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.
Despite its fundamental role for carbon (C) and nutrient cycling, rhizodeposition remains ‘the hidden half of the hidden half’: it is highly dynamic and rhizodeposits are rapidly incorporated into ...microorganisms, soil organic matter, and decomposed to CO2. Therefore, rhizodeposition is rarely quantified and remains the most uncertain part of the soil C cycle and of C fluxes in terrestrial ecosystems. This review synthesizes and generalizes the literature on C inputs by rhizodeposition under crops and grasslands (281 data sets). The allocation dynamics of assimilated C (after 13C‐CO2 or 14C‐CO2 labeling of plants) were quantified within shoots, shoot respiration, roots, net rhizodeposition (i.e., C remaining in soil for longer periods), root‐derived CO2, and microorganisms. Partitioning of C pools and fluxes were used to extrapolate belowground C inputs via rhizodeposition to ecosystem level. Allocation from shoots to roots reaches a maximum within the first day after C assimilation. Annual crops retained more C (45% of assimilated 13C or 14C) in shoots than grasses (34%), mainly perennials, and allocated 1.5 times less C belowground. For crops, belowground C allocation was maximal during the first 1–2 months of growth and decreased very fast thereafter. For grasses, it peaked after 2–4 months and remained very high within the second year causing much longer allocation periods. Despite higher belowground C allocation by grasses (33%) than crops (21%), its distribution between various belowground pools remains very similar. Hence, the total C allocated belowground depends on the plant species, but its further fate is species independent. This review demonstrates that C partitioning can be used in various approaches, e.g., root sampling, CO2 flux measurements, to assess rhizodeposits’ pools and fluxes at pot, plot, field and ecosystem scale and so, to close the most uncertain gap of the terrestrial C cycle.
Despite its fundamental role for carbon (C) and nutrient cycling, rhizodeposition remains “the hidden half of the hidden half”: it is highly dynamic and rhizodeposits are rapidly incorporated into microorganisms, soil organic matter, and decomposed to CO2. Therefore, rhizodeposition is rarely quantified and remains the most uncertain part of C fluxes in terrestrial ecosystems. This review synthesizes and generalizes the literature on C inputs by rhizodeposition under crops and grasslands.
The burgeoning global market for soil microbial inoculants for use in agriculture is being driven by pressure to increase sustainable crop production by managing pests and diseases without ...environmental impacts. Microbial inoculants, based predominantly on bacteria and fungi, are applied to soil as alternatives to conventional inorganic fertilizers (biofertilizers) or to carry out specific functions including biocontrol of pests and diseases (biopesticides), or for bioremediation and enhancement of soil characteristics. While some soil inoculants such as rhizobia have a long and successful history of use, others have performed inconsistently in the field and failed to live up to their promise suggested by laboratory testing. A more precise understanding of the ecology and modes of action of inoculant strains is key to optimizing their efficacy and guiding their targeted use to situations where they address key limitations to crop production. This will require greater collaboration between science disciplines, including microbiology, plant and soil science, molecular biology and agronomy. Inoculants must be produced and formulated to ensure their effective establishment in the soil and practicality of implementation alongside existing cropping practices. New approaches to strain selection and construction of beneficial microbial consortia should lead to more efficacious inoculant products. Extensive and rigorous field evaluation of inoculants under a range of soil and environmental conditions has rarely been undertaken and is urgently needed to validate emerging inoculant products and underpin successful implementation by growers, especially in a market that is largely unregulated at present.
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