Field-grown B.stricta rhizosphere microbiomes exhibit minimal diel changes in microbial membership and potential function

Fasta file of raw data, csv metadata for fasta reads, and cleaned phyloseq object containing bacterial 16S rRNA transcript and 16S rRNA gene reads.

Abstract for paper is as follows: The rhizosphere microbiome greatly affects plant health and fitness. Quantifying bacterial responses to fine-scale plant-mediated changes in the rhizosphere, such as those associated with diel cycling of host plant physiology, will increase our understanding of microbial community assembly patterns. Here, we used 16S rRNA biomarker gene (DNA) and transcript (RNA) sequencing to characterize changes in the rhizosphere community membership and activity over short timescales in field-grown Boechera stricta plants. Microbial communities characterized by 16S-rRNA-transcripts, which serve as a proxy for microbial activity, showed greater sensitivity to fine-scale environmental changes than did communities characterized by 16S-rRNA biomarker gene sequencing, which reflects microbial presence/absence. Significant differences were seen between overall communities characterized by RNA vs. DNA, with RNA-derived communities showing more significant differences between the rhizosphere and control soil communities within phyla and in differential abundance analysis of genera. Communities reconstructed from RNA were also more sensitive to the effects of field block and collection timepoint. Using differential abundance analysis showed five genera to have significantly (p<0.05) differential abundance in the rhizosphere soil between the pre-dawn (AM) and early afternoon (PM) timepoints based on 16S rRNA transcripts, including the close plant associated genus Curtobacterium. However, when variance was partitioned between day of collection, the amplitude of the signal between timepoints was not significant. In sum, community composition and activity was highly sensitive to abiotic factors expressed over the small spatial scale of field blocks and short 24-hr periods between collection days, but showed minimal to no diel patterning.