Pedosphere 31(6): 954--963, 2021
ISSN 1002-0160/CN 32-1315/P
©2021 Soil Science Society of China
Published by Elsevier B.V. and Science Press
Distribution characteristics and diversities of cbb and coxL genes in paddy soil profiles from southern China
Wentao PENG1,2, Yan WANG1, Xiuxiu ZHU1, Liufeng XU1, Juan ZHAO1, Zhongli CUI1, Hui CAO1
1College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing 210095 (China)
2Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101 (China)
ABSTRACT
      The Calvin-Benson-Bassham cycle and Wood-Ljungdahl pathway are two well-known ones in the six carbon sequestration pathways, but the current knowledge of their occurrence in different layers of agricultural soil profiles is poor. In this study, the diversities of three genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), i.e., genes encoding the green-like (cbbLG) and red-like (cbbLR) forms of RubisCO I and encoding RubisCO II (cbbM), and the gene encoding carbon monoxide dehydrogenase large subunit (coxL) from five paddy soils in southern China were investigated by real-time quantitative polymerase chain reaction, restriction fragment length polymorphism (RFLP) analysis, and clone library. The abundances of the four genes ranged from 107 to 109 copies g-1 soil, and the cbbLR gene outnumbered the other three genes in all soil samples, suggesting important roles they play in carbon dioxide (CO2) fixation. In addition, it was found that the copy numbers of cbbLR and cbbLG decreased with increasing soil depth, while the copy numbers of cbbM and coxL decreased in the shallow depths but increased with increasing soil depth. The results of RFLP showed a larger Shannon index (H) in the deeper soil layers among the four gene clone libraries, indicating that the community diversity in these soil layers was greater. The cbbLG gene had relatively low diversity (at genus level), and most of the sequences were classified as Sideroxydans and Thiobacillus. In contrast, the highly diverse groups were found in the other three gene clone libraries (cbbLR, cbbM, and coxL), most of which were distantly related to known sequences, even forming separate clusters. In summary, this study provides a new insight into CO2 fixers along agricultural soil profiles by comparing four bacterial genes.
Key Words:  Calvin-Benson-Bassham cycle,carbon dioxide fixation,carbon monoxide dehydrogenase,ribulose-1,5-bisphosphate carboxylase/oxygenase
Citation: Peng W T, Wang Y, Zhu X X, Xu L F, Zhao J, Cui Z L, Cao H. 2021. Distribution characteristics and diversities of cbb and coxL genes in paddy soil profiles from southern China. Pedosphere. 31(6): 954–963.
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