Studying the entire protist community in ecologically relevant soil microcosms

The role of protists in soil biogeochemical processes remains poorly understood and quantified due to the lack of appropriate methodologies to study them independently from other soil biota under conditions emulating natural soil. Here we present a methodological breakthrough for the selective removal of protists using gamma irradiation and the subsequent reinoculation with metazoan-free soil powder inoculum that allows reconstructing a complex microbial food web comprising the native microflora and soil protist communities, without other fauna. Culturable flagellates and ciliates were totally removed by a radiation of 6 kGy, while a significant fraction of the amoebae survived (8% of the entire protist population) at 16 kGy but were totally removed at 27 kGy. Reinoculation successfully established a protist community of similar size and composition as the control soil as assessed by both meta transcriptomics analysis and microscopic observation after cultivation. The disturbance of the microflora community was limited and acceptable from 6 to 16 kGy doses. This methodology opens up exciting new perspectives for studying the ecological roles of the entire protist community or specific groups thereof (flagellates and ciliates) in real soil and in the presence of a viable native microflora community.