Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences

Abstract

Microbes are key components of the soil environment and are important contributors to the sustainability of agricultural systems, which is especially significant for biofuel crops growing on marginal lands. We studied bacterial communities in the rhizosphere of five biofuel crops cultivated in four locations in Michigan to determine which factors were correlated to changes in the structure of those communities. Three of these sites were marginal lands in that two were not suitable for conventional agriculture and one was regulated as a brownfield due to prior industrial pollution. Bacterial community composition and structure were assessed by 454 sequencing of the 16S rRNA gene. A total of 387,111 sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as plant species, soil attributes, and location. The most abundant bacterial phyla found in the rhizosphere of all crops were Acidobacteria, Proteobacteria, Actinobacteria, and Verrucomicrobia. Bacterial communities grouped by location rather than by crop and their structures were correlated to soil attributes, principally pH, organic matter, and nutrients. The effect of plant species was low but significant, and interactions between locations, plant species, and soil attributes account for most of the explained variation in the structure of bacterial communities, showing a complex relationship between bacterial populations and their environment. Bacterial diversity was higher in the agricultural sites compared to adjacent forest sites, indicating that the cultivation of those biofuel crops increased the rRNA diversity.

Contrasting Effects of Chinese Fir Plantations of Different Stand Ages on Soil Enzyme Activities and Microbial Communities

“…The microbial compositions of Chinese fir plantations of different ages were different. The bacterial dominance of Acidobacteria, Proteobacteria, Actinobacteria, Chloroflexi, and Firmicutes and the fungal dominance of Ascomycota, Basidiomycota and Zygomycota in the present study have been observed in various soils types [45][46][47][48][49], indicating that these microbial phyla play important roles in soil ecosystems. Changes in microbial community composition indicate changes in soil ecological environment and function [50,51].…”

Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil

“…In contrasting soils, such as deserts and forests, significantly fewer FP-CAZy core sequences could be identified, suggesting that the soil environment, which can be geographically specific, is important for defining a soil core and its functional potential. This result has been reported previously where soil type was the critical driver of microbial community compositional differences [53,54]. For metagenomic studies, this observation has implications for the genomic or functional level that should be compared between studies.…”

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

“…DNA extraction and SSU rRNA gene amplification methods were described previously (29). The SSU rRNA gene amplicons from the first sample were sequenced by the Joint Genome Institute (JGI) in their standard work flow, which used 454 GS FLX and Titanium platforms and a primer set (926F, AAACTYAAAKGAATTGACGG; 1392R, ACGGGCGG TGTGTRC) that targeted the V6-V8 variable region of bacteria, archaea, and eukaryotes.…”