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

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

doi:10.1007/s00374-021-01544-6

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

Journal Article · Sun Feb 14 00:00:00 EST 2021 · Biology and Fertility of Soils

DOI:https://doi.org/10.1007/s00374-021-01544-6· OSTI ID:1846010

Zhang, Bangzhou ^[1]; Penton, C. Ryan ^[2]; Yu, Zhenhua ^[3]; Xue, Chao ^[4]; Chen, Qiongyun ^[5]; Chen, Zhangran ^[6]; Yan, Changsheng ^[5]; Zhang, Qiang ^[5]; Zhao, Mengxin ^[7]; Quensen, John F. ^[8]; Tiedje, James M. ^[8]

Michigan State Univ., East Lansing, MI (United States); Xiamen Univ. (China); Michigan State University Center for Microbial Ecology
Arizona State Univ., Mesa, AZ (United States); Arizona State Univ., Tempe, AZ (United States)
Michigan State Univ., East Lansing, MI (United States); Chinese Academy of Sciences (CAS), Harbin (China)
Michigan State Univ., East Lansing, MI (United States); Nanjing Agricultural Univ. (China)
Xiamen Univ. (China)
Michigan State Univ., East Lansing, MI (United States); Xiamen Univ. (China)
Michigan State Univ., East Lansing, MI (United States); Chinese Academy of Agricultural Sciences, Beijing (China)
Michigan State Univ., East Lansing, MI (United States)

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, here 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. provides a more comprehensive assessment of denitrifier gene hosts, their ecological patterns, and the degree of novelty in retrieved gene sequences.

View Accepted Manuscript (DOE)

Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Sponsoring Organization:: National Natural Science Foundation of China (NSFC); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FC02-07ER64494; SC0018409

OSTI ID:: 1846010

Journal Information:: Biology and Fertility of Soils, Journal Name: Biology and Fertility of Soils Journal Issue: 4 Vol. 57; ISSN 0178-2762

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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NGS
higher coverage
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primer design
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A new primer set for Clade I nosZ that recovers genes from a broader range of taxa

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