Seasonality drives microbiome composition and nitrogen cycling in soil below biocrusts

Biological soil crusts (biocrusts) recently discovered in agroecosystems have the potential to enrich soil moisture and nitrogen (N) concentrations and structure the subsurface microbiome. In citrus agroecosystems, year-round N availability is vital for production, with vegetative flushes in the spring and fall and fruit development in the fall and winter. Due to the N demand and natural formation of biocrusts in citrus orchards, we investigated the influence of biocrusts on soil moisture content, N cycling, and microbiome composition in the upper root zone of a sandy soil citrus orchard (Florida, USA). Soils sampled from below biocrusts (1–5 cm) were collected at eight sampling dates over a one-year period in the orchard from biocrust-covered and proximate bare areas. Samples were analyzed for moisture content, soluble and microbial N pools, and potential ammonia oxidation. Bacterial and fungal communities were characterized using the 16S rRNA gene and ITS region sequences, respectively, at five sampling dates from September 2019 through March 2020. Biocrust presence and sampling date significantly impacted soil moisture and soluble and microbial N pools ( p < 0.05). Soil moisture and inorganic N were enriched below biocrusts compared to below bare soil controls during the dry season from fruit set through harvest. Microbial biomass N and potential ammonia oxidation activity were also higher in September and November during fruit set. During fruit set and maturation, there was a corresponding greater abundance of copiotrophic bacteria and fungi capable of heterotrophic nitrification in soil below biocrusts. Overall, these results indicate soil under biocrusts had increased moisture, N concentrations, and relative abundances of microbiota with functional potential for cycling N. These results support a potential role for biocrust influence on crop N availability and soil health during periods of plant nutrient demand. • Biocrust impact on the soil microbiome varied by season. • Soil nitrogen cycling potential increased during the dry season. • Biocrust presence significantly impacted soil moisture and nitrogen concentrations. • Biocrusts increased abundance of fungi capable of heterotrophic nitrification. • Variance in fungal community composition explained potential ammonia oxidation activity.