Microbial communities vary across soil aggregates and bulk soil samples

Soils are characterised by the vast diversity of bacteria, archaea and fungi which collectively guarantee ecosystem functioning. Physical and chemical heterogeneity, and fragmentation of the soil pore network have been suggested to give rise to diverse distinct microbial communities at the small-scale. Yet little is known about structure of communities at the small-scale and its drivers. Here, we compared bacterial and archaeal, and fungal composition and richness of individual hand-picked 2-millimeter-sized soil aggregates and standard bulk soil samples. To disentangle what factors drive community composition and richness at the millimetre-scale, we concurrently determined microbial community composition and richness, carbon and nitrogen content, natural isotopic ratio and soil water content of individual aggregates and recorded spatial distribution of aggregates at the field site. We demonstrate that bulk soil samples and aggregates systematically differed in microbial community composition and richness. Aggregate-communities markedly varied in composition and richness. Soil depth and horizontal sampling location strongly impacted community composition of aggregates. Also, organic matter concentration and recycling status and soil moisture were linked with community composition and richness. Our data suggests that variability of microbial communities at the millimetre-scale allows large overall richness. And claim that it partly originates from environmental heterogeneity of the soil matrix at the millimetre-scale. Sequencing was performed at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna under the project IDs JMF-2011-I.