Xue, K., L. Wu, Y. Deng, Z. He, J. V. Nostrand, G. P. Robertson, T. M. Schmidt, and J. Zhou. 2013. Functional gene differences in soil microbial communities from conventional, low-input and organic farmlands. Applied and Environmental Microbiology 79:1284-1292.
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 ©/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, USA. Compared to CT, a higher diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from either CT or LI. 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 that all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3-, NH4+, available phosphorus and potassium contents) 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 NO3- concentration and denitrification genes, NH4+ concentration and ammonification genes, plus N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.
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