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Abstract

The soil microbiome, existing as interconnected communities closely
associated with soil aggregates, is the key driver in nutrient cycling.
However, the underlying genomic information encoding the machinery of
the soil microbiome involved in nutrient cycling at the soil aggregate
scale is barely known. Here comparative metagenomics and genome binning
were applied to investigate microbial functional profiles at the soil
aggregate scale under different organic material amendments in a
long-term field experiment. Soil samples were sieved into large
macroaggregates (>2 mm), macroaggregates (0.25-2 mm) and microaggregates
(<0.25 mm). Microbial taxonomic and functional alpha diversity were
significantly correlated to soil NO3- and SOC. The highest abundance of
nasB, nirK, and amoA genes, which are responsible for denitrification
and ammonia oxidizers driving nitrification, was observed in
microaggregates. Both manure and peat treatments significantly decreased
the abundance of napA and nrfA that encode enzymes involved in
dissimilatory nitrate reduction to ammonium (DNRA). As a biomarker for
soil inorganic P solubilization, the relative abundance of gcd was
significantly increased in macroaggregates and large macroaggregates.
Three nearly complete genomes of Nitrososphaeraceae (AOA) and seven
bacterial genomes were shown to harbor a series of genes involved in
nitrification and P solubilization, respectively. Our study provides
comprehensive insights into the microbial genetic potential for DNRA and
P-solubilizing activity across different soil aggregate fractions and
fertilization regimes.