Environmental Science & Technology · 2025 · 15 citations · 80 references
AgricultureMicrobiologySoil SciencesMetagenomicsMicrobial EcologySoil MicrobiologyNitrogen FixationNitrogen Fixation In SoilsRhizosphere BiogeochemistryRhizosphere EcologyRhizosphere Nutrient DynamicsSoil Microbial PhysiologyAcetylene Reduction AssayBiotransformationContaminated SoilDissimilatory Nitrate ReductionMethylated Arsenic CompoundsNitrate ReductionNitrite Reductase ActivityRhizosphere Metagenomics
Plants can recruit microorganisms to enhance soil arsenic (As) removal and nitrogen (N) turnover, but how microbial As methylation in the rhizosphere is affected by N biotransformation is not well understood. Here, we used acetylene reduction assay, arsM gene amplicon, and metagenome sequencing to evaluate the influence of N biotransformation on As methylation in the rhizosphere of Vetiveria zizanioides, a potential As hyperaccumulator. V. zizanioides was grown in mining soils (MS) and artificial As-contaminated soils (AS) over two generations in a controlled pot experiment. Results showed that the content of dimethylarsinic acid in the rhizosphere was significantly positively correlated with the rate of N fixation and the activity of nitrite reductase. The As-methylating species (e.g., Flavisolibacter and Paraflavitalea ) were significantly enriched in the root-associated compartments in the second generation of MS and AS. Notably, higher abundance of genes involved in N fixation ( nifD, nifK ) and dissimilatory nitrate reduction to ammonium ( narG / H, nirB / D / K / S ) was detected in the second generation of MS than in the first generation. The metabolic pathway analysis further demonstrated that N fixing-stimulative and DNRA-stimulative As-methylating species could provide ammonium to enhance the synthesis of S -adenosyl- l -methionine, serving as methyl donors for soil As methylation. This study highlights two important N conversion-stimulative As-methylating pathways and has important implications for enhancing phytoremediation in As-contaminated soils.
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Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt, Gwo-Liang Chen, Philip LoCascio et al. · BMC Bioinformatics · 2010 · 13.1K citations · Full text