。

研究结论：结合生理学与基因组学数据，本研究证实常见土壤菌种地衣芽孢杆菌并不具备反硝化能力，但可通过发酵型异化硝酸盐/亚硝酸盐还原为铵（DNRA）途径生成一氧化二氮，且伴随一氧化二氮的产生。鉴于地衣芽孢杆菌广泛分布且在实验室中易于培养，其是进一步探究DNRA菌一氧化二氮生成的实际机制及其原位相关性的理想研究对象。