Functional potential of soil microbial communities in the maize rhizosphere.
Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds.
Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America; Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.
Xiangzhen
X
Li
Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, CAS, Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, PR China.
Junpeng
J
Rui
School of Marine Sciences, Ningbo, Zhejiang, China.
Jingbo
J
Xiong
Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.
Jiabao
J
Li
Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States of America.
Zhili
Z
He
Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States of America.
Jizhong
J
Zhou
Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.
Anthony C
AC
Yannarell
Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.
Roderick I
RI
Mackie
D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D005798:Genes, Bacterial; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D058441:Rhizosphere; D012988:Soil Microbiology; D003313:Zea mays / Q000382:microbiology*