Microbial composition and functions in the rhizosphere-an important microbial hotspot-are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA ...amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions. The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin-antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11-182%), while genes involved in nitrification were strongly depleted.
Polyaromatic hydrocarbons (PAHs) are considered as hazardous organic priority pollutants. PAHs have immense public concern and critical environmental challenge around the globe due to their toxic, ...carcinogenic, and mutagenic properties, and their ubiquitous distribution, recalcitrance as well as persistence in environment. The knowledge about harmful effects of PAHs on ecosystem along with human health has resulted in an interest of researchers on degradation of these compounds. Whereas physico-chemical treatment of PAHs is cost and energy prohibitive, bioremediation i.e. degradation of PAHs using microbes is becoming an efficient and sustainable approach. Broad range of microbes including bacteria, fungi, and algae have been found to have capability to use PAHs as carbon and energy source under both aerobic and anaerobic conditions resulting in their transformation/degradation. Microbial genetic makeup containing genes encoding catabolic enzymes is responsible for PAH-degradation mechanism. The degradation capacity of microbes may be induced by exposing them to higher PAH-concentration, resulting in genetic adaptation or changes responsible for high efficiency towards removal/degradation. In last few decades, mechanism of PAH-biodegradation, catabolic gene system encoding catabolic enzymes, and genetic adaptation and regulation have been investigated in detail. This review is an attempt to overview current knowledge of microbial degradation mechanism of PAHs, its genetic regulation with application of genetic engineering to construct genetically engineered microorganisms, specific catabolic enzyme activity, and application of bioremediation for reclamation of PAH-contaminated sites. In addition, advanced molecular techniques i.e. genomic, proteomic, and metabolomic techniques are also discussed as powerful tools for elucidation of PAH-biodegradation/biotransformation mechanism in an environmental matrix.
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