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ARS Home » Plains Area » Fort Collins, Colorado » Center for Agricultural Resources Research » Soil Management and Sugarbeet Research » Research » Publications at this Location » Publication #336469
Title: Bacterial microbiome and nematode occurrence in different potato agricultural soils

Author
item CASTILLO, JUAN - Colorado State University
item VIVANCO, JORGE - Colorado State University
item Manter, Daniel

Submitted to: Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2017
Publication Date: 5/20/2017
Citation: Castillo, J.D., Vivanco, J.M., Manter, D.K. 2017. Bacterial microbiome and nematode occurrence in different potato agricultural soils. Microbial Ecology. doi:10.1007/s00248-017-0990-2.

Interpretive Summary: Currently there is a growing interest in the study of soil and rhizosphere microbiome to understand the soil community composition and biodiversity, and the impact their interactions have on plants. The soil ecosystem is a complex and diverse environment that contains millions of bacteria and fungi, nematodes, mites, earthworms, and arthropods species in a single gram of soil. It has been demonstrated that the diversity of underground microorganisms significantly determines the aboveground biodiversity and ecosystem functioning. For the specific case of agricultural ecosystems, intensive agriculture is causing soil degradation, loss of biodiversity, reduction of soil-food trophic levels (predators), and decreasing functional groups with larger biomass (earthworms, enchytraeids, collembolans, mites). Hence, there is a need to understand soil microbial community, diversity and ecology, and beneficial or deleterious plant-microbe interactions in order to develop a more sustainable agriculture. The use molecular biology techniques to study the soil and rhizosphere bacterial microbiome, and the use of soil free-living nematodes as soil-health bioindicators can be used as tools to understand soil interactions within an agricultural system. In this work, nematode and microbial community composition in five different potato farms were analyzed to determine negative and positive correlations between any bacterial genus and P. neglectus and M. chitwoodi. Farms showed differences in bacterial communities, percentage of bacterivorous and fungivorous nematodes, and numbers of P. neglectus and M. chitwoodi. Our results suggest that the genera Bacillus spp., Arthrobacter spp., and Lysobacter spp. present in Colorado soils can explain the lower populations of P. neglectus and M. chitwoodi. Further studies will isolate and identify bacterial strains of these genera, and evaluate their nematode-antagonistic activity.

Technical Abstract: Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato crops of the San Luis Valley, Colorado. Bacterial microbiome (16S rRNA copies per gram of soil) and nematode communities (nematodes per 200 gr of soil) from five different potato farms were analyzed to determine negative and positive correlations between any bacterial genus and P. neglectus and M. chitwoodi. Farms showed differences in bacterial communities, percentage of bacterivorous and fungivorous nematodes, and numbers of P. neglectus and M. chitwoodi. The farm with the lowest population of P. neglectus and M. chitwoodi had higher abundances of the bacterial genera Bacillus spp., Arthrobacter spp., and Lysobacter spp., and the soil nematode community was composed by more than 30% of fungivorous nematodes. In contrast, the farm with higher numbers of P. neglectus and M. chitwoodi had a lower abundance of the above mentioned bacterial genera, higher abundance of Burkholderia spp. and less than 25% of fungivorous nematodes. The a-Proteobacteria: Rhodoplanes, Phenylobacterium and Kaistobacter positively correlated with M. chitwoodi, and the Bacteroidia and '-Proteobacteria positively correlated with P. neglectus. Our results suggest that the genera Bacillus spp., Arthrobacter spp., and Lysobacter spp. present in Colorado soils can explain the lower populations of P. neglectus and M. chitwoodi. Further studies will isolate and identify bacterial strains of these genera, and evaluate their nematode-antagonistic activity.