Understanding soil bacterial communities for sustainable agriculture

Abstract

Nutrient loss from synthetic fertilizer use contributes to poor water quality, conversion of native landscapes to agricultural production reduces biodiversity, and antibiotic use in animal production contributes to antibiotic resistance. Therefore, agriculture can have adverse effects on local and global environments. Soil bacteria mediate processes that can influence the impact of agriculture on the environment. Characterizing soil bacterial communities in response to changes in agricultural management may inform scientific understanding of how management decisions can alter soil bacteria. Several management practices aim to reduce the impact of agriculture on the environment and improve its sustainability. Offsetting synthetic fertilizer use with organic amendments can reduce nitrate losses and improve water quality. However, the microbially mediated and hard to predict the release of plant-available nutrients from organic amendments can limit their adoption and use. Installation of prairie strips as a conservation practice can reduce sediment loss and provide habitat for native animals, improving diversity. However, the impact of prairie strips on the soil bacterial community remains under characterized. Grasses can filter antibiotics and antibiotic resistance genes in runoff water from manure treated fields, though the ability of prairie strips to reduce antibiotic resistance in runoff water is not understood. The experiments described in this dissertation contribute to a scientific understanding of soil bacteria's response to organic amendment and prairie strip installation, as well as the impact of prairie strips on attenuating the transport of manure associated bacteria and antibiotic resistance genes. Soil bacterial communities' response to organic amendments of varying quality was compared against soil receiving no amendment during an incubated microcosm study. Soil bacterial communities exhibited community similarity in two temporal groupings in all amended and un-amended soils. In response to organic several bacterial taxa became significantly more abundant in amended soils and were associated with amendment quality. Alpha and beta diversity of soil bacteria were compared between agricultural soil and prairie strip soil at two sites. Prairie strips examined were less than five years old and did not significantly differ from agricultural soils at the two sites. Bacterial richness, Shannon's diversity, and Simpson's diversity were significantly greater in prairie soils than agricultural soils at one site and only in response to rainfall. The abundance of manure-associated bacteria in runoff water was compared between plots receiving manure without prairie strips and plots receiving manure. Prairie strip appended plots had lower abundances of manure associated taxa and lower detection of antibiotic resistance genes than plots without prairie strips. Conservation practices designed to reduce nutrient loss, such as the use of composts or the installation of prairie strips, are essential practices that can improve agricultural sustainability, yet have impacts on bacterial dynamics that are not well understood. Characterizing bacterial communities in soils under various conservation practices will inform our understanding of how these practices impact the soil bacterial community.