Evidence of variability in the structure and recruitment of rhizospheric and endophytic bacterial communities associated with arable sweet sorghum (Sorghum bicolor (L) Moench)

Abstract

(167 words)Sorghum is the second most cultivated crop in Africa and is a staple food source of many African communities. Exploiting the associated plant growth promoting bacteria (PGPB) has potential as an agricultural biotechnology strategy to enhance sorghum growth, yield and nutritional properties. Here we use Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE) to evaluate the factors that potentially shape rhizospheric and endophytic bacterial communities associated with sorghum farmed in South Africa. Microbial diversity was typically higher in the rhizosphere and rhizoplane compared to the endophytic zones (root, shoot and stem). Geographical location was one of the main drivers in describing microbial community assemblages found in rhizospheric and endophytic sorghum-linked niches. NO 3 -N, total nitrogen and pH were clearly identified as the main abiotic factors shaping sorghum-associated soil communities.Our results also suggest that specific bacterial taxa with potential N-fixing capacities (Acetobacter sp., Azospirillum sp., Pantoea sp., Bacillus sp. and cyanobacteria) are consistently detected in sorghum-created rhizospheric and endophytic environments, irrespective of environmental factor effects.

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

“…However, in this study, sorghum stem communities were slightly more diverse than sorghum root communities. This further supports the hypothesis that only a small proportion of sorghum-associated endophytic bacteria are specifically recruited to different niches, whereas the bulk of the endophytic community is composed of opportunistic endophytes that are subjected to minimal selective pressure (Ramond et al, 2013). Dominant phylotypes in sorghum included ecologically and biotechnologically significant bacterial genera.…”

“…This indicates that the DNA extraction procedure introduces significant bias, thereby influencing the interpretation of the microbial community observed. PCR-based metagenomic approaches such as DGGE Ramond et al, 2013), t-RFLP (Sessitsch et al, 2012;Ding et al, 2013) and next generation sequencing (Gottel et al, 2011;Lucero et al, 2011;Ìnceoğlu et al, 2011;Molina et al, 2012) are continuously used to elucidate the structure and ecological roles of plant-associated (and other) microbial communities. However, few, if any, of these studies share the same DNA extraction protocol and/or are preceded by an evaluation of DNA extraction procedures to select the most efficient.…”

“…In one study, bacterial isolates from sorghum tissues were affiliated to the phyla Firmicutes, Actinobacteria, α-Proteobacteria and β-Proteobacteria, with no further characterisation (Grönemeyer et al, 2012). Ramond et al (2013) showed that the diversity of sorghum associated endophytic bacteria is lower than that of rhizospheric communities using t-RFLP and DGGE; however, the low resolution of the two fingerprinting techniques made it difficult to assign taxonomy for the recovered OTUs. Despite this, sorghum has been used widely as a host organism in the study of PGPeBs such as Gluconacetobacter species and Bacillus sp.…”

Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent

“…In addition, geographic location and soil characteristics are the main factors explaining the variability in the structure of the bacterial community in the rhizosphere of sorghum [9]. Moreover, in an earlier study, we found soil to be the most important factor on sorghum rhizosphere bacterial community assembly followed by plant growth stage and plant genotype [10].…”

Research priorities for harnessing plant microbiomes in sustainable agriculture

“…Progress has been made towards the establishment of model host–microbiome systems for the legume Medicago [42], Populus [43], rice [13,15,44–46], Sorghum [47], Miscanthus [48], maize [49,50], and tomato [51]. All of these model organisms have fully sequenced genomes and growing communities of researchers to extend their utility for microbiome research.…”