Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes

Agroecosystem management practices, plant-microbe interactions, and climate are all factors that influence soil microbial community diversity and functionality. Herein, we assessed diversity of soil bacterial-archaeal assemblages and denitrification gene markers in a long-term tillage field experiment. We evaluated bulk and rhizosphere soils from two crop years (corn and soybean) of a three-year rotation of corn-soybean-small grain + cover crop. Soil samples were collected at three growth stages from corn and soybean plants and across three tillage practices that had been applied every year for 40 years. Tillage practices represented three levels of disturbance intensity ranging from low (no-till) to intermediate (chisel-disk) to high (moldboard plow) intensities. Bacterial assemblage diversity differed in soils having contrasting tillage histories and from bulk or rhizosphere soil (compartments), crop year, and growth stage. Compared to plowed and chisel-disked soils, no-till soils had lower abundances of denitrification genes, higher abundances of genes for dissimilatory nitrate reduction to ammonium (DNRA), and higher abundances of family-level taxa associated with archaeal nitrification and anammox. Soybean rhizospheres exerted stronger selection on bacterial-archaeal composition and diversity relative to corn rhizospheres. Abundances of N genes were grouped by factors related to weather, as well as management and soil compartment, which could impact activity related to denitrification and DNRA. Low intensity tillage may provide an option to reduce potential ‘hot spots’ or ‘hot moments’ for N losses in agricultural soils, although weather and crop type are also important factors that can influence how tillage affects microbial assemblages and microbial N use.