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Effect of land use on the abundance and diversity of autotrophic bacteria as measured by ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large subunit gene abundance in soils

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Abstract

Elucidating the biodiversity of CO2-assimilating bacterial communities under different land uses is critical for establishing an integrated view of the carbon sequestration in agricultural systems. We therefore determined the abundance and diversity of CO2 assimilating bacteria using terminal restriction fragment length polymorphism and quantitative PCR of the cbbL gene (which encodes ribulose-1,5-biphosphate carboxylase/oxygenase). These analyses used agricultural soils collected from a long-term experiment (Pantang Agroecosystem) in subtropical China. Soils under three typical land uses, i.e., rice–rice (RR), upland crop (UC), and paddy rice–upland crop rotation (PU), were selected. The abundance of bacterial cbbL (0.04 to 1.25 × 108 copies g−1 soil) and 16S rDNA genes (0.05–3.00 × 1010 copies g−1 soil) were determined in these soils. They generally followed the trend RR > PU > UC. The cbbL-containing bacterial communities were dominated by facultative autotrophic bacteria such as Mycobacterium sp., Rhodopseudomonas palustris, Bradyrhizobium japonicum, Ralstonia eutropha, and Alcaligenes eutrophus. Additionally, the cbbL-containing bacterial community composition in RR soil differed from that in upland crop and paddy rice–upland crop rotations soils. Soil organic matter was the most highly statistically significant factor which positively influenced the size of the cbbL-containing population. The RR management produced the greatest abundance and diversity of cbbL-containing bacteria. These results offer new insights into the importance of microbial autotrophic CO2 fixation in soil C cycling.

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Abbreviations

T-RFLP:

Terminal restriction fragment length polymorphism

CO2 :

Carbon dioxide

SOC:

Soil organic C

RR:

Rice–rice

UC:

Upland crop

TRF:

Terminal restriction fragment

PU:

Paddy rice–upland crop rotation

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Acknowledgments

This work was supported by the “Strategic Priority Research Program—Climate Change: Carbon Budget and Related Issues” of the Chinese Academy of Sciences (XDA05050505), National Natural Science Foundation of China (41090283; 41271279), the CAS/SAFEA International Partnership Program for Creative Research Teams (KZCX2-YW-T07; 20100491005-8) and the Knowledge Innovation Program of the Chinese Academy of Sciences (ISACX-LYQY-QN-1103).

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Authors and Affiliations

  1. Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, China

    Hongzhao Yuan, Tida Ge, Xiaohong Wu, Shoulong Liu, Ping Zhou, Xiaojuan Chen & Jinshui Wu

  2. Horticulture & Landscape College, Hunan Agricultural University, Changsha, Hunan, 410128, China

    Shenying Zou

  3. Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK

    Phil Brookes

  4. Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha City, Hunan Province, 410125, China

    Jinshui Wu

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  1. Hongzhao Yuan
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  2. Tida Ge
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Correspondence to Jinshui Wu.

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Yuan, H., Ge, T., Zou, S. et al. Effect of land use on the abundance and diversity of autotrophic bacteria as measured by ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large subunit gene abundance in soils. Biol Fertil Soils 49, 609–616 (2013). https://doi.org/10.1007/s00374-012-0750-x

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