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

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

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Denitrification is an important global N cycle process. The gene encoding NosZ that converts nitrous oxide (N2O) to N2 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.

Original languageEnglish (US)
Pages (from-to)523-531
Number of pages9
JournalBiology and Fertility of Soils
Volume57
Issue number4
DOIs
StatePublished - May 2021

Keywords

  • Clade I
  • Higher coverage
  • NGS
  • Primer design
  • Soil type
  • nosZ

ASJC Scopus subject areas

  • Microbiology
  • Agronomy and Crop Science
  • Soil Science

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