干旱区生态环境知识资源中心(Arid): A new primer set for Clade I nosZ that recovers genes from a broader range of taxa

Arid

DOI	10.1007/s00374-021-01544-6
	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.
通讯作者	Tiedje, JM (corresponding author), Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA.
来源期刊	BIOLOGY AND FERTILITY OF SOILS
ISSN	0178-2762
EISSN	1432-0789
出版年	2021
卷号	57 期号:4 页码:523-531
英文摘要	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.
英文关键词	nosZ Clade I Primer design NGS Higher coverage Soil type
类型	Article
语种	英语
收录类别	SCI-E
WOS记录号	WOS:000617820600002
WOS关键词	NITROUS-OXIDE REDUCTASE ; N2O EMISSIONS ; DENITRIFIERS ; DIVERSITY ; COMMUNITY ; FERTILIZATION ; ABUNDANCE ; BACTERIA
WOS类目	Soil Science
WOS研究方向	Agriculture
来源机构	Arizona State University
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/349705
作者单位	[Zhang, Bangzhou; Yu, Zhenhua; Xue, Chao; Chen, Zhangran; Zhao, Mengxin; Quensen, John F.; Tiedje, James M.] Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA; [Zhang, Bangzhou] Xiamen Univ, Zhongshan Hosp, Dept Gastroenterol, Xiamen, Peoples R China; [Penton, C. Ryan] Arizona State Univ, Ctr Fundamental & Appl Microbi, Biodesign Inst, Tempe, AZ USA; [Penton, C. Ryan] Arizona State Univ, Coll Integrat Sci & Arts, Fac Sci & Math, Mesa, AZ USA; [Yu, Zhenhua] Chinese Acad Sci, Northeast Inst Geog & Agroecol, Key Lab Mollisols Agroecol, Harbin, Peoples R China; [Xue, Chao] Nanjing Agr Univ, Natl Engn Res Ctr Organ Based Fertilizers, Jiangsu Collaborat Innovat Ctr Solid Organ Waste, Jiangsu Prov Key Lab Solid Organ Waste Utilizat, Nanjing, Peoples R China; [Chen, Qiongyun; Chen, Zhangran; Yan, Changsheng; Zhang, Qiang] Xiamen Univ, Sch Med, Inst Microbial Ecol, Xiamen, Peoples R China; [Zhao, Mengxin] Chinese Acad Agr Sci, Inst Plant Protect, State Key Lab Biol Plant Dis & Insect Pests, Beijing,...
推荐引用方式 GB/T 7714	Zhang, Bangzhou,Penton, C. Ryan,Yu, Zhenhua,et al. A new primer set for Clade I nosZ that recovers genes from a broader range of taxa[J]. Arizona State University,2021,57(4):523-531.
APA	Zhang, Bangzhou.,Penton, C. Ryan.,Yu, Zhenhua.,Xue, Chao.,Chen, Qiongyun.,...&Tiedje, James M..(2021).A new primer set for Clade I nosZ that recovers genes from a broader range of taxa.BIOLOGY AND FERTILITY OF SOILS,57(4),523-531.
MLA	Zhang, Bangzhou,et al."A new primer set for Clade I nosZ that recovers genes from a broader range of taxa".BIOLOGY AND FERTILITY OF SOILS 57.4(2021):523-531.