%0 Journal Article %T A new primer set for Clade I nosZ that recovers genes from a broader range of taxa %A Zhang, B. %A Penton, C. R. %A Yu, Z. %A Xue, C. %A Chen, Q. %A Chen, Z. %A Yan, C. %A Zhang, Q. %A Zhao, M. %A Quensen, J. F. %A Tiedje, J. M. %J Biology and Fertility of Soils %V 57 %P 523-531 %D 2021 %X
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.
%R 10.1007/s00374-021-01544-6 %M KBS.3934