Impact of Harvest on Switchgrass Leaf Microbial Communities.

Esther Singer,Elizabeth M Carpenter,Thomas E Juenger,Jason Bonnette,Tanja Woyke

doi:10.3390/genes13010022

Esther Singer, Elizabeth M Carpenter + Show 3 more

Open Access

https://doi.org/10.3390/genes13010022

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Abstract

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.

Highlights

Plant microbial communities vary in structure and function across diverse plant species [1], genotypes [2], ecosystems [3], soil types [4], and soil and plant treatments [5], as showcased by many amplicon sequencing studies
We used amplicon sequencing to analyze the bacterial, archaeal and fungal communities associated with leaf surface and leaf endosphere compartments of four switchgrass genotypes that were either harvested or not harvested, and in the presence and absence of fertilization
Because we did not measure microbial biomass, we can only speculate about whether unharvested leaf endosphere (LE) samples failed during sequencing due to a biological or a technical cause

Summary

Introduction

Plant microbial communities vary in structure and function across diverse plant species [1], genotypes [2], ecosystems [3], soil types [4], and soil and plant treatments [5], as showcased by many amplicon sequencing studies. Leaves generally host lower microbial biomass than roots, some of the insights obtained from phyllosphere microbial community studies show that leaf microbiota provide plant growth-promoting benefits. Various Methylobacter spp. can oxidize and assimilate methanol released by plant leaves as a byproduct of pectin formation during cell wall synthesis [14], and leaf-colonizing Cyanobacteria and Gammaproteobacteria spp. aid in N2 fixation in the plant species Carludovica drudei, Grias cauliflora and Costus leavis [15]

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