Abstract
Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. The aim of this study was to investigate the bacterial communities profiles in some native plants and samples of the Moroccan phosphate mine ecosystem by assessing the percentages of taxonomic identification using six hypervariable regions of the 16S rRNA. The rhizosphere of the three wild plants in the Moroccan phosphate mine is characterized by interesting bacterial diversity including Proteobacteria (62.24%, 71.15% and 65.61%), Actinobacteria (22.53%, 15.24%, 22.30%), Bacteroidetes (7.57%; 4.23%; 7.63%), and Firmicutes (5.82%; 1.17%; 2.83%). The bulk phosphate mine samples were dominated by Actinobacteria with average relative abundance of 97.73% that are different from those inferred in the rhizosphere samples of the native plants. The regions V3, V4 and V67 performed better in the taxonomic profiling at different taxonomic levels. Results indicated that both plant genotype and mainly soil conditions may be involved in the shaping of bacterial diversity. Such indication was also confirmed by the prediction of functional profiles that showed enrichment of many functions related to biological nitrogen fixation in the rhizosphere of native plants and the stress related functions in the bulk phosphate mine in comparison with the wheat rhizosphere samples.
Highlights
Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions
Its sequences serve as a marker of choice in order to infer the microbiome composition. 16S rRNA gene is universally present in bacteria and archaebacteria, it contains conserved, variable and hypervariable regions allowing taxonomical classification and separation
To investigate the microbiome associated with native plants that grow in phosphate mines in Morocco and its comparison with the phosphate bulk soil samples and the rhizosphere of wheat crop, a total of 15 samples were subjected to 16S rRNA sequencing analysis using Ion Torrent PGMTM sequencing platform
Summary
Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. Despite the continuous improvements in cultivation-dependent techniques, an often cited estimate indicated that only 1% of extant bacteria can be isolated in culture and as much as 99% or more of the microorganisms present in many natural environments are not readily c ulturable[13,14] This traditional approach is still required in order to isolate single strains that can be applied as inoculum, the next-generation sequencing (NGS) molecular methods are, nowadays, widely used to profile microbial communities and their dynamic in different plants and plant compartments[15]. Barb et al.[21] analyzed the six hypervariable regions of the 16S marker gene by using the Ion 16STM metagenomics kit to study the oral microbiome diversity They developed a novel analytical pipeline with the V4 region enabled the best resolution of bacterial communities profiling up to both family and genus levels. The ability of some native isolates from Atacama desert to act as plant growth promoting bacteria (PGPB) was confirmed in wheat plants, they showed greater protection against salt stress[26]
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