Pedosphere 29(3): 298--310, 2019
ISSN 1002-0160/CN 32-1315/P
©2019 Soil Science Society of China
Published by Elsevier B.V. and Science Press
Functional Metagenomics to Mine Soil Microbiome for Novel Cadmium Resistance Genetic Determinants
ZHENG Xin1, CHEN Liang1, CHEN Miaomiao1, CHEN Jinghao1,2, LI Xiaofang1,3
1Key Laboratory for Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021(China);
2University of Chinese Academy of Sciences, Beijing 100049(China);
3Environment Center, Sustainable Minerals Institute, The University of Queensland, Brisbane 4072(Australia)
      Metal resistance genes are valuable resources for genetic engineering of bioremediation tools. In this study, novel genetic determinants involved in cadmium (Cd) resistance were identified using a small-insert metagenomic DNA library constructed from an arable soil microbiome. A total of 16 recombinant plasmids harboring 49 putative open reading frames (ORFs) were found to be associated with enhanced Cd tolerance. In addition to several ORFs for ion transport/chelation and stress response, most ORFs were assumed to be associated with non-direct metal resistance mechanisms such as energy metabolism, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, and signal transduction. Furthermore, 13 ORFs from five clones selected at random were cloned and subject to Cd resistance assay. Eight of these ORFs were positive for Cd resistance when expressed in Escherichia coli, among which four ORFs significantly reduced Cd accumulation and one increased Cd enrichment of the host cells. Notably, C1-ORF1, potentially encoding a histidine kinase-like adenosine triphosphatase, was the most effective Cd resistance determinant and reduced host Cd accumulation by 33.9%. These findings highlight the vast capacity of soil microbiome as a source of gene pool for bioengineering. The novel genetic determinants for Cd resistance identified in this study merit further systematic explorations into their molecular mechanisms.
Key Words:  bioremediation,genetic engineering,histidine kinase,metal resistance gene,open reading frame,recombinant plasmid
Citation: Zheng X, Chen L, Chen M M, Chen J H, Li X F. 2019. Functional metagenomics to mine soil microbiome for novel cadmium resistance genetic determinants. Pedosphere. 29(3):298-310.
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