Variations in the diversity of soil bacterial and archaeal communities in response to different long-term fertilization regimes in maize fields

Understanding the effect of different agricultural practices on soil microbiome is very important since it has a decisive role in the multifunctionality of soils. Our research aimed to reveal and compare the changes in the composition of soil bacterial and archaeal communities in response to cultivation and fertilization regimes. Soil samples were collected from a long-term (60-year-old) field experiment with maize (Zea mays L.) monoculture under inorganic fertilization, combined fertilization (inorganic and farmyard manure) and without fertilization, and a nearby fallow land five times over a crop cycle. The bacterial and archaeal community compositions were revealed by amplicon sequencing of the 16S rRNA genes on Illumina MiSeq platform. Significant differences were observed between cultivated soils and fallow land, as well as among cultivated soils under different fertilization regimes in both bacterial and archaeal community structures. Many taxa (e.g. Gaiella, Burkholderiaceae, Saprospiraceae, Rhodoplanes, MB-A2-108 and Cand. Nitrososphaera) were found to be more abundant in the fallow land than in the cultivated soils. The exclusive use of inorganic fertilizer resulted in a significantly different bacterial and archaeal community structure with higher relative abundance of sequences affiliated with mostly acidotolerant taxa (e.g. Bryobacter, Cand. Solibacter, Acidibacteriales, WPS-2 and Cand. Nitrosotalea). These taxa were not enriched in the combined fertilizer treatment, even though the manure was applied only once every four years. The results demonstrated a strong effect of inorganic fertilizers on the soil bacterial and archaeal communities, however, these effects can be decreased by the application of farmyard manure.