Functional gene differences in soil microbial communities from conventional, low-input and organic farmlands. Xue, K., Wu, L., Deng, Y., He, Z., Nostrand, J., Robertson, G. P., Schmidt, T. M., & Zhou, J. Applied and Environmental Microbiology, 2013.
abstract   bibtex   
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, 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.
@article{xue_functional_2013,
	title = {Functional gene differences in soil microbial communities from conventional, low-input and organic farmlands},
	volume = {79},
	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, 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.},
	journal = {Applied and Environmental Microbiology},
	author = {Xue, K. and Wu, L. and Deng, Y. and He, Z. and Nostrand, J.V. and Robertson, G. P. and Schmidt, T. M. and Zhou, J.},
	year = {2013},
	keywords = {KBS}
}

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