Synthetic physical contact-remodeled rhizosphere microbiome for enhanced phytoremediation

Magnetic nanoparticle-assisted colonization of synthetic bacteria on plant roots for improved phytoremediation of heavy metals

Seed-associated microbiomes can impact the later colonization of a plant rhizosphere microbiome. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome may intervene in the assembly of a rhizosphere microbiome. In this study, the fungus Trichoderma guizhouense NJAU4742 was introduced to both maize and watermelon seed microbiomes by seed coating. Application was found to significantly promote seed germination and improve plant growth and rhizosphere soil quality. The activities of acid phosphatase, cellulase, peroxidase, sucrase, and α-glucosidase increased significantly in two crops. The introduction of Trichoderma guizhouense NJAU4742 also led to a decrease in the occurrence of disease. Coating with T. guizhouense NJAU4742 did not alter the alpha diversities of the bacterial and fungal communities but formed a key network module that contained both Trichoderma and Mortierella. This key network module comprised of these potentially beneficial microorganisms was positively linked with the belowground biomass and activities of rhizosphere soil enzymes but negatively correlated with disease incidence. Overall, this study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome. IMPORTANCE Seed-associated microbiomes can impact the rhizosphere microbiome assembly and function display. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome with the beneficial microbes may intervene in the assembly of a rhizosphere microbiome. Here, we introduced T. guizhouense NJAU4742 to the seed microbiome by seed coating. This introduction led to a decrease in the occurrence of disease and an increase in plant growth; furthermore, it formed a key network module that contained both Trichoderma and Mortierella. Our study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome.

Nitrogen fixing nodules are formed on the roots and stems of the tropical legume Sesbania rostrata by Azorhizobium caulinodans as a result of crack entry invasion of emerging lateral roots. Advantage was taken of this invasion capability of A. caulinodans to determine whether inoculation of the non-legume wheat with A. caulinodans would result in the endophytic establishment of azorhizobia within wheat roots. Advantage was also taken of the oxygen tolerance of the nitrogenase of free-living azorhizobia to assess the extent to which the endophytic establishment of azorhizobia in wheat roots would provide a niche for nitrogen fixation of benefit to the plant. Wheat was inoculated with A. caulinodans and grown in pots under controlled conditions, without added growth reglators and without addition of fixed nitrogen. Microscopic examination of the short lateral roots of inocluated wheat showed invasion of azorhizobia between cells of the cortex, within the xylem and the root meristem Acetylene reduction assays combined with analysis of tissue nitrogen levels indicated the likelihood that colonization led to nitrogenase activity. Inoculated wheat showed significant increases in dry weight and nitrogen content as compared with uninoculated controls. We discuss the extent to which this nitrogen fixation is likely to involve symbiotic nitrogen fixation, and we indicate the need for field trials to determine the extent to which inolculation of wheat with A. caulinodans will reduce the requirement for inputs of nitrogenous fertilizers.

The quest for increasing agricultural yield due to increasing population pressure and demands for healthy food has inevitably led to the indiscriminate use of chemical fertilizers. On the contrary, the exposure of the crops to abiotic stress and biotic stress interferes with crop growth further hindering the productivity. Sustainable agricultural practices are of major importance to enhance production and feed the rising population. The use of plant growth promoting (PGP) rhizospheric microbes is emerging as an efficient approach to ameliorate global dependence on chemicals, improve stress tolerance of plants, boost up growth and ensure food security. Rhizosphere associated microbiomes promote the growth by enhancing the uptake of the nutrients, producing plant growth regulators, iron chelating complexes, shaping the root system under stress conditions and decreasing the levels of inhibitory ethylene concentrations and protecting plants from oxidative stress. Plant growth-promoting rhizospheric microbes belong to diverse range of genera including Acinetobacter, Achromobacter, Aspergillus, Bacillus, Burkholderia, Flavobacterium, Klebsiella, Micrococcus, Penicillium, Pseudomonas, Serratia and Trichoderma. Plant growth promoting microbes are an interesting aspect of research for scientific community and a number of formulations of beneficial microbes are also commercially available. Thus, recent progress in our understanding on rhizospheric microbiomes along with their major roles and mechanisms of action under natural and stressful conditions should facilitate their application as a reliable component in the management of sustainable agricultural system. This review highlights the diversity of plant growth promoting rhizospheric microbes, their mechanisms of plant growth promotion, their role under biotic and abiotic stress and status of biofertilizers. The article further focuses on the role of omics approaches in plant growth promoting rhizospheric microbes and draft genome of PGP microbes.

BackgroundSoil microbiomes are considered a cornerstone of the next green revolution, and plant growth-promoting bacteria (PGPB) are critical for microbiome engineering. However, taking plant-beneficial microorganisms from discovery to agricultural application remains challenging, as the mechanisms underlying the interactions between beneficial strains and plants in native soils are still largely unknown. Increasing numbers of studies have indicated that strains introduced to manipulate microbiomes are usually eliminated in soils, while others have reported that application of PGPB as inocula significantly improves plant growth. This contradiction suggests the need for a deeper understanding of the mechanisms underlying microbe-induced growth promotion.ResultsWe showed PGPB-induced long-term plant growth promotion after elimination of the PGPB inoculum in soils and explored the three-way interactions among the exogenous inoculum, indigenous microbiome, and plant, which were key elements of the plant growth-promoting process. We found the rhizosphere microbiome assembly was mainly driven by plant development and root recruitments greatly attenuated the influence of inocula on the rhizosphere microbiome. Neither changes in the rhizosphere microbiome nor colonization of inocula in roots was necessary for plant growth promotion. In roots, modification of DNA methylation in response to inoculation affects gene expression related to PGPB-induced growth promotion, and disruptions of the inoculation-induced DNA methylation patterns greatly weakened the plant growth promotion. Together, our results showed PGPB-induced DNA methylation modifications in roots mediated the promotion process and these modifications remained functional after elimination of the inoculum from the microbiome.ConclusionThis study suggests a new mechanism in which PGPB affect DNA methylation in roots to promote plant growth, which provides important insights into microbiome–plant interactions and offers new strategies for plant microbiome engineering beyond the perspective of maintaining inoculum persistence in soils.4DAt-NxeARCpvmCXo93oLmVideo abstractGraphical abstract

Rhizosphere is the portion of soil that is exposed to the root activity. It is hot spot for microbial activities which support the plant growth and development in different ways. Microbial communities in the rhizosphere referred as rhizosphere microbiome are one of the most diverse regions of the ecosystem existing on Earth. Rhizosphere microbiome is biologically the most diverse part of the ecosystem which contains a large number of microbial communities which interact with the plants differently like the good, the bad, and the ugly microbes of rhizosphere. The good ones are beneficial microbes of the rhizosphere which are involved in plant growth promotion through nutrient uptake in plants, antagonism to plant pathogens, and plant tolerance against abiotic stresses. However, the bad ones are plant parasitic fungi and nematodes which cause diseases of economic importance in important crop plants and result in serious issues of reduction in productivity and food security. Similarly, some rhizosphere microbes avail the opportunity to invade the human body through different courses and cause infectious diseases. These opportunistic microbes are “the ugly” ones as they are the most deleterious in nature. In this chapter, we have discussed in detail the good, the bad, and the ugly members of rhizosphere microbiome. Moreover, we have given a comprehensive account of bolts and nuts of rhizosphere and engineering of rhizosphere for agriculturally sustainability.

Streptomyces partum Act12 and Streptomyces roche D74 are biocontrol strains that can promote plant growth and enhance stress resistance in different crops. However, their effects on the rhizosphere microbiome and the role of the reassembled microbiome in plant growth promotion and stress resistance enhancement remain unclear. This study investigated the variation in the rhizosphere microbiome induced by Streptomyces application through a cucumber (Cucumis sativus L. cv. “Youliang”) pot experiment. The bacterial and fungal communities of rhizosphere soils inoculated with and without Streptomyces were, respectively, compared based on 16S rRNA and internal transcribed spacer rRNA gene sequences. Following Streptomyces application, the bacterial alpha diversity increased significantly, while the fungal alpha diversity exhibited the opposite trend. The bacterial and fungal communities’ compositions clearly shifted in the inoculated soil. Compared with the uninoculated control, the relative abundance of the genus Streptomyces increased by 68.3%, and the bacterial co-occurrence network in the rhizosphere soil was enriched significantly. The relative abundance of bacteria associated with nitrogen fixation was increased by 7.5% following Streptomyces application. Based on the results of this study, we conclude that the application of Streptomyces Act12 and D74 can be used to reassemble and optimize the rhizosphere microbiome of cucumber, which is conducive to plant survival.

Impact of co-inoculation with plant-growth-promoting rhizobacteria and rhizobium on the biochemical responses of alfalfa-soil system in copper contaminated soil

Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.

Plants are no more considered as organisms but as complex communities harbouring diverse microbes both on its outer as well as inner surfaces and environment. Plant microbiome represents the complex microbial communities associated directly or indirectly with a plant. It can be broadly categorized into endophytic, epiphytic and rhizospheric microbiome. Therefore, complex interactions between different said zones lead to a plant microbiome. Interestingly, plant microbiome involves pathogenic as well as non-pathogenic microbes. Non-pathogenic members include neutral as well as symbiotic members. Applications of plant-associated microbes hold a plethora of promises in diverse fields, viz. biotransformation, biodegradation, phytoremediation, seed production, seed predation, plant growth promotion, stress tolerance, biocatalysis, biofuel production, biocontrol, agricultural importance, source of novel natural products, biosynthesis and many more. There is an urgent need to explore and understand the hyperdiversity as well as functional potential of these microbial communities not just for the sake of sustaining ecosystem services but to maintain the beneficial use of biodiversity to mankind. For sustainable development of the human world, sustainable agriculture is the need of the hour. Plant microbiome communities are reported to play important roles in soil improvement, plant growth promotion and stress resistance. They are bestowed with the distinguished features of atmospheric nitrogen fixation, bioactive metabolite and phytohormone production, plant disease suppression, nutrient cycling enhancement and many more. Microbial mutualism offers a novel approach to develop microbial inoculants for use in agricultural biotechnology. The microbial inoculants offer several advantages as they are more safe, have reduced environmental cost, have lesser negative impacts on human health, are active in small quantities and have many more positive applications. These products can plausibly be used as biofertilizers and/or biocontrol agents, plant strengtheners, phytostimulators and biopesticides. It is a well-established fact that plants cannot survive in the absence of microbial associations. Therefore, deep understanding of the plant microbiome as a whole is essential in order to explore the same for better and sustainable agriculture.

Saline-alkali soil has poor fertility and low organic matter content, which are key factors that limit agricultural productivity. Intercropping systems can enhance biodiversity in farmlands, thereby increasing the organic matter content. During this process, soil microorganisms respond to environmental changes. Therefore, we conducted a three-year intercropping enhancement experiment using saline-alkali soil. To avoid nutrient and microbial differences caused by the varying nutrient demands of different crop types, we systematically sampled the tillage layer of the soil (0–20 cm) from the subsequent crop (wheat season) in the intercropping systems. We found that compared to the control group, the three intercropping systems significantly increased the nutrient content in saline-alkali soil, including total nitrogen, total phosphorus, total potassium, organic matter, available nitrogen, and available potassium. Notably, there were significant increases in total nitrogen, organic matter, and available potassium. The intercropping systems had varying effects on the alpha and beta diversities of soil bacteria and fungi. Specifically, the effect of intercropping on fungal alpha diversity was significantly greater than that on bacterial alpha diversity, whereas its effect on bacterial beta diversity was greater than that on fungal beta diversity. Additionally, intercropping influenced microbial community composition, increasing the abundance of Acidobacteria and Gemmatimonadetes and decreasing the abundance of Actinobacteria. It also increased the abundance of Ascomycota and Mortierella and decreased the abundance of Basidiomycota. Total nitrogen and soil organic matter were identified as the primary environmental factors that significantly affected bacterial community composition; however, they had no significant impact on fungal communities. Intercropping had different effects on the fungal and bacterial networks. It increased the stability and complexity of the bacterial network. However, although it improved the stability of the fungal network, intercropping reduced its complexity. In summary, intercropping with leguminous plants is an effective way to enhance soil nutrients, particularly organic matter, in saline-alkali soils. Simultaneously, intercropping affects the soil microbial community structure of subsequent crops; however, the responses of bacteria and fungi to intercropping are significantly different. The results of this study provide data support for improving saline-alkali land through planting systems.

Bacterial communities in the rhizosphere and endorhizosphere of plants show distinct composition, function, and ecological roles during adaptation to diverse habitats. This study examines how rhizosphere and endophytic microbes associated with Aeluropus sinensis-a salt-excreting halophyte-contribute to its salt tolerance across saline-alkali environments. Microbial diversity and composition were analyzed via 16S rRNA gene amplicon sequencing. Soil physicochemical properties were measured to evaluate environmental effects. Linear regression assessed microbial-environment relationships, and co-occurrence networks identified key taxa and their adaptive strategies along environmental gradients. Soil salinity significantly affected rhizosphere bacterial diversity, with moderate levels increasing richness. Proteobacteria dominated both root and rhizosphere microbiomes across habitats. The endorhizosphere community strongly correlated with soil nutrients such as available phosphorus (AP) and total nitrogen (TN). Co-occurrence analysis reveals that chemoheterotrophic microbes in the A. sinensis rhizosphere employ distinct adaptive strategies across gradients, and ammonia-oxidizing bacteria (AOB) may support nitrogen cycling in the Yellow River Delta saline-alkaline ecosystem. This study underscores microbial adaptability in salt-tolerant grasses, demonstrating that comparing rhizosphere and endorhizosphere microbiomes in Poaceae under stress improves understanding of microbial functions in harsh environments.

Soil samples were collected in a typical short-term flooding wetland with two dominate vegetation types (i.e., Phragmites australis and Suaeda salsa) of the Yellow River Delta of China. Path analysis was applied to investigate the relationship between soil nitrogen and selected 12 soil properties. Correlation analysis showed that soil total nitrogen was significantly correlated with total carbon, nitrate nitrogen, available phosphorous, total potassium, total sulfur and soil organic matter (P <0.01). Path analysis demonstrated that total carbon, nitrate nitrogen and soil organic matter had higher direct and indirect positive effects to total nitrogen, whereas bulk density and salt exhibited higher negative effects. Additionally, available phosphorous, total potassium, total sulfur exhibited indirect effects on total nitrogen through total carbon.

Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp.

Chapter 9 - Involvement of soil parameters and rhizosphere microbiome in sustainable crop productivity