CPR from Cullars Rotation top soil - shotgun metagenomics and 16S analysis (16S, Shotgun, and MAGs)

Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms that are predicted to play important ecological roles in biogeochemical cycles. Recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. To better access CPR genomes, we enriched for ultra-small bacterial cells from soil samples. This strategy was applied to study CPR taxa from soils sampled from the Cullars Rotation, a soil fertility experiment initiated in 1911 that includes 14 different soil fertility treatments. From these treatment groups 42 samples were shotgun sequenced, enabling the reconstruction of 26 quality CPR metagenome-assembled genomes (MAGs). Moreover, 4 plots with the msot striking community shifts were selected for 16S analysis of the entire soil microbiota in order to identify potential CPR symbionts. Our study was able to reconstruct the CPR community from soils, revealing a prevalence of Saccharibacteria which also carried the ability to degrade plant biomass. We identified that CPR community shifts were not correlated to nutrient levels, nor were them associated with other specific bacteria as symbionts, instead they responded to shifts in pH and heavy metal concentrations. Our findings shed light in the ecology of this group in soils revealing their distribution and association patterns.