Composition and potential functional roles of soil fungal communities on arid farms in Arequipa (Southern Peru) characterized using SMRT sequencing

Abstract Small farms near Arequipa, Peru face many challenges including crop diseases caused by soil-borne fungal pathogens. Identifying fungi in these soils and factors that shift the balance between pathogenic and beneficial lifestyles will aid in the development of more effective and sustainable disease control strategies. In this study, the composition and potential functional roles of soil fungal communities on 12 farms was characterized using SMRT sequencing. Communities were compared with soil physiochemical properties and farms grouped based on location (River vs. Canal), and farm age (Old, New, Very New) to investigate possible drivers of community structure and function. Communities were dominated by the Ascomycota phylum, and Fusarium, Alternaria and Cladosporium genera. The majority of phylotypes were saprotrophs, however, an unusually large fraction were pathotrophs (14-29%), and 10% of the entire community were plant pathogens. There were correlations between saprophytic and pathogenic phylotypes with soil pH, organic matter, nitrogen and phosphorous, though the strongest driver of community structure were cobalt and nickel. Dominant pathogenic phylotypes in river and canal farms differed indicating the need for more site-specific intervention strategies. Age was positively correlated with a decline in saprotrophs and increase in pathotrophs highlighting the need to replenish soil organic matter. Correlations between individual phylotypes could mediate disease outbreaks and should be explored in future studies. Results of this study confirm that soils in this unique agroecosystem are highly conducive to the survival of soil-borne pathogens, though it should be possible to suppress these organisms via more targeted soil management practices.