Carbon amendments influence composition and functional capacities of indigenous soil bacterial communities

Authors: DUNDORE-ARIAS, JOSE PABLO - University Of Minnesota; Castle, Sarah; FELICE, LAURA - University Of Minnesota; DILL-MACKY, RUTH - University Of Minnesota; KINKEL, LINDA - University Of Minnesota

Submitted to: Frontiers in Molecular Biosciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2019
Publication Date: 1/9/2020
Citation: Dundore-Arias, J., Castle, S.C., Felice, L., Dill-Macky, R., Kinkel, L.L. 2020. Carbon amendments influence composition and functional capacities of indigenous soil bacterial communities. Frontiers in Molecular Biosciences. 6(151):1-12. https://doi.org/10.3389/fmolb.2019.00151.
DOI: https://doi.org/10.3389/fmolb.2019.00151

Interpretive Summary: Additions of organic matter are recognized for their potential to increase microbial activity and biomass in soil, but little is known about how specific carbon compound additions shape soil microbial communities and their functional capacities in agricultural systems. Using soils from two field sites, we evaluated soil chemistry, bacterial communities, and functional characteristics of the bacterial genus Streptomyces, in response to periodic carbon substrate additions after a period of nine months. In the lab, soils were amended with a low or high concentration of carbon compounds commonly found in soils (glucose, fructose, malic acid, or a mixture of all compounds). Carbon additions resulted in differences in soil chemical properties and the antibiotic inhibitory capacities of Streptomyces. At both sites, carbon additions, regardless of concentration or type, significantly influenced bacterial community compositions and which specific bacterial groups were present. There is growing interest in harnessing the functional capacities of soil microbial communities to increase agricultural crop production. These results suggest that manipulation of soil carbon resource availability through carbon compound additions has the potential to selectively change the functions of specific microbial groups, potential enhancing pathogen suppression by the soil community.

Technical Abstract: Soil organic nutrient amendments are recognized for their potential to improve microbial activity and biomass in the soil. However, the specific selective impacts of carbon amendments on indigenous microbiomes and their metabolic functions in agricultural soils remain underexplored. We investigated the changes in soil chemical characteristics and phenotypes of Streptomyces communities following carbon amendments to soil. Mesocosms were established with soil from two field sites varying in soil organic matter content (low organic mater, LOM; high organic matter, HOM), that were amended at intervals over nine months with low or high dose solutions of glucose, fructose, malic acid, a mixture of these compounds, or water only (non-amended control). Significant shifts in soil chemical characteristics and antibiotic inhibitory capacities of indigenous Streptomyces were observed in response to carbon additions. High dose amendments consistently increased soil total carbon, while amendments with malic acid reduced soil pH. In LOM soils, higher frequencies of Streptomyces inhibitory against both bacterial (Streptomyces scabies) and fungal (Fusarium oxyxporum) pathogens were observed in response to soil carbon additions. Additionally, to determine if shifts in Streptomyces functional characteristics correlated with microbiome composition, we evaluated composition of bacterial communities using 16S rRNA gene sequencing. Regardless of dose, community composition differed significantly among carbon-amended and non-amended soils from both sites. Carbon type and dose had significant effects on bacterial community composition in both LOM and HOM soils. Relationships among microbial community richness, diversity, and soil characteristics were unique among soils from different sites. These results suggest that manipulation of soil resource availability has the potential to selectively modify the functional capacities of soil microbiomes, and specifically to enhance pathogen inhibitory microbial communities of high value to agricultural systems.