Một bộ mồi mới cho Clade I nosZ phục hồi gen từ một khoảng rộng hơn của taxa

Biology and Fertility of Soils - Tập 57 - Trang 523-531 - 2021
Bangzhou Zhang1,2, C. Ryan Penton3,4, Zhenhua Yu1,5, Chao Xue1,6, Qiongyun Chen7, Zhangran Chen1,7, Changsheng Yan7, Qiang Zhang7, Mengxin Zhao1,8, John F. Quensen1, James M. Tiedje1
1Center for Microbial Ecology, Michigan State University, East Lansing, USA
2Department of Gastroenterology, Zhongshan Hospital, Xiamen University, Xiamen, China
3Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, USA
4College of Integrative Sciences and Arts, Faculty of Science and Mathematics, Arizona State University, Mesa, USA
5Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
6Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
7Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
8State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China

Tóm tắt

Quá trình khử nitrat là một quá trình quan trọng trong chu trình nitơ toàn cầu. Gen mã hóa NosZ, gen chuyển đổi khí nitrous oxide (N2O) thành N2, đã được sử dụng rộng rãi như một dấu sinh học để nghiên cứu cộng đồng khử nitrat. Tuy nhiên, các mồi PCR thông thường chỉ nhắm tới một phạm vi hạn chế trong Clade I nosZ có đa dạng di truyền, và các sản phẩm khuếch đại quá dài để giải trình tự trên các nền tảng NGS hiện tại. Để giải quyết những vấn đề này, chúng tôi đã phát triển một bộ mồi PCR mới khuếch đại một vùng 355-bp của Clade I nosZ và thu được sự bao phủ thuế phân loại rộng hơn so với các mồi thông thường trong các thử nghiệm in silico. Khi so sánh với bộ mồi nosZF_nosZR_Rich_2003 được sử dụng rộng rãi, sử dụng cùng mẫu đất và cùng độ sâu giải trình tự, bộ mồi mới đã thu hồi gen từ bốn lần nhiều loài độc nhất hơn, với các chỉ số đa dạng tổng quát cao hơn một cách nhất quán. Bộ mồi mới hoạt động tốt với các nền tảng giải trình tự khác nhau (Ion Torrent và Illumina), và trong một loạt các mẫu đất từ Bắc cực đến nhiệt đới, từ sa mạc đến nông nghiệp, và từ bề mặt đến tầng đất thấp với khối lượng sinh khối rất thấp, với sự khác biệt đáng kể về đa dạng và thành phần của cộng đồng khử nitrat. Bộ mồi mới này cho Clade I cùng với các mồi gần đây được báo cáo cho Clade II bởi Chee-Sanford et al. (J Microbiol Meth 172:105908, 2020) cung cấp một đánh giá toàn diện hơn về các chủ thể gen khử nitrat, các mẫu sinh thái của chúng và mức độ độc đáo trong các trình tự gen được thu hồi.

Từ khóa

#khử nitrat #gen NosZ #Clade I #đa dạng di truyền

Tài liệu tham khảo

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