Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity
Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity
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DOI：
10.1111/1462-2920.13643
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发表时间：
2017-03-01
影响因子：
5.1
通讯作者：
Neufeld, Josh D.
中科院分区：
文献类型：
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作者：
Coyotzi, Sara;Doxey, Andrew C.;Neufeld, Josh D.
反硝化作用将作为肥料施用的氮转化并释放N2 O，这是一种潜在的温室气体。关于农业土壤中丰富和活跃的微生物的身份知之甚少。我们耦合DNA稳定同位素探针（DNA-SIP）与流通反应器（FTR）检测活性农业土壤微生物。将FTR与硝酸盐和C-13（6）-葡萄糖在缺氧条件下孵育，并在多个时间点取样。通过16 S rRNA基因指纹图谱、扩增子和鸟枪宏基因组测序分析来自活性微生物的标记DNA。各研究中心和时间点的重组分分类学代表一致，包括β-变形菌（71%; Janthinobacterium、Acidovorax、Azoarcus和Dechloromonas）、α-变形菌（8%;根瘤菌）、γ-变形菌（4%;假单胞菌）和放线菌（4%;链霉菌科）。大多数亚硝酸还原酶读数来自注释为含铜形式（nirK）的重DNA。基于匹配nirK基因的读段的活性转录因子的生物学分类与通过一氧化氮（norB）和RNA聚合酶（rpoB）注释获得的生物学分类相当，但不是一氧化二氮还原酶基因（nosZ）。从重DNA回收的宏基因组的分析表明，广泛的nirK序列家族的多样性，包括新的分类组，没有被现有的引物捕获。
Denitrification transforms nitrogen applied as fertilizer and emits N2O, which is a potent greenhouse gas. Very little is known about the identities of abundant and active denitrifiers in agricultural soils. We coupled DNA stable-isotope probing (DNA-SIP) with flow-through reactors (FTRs) to detect active agricultural soil denitrifiers. The FTRs were incubated with nitrate and C-13(6)-glucose under anoxic conditions and sampled at multiple time points. Labelled DNA from active microorganisms was analyzed by 16S rRNA gene fingerprinting, amplicon and shotgun metagenomic sequencing. Taxonomic representation of heavy fractions was consistent across sites and timepoints, including Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus and Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas) and Actinobacteria (4%; Streptomycetaceae). Most nitrite-reductase reads from heavy DNA annotated to the copper-containing form (nirK). Assigned taxonomies of active denitrifiers based on reads matching the nirK gene were comparable to those obtained through nitric oxide (norB) and RNA polymerase (rpoB) annotations but not the nitrous oxide reductase gene (nosZ). Analysis of recovered metagenomes from heavy DNA demonstrated extensive nirK sequence family diversity, including novel taxonomic groups that are not captured by existing primers.