Relationships between yield, rotation length, and abundance of Olpidium brassicae and Pyrenochaeta sp. in the rhizosphere of oilseed rape

Oilseed rape yields in the UK have been found to decline with more frequent cropping in a rotation. Previously, two soil-borne organisms (Olpidium brassicae (Chytridiomycota) and Pyrenochaeta sp. (Ascomycota)) were identified as having high relative abundance in rhizosphere fungal communities associated with oilseed rape crops where yield decline had been recorded. In order to better understand these organisms' association with the oilseed rape crop, the current study was designed to investigate the fungal rhizosphere microbiome of oilseed rape grown in a wide range of rotational frequencies. Samples collected from a long-term rotation trial site at three time points through the growing season were used to determine fungal community composition, and quantification of O. brassicae and Pyrenochatea sp. Analyses showed the combined root and rhizosphere fungal communities were similar across all oilseed rape rotations, largely due to the high relative abundance of O. brassicae, irrespective of cropping frequency. Olpidium brassicae abundance peaked in March (mid-season) in all rotations, before declining in abundance by June (pre-harvest). In contrast, Pyrenochaeta sp. increased in abundance throughout the season, with significantly higher levels reached in June than earlier in the season. Pyrenochaeta sp. had a greater abundance early in the season (January) in continuously grown and alternate oilseed rape (grown one year in two) than in rotations with longer gaps between oilseed rape crops This study concludes that O. brassicae cannot be solely associated with yield decline of OSR observed in short rotation cropping due to its prevalence in the extended rotations examined (up to 6-year gap)

Nutrient (C, N and P) enrichment induces significant changes in the soil metabolite profile and microbial carbon partitioning

The cycling of soil organic matter (SOM) and carbon (C) within the soil is governed by the presence of key macronutrients, particularly nitrogen (N) and phosphorus (P). The relative ratio of these nutrients has a direct effect on the potential rates of microbial growth and nutrient processing in soil and thus is fundamental to ecosystem functioning. However, the effect of changing soil nutrient stoichiometry on the small organic molecule (i.e., metabolite) composition and cycling by the microbial community remains poorly understood. Here, we aimed to disentangle the effect of stoichiometrically balanced nutrient addition on the soil metabolomic profile and apparent microbial carbon use efficiency (CUE) by adding a labile C source (glucose) in combination with N and/or P. After incorporation of the added glucose into the microbial biomass (48 h), metabolite profiling was undertaken by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). 494 metabolites were identified across all treatments mainly consisting of lipids (n = 199), amino acids (n = 118) and carbohydrates (n = 43), >97% of which showed significant changes in concentration between at least one treatment. Overall, glucose-C addition generally increased the synthesis of other carbohydrates in soil, while addition of C and N together increased peptide synthesis, indicative of protein formation and turnover. The combination of C and P significantly increased the number of fatty acids synthesised. There was no significant change in the PLFA-derived microbial community structure or microbial biomass following C, N and P addition. Further, N addition led to an increase in glucose-C partitioning into anabolic processes (i.e., increased CUE), suggesting the microbial community was N, but not P limited. Based on the metabolomic profiles observed here, we conclude that inorganic nutrient enrichment causes substantial shifts in both primary and secondary metabolism within the microbial community, leading to changes in resource flow and thus soil functioning, however, the microbial community illustrated significant metabolic flexibility

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

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

Cultivar-level genotype differences influence diversity and composition of lettuce (Lactuca sp.) phyllosphere fungal communities

Different lettuce genotypes supported significantly different phyllosphere fungal communities. Phyllosphere fungal diversity was low and fungi fell into five similarity groups. These groups were represented in significantly different proportions throughout 26 lettuce accessions indicating cultivar-level variation in the fungal colonization of the lettuce phyllosphere. Significant differences in the proportions of the two dominant groups (with similarity to Cladosporium spp. and Sporobolomyces roseus) were identified between parental lines of two lettuce mapping populations providing opportunities to further investigate the genetic control of cultivar-level variation in fungal phyllosphere colonisation