Short- and long-term effects of continuous compost amendment on soil microbiome community

Abstract

Organic amendment, especially use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches carbon and nitrogen soil reservoirs. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over four years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 l/m2). Microbial community dynamic in the soils was examined by high- and low-time-resolution analyses. Annual analyses community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9 -10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to one month, followed by a mild response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost-dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost related indicator taxa and compost derived core microbiome at both sites. Overall, this study describes changes of the ecology of soil microbiome as a response to compost vs. conventional fertilization in a time-dependent manner.