Diversity, Plant Growth Promoting Attributes, and Agricultural Applications of Rhizospheric Microbes

Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.

Rhizobacterial mediated interactions in Curcuma longa for plant growth and enhanced crop productivity: a systematic review

Turmeric (Curcuma longa L.), a significant commercial crop of the Indian subcontinent is widely used as a condiment, natural dye, and as a cure for different ailments. Various bioactive compounds such as turmerones and curcuminoids have been isolated from C. longa that have shown remarkable medicinal activity against various ailments. However, reduced soil fertility, climatic variations, rapid urbanization, and enhanced food demand, pose a multifaceted challenge to the current agricultural practices of C. longa. Plant growth-promoting microbes play a vital role in plant growth and development by regulating primary and secondary metabolite production. Rhizospheric associations are complex species-specific interconnections of different microbiota with a plant that sustain soil health and promote plant growth through nutrient acquisition, nitrogen fixation, phosphate availability, phytohormone production, and antimicrobial activities. An elaborative study of microbiota associated with the roots of C. longa is essential for rhizospheric engineering as there is a huge potential to develop novel products based on microbial consortium formulations and elicitors to improve plant health, stress tolerance, and the production of secondary metabolites such as curcumin. Primarily, the purpose of this review is to implicate the rhizospheric microbial flora as probiotics influencing overall C. longa health, development, and survival for an increase in biomass, enhanced yield of secondary metabolites, and sustainable crop production.

Mechanisms and Applications of Bacterial Inoculants in Plant Drought Stress Tolerance

Agricultural systems are highly affected by climatic factors such as temperature, rain, humidity, wind, and solar radiation, so the climate and its changes are major risk factors for agricultural activities. A small portion of the agricultural areas of Brazil is irrigated, while the vast majority directly depends on the natural variations of the rains. The increase in temperatures due to climate change will lead to increased water consumption by farmers and a reduction in water availability, putting production capacity at risk. Drought is a limiting environmental factor for plant growth and one of the natural phenomena that most affects agricultural productivity. The response of plants to water stress is complex and involves coordination between gene expression and its integration with hormones. Studies suggest that bacteria have mechanisms to mitigate the effects of water stress and promote more significant growth in these plant species. The underlined mechanism involves root-to-shoot phenotypic changes in growth rate, architecture, hydraulic conductivity, water conservation, plant cell protection, and damage restoration through integrating phytohormones modulation, stress-induced enzymatic apparatus, and metabolites. Thus, this review aims to demonstrate how plant growth-promoting bacteria could mitigate negative responses in plants exposed to water stress and provide examples of technological conversion applied to agroecosystems.

Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils

Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all four crops when grown in disrupted soils. In summary, soil disruption followed by crop introduction amplified the plant colonization of potential beneficial bacterial genera in the rhizosphere.

Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions

Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes' rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.

Increasing aridity shapes beta diversity and the network dynamics of the belowground fungal microbiome associated with Opuntia ficus-indica

AIMS

The effects of aridity on soil and water-use efficient (WUE) crop species are relatively well known. However, the understanding of its impacts on the dynamics of below-ground microorganisms associated with plant roots is less well understood.

METHODS

To investigate the influence of increasing aridity on the dynamics of the fungal communities, samples from the root endosphere and rhizosphere associated with the prickly pear cactus trees (Opuntia ficus-indica) growing along the aridity gradient were collected and the internal transcribed spacer (ITS) were sequenced. The diversity and network analyses of fungal taxa were determined along with standard measurements of soil parameters.

RESULTS

We found that (i) the fungal community exhibited similar alpha diversity and shared a set of core taxa within the rhizosphere and endosphere, but there was significant beta diversity differences; (ii) the relative abundance of major phyla was higher in the rhizosphere than in the endosphere; (iii) arbuscular endomycorrhizal colonization was highest in the humid climate and decreased under lower-arid, and was negatively correlated with increased concentration of Ca²⁺ in the soil; (iv) increased aridity correlated with increased connectivity of the soil microbial-root fungal networks in the arid soils, producing a highly cohesive network in the upper-arid area; and (v) distinct fungal hubs sculpt the fungal microbiome network structure in the rhizosphere and endosphere within each bioclimatic zone.

CONCLUSIONS

Our findings highlight the importance of gradient analysis-based correlation network as a powerful approach to understand changes in the diversity, the dynamics, and the structure of fungal communities associated with the rhizosphere-endosphere interaction and led to the identification of microbes at each bioclimatic zone that are potentially involved in promoting the survival, protection, and growth of Opuntia trees. The variability of fungal hubs composition depending on plant compartment and bioclimatic zone will give key implications for the application of rhizospheric fungi and endophytes as microbial inoculants in agriculture, as well as in the conservation and restoration of cacti plants in arid and semi-arid lands against the backdrop of climate change. Overall, this study will enhance our understanding of the microbiomes'dynamic of CAM plants in nature.