Differential responses of prokaryotic and fungal communities in soil microenvironments to drying and wetting as affected by soil aggregate isolation method

• Microbial communities are altered by aggregate separation method. • Wet sieving increased microbial diversity in comparison to dry sieving. • Soil prokaryotic and fungal communities responded differently to dry and wet sieving. • Ribosomal RNA copy number and genome size showed high abundances in drier soils. Microorganisms live in communities within and on the surface of soil aggregates of varying sizes. A growing body of evidence suggests that different size fractions of aggregates are habitats for distinct microbial communities, but comparisons have been difficult owing to different aggregate separation methods. Two aggregate isolation methods, dry and wet sieving, originating from field moist and dried soils were used to investigate their effects on the prokaryotic and fungal communities in four aggregate size fractions (large macroaggregates (>2000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm), and silt & clay (