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

Intracellular metabolite pool changes in response to nutrient depletion induced metabolic switching in Streptomyces coelicolor

Abstract: A metabolite profiling study of the antibiotic producing bacterium Streptomyces coelicolor A3(2) has been performed. The aim of this study was to monitor intracellular metabolite pool changes occurring as strains of S. coelicolor react to nutrient depletion with metabolic re-modeling, so-called metabolic switching, and transition from growth to secondary metabolite production phase. Two different culture media were applied, providing depletion of the key nutrients phosphate and L-glutamate, respectively, as the triggers for metabolic switching. Targeted GC-MS and LC-MS methods were employed to quantify important primary metabolite groups like amino acids, organic acids, sugar phosphates and other phosphorylated metabolites, and nucleotides in time-course samples withdrawn from fully-controlled batch fermentations. A general decline, starting already in the early growth phase, was observed for nucleotide pools and phosphorylated metabolite pools for both the phosphate and glutamate limited cultures. The change in amino acid and organic acid pools were more scattered, especially in the phosphate limited situation while a general decrease in amino acid and non-amino organic acid pools was observed in the L-glutamate limited situation. A phoP deletion mutant showed basically the same metabolite pool changes as the wild-type strain M145 when cultivated on phosphate limited medium. This implies that the inactivation of the phoP gene has only little effect on the detected metabolite levels in the cell. The energy charge was found to be relatively constant during growth, transition and secondary metabolite production phase. The results of this study and the employed targeted metabolite profiling methodology are directly relevant for the evaluation of precursor metabolite and energy supply for both natural and heterologous production of secondary metabolites in S. coelicolor

Fate and effects of enrofloxacin in aquatic systems under different light conditions

The fate and effects of fluoroquinolone antibacterials (FQ) in the environment is of significance because of apparent increased FQ resistance in environmental and clinical organisms. Here we simultaneously assessed the fate and effects of enrofloxacin (enro), an FQ often used in agriculture, on the chemistry and in situ microbial communities in receiving waters. We added enro to 25 mu g/L in nine outdoor mesocosms maintained under three light conditions (in triplicate): full sunlight typical of the upper epilimnion (100% full-light exposure, FLE), partial shading typical of the lower epilimnion (28% FILE), and near-complete shading typical of the hypolimnion (0.5% FILE). Enro disappearance and ciprofloxacin (cipro) formation were monitored overtime using LC/MS, and water chemistry and ambient microbial communities (using denaturing gradient gel electrophoresis; DGGE) were characterized. Enro half-lives were 0.8, 3.7, and 72 days for the 100%, 28%, and 0.5% FLE treatments, respectively, creating three distinct FQ exposure scenarios. Although FQ exposures ranged from similar to 6 mu g/L for 24 h to similar to 21 mu g/L for 30 days, no statistically significant exposure effects were noted in water quality or microbial communities (as indicated by whole-community 16S rDNA DGGE analysis and specific amplification of the QRDR region of gyrase A). Small changes in water chemistry were noted over time; however, changes could not be specifically attributed to FQs. In general, enro addition had minimal effect on water column conditions at the levels and durations used here; however, further investigation is needed to assess effects in aquatic sediments