Abstract
We aimed to understand how crop practices such as tillage, crop management and cover crop use affect aggregate microhabitats for nitrogen (N)-cycling microorganisms. We quantified the abundance of five N-cycling functional genes: two genes related to ammonia oxygenation (amoA from archaea and bacteria), two nitrite reducers (nirS and nirK) and one for nitrous oxide reduction (nosZ) as well as total eubacteria (16S) in two soil aggregate fractions. These fractions were total (occluded and non-occluded) microaggregates (tMi) and total silt and clay (tS + C) from a field trial under conventional and organic crop management combined with intensive or conservation tillage and four different cover crops. Although we found no clear associations between abundances of different functional genes in aggregate fractions, abundance of nosZ and amoA AOA changed almost exclusively in the tMi, suggesting that this fraction may mediate soil microbial response to crop management practices. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the nosZ gene indicated that aggregate fractions host different microbial communities, therefore providing distinct microhabitats.
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