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The capacity of nine species of white rot fungus from a variety of basidiomycete orders to degrade contrasting mono-aromatic pesticides was investigated. There was no relationship between degradation of the dye Poly R-478, a presumptive test for ligninolytic potential, and degradation of the highly available pesticides diuron, metalaxyl, atrazine or terbuthylazine in liquid culture. However, there were significant positive correlations between the rates of degradation of the different pesticides. Greatest degradation of all the pesticides was achieved by Coriolus versicolor, Hypholoma fasciculare and Stereum hirsutum. After 42 days, maximum degradation of diuron, atrazine and terbuthylazine was above 86%, but for metalaxyl less than 44%. When grown in the organic matrix of an on-farm "biobed" pesticide remediation system, relative degradation rates of the highly available pesticides by C. versicolor, H. fasciculare and S. hirsutum showed some differences to those in liquid culture. While H. fasciculare and C. versicolor were able to degrade about a third of the poorly available compound chlorpyrifos in biobed matrix after 42 days, S. hirsutum, which was the most effective degrader of the available pesticides, showed little capacity to degrade the compound.

Bacteria from Pinus sylvestris-Suillus luteus mycorrhizas were isolated, characterised, and their effects on P. sylvestris-S. luteus interactions and plant growth investigated in vitro. The isolates formed five distinct phenotypic and physiological groups. Two of the groups, accounting for 34 of the 55 isolates, consisted of Bacillus spp., with three subgroups represented. The other groups contained Burkholderia spp., Serratia spp. and Pseudomonas spp. Representatives from each bacterial group were used in microcosm experiments to investigate bacterial effects on P. sylvestris-S. luteus interactions. Most Bacillus isolates stimulated growth of S. luteus along the P. sylvestris root, while isolates of Pseudomonas and Serratia inhibited root colonisation by the fungus. Burkholderia and Serratia isolates inhibited ectomycorrhiza formation by 97 and 41% respectively, while a single Bacillus isolate doubled the formation of first order ectomycorrhizal roots. There were no clear relationships between effects of the bacteria on root colonisation by the fungus after 4 weeks, and chitinase production or subsequent ectomycorrhiza formation. However, isolates that inhibited ectomycorrhiza formation appeared to associate preferentially with ectomycorrhizal roots. Several isolates enhanced plant growth substantially, although these effects were unrelated to either root colonisation by the fungus or ectomycorrhiza formation.

Background The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. Results Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of “Kill-the-Winner” dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of “viral priming,” which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. Conclusions Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability.

Crop protection products (CPPs) are subject to strict regulatory evaluation, including laboratory and field trials, prior to approval for commercial use. Laboratory tests lack environmental realism, while field trials are difficult to control. Addition of environmental complexity to laboratory systems is therefore desirable to mimic a field environment more effectively. We investigated the effect of non-UV light on the degradation of eight CPPs (chlorotoluron, prometryn, cinosulfuron, imidacloprid, lufenuron, propiconazole, fludioxonil, and benzovindiflupyr) by addition of non-UV light to standard OECD 307 guidelines. Time taken for 50% degradation of benzovindiflupyr was halved from 373 to 183 days with the inclusion of light. Similarly, time taken for 90% degradation of chlorotoluron decreased from 79 to 35 days under light conditions. Significant reductions in extractable parent compound occurred under light conditions for prometryn (4%), imidacloprid (8%), and fludioxonil (24%) compared to dark controls. However, a significantly slower rate of cinosulfuron (14%) transformation was observed under light compared to dark conditions. Under light conditions, nonextractable residues were significantly higher for seven of the CPPs. Soil biological and chemical analyses suggest that light stimulates phototroph growth, which may directly and/or indirectly impact CPP degradation rates. The results of this study strongly suggest that light is an important parameter affecting CPP degradation, and inclusion of light into regulatory studies may enhance their environmental realism.