A new primer set for Clade I nosZ that recovers genes from a broader range of taxa

文献类型： 外文期刊

第一作者： Zhang, Bangzhou

作者： Zhang, Bangzhou;Yu, Zhenhua;Xue, Chao;Chen, Zhangran;Zhao, Mengxin;Quensen, John F.;Tiedje, James M.;Zhang, Bangzhou;Penton, C. Ryan;Penton, C. Ryan;Yu, Zhenhua;Xue, Chao;Chen, Qiongyun;Chen, Zhangran;Yan, Changsheng;Zhang, Qiang;Zhao, Mengxin

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关键词： nosZ; Clade I; Primer design; NGS; Higher coverage; Soil type

期刊名称：BIOLOGY AND FERTILITY OF SOILS （ 影响因子：6.432； 五年影响因子：6.332 ）

ISSN： 0178-2762

年卷期： 2021 年 57 卷 4 期

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收录情况： SCI

摘要： Denitrification is an important global N cycle process. The gene encoding NosZ that converts nitrous oxide (N2O) to N-2 has been widely used as a biomarker to study denitrifying communities. However, conventional PCR primers target a limited range of the genetically diverse Clade I nosZ, and the amplicons are too long for sequencing on current NGS platforms. To address these issues, we developed a new PCR primer set that amplifies a 355-bp region of Clade I nosZ and captures broader taxonomic coverage than conventional primers in in silico tests. When compared with the widely used nosZF_nosZR_Rich_2003 set using the same soil samples and the same sequencing depth, the new set retrieved genes from four times more unique species, with consistently higher general diversity-based metrics. The new primer set performed well with different sequencing platforms (Ion Torrent and Illumina), and among a wide variety of soils from polar to tropical, desert to agricultural, and surface to a very low biomass subsoil, with significant differences in denitrifying community diversity and composition. This new primer set for Clade I together with the primers recently reported for Clade II by Chee-Sanford et al. (J Microbiol Meth 172:105908, 2020) provides a more comprehensive assessment of denitrifier gene hosts, their ecological patterns, and the degree of novelty in retrieved gene sequences.

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