Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.
Droughts are occurring with increased frequency and duration in tropical rainforests due to climate change, having a significant impact on soil C dynamics. The role of microbes as drivers of changing C flow, particularly in relation to volatile organic compound (VOC) cycling, remains largely unknown. Here, we aimed to characterize microbial responses to drought using an integrative, multiple 'omics approach, and hypothesized that microbial communities will adapt by altering their C allocation strategies. Specifically, during pre-drought, primary metabolic pathways will be more active with microbes using C towards growth, whereas during drought, microbes will divert C to secondary metabolite (including VOC) production in response to stress. To test this, we conducted an ecosystem-wide 66-day drought experiment in the tropical rainforest biome at Biosphere 2, a glass-and steel-enclosed facility near Tucson, AZ. To track carbon allocation by microbes, we injected C1 or C2 positionspecific 13C-pyruvate solution into a 25 cm2 region within a soil flux chamber collar (n=6 locations) and measured C isotope ratios of VOC and CO2 emissions. Soil was collected at 0, 6, and 48 hours after pyruvate addition to examine responses in soil metatranscriptomics, metagenomics, and metabolomics (1H nuclear magnetic resonance [NMR] and Fourier-transform ion cyclotron resonance [FTICR]). Our results indicated that 13CO2 (primarily emitted from C1-13C-pyruvate) fluxes decreased during drought, indicating diminished microbial activity. 13C-VOCs (primarily emitted from C2-13C-pyruvate) fluxes also differed between pre-drought and drought. Furthermore, drought-induced increases in activity of VOC-producing metabolic pathways, including acetate and acetone biosynthesis, were evident, as inferred from volatilome, metabolome, and metatranscriptome data. Overall, these results indicate that integration of multiple 'omics datasets reveal specific impacts of drought on microbial activity affecting carbon flow in the tropical rainforest soil.
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