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 (<53 μm)) using metabarcoding of the 16S rRNA gene and internal transcribed spacer. While prokaryotic community composition among treatments in each of the four size fractions was different, the composition and alpha diversity for fungi were more resistant to change in large and small macroaggregates than in the microaggregate and silt & clay fractions. The average prokaryotic ribosomal RNA copy number and genome size increased in all aggregate size fractions when soils were dried before sieving. Decisions on which aggregate separation method to use depend heavily on the questions one is interested in, but soil storage conditions between sample collection and sieving are highlighted as driving the biggest differences in microbial community composition.