Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils

Abstract

In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources.

Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India

“…Two phylotypes (RS23, RS17) were related to Salinimicrobium catena isolated from sediments of oil fields in the South China Sea [29] within Flavobacteriaceae. The Acidobacteria group was dominant in the AS clone library and the sequences were related (88-99%) to uncultured Solibacter isolated from hydrocarbon contaminated soils [30], and uncultured Acidobacteria isolated from the heavy metal contaminated soils [31]. No phylotype from SS2 was found related to this group.…”

Culture-Independent Phylogenetic Analysis of the Microbial Community in Industrial Sugarcane Bagasse Feedstock Piles

“…This microbial biodiversity reflects the relatively aerobic nature below the bagasse pile surface under the collection conditions. Comparative analysis based on 16S rDNA sequences revealed that the bacterial community in the bagasse pile was mostly related to the bacteria in the soil and compost (EU676446, GQ360076), 23) especially from high-temperature sites (AM749771, GU113028), 24) A substantial number of the sequences were also related to the microbial assemblage in geothermal ecosystems e.g., hot spring, 11) and the thermophilic cyanobacterial mat (EF032761) as well as in waste water sludge (FJ536903). 25) Although the analysis might have been biased due to the availability of sequences from different environments in the existing databases, this suggests significant similarities and differences between the microbial groups in bagasse piles and other ecosystems.…”

Phytotoxicity analysis of extracts from compost and their ability to inhibit soil-borne pathogenic fungi and reduce root-knot nematodes

“…The denaturing gradient gel electrophoresis (DGGE) analysis was conducted according to the methods described by Nakatsu et al (2000) and Navarro-Noya et al (2010). The DGGE gels were analyzed with the Quantity One software (Bio-Rad).…”