Bulk soil bacterial community structure and function respond to long-term organic and conventional agricultural management

Authors: Bakker, Matthew; Looft, Torey; Alt, David; DELATE, KATHLEEN - Iowa State University; Cambardella, Cynthia

Submitted to: Canadian Journal of Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2018
Publication Date: 7/30/2018
Publication URL: http://handle.nal.usda.gov/10113/6440083
Citation: Bakker, M.G., Looft, T., Alt, D.P., Delate, K., Cambardella, C.A. 2018. Bulk soil bacterial community structure and function respond to long-term organic and conventional agricultural management. Canadian Journal of Microbiology. 64(12):901-914. https://doi.org/10.1139/cjm-2018-0134.
DOI: https://doi.org/10.1139/cjm-2018-0134

Interpretive Summary: The activities of microorganisms in soil have important impacts on soil quality, nutrient availability and the exchange of gases with the atmosphere. If we understood how agricultural management impacts soil microorganisms, we might be able to encourage beneficial activities of soil microorganisms. We compared the communities of soil microorganisms from field plots that have been managed using either conventional or organic approaches for the past 17 years. Our results show that communities of bacteria and fungi in soil differed between these two management approaches, and that particular microorganisms were favored by each type of agricultural management. These impacts on communities of soil microorganisms accompanied changes to soil physical and chemical properties. We also looked at the abundance of particular genes that enable certain soil microorganisms to exchange important atmospheric gases. The abundance of these genes also varied with agricultural management. Thus, agricultural management choices had an impact on the kinds of microorganisms that were present in field soil, and the kinds of activities they could perform. As we refine our understanding of these processes, it may become possible to use agricultural management to foster beneficial activities performed by soil microorganisms.

Technical Abstract: The degree to which bulk soil microbiomes respond to management practices has bearing on the sustainability of our production systems and the potential to eventually manage soil microbiology to allow for sustained or increased productivity under reduced inputs. Over two years, we contrasted the bulk soil microbiomes associated with long-term field management under organic and conventional paradigms, in a commodity crop production setting in the Midwest region of the United States. The resulting profiles of fungal and prokaryote communities in bulk soils contribute to our understanding of the natural history of many poorly understood taxa. There were significant changes to bulk soil fungal (1 out of 2 years) and prokaryote (2 out of 2 years) communities in response to agricultural management. Particular taxa responded to management consistently across both years; OTUs belonging to Acidobacteria Subgroup 6, Microvirga, Planctomyces, and Verrucomicrobiaceae were enriched under organic management, while OTUs belonging to Chloroflexi, Chthoniobacterales, Crenarchaeota, Planctomyces, and Sphingomonas were enriched under conventional management. Structural changes to soil microbiomes accompany changes to soil edaphic properties. Changes in the abundance of functional genes related to the cycling of greenhouse gases were also evident. Particulate methane monooxygenase genes were more frequent in soil under organic management, while soluble methane monooxygenase were more frequent in soil under conventional management in one of two years. Clade II nitrous oxide reductase genes were significantly less frequent in soils under second year alfalfa compared to soils under corn. Results demonstrate that bulk soil microbial community structure and function are sensitive to agricultural management. In time, deliberate management of soil microbiomes may enhance provision of ecosystem services.