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

Journal Article · · Biology and Fertility of Soils
 [1];  [2];  [3];  [4];  [5];  [1];  [5];  [5];  [6];  [7];  [7]
  1. Michigan State Univ., East Lansing, MI (United States); Xiamen Univ. (China)
  2. Arizona State Univ., Mesa, AZ (United States); Arizona State Univ., Tempe, AZ (United States)
  3. Michigan State Univ., East Lansing, MI (United States); Chinese Academy of Sciences (CAS), Harbin (China)
  4. Michigan State Univ., East Lansing, MI (United States); Nanjing Agricultural Univ. (China)
  5. Xiamen Univ. (China)
  6. Michigan State Univ., East Lansing, MI (United States); Chinese Academy of Agricultural Sciences, Beijing (China)
  7. Michigan State Univ., East Lansing, MI (United States)
+ Show Author Affiliations

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.

Research Organization:
Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Natural Science Foundation of China (NSFC)
Grant/Contract Number:
SC0018409; FC02-07ER64494; 81800517
OSTI ID:
1846010
Journal Information:
Biology and Fertility of Soils, Vol. 57, Issue 4; ISSN 0178-2762
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
nosZ
Clade I
primer design
NGS
higher coverage
soil type