title: Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands.
abstract: Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO(3)(-), NH(4)(+), available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO(3)(-) concentration and denitrification genes, NH(4)(+) concentration and ammonification genes, and N(2)O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.
authors.affiliation: Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Xue
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.forename: Ye
authors.initials: Y
authors.lastname: Deng
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.forename: Joy
authors.initials: J
authors.lastname: Van Nostrand
authors.forename: Philip G
authors.initials: PG
authors.lastname: Robertson
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Schmidt
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D000383:Agriculture / Q000379:methods; D058448:Biota; D002244:Carbon / Q000378:metabolism; D005798:Genes, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics; D054892:Metagenome; D008824:Michigan; D046228:Microarray Analysis; D009584:Nitrogen / Q000378:metabolism; D010758:Phosphorus / Q000378:metabolism; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D013455:Sulfur / Q000378:metabolism
chemical_list: D012987:Soil; D010758:Phosphorus; D013455:Sulfur; D002244:Carbon; D009584:Nitrogen