Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440, Bayreuth, Germany.
Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.
Microb Ecol. 2020 Jul;80(1):243-247. doi: 10.1007/s00248-020-01482-0. Epub 2020 Jan 27.
Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N and O. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 10-3.2 × 10 gene copies g soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.
微生物在土壤和沉积物的氮循环和温室气体排放中起着至关重要的作用。最近发现的需氧脱氮菌被提议通过一氧化氮歧化直接将硝酸盐和亚硝酸盐还原为 N 和 O 来减少硝酸盐和亚硝酸盐。到目前为止，这些微生物的生态作用还没有被很好地理解。对需氧脱氮菌进行靶向研究的唯一可用工具是它们各自的maker 基因，即一氧化氮歧化酶（nod）。在这里，我们建立了使用 PacBio 长读测序扩增 nod 基因来研究需氧脱氮菌的多样性和群落结构的方法。我们以农业土壤和湖泊沉积物为例，研究了两组不同的环境样本。获得的圆形一致序列（约 1.0 kb）涵盖了大多数 NO 歧化酶的取代特征，允许对需氧脱氮菌进行可靠的分类。不同的栖息地揭示了不同的 nod 基因库和群落结构，大多数序列类型与尚未鉴定的环境 nod 谱系有关。nod 基因的丰度范围为 2.2×10-3.2×10 个基因拷贝 g 土壤或沉积物，占总细菌 16S rRNA 基因计数的高达 3%。本研究表明，nod 基因靶向长读测序可以成为研究这些新型微生物生态学的有力工具，研究结果还表明，需氧脱氮菌在不同的陆地样本中普遍存在且丰富，它们可能在氮转化中发挥着重要但尚未被忽视的作用。
