mSystems · 2022 · 28 citations · 64 references
AgricultureAgronomyPlant SciencesMicrobial EcologyPlant-microbe InteractionsSoil MicrobiologyPlant MicrobiomeRhizosphere BiologyRhizosphere EcologyRhizosphere InteractionsRhizosphere MicrobiologyRhizosphere ProcessesNitrogen MineralizationRhizosphere Bacterial CommunitiesRhizosphere FunctionRhizosphere Microbial EcologyRhizosphere Microbial InteractionsRhizosphere MicrobiomesRhizosphere Phosphorus CyclingRhizosphere Phosphorus Dynamics
plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.
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DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen et al. · Nature Methods · 2016 · 36.3K citations
Twelve years of SAMtools and BCFtools
Petr Danecek, James Bonfield, Jennifer Liddle et al. · GigaScience · 2021 · 15.9K citations · Full text