UC Davis

Most soil microorganisms live in communities within and on the surface of soil aggregates, the three-dimensional complexes composed of organic materials and particles that make up the soil physical structure. Soil aggregates vary considerably in physical and chemical properties by size, making them unique habitats for distinct microbial communities and metabolisms. However, this fine-scale spatial variability for microbes has received relatively little attention, and a better understanding of microbial community dynamics at these levels is crucial for predicting microbially-mediated soil functional responses to changing environments. This dissertation investigates the microbial communities in soil aggregates using three approaches. First, soil carbon (C) and aggregation dynamics were studied in an agricultural field experiment comparing the long-term impacts of manure compost and mineral fertilizer on C storage. Compost amendments increased soil total C, microbial biomass C, and maintained aggregate stability compared to mineral fertilizer. The prokaryotic community differed in composition between aggregates of different size fractions ranging from large macroaggregates (> 2 mm) to silt & clay (< 250 μm) and showed an increased capacity for potential degradation of aromatic C compounds with compost amendment. This suggests that yearly additions of compost can increase the diversity of substrates for microbes to increase biomass and aggregation through microbial activities. Next, because consistent relationships between microbial communities and aggregate size have remained elusive in the literature, two commonly used aggregate isolation methods, dry and wet sieving, were compared to identify their effects on prokaryotic and fungal communities in soils with different starting moistures. While the prokaryotic community was different by sieving treatment in each aggregate size fraction, the alpha diversity and composition of the fungal community were more resistant to change in the large and small macroaggregates than in the microaggregates and silt & clay. Drying soils prior to sieving favored spore-forming fast-growing generalist prokaryotes and fungal saprotrophs, whereas rewetting soils through wet sieving resulted in more slow-growing specialist prokaryotes and fungal pathogens. These results show that dry and wet sieving soils with different starting moistures can drastically affect the microbial communities in aggregates through drying and wetting dynamics. Finally, to better understand the different microbial taxa driving different functions in soil aggregates, a shotgun metagenomics approach was used to analyze the taxonomic and functional gene composition with the metabolic output of the microbiome in four size fractions of aggregates. Higher abundances of genes for the degradation of plant-derived compounds and biofilm formation were found in the macroaggregates, while the microaggregates and silt & clay were more enriched in genes for biomass recycling and anaerobic respiration. Both taxonomic profiling and reconstruction of genomes from metagenomes revealed a higher abundance of ammonia-oxidizing archaea (AOA) in macroaggregates, and further analysis of their genomic content revealed complementary metabolisms potentially enabling distinct AOA lineages to colonize different niches within the same habitat. These results characterize macroaggregates and microaggregates as resource-rich and resource-poor environments for microbes, respectively, and in conjunction with the other chapters in this dissertation, advances knowledge of the composition, stability, and function of microbial communities stratified in soil aggregates of different size.