Plant associated microbial populations in organic and conventional Mid Atlantic cropping systems with and without glyphosate
Our objective was to determine if the application of the herbicide glyphosate to resistant corn or soybean plants indirectly shifts the structure of the plant associated microbial community in endophytic association with the plant. To achieve these goals we utilized the USDA Beltsville LTAR site, Farming Systems Project (FSP), a site that has maintained 20 years of organic and conventional corn/soybean/wheat cropping systems in field scale replicated plots. Microplots were established within rotations of either Chisel-till (CT), No-till, Organic 3 year or Organic 6 year. Bulk and rhizosphere soils, roots, shoots and nodules were collected prior to glyphosate application and again 20 days after application. Roots were assessed for endophytic fungal community. Culture based analysis and DNA/RNA were extracted from the bulk and rhizosphere soils, soybean nodules and xylem and phloem from shoots over two years among four cropping rotations. Metagenomic libraries were constructed from extracts of soil and plant tissues and illumina high throughput sequencing was used to asses the fungal and bacterial community structure before and after glyphosate treatment among this diverse array of farming systems which represent the highest acreage management regime among organic and conventional farmers in the Mid-Atlantic region.
We detected increases in root endophytic density of both fungi and bacteria over two seasons. Early season measurements of root fungal endophytes revealed an average of 10 colony forming unit (CFU)/ 100 cm of root, whereas when the plants reached reproductive stages the average endophyte density had increased to 40-60 CFU/ 100 cm of root. Analysis of soybean nodule endophyte community using 16s gene amplification, classified by the Ribosomal Database Project, revealed 12 nitrogen fixing species among soybean in our field sites with Bradyrhizobium, Rhizobium, Pseudomonas being among the most common genera. Xylem and phloem 16s clone library construction and selective media based culturing identified 30-40 genera of bacteria living within the vasculature of the corn and soybean plants. Metagenomic sequencing of microbial 16s and ITS genes from plow layer (Ap horizon) or deeper soils demonstrated that among organic and conventional systems soil depth is a primary driver of microbial community structure. Principle component analysis indicated that regardless farming system, microbial communities below the plow layer are significantly less diverse then communities in the plow layer. Within the plow layer, when comparing rhizosphere and bulk soils, subtle farming system level effects were detected, influencing the structure of the plant associated microbial community.