Sixty root nodule isolates of soybean rhizobia indigenous to eight field sites in India were characterized using PCR-RFLP for repeated sequence RSalpha a 1195-bp DNA fragment, indole acetic acid production, and nitrogenase activity. Site-dependent variations were observed in terms of IAA production and nitrogenase activities. RSalpha was conserved in slow-growing soybean rhizobia across locations and sites and was absent in other Rhizobiaceae members and other bacterial genera. The results suggest that RSalpha can be a useful molecular marker for slow-growing soybean rhizobia. The study also showed the low presence of soybean nodulating fast growers in Indian soils.
The composition of rhizosphere microorganisms in soils can vary greatly across space, plant species, soil type, root architecture and growth stage (Berg and Smalla 2009). Physicochemical and biological features have an important role in the soil for the establishment of plant-microbe interactions (Janssen 2006). As it was demonstrated, soil pH, structure, oxygen and nutrition levels in the rhizosphere differ from those in the bulk soil (Roesch et al. 2007). The soil is considered to harbour the most diverse bacterial communities on earth providing habitats for them (Roesch et al. 2007). Soil microbial communities play an important role in plant health, soil quality and ecosystem sustainability of agricultural systems (Rincon-Florez et al. 2013). Bacterial communities are important drivers for all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil (Roesch et al. 2007, Rincon-Florez et al. 2013). There are biotic and abiotic factors that are assumed to influence the structural and functional diversity of bacterial communities in the rhizosphere soil, such as climate, season, herbicide application, management practices (Galazka et al. 2017a,b), integrated livestock-crop system (Acosta-Martínez Soils harbour enormously diverse bacterial communities that interact specifically with plants generating beneficial interactions between them. This study was the first approach to assess bacterial communities before sowing with three cotton genotypes, including both transgenic and conventional ones. The structure of bacterial communities was identified using the next generation sequencing analysis, ion torrent PGM (Personal Genome Machine™) sequencer technology, based on the V2-V3 16S rRNA gene region. Quantitative insights into microbial ecology pipeline were used to identify the structure and diversity of bacterial communities in bulk soil samples collected in the northeast of Mexico. Bulk soil textures and chemical properties, including most nutrients, were homogeneous in these bulk soil samples. Relative abundance analysis showed similar bacterial community structures. Dominant taxonomic phyla were Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria, Gemmatimonadetes and Bacteroidetes, whereas the main families were Bacillaceae, Chitinophagaceae and Rhodospirillaceae with an abundance average of BS1 (bulk soil sample), BS2 and BS3 (24.85, 19.74 and 19.71%, respectively). Alpha diversity analysis showed a high diversity (Shannon and Simpson index) and a large value of the observed species found in bulk soils samples. These results allowed establishing the previous bacterial structural community in an unused soil before sowing it with a transgenic crop for the first time.
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