Plant-microbe interactions in the rhizosphere for smarter and more sustainable crop fertilization: the case of PGPR-based biofertilizers

Biofertilizers based on plant growth promoting rhizobacteria (PGPR) are nowadays gaining increasingly attention as a modern tool for a more sustainable agriculture due to their ability in ameliorating root nutrient acquisition. For many years, most research was focused on the screening and characterization of PGPR functioning as nitrogen (N) or phosphorus (P) biofertilizers. However, with the increasing demand for food using far fewer chemical inputs, new investigations have been carried out to explore the potential use of such bacteria also as potassium (K), sulfur (S), zinc (Zn), or iron (Fe) biofertilizers. In this review, we update the use of PGPR as biofertilizers for a smarter and more sustainable crop production and deliberate the prospects of using microbiome engineering-based methods as potential tools to shed new light on the improvement of plant mineral nutrition. The current era of omics revolution has enabled the design of synthetic microbial communities (named SynComs), which are emerging as a promising tool that can allow the formulation of biofertilizers based on PGPR strains displaying multifarious and synergistic traits, thus leading to an increasingly efficient root acquisition of more than a single essential nutrient at the same time. Additionally, host-mediated microbiome engineering (HMME) leverages advanced omics techniques to reintroduce alleles coding for beneficial compounds, reinforcing positive plant-microbiome interactions and creating plants capable of producing their own biofertilizers. We also discusses the current use of PGPR-based biofertilizers and point out possible avenues of research for the future development of more efficient biofertilizers for a smarter and more precise crop fertilization. Furthermore, concerns have been raised about the effectiveness of PGPR-based biofertilizers in real field conditions, as their success in controlled experiments often contrasts with inconsistent field results. This discrepancy highlights the need for standardized protocols to ensure consistent application and reliable outcomes.

Assessment of the Microbial Communities in Soil Contaminated with Petroleum Using Next-Generation Sequencing Tools

Microbial communities are known to play a principal role in petroleum degradation. This study tries to determine the composition of bacteria in selected crude oil-contaminated soil from Tabasco and Tamaulipas states, Mexico. We determined the microbial populations living under these conditions. We evaluated the structure and diversity of bacterial communities in the contaminated soil samples. The most abundant phylum is proteobacteria. Next Generation Sequencing (NGS) analysis of the sampled soils from both states revealed that this phylum has the most relative abundance among the identified bacteria phyla. The heatmap represented the relative percentage of each genus within each sample and clustered the four samples into two groups. Moreover, this allowed us to identify many genera in alkaline soil from Tamaulipas, such as Skermanella sp., Azospirillum sp. and Unclassified species from the Rhodospirillaceae family in higher abundance. Meanwhile, in acidic soil from Tabasco, we identified Thalassospira, Unclassified members of the Sphingomonadaceae family and Unclassified members of the Alphaproteobacteria class with higher abundance. Alpha diversity analysis showed a low diversity (Shannon and Simpson index); Chao observed species in both Regions. These results suggest that the bacteria identified in these genera may possess the ability to degrade petroleum, and further studies in the future should elucidate their role in petroleum degradation.

Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review

Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil–plant–microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.

Nano-Restoration for Sustaining Soil Fertility: A Pictorial and Diagrammatic Review Article

Soil is a real treasure that humans cannot live without. Therefore, it is very important to sustain and conserve soils to guarantee food, fiber, fuel, and other human necessities. Healthy or high-quality soils that include adequate fertility, diverse ecosystems, and good physical properties are important to allow soil to produce healthy food in support of human health. When a soil suffers from degradation, the soil’s productivity decreases. Soil restoration refers to the reversal of degradational processes. This study is a pictorial review on the nano-restoration of soil to return its fertility. Restoring soil fertility for zero hunger and restoration of degraded soils are also discussed. Sustainable production of nanoparticles using plants and microbes is part of the process of soil nano-restoration. The nexus of nanoparticle–plant–microbe (NPM) is a crucial issue for soil fertility. This nexus itself has several internal interactions or relationships, which control the bioavailability of nutrients, agrochemicals, or pollutants for cultivated plants. The NPM nexus is also controlled by many factors that are related to soil fertility and its restoration. This is the first photographic review on nano-restoration to return and sustain soil fertility. However, several additional open questions need to be answered and will be discussed in this work.

The Metabolic Potential of Endophytic Actinobacteria Associated with Medicinal Plant Thymus roseus as a Plant-Growth Stimulator

Bio-fertilizer practice considers not only economical but also environmentally friendly, sustainable agriculture. Endophytes can play important beneficiary roles in plant development, directly, indirectly, or synergistically. In this study, the majority of our endophytic actinobacteria were able to possess direct plant growth-promoting (PGP) traits, including auxin (88%), ammonia (96%), siderophore production (94%), and phosphate solubilization (24%), along with cell-wall degrading enzymes such as protease (75%), cellulase (81%), lipase (81%), and chitinase (18%). About 45% of tested strains have an inhibitory effect on the phytopathogen Fusarium oxysporum, followed by 26% for Verticillium dahlia. Overall, our results showed that strains XIEG63 and XIEG55 were the potent strains with various PGP traits that caused a higher significant increase (p ≤ 0.05) in length and biomass in the aerial part and roots of tomato and cotton, compared to the uninoculated plants. Our data showed that the greatest inhibition percentages of two phytopathogens were achieved due to treatment with strains XIEG05, XIEG07, XIEG45, and XIEG51. The GC-MS analysis showed that most of the compounds were mainly alkanes, fatty acid esters, phenols, alkenes, and aromatic chemicals and have been reported to have antifungal activity. Our investigation emphasizes that endophytic actinobacteria associated with medicinal plants might help reduce the use of chemical fertilization and potentially lead to increased agricultural productivity and sustainability.

The Effects of the Microbial Biostimulants Approved by EU Regulation 2019/1009 on Yield and Quality of Vegetable Crops

The use of microbial biostimulants such as plant growth-promoting rhizobacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) has gained popularity in recent years as a sustainable approach to boost yield as well as the quality of produce. The beneficial effects of microbial biostimulants have been reported numerous times. However, information is missing concerning quantitative assessment of the overall impact of microbial biostimulants on the yield and quality of vegetable crops. Here we provide for the first time a comprehensive, semi-systematic review of the effects of microbial biostimulants allowed by Regulation (EU) 2019/1009, including microorganisms belonging to the AMF (phylum Glomeromycota), or to Azospirillum, Azotobacter and Rhizobium genera, on vegetable crops' quality and yield, with rigorous inclusion and exclusion criteria based on the PRISMA method. We identified, selected and critically evaluated all the relevant research studies from 2010 onward in order to provide a critical appraisal of the most recent findings related to these EU-allowed microbial biostimulants and their effects on vegetable crops' quality and yield. Moreover, we highlighted which vegetable crops received more beneficial effects from specific microbial biostimulants and the protocols employed for plant inoculation. Our study is intended to draw more attention from the scientific community to this important instrument to produce nutrient-dense vegetables in a sustainable manner. Finally, our semi-systematic review provides important microbial biostimulant application guidelines and gives extension specialists and vegetable growers insights into achieving an additional benefit from microbial biostimulant application.

Tracking and plant growth-promoting effect of Paraburkholderia tropica MTo-293 applied to Solanum lycopersicum

Paraburkholderia tropica MTo-293 was applied as an experimental bio-input to Solanum lycopersicum (tomato) cv. Platense. Different plant growth systems and inoculation strategies were tested to evaluate P. tropica plant colonization at the seedling stage (growth chamber) using culture-dependent and -independent techniques. The effect of P. tropica on plant growth was evaluated in the growth chamber and greenhouse (productive stage) by biomass accumulation and fruit production, respectively. P. tropica was able to colonize the surface and inner root and stem of tomato seedlings regardless of the inoculation strategy-at sowing and/or before transplanting-showing the competitive nature of P. tropica in nonsterile substrate systems. A nested polymerase chain reaction was validated to track P. tropica in tomato plants even in the inner stem with endophytic P. tropica populations of less than 10²  CFU g^-1 of fresh weight. Efficient colonization of P. tropica correlated with a positive effect on tomato growth when applied at sowing and/or before transplanting: plant growth promotion was observed not only at the seedling stage but also at productive stages improving crop yield in two different seasons. To our knowledge, this report is the first to track and evaluate the plant growth-promoting effect of P. tropica MTo-293 in tomato plants grown in nonsterile substrate systems.

Management of abiotic stresses by microbiome-based engineering of the rhizosphere

Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stresses, efforts have accelerated in this direction. Though still in its infancy, microbiome-based engineering has gained popularity because of its advantages over microbe-based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by introduction to the conventional approach of microbe-based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focusses on the significance of rhizospheric microbiome, and harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host-mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of combinatorial scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.

Micronutrients in Food Production: What Can We Learn from Natural Ecosystems?

Soil micronutrients limit crop productivity in many regions worldwide, and micronutrient deficiencies affect over two billion people globally. Microbial biofertilizers could combat these issues by inoculating arable soils with microorganisms that mobilize micronutrients, increasing their availability to crop plants in an environmentally sustainable and cost-effective manner. However, the widespread application of biofertilizers is limited by complex micronutrient–microbe–plant interactions, which reduce their effectiveness under field conditions. Here, we review the current state of seven micronutrients in food production. We examine the mechanisms underpinning microbial micronutrient mobilization in natural ecosystems and synthesize the state-of-knowledge to improve our overall understanding of biofertilizers in food crop production. We demonstrate that, although soil micronutrient concentrations are strongly influenced by soil conditions, land management practices can also substantially affect micronutrient availability and uptake by plants. The effectiveness of biofertilizers varies, but several lines of evidence indicate substantial benefits in co-applying biofertilizers with conventional inorganic or organic fertilizers. Studies of micronutrient cycling in natural ecosystems provide examples of microbial taxa capable of mobilizing multiple micronutrients whilst withstanding harsh environmental conditions. Research into the mechanisms of microbial nutrient mobilization in natural ecosystems could, therefore, yield effective biofertilizers to improve crop nutrition under global changes.

Bioinoculants-Natural Biological Resources for Sustainable Plant Production

Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.

Physiological and Molecular Investigation of Urea Uptake Dynamics in Cucumis sativus L. Plants Fertilized With Urea-Doped Amorphous Calcium Phosphate Nanoparticles

At present, the quest for innovative and sustainable fertilization approaches aiming to improve agricultural productivity represents one of the major challenges for research. In this context, nanoparticle-based fertilizers can indeed offer an interesting alternative with respect to traditional bulk fertilizers. Several pieces of evidence have already addressed the effectiveness of amorphous calcium phosphate-based nanoparticles as carriers for macronutrients, such as nitrogen (N), demonstrating increase in crop productivity and improvement in quality. Nevertheless, despite N being a fundamental nutrient for crop growth and productivity, very little research has been carried out to understand the physiological and molecular mechanisms underpinning N-based fertilizers supplied to plants via nanocarriers. For these reasons, this study aimed to investigate the responses of Cucumis sativus L. to amorphous calcium phosphate nanoparticles doped with urea (U-ACP). Urea uptake dynamics at root level have been investigated by monitoring both the urea acquisition rates and the modulation of urea transporter CsDUR3, whereas growth parameters, the accumulation of N in both root and shoots, and the general ionomic profile of both tissues have been determined to assess the potentiality of U-ACP as innovative fertilizers. The slow release of urea from nanoparticles and/or their chemical composition contributed to the upregulation of the urea uptake system for a longer period (up to 24 h after treatment) as compared to plants treated with bulk urea. This prolonged activation was mirrored by a higher accumulation of N in nanoparticle-treated plants (approximately threefold increase in the shoot of NP-treated plants compared to controls), even when the concentration of urea conveyed through nanoparticles was halved. In addition, besides impacting N nutrition, U-ACP also enhanced Ca and P concentration in cucumber tissues, thus having possible effects on plant growth and yield, and on the nutritional value of agricultural products.

Iron Biofortification in Rice: An Update on Quantitative Trait Loci and Candidate Genes

Rice is the most versatile model for cereals and also an economically relevant food crop; as a result, it is the most suitable species for molecular characterization of Fe homeostasis and biofortification. Recently there have been significant efforts to dissect genes and quantitative trait loci (QTL) associated with Fe translocation into rice grains; such information is highly useful for Fe biofortification of cereals but very limited in other species, such as maize (Zea mays) and wheat (Triticum aestivum). Given rice's centrality as a model for Poaceae species, we review the current knowledge on genes playing important roles in Fe transport, accumulation, and distribution in rice grains and QTLs that might explain the variability in Fe concentrations observed in different genotypes. More than 90 Fe QTLs have been identified over the 12 rice chromosomes. From these, 17 were recorded as stable, and 25 harbored Fe-related genes nearby or within the QTL. Among the candidate genes associated with Fe uptake, translocation, and loading into rice grains, we highlight the function of transporters from the YSL and ZIP families; transporters from metal-binding molecules, such as nicotianamine and deoxymugineic acid; vacuolar iron transporters; citrate efflux transporters; and others that were shown to play a role in steps leading to Fe delivery to seeds. Finally, we discuss the application of these QTLs and genes in genomics assisted breeding for fast-tracking Fe biofortification in rice and other cereals in the near future.