Harnessing Soil Microbes to Improve Plant Phosphate Efficiency in Cropping Systems

Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem

Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.

How do high phosphate concentrations affect soil microbial communities after a century of ecosystem self-reclamation?

The use of rock phosphate (RP) instead of soluble phosphate fertilizers is preferred for the development of more sustainable agriculture. However, the impact of high concentrations in RP on bacterial and fungal communities remains poorly documented. Thus, next-generation sequencing was used to characterize bacterial and fungal communities in the soils and roots of four plant species growing naturally in a self-restored ecosystem, on former open-pit phosphate mines where past exploitation generated locally a substantial phosphate enrichment of the soil. Our results show that bacterial communities are dominated by Actinobacteria and Proteobacteria phyla, while the Ascomycota and Basidiomycota phyla predominate in the fungal community. The alpha and beta diversities of both bacterial and fungal communities differ significantly between the root and soil compartments but are not significantly affected by RP inputs. However, Amplicon Sequence Variants (ASVs) indicative of RP-enriched soils have been identified; among them are bacteria representative of Streptomyces, Bacillus, Mycobacterium or Agromyces. Implications of these results open new ways of reflection to understand the microbial response following RP-inputs and long-term soil restoration, as well as to formulate microbial-based bioinoculants for sustainable agriculture applications based on microorganisms better adapted to high concentrations of RP.

Phosphatases: Decoding the Role of Mycorrhizal Fungi in Plant Disease Resistance

Mycorrhizal fungi, a category of fungi that form symbiotic relationships with plant roots, can participate in the induction of plant disease resistance by secreting phosphatase enzymes. While extensive research exists on the mechanisms by which mycorrhizal fungi induce resistance, the specific contributions of phosphatases to these processes require further elucidation. This article reviews the spectrum of mycorrhizal fungi-induced resistance mechanisms and synthesizes a current understanding of how phosphatases mediate these effects, such as the induction of defense structures in plants, the negative regulation of plant immune responses, and the limitation of pathogen invasion and spread. It explores the role of phosphatases in the resistance induced by mycorrhizal fungi and provides prospective future research directions in this field.

Phospholipase-mediated phosphate recycling during plant leaf senescence

BACKGROUND

Phosphorus is a macronutrient necessary for plant growth and development and its availability and efficient use affect crop yields. Leaves are the largest tissue that uses phosphorus in plants, and membrane phospholipids are the main source of cellular phosphorus usage.

RESULTS

Here we identify a key process for plant cellular phosphorus recycling mediated by membrane phospholipid hydrolysis during leaf senescence. Our results indicate that over 90% of lipid phosphorus, accounting for more than one-third of total cellular phosphorus, is recycled from senescent leaves before falling off the plants. Nonspecific phospholipase C4 (NPC4) and phospholipase Dζ2 (PLDζ2) are highly induced during leaf senescence, and knockouts of PLDζ2 and NPC4 decrease the loss of membrane phospholipids and delay leaf senescence. Conversely, overexpression of PLDζ2 and NPC4 accelerates the loss of phospholipids and leaf senescence, promoting phosphorus remobilization from senescent leaves to young tissues and plant growth. We also show that this phosphorus recycling process in senescent leaves mediated by membrane phospholipid hydrolysis is conserved in plants.

CONCLUSIONS

These results indicate that PLDζ2- and NPC4-mediated membrane phospholipid hydrolysis promotes phosphorus remobilization from senescent leaves to growing tissues and that the phospholipid hydrolysis-mediated phosphorus recycling improves phosphorus use efficiency in plants.

Characterization of a novel root-associated diazotrophic rare PGPR taxa, Aquabacter pokkalii sp. nov., isolated from pokkali rice: new insights into the plant-associated lifestyle and brackish adaptation

Salinity impacts crop growth and productivity and lowers the activities of rhizosphere microbiota. The identification and utilization of habitat-specific salinity-adapted plant growth-promoting rhizobacteria (PGPR) are considered alternative strategies to improve the growth and yields of crops in salinity-affected coastal agricultural fields. In this study, we characterize strain L1I39T, the first Aquabacter species with PGPR traits isolated from a salt-tolerant pokkali rice cultivated in brackish environments. L1I39T is positive for 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation and can promote pokkali rice growth by supplying fixed nitrogen under a nitrogen-deficient seawater condition. Importantly, enhanced plant growth and efficient root colonization were evident in L1I39T-inoculated plants grown under 20% seawater but not in zero-seawater conditions, identifying brackish conditions as a key local environmental factor critical for L1I39T-pokkali rice symbiosis. Detailed physiological studies revealed that L1I39T is well-adapted to brackish environments. In-depth genome analysis of L1I39T identified multiple gene systems contributing to its plant-associated lifestyle and brackish adaptations. The 16S rRNA-based metagenomic study identified L1I39T as an important rare PGPR taxon. Based on the polyphasic taxonomy analysis, we established strain L1I39T as a novel Aquabacter species and proposed Aquabacter pokkalii sp nov. Overall, this study provides a better understanding of a marine-adapted PGPR strain L1I39T that may perform a substantial role in host growth and health in nitrogen-poor brackish environments.

Soil phosphorus transformation and plant uptake driven by phosphate-solubilizing microorganisms

Phosphorus (P) is an important nutrient for plants, and a lack of available P greatly limits plant growth and development. Phosphate-solubilizing microorganisms (PSMs) significantly enhance the ability of plants to absorb and utilize P, which is important for improving plant nutrient turnover and yield. This article summarizes and analyzes how PSMs promote the absorption and utilization of P nutrients by plants from four perspectives: the types and functions of PSMs, phosphate-solubilizing mechanisms, main functional genes, and the impact of complex inoculation of PSMs on plant P acquisition. This article reviews the physiological and molecular mechanisms of phosphorus solubilization and growth promotion by PSMs, with a focus on analyzing the impact of PSMs on soil microbial communities and its interaction with root exudates. In order to better understand the ability of PSMs and their role in soil P transformation and to provide prospects for research on PSMs promoting plant P absorption. PSMs mainly activate insoluble P through the secretion of organic acids, phosphatase production, and mycorrhizal symbiosis, mycorrhizal symbiosis indirectly activates P via carbon exchange. PSMs can secrete organic acids and produce phosphatase, which plays a crucial role in soil P cycling, and related genes are involved in regulating the P-solubilization ability. This article reviews the mechanisms by which microorganisms promote plant uptake of soil P, which is of great significance for a deeper understanding of PSM-mediated soil P cycling, plant P uptake and utilization, and for improving the efficiency of P utilization in agriculture.

Green manure incorporation enhanced soil labile phosphorus and fruit tree growth

Introduction

The incorporation of green manures substantially enhances the conversion of external phosphorus (P) fertilizers and soil-reserved P into forms readily available to plants. The study aims to evaluate the influence of green manure additions on soil phosphorus dynamics and citrus growth, considering different green manure species and initial soil phosphorus levels. Additionally, the research seeks to elucidate the microbiological mechanisms underlying the observed effects.

Methods

A citrus pot experiment was conducted under both P-surplus (1.50 g·P·kg-1) and P-deficient (0.17 g·P·kg-1) soils with incorporating legume (Leg), non-legume (Non-Leg) or no green manure residues (CK), and 18O-P labeled KH2PO4 (0.5 g, containing 80‰ δ18Op) was additionally introduced to trace the turnover characteristics of chemical P fertilizer mediated by soil microorganisms.

Results and discussion

In P-surplus soil, compared with the CK treatment, the Leg treatment significantly increased soil H2O-Pi (13.6%), NaHCO3-Po (8.9%), NaOH-Pi (9.5%) and NaOH-Po (30.0%) content. It also promoted rapid turnover of P sources into H2O-Pi and NaHCO3-Pi pools by enhancing the phoC (576.6%) gene abundance. In contrast, the Non-Leg treatment significantly augmented soil H2O-Pi (9.2%) and NaHCO3-Po (8.5%) content, facilitating the turnover of P sources into NaHCO3-Pi pools. Under P-deficient soil conditions, compared with the CK treatment, the Leg treatment notably raised soil H2O-Pi (150.0%), NaHCO3-Pi (66.3%), NaHCO3-Po (34.8%) and NaOH-Pi (59.0%) content, contributing to the transfer of P sources into NaHCO3-Pi and NaOH-Pi pools. This effect was achieved through elevated ALP (33.8%) and ACP (12.9%) activities and increased pqqC (48.1%), phoC (42.9%), phoD (21.7%), and bpp (27.4%) gene abundances. The Non-Leg treatment, on the other hand, led to significant increases in soil NaHCO3-Pi (299.0%) and NaHCO3-Po (132.6%) content, thereby facilitating the turnover of P sources into NaHCO3-Pi and NaOH-Pi pools, except for the phoC gene abundance. Both Leg and Non-Leg treatments significantly improved citrus growth (7.3-20.0%) and P uptake (15.4-42.1%) in P-deficient soil but yielded no substantial effects in P-surplus soil. In summary, introducing green manure crops, particularly legume green manure, emerges as a valuable approach to enhance soil P availability and foster fruit tree growth in orchard production.

Phosphate-solubilizing bacteria: Their agroecological function and optimistic application for enhancing agro-productivity

Phosphorus (P) is a limiting nutrient in the soil-plant nutrient cycling. Although the exogenous application of chemical P fertilizers can satisfy crop P requirements during critical growth phases. While excessive P fertilizers use results in low phosphorus acquisition efficiency (PAE), it has serious environmental consequences and hastens the depletion of P mineral reserves. Phosphate-solubilizing bacteria (PSB) have the potential to make insoluble phosphate available to plants through solubilization and mineralization, increasing crop yields while maintaining environmental sustainability. Existing reviews mainly focus on the beneficial effects of PSB on crop performance and related mechanisms, while few of them elucidate the action mechanisms of PSB in soil-microbe-plant interactions for crop cultivation with high yield efficiency. Hence, this study provides a comprehensive review of the physicochemical and molecular mechanisms (e.g., root exudates, extracellular polysaccharides, organic acids, phosphatases, and phosphate-specific transport systems) of PSB to facilitate the P cycle in the soil-plant systems. Further, the potential of commercial applications of PSB (e.g., genetic engineering, seed priming and coating) are also discussed in order to highlight their contribution to sustainable agriculture. Finally, existing challenges and future prospects in agricultural applications are proposed. In conclusion, we firmly believe that PSB represent a highly significant biotechnological tool for enhancing agricultural productivity and offers a wide range of extensive potential applications.

The Splicing Factor OsSCL26 Regulates Phosphorus Homeostasis in Rice

Phosphorus (P) is an essential nutrient for plant growth. However, its deficiency poses a significant challenge for crop production. To overcome the low P availability, plants have developed various strategies to regulate their P uptake and usage. In this study, we identified a splicing factor, OsSCL26, belonging to the Serine/arginine-rich (SR) proteins, that plays a crucial role in regulating P homeostasis in rice. OsSCL26 is expressed in the roots, leaves, and base nodes, with higher expression levels observed in the leaf blades during the vegetative growth stage. The OsSCL26 protein is localized in the nucleus. Mutation of OsSCL26 resulted in the accumulation of P in the shoot compared to the wild-type, and the dwarf phenotype of the osscl26 mutant was alleviated under low P conditions. Further analysis revealed that the accumulated P concentrations in the osscl26 mutant were higher in the old leaves and lower in the new leaves. Furthermore, the P-related genes, including the PHT and SPX family genes, were upregulated in the osscl26 mutant, and the exclusion/inclusion ratio of the two genes, OsSPX-MFS2 and OsNLA2, was increased compared to wild-type rice. These findings suggest that the splicing factor OsSCL26 plays a pivotal role in maintaining P homeostasis in rice by influencing the absorption and distribution of P through the regulation of the transcription and splicing of the P transport genes.

Co-Inoculation of Non-Symbiotic Bacteria Bacillus and Paraburkholderia Can Improve the Soybean Yield, Nutrient Uptake, and Soil Parameters

Due to its nutritional value and oil, soybean (Glycine max L.) became an economic crop in India and worldwide. The current study investigated the effect of forest-associated plant growth-promoting rhizobacteria (PGPR) on soybean yield and grain nutrient content. Five potential bacteria were used in this study based on their PGPR traits. The pot assay result with two crops (soybean and chickpea) confirmed the growth promotion activity of the two strains (Bacillus subtilis MpS15 and Paraburkholderia sabiae NvS21). The result showed significant (p < 0.05) enhancement in plant length and biomass with the seed treatment with strains (MpS15 and NvS21) compared to the control. Later both biocompatible potential strains were used in field experiments as individuals and consortia. Seed treatment of consortia significantly improves the nodulation and photosynthetic content more than individual treatments and control. Compared to the control, the co-inoculation of MpS15 and NvS21 increased soybean grain, straw yield, and grain NPK contents. Interestingly, soil parameters (organic carbon, available NPK) showed a strong correlation (p < 0.05) with plant parameters and nutrient uptake. Overall, our study provides strong relationships between soil parameters, microbial inoculum as consortia, and soybean performance, and these strains may be utilized as bioinoculant in future.

The Importance of Microorganisms for Sustainable Agriculture-A Review

In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.

Plant-soil-microbes: A tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices

Plants can achieve their proper growth and development with the help of microorganisms associated with them. Plant-associated microbes convert the unavailable nutrients to available form and make them useful for plants. Besides nutrient acquisition, soil microbes also inhibit the pathogens that cause harm to plant growth and induces defense response. Due to the beneficial activities of soil nutrient-microbe-plant interactions, it is necessary to study more on this topic and develop microbial inoculant technology in the agricultural field for better crop improvement. The soil microbes can be engineered, and plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting bacteria (PGPB) technology can be developed as well, as its application can be improved for utilization as biofertilizer, biopesticides, etc., instead of using harmful chemical biofertilizers. Moreover, plant growth-promoting microbe inoculants can enhance crop productivity. Although, scientists have discussed several tools and techniques by omics and gene editing approaches for crop improvement to avoid biotic and abiotic stress and make the plant healthier and more nutritive. However, beneficial soil microbes that help plants with the nutrient acquisition, development, and stress resistance were ignored, and farmers started utilizing chemical fertilizers. Thus, this review attempts to summarize the interaction system of plant microbes, the role of beneficiary soil microbes in the rhizosphere zone, and their role in plant health promotion, particularly in the nutrition acquisition of the plant. The review will also provide a better understanding of soil microbes that can be exploited as biofertilizers and plant growth promoters in the field to create environmentally friendly, sustainable agriculture systems.

Mycorrhiza-mediated potassium transport in Medicago truncatula can be evaluated by using rubidium as a proxy

Arbuscular mycorrhizal (AM) fungi considerably improve plant nutrient acquisition, particularly phosphorus and nitrogen. Despite the physiological importance of potassium (K⁺) in plants, there is increasing interest in the mycorrhizal contribution to plant K⁺ nutrition. Yet, methods to track K⁺ transport are often costly and limiting evaluation opportunities. Rubidium (Rb⁺) is known to be transported through same pathways as K⁺. As such our research efforts attempt to evaluate if Rb⁺ could serve as a viable proxy for evaluating K⁺ transport in AM symbiosis. Therefore, we examined the transport of K⁺ in Medicago truncatula colonized by the AM fungus Rhizophagus irregularis isolate 09 having access to various concentrations of Rb⁺ in custom-made two-compartment systems. Plant biomass, fungal root colonization, and shoot nutrient concentrations were recorded under sufficient and limited K⁺ regimes. We report that AM plants displayed higher shoot Rb⁺ and K⁺ concentrations and a greater K⁺:Na⁺ ratio relative to non-colonized plants in both sufficient and limited K⁺ conditions. Consequently, our results indicate that Rb⁺ can be used as a proxy to assess the movement of K⁺ in AM symbiosis, and suggest the existence of a mycorrhizal uptake pathway for K⁺ nutrition in M. truncatula.

Physiological and transcriptomic response of Medicago truncatula to colonization by high- or low-benefit arbuscular mycorrhizal fungi

Arbuscular mycorrhizal (AM) fungi form a root endosymbiosis with many agronomically important crop species. They enhance the ability of their host to obtain nutrients from the soil and increase the tolerance to biotic and abiotic stressors. However, AM fungal species can differ in the benefits they provide to their host plants. Here, we examined the putative molecular mechanisms involved in the regulation of the physiological response of Medicago truncatula to colonization by Rhizophagus irregularis or Glomus aggregatum, which have previously been characterized as high- and low-benefit AM fungal species, respectively. Colonization with R. irregularis led to greater growth and nutrient uptake than colonization with G. aggregatum. These benefits were linked to an elevated expression in the roots of strigolactone biosynthesis genes (NSP1, NSP2, CCD7, and MAX1a), mycorrhiza-induced phosphate (PT8), ammonium (AMT2;3), and nitrate (NPF4.12) transporters and the putative ammonium transporter NIP1;5. R. irregularis also stimulated the expression of photosynthesis-related genes in the shoot and the upregulation of the sugar transporters SWEET1.2, SWEET3.3, and SWEET 12 and the lipid biosynthesis gene RAM2 in the roots. In contrast, G. aggregatum induced the expression of biotic stress defense response genes in the shoots, and several genes associated with abiotic stress in the roots. This suggests that either the host perceives colonization by G. aggregatum as pathogen attack or that G. aggregatum can prime host defense responses. Our findings highlight molecular mechanisms that host plants may use to regulate their association with high- and low-benefit arbuscular mycorrhizal symbionts.

Diversity and Phosphate Solubilization Efficiency of Phosphate Solubilizing Bacteria Isolated from Semi-Arid Agroecosystems of Eastern Kenya

Phosphorus (P) is a major nutrient required for plant growth but it forms complexes with other elements in soil upon application. A cost-effective way of availing P to plants is by use of Phosphate Solubilizing Bacteria (PSB). There is a wide range of PSB suited for diverse agro-ecologies. A large part of Eastern Kenya especially the lower altitude regions are semi-arid with nutrient depleted soils and predominated by low-income smallholders farmers who do not afford costly inorganic fertilizers. To alleviate poor soil nutrition in this agroecosystem, we sought to study the diversity of phosphate solubilizing bacteria and their phosphate solubilization efficiency. The bacteria were selectively isolated in Pikovskaya’s agar media. Bacterial colonies were enumerated as Colony Forming Units and morphological characterization determined by analyzing morphological characteristics. Genetic characterization was determined based on sequencing of 16S rRNA. A total of 71 PSB were isolated and they were placed into 23 morphological groups. Correlation analysis showed a negative correlation between phosphate solubilizing bacteria and the levels of phosphorus, iron, calcium, magnesium and soil pH. Analysis of 16S rRNA sequences revealed that the genetic sequences of the isolates matched the strains from the genera Burkholderia, Pseudomonas, Bacillus, Enterobacter, Pantoea, Paraburkholderia, Cronobacter, Ralstonia, Curtobacterium, and Massilia deposited in NCBI Database. Analysis of Molecular Variance showed that variation within populations was higher than that of among populations. Phosphate solubilization index values ranged between 1.143 and 5.883. Findings on biodiversity of phosphate solubilizing bacteria led to identification of 10 candidate isolates for plant growth improvement and subsequently, bio-fertilizer development.

Composition and functioning of the soil microbiome in the highest altitudes of the Italian Alps and potential effects of climate change

As the European Alps are experiencing a strong climate warming; this study analyzed the soil microbiome at different altitudes and among different vegetation types at the Stelvio Pass (Italian Alps), aiming to i) characterize the composition and functional potential of the microbiome of soils and their gene expression during the peak vegetative stage; ii) explore the potential short-term (using open top chambers) and long-term (space-for-time substitutions) effects of increasing temperature on the alpine soil microbiome. We found that the functional potential of the soil microbiome and its expression differed among vegetation types. Microbial α-diversity increased along the altitudinal gradient. At lower altitude, shrubland had the highest proportion of fungi, which was correlated with higher amounts of CAZymes, specific for degrading fungal biomass and recalcitrant plant biopolymers. Subalpine upward vegetation shift could lead a possible loss of species of alpine soils. Shrub encroachment may accelerate higher recalcitrant C decomposition and reduce total ecosystem C storage, increasing the efflux of CO2 to the atmosphere with a positive feedback to warming. Five years of warming had no effect on the composition and functioning of microbial communities, indicating that longer-term warming experiments are needed to investigate the effects of temperature increases on the soil microbiome.

Efficiency of the Hydroponic System as an Approach to Confirm the Solubilization of CaHPO4 by Microbial Strains Using Glycine max as a Model

The sustainable development of agriculture can be stimulated by the great market availability of bio-inputs, including phosphate-solubilizing microbial strains. However, these strains are currently selected using imprecise and questionable solubilization methodologies in solid or liquid media. We hypothesized that the hydroponic system could be a more efficient methodology for selecting phosphate-solubilizing strains as plant growth promoters. This methodology was tested using the plant Glycine max as a model. The growth-promoting potential of the strains was compared with that of the Biomaphos® commercial microbial mixture. The obtained calcium phosphate (CaHPO₄) solubilization results using the hydroponic system were inconsistent with those observed in solid and liquid media. However, the tests in liquid medium demonstrated poor performances of Codinaeopsis sp. (328EF) and Hamigera insecticola (33EF) in reducing pH and solubilizing CaHPO₄, which corroborates with the effects of biotic stress observed in G. max plants inoculated with these strains. Nevertheless, the hydroponic system allowed the characterization of Paenibacillus alvei (PA12), which is also efficient in solubilization in a liquid medium. The bacterium Lysinibacillus fusiformis (PA26) was the most effective in CaHPO₄ solubilization owing to the higher phosphorus (P) absorption, growth promotion, and physiological performance observed in plants inoculated with this bacterium. The hydroponic method proved to be superior in selecting solubilizing strains, allowing the assessment of multiple patterns, such as nutritional level, growth, photosynthetic performance, and anatomical variation in plants, and even the detection of biotic stress responses to inoculation, obtaining strains with higher growth promotion potential than Biomaphos®. This study proposed a new approach to confirm the solubilizing activity of microorganisms previously selected in vitro and potentially intended for the bio-input market that are useful in P availability for important crops, such as soybeans.

Prospect and Challenges for Sustainable Management of Climate Change-Associated Stresses to Soil and Plant Health by Beneficial Rhizobacteria

Climate change imposes biotic and abiotic stresses on soil and plant health all across the planet. Beneficial rhizobacterial genera, such as Bacillus, Pseudomonas, Paraburkholderia, Rhizobium, Serratia, and others, are gaining popularity due to their ability to provide simultaneous nutrition and protection of plants in adverse climatic conditions. Plant growth-promoting rhizobacteria are known to boost soil and plant health through a variety of direct and indirect mechanisms. However, various issues limit the wider commercialization of bacterial biostimulants, such as variable performance in different environmental conditions, poor shelf-life, application challenges, and our poor understanding on complex mechanisms of their interactions with plants and environment. This study focused on detecting the most recent findings on the improvement of plant and soil health under a stressful environment by the application of beneficial rhizobacteria. For a critical and systematic review story, we conducted a non-exhaustive but rigorous literature survey to assemble the most relevant literature (sorting of a total of 236 out of 300 articles produced from the search). In addition, a critical discussion deciphering the major challenges for the commercialization of these bioagents as biofertilizer, biostimulants, and biopesticides was undertaken to unlock the prospective research avenues and wider application of these natural resources. The advancement of biotechnological tools may help to enhance the sustainable use of bacterial biostimulants in agriculture. The perspective of biostimulants is also systematically evaluated for a better understanding of the molecular crosstalk between plants and beneficial bacteria in the changing climate towards sustainable soil and plant health.

Rhizosphere Bacteria in Plant Growth Promotion, Biocontrol, and Bioremediation of Contaminated Sites: A Comprehensive Review of Effects and Mechanisms

Agriculture in the 21st century is facing multiple challenges, such as those related to soil fertility, climatic fluctuations, environmental degradation, urbanization, and the increase in food demand for the increasing world population. In the meanwhile, the scientific community is facing key challenges in increasing crop production from the existing land base. In this regard, traditional farming has witnessed enhanced per acre crop yields due to irregular and injudicious use of agrochemicals, including pesticides and synthetic fertilizers, but at a substantial environmental cost. Another major concern in modern agriculture is that crop pests are developing pesticide resistance. Therefore, the future of sustainable crop production requires the use of alternative strategies that can enhance crop yields in an environmentally sound manner. The application of rhizobacteria, specifically, plant growth-promoting rhizobacteria (PGPR), as an alternative to chemical pesticides has gained much attention from the scientific community. These rhizobacteria harbor a number of mechanisms through which they promote plant growth, control plant pests, and induce resistance to various abiotic stresses. This review presents a comprehensive overview of the mechanisms of rhizobacteria involved in plant growth promotion, biocontrol of pests, and bioremediation of contaminated soils. It also focuses on the effects of PGPR inoculation on plant growth survival under environmental stress. Furthermore, the pros and cons of rhizobacterial application along with future directions for the sustainable use of rhizobacteria in agriculture are discussed in depth.

Characterization of Erwinia gerundensis A4, an Almond-Derived Plant Growth-Promoting Endophyte

The rapidly increasing global population and anthropogenic climate change have created intense pressure on agricultural systems to produce increasingly more food under steadily challenging environmental conditions. Simultaneously, industrial agriculture is negatively affecting natural and agricultural ecosystems because of intensive irrigation and fertilization to fully utilize the potential of high-yielding cultivars. Growth-promoting microbes that increase stress tolerance and crop yield could be a useful tool for helping mitigate these problems. We investigated if commercially grown almonds might be a resource for plant colonizing bacteria with growth promotional traits that could be used to foster more productive and sustainable agricultural ecosystems. We isolated an endophytic bacterium from almond leaves that promotes growth of the model plant Arabidopsis thaliana. Genome sequencing revealed a novel Erwinia gerundensis strain (A4) that exhibits the ability to increase access to plant nutrients and to produce the stress-mitigating polyamine spermidine. Because E. gerundensis is known to be able to colonize diverse plant species including cereals and fruit trees, A4 may have the potential to be applied to a wide variety of crop systems.

Long-term cover crops improved soil phosphorus availability in a rain-fed apple orchard

The objective of this present study was to understand the distribution patterns of various forms of soil phosphorus (P) and the biotic and abiotic factors affecting the soil P fractions under long-term cover crops. Here, we investigated the characteristics of soil P forms, community structure of P-solubilizing bacteria (using 16S rRNA) and the related enzyme activity under clean tillage (CT), 14 years of white clover (WC, Trifolium repens L.) and orchard grass (OG, Dactylis glomerata L.) cover crops in a rain-fed apple orchard on the Weibei Loess Plateau, China. Relative to CT treatment, long-term cover crops enhanced the bioavailability of soil P by increasing the contents of total phosphorus (TP), microbial phosphorus (MBP), organic phosphorus (Po) and certain forms of inorganic phosphorus (e.g. Al-P, Ca₂-P, Ca₈-P and Fe-P) in the surface soil, in addition, WC treatment also increase the available P (AP) contents in the topsoil. A redundant analysis (RDA) showed that soil organic matter (SOM), NH₄⁺-N and pH were the key environmental factors affecting the morphological changes of soil P. In addition, the effects of long-term cover crops on soil P forms were mainly concentrated in the topsoil, and the WC treatment had a greater impact on soil P composition than the OG treatment. Interestingly, long-term cover crops effectively increased the abundances of P-solubilizing bacteria, such as Streptomyces, Sphingomonas, Nocardioides and Haliangium, and enhanced the alkaline phosphatase (ALP) activity. Overall, long-term cover crops were an effective strategy to activate soil P as they improve the soil environment.

Global Profiling of Phosphorylation Reveals the Barley Roots Response to Phosphorus Starvation and Resupply

Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress; however, its functions in P starvation/resupply are largely unknown for barley (Hordeum vulgare) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein-protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.

Accessing Legacy Phosphorus in Soils

Repeated applications of phosphorus (P) fertilizers result in the buildup of P in soil (commonly known as legacy P), a large fraction of which is not immediately available for plant use. Long-term applications and accumulations of soil P is an inefficient use of dwindling P supplies and can result in nutrient runoff, often leading to eutrophication of water bodies. Although soil legacy P is problematic in some regards, it conversely may serve as a source of P for crop use and could potentially decrease dependence on external P fertilizer inputs. This paper reviews the (1) current knowledge on the occurrence and bioaccessibility of different chemical forms of P in soil, (2) legacy P transformations with mineral and organic fertilizer applications in relation to their potential bioaccessibility, and (3) approaches and associated challenges for accessing native soil P that could be used to harness soil legacy P for crop production. We highlight how the occurrence and potential bioaccessibility of different forms of soil inorganic and organic P vary depending on soil properties, such as soil pH and organic matter content. We also found that accumulation of inorganic legacy P forms changes more than organic P species with fertilizer applications and cessations. We also discuss progress and challenges with current approaches for accessing native soil P that could be used for accessing legacy P, including natural and genetically modified plant-based strategies, the use of P-solubilizing microorganisms, and immobilized organic P-hydrolyzing enzymes. It is foreseeable that accessing legacy P will require multidisciplinary approaches to address these limitations.

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.

Integrated use of phosphate-solubilizing Bacillus subtilis strain IA6 and zinc-solubilizing Bacillus sp. strain IA16: a promising approach for improving cotton growth

Mineral nutrition of crop plants is one of the major challenges faced by modern agriculture, particularly in arid and semi-arid regions. In alkaline calcareous soils, the availability of phosphorus and zinc is critically less due to their fixation and precipitation as complexes. Farmers use fertilizers to fulfill crop requirements, but their efficacy is less, which increases production costs. Plant growth-promoting rhizobacteria (PGPR) can improve the availability of crop nutrients through solubilizing the insoluble compounds of phosphorus and zinc in soil. In the present study, a total of 40 rhizobacterial isolates were isolated from cotton rhizosphere and screened for improving cotton growth through the solubilization of phosphorus and zinc. Out of these 40 isolates, seven isolates (IA2, IA3, IA6, IA7, IA8, IA13, and IA14) efficiently solubilized insoluble rock phosphate while seven isolates (IA10, IA16, IA20, IA23, IA24, IA28, and IA30) were more efficient in solubilizing insoluble zinc oxide. In liquid media, strain IA7 (2.75 μg/mL) solubilized the highest amount of phosphate while the highest concentration of soluble zinc was observed in the broth inoculated with strain IA20 (3.94 μg/mL). Seven phosphate-solubilizing and seven zinc-solubilizing strains were evaluated using jar trial to improve the growth of cotton seedlings, and the results were quite promising. All the inoculated treatments showed improvement in growth parameters in comparison with control. Best results were shown by the combined application of IA6 and IA16, followed by the combination of strains IA7 and IA20. Based on the jar trial, the selected isolates were further characterized by plant growth-promoting characters such as siderophores production, HCN production, ammonia production, and exopolysaccharides production. These strains were identified through 16S rRNA sequencing as Bacillus subtilis IA6 (accession # MN005922), Paenibacillus polymyxa IA7 (accession # MN005923), Bacillus sp. IA16 (accession # MN005924), and Bacillus aryabhattai IA20 (accession # MN005925). It is hence concluded that the integrated use of phosphate-solubilizing and zinc-solubilizing strains as potential inoculants can be a promising approach for improving cotton growth under semi-arid conditions.

Tightening the Phosphorus Cycle through Phosphorus-Efficient Crop Genotypes

We are facing unprecedented phosphorus (P) challenges, namely P scarcity associated with increasing food demand, and an oversupply of P fertilisers, resulting in eutrophication. Although we need a multidisciplinary approach to systematically enhance P-use efficiency, monodisciplinary studies still prevail. Here, we propose to tighten the P cycle by identifying P-efficient crop genotypes, integrating four plant strategies: increasing P-acquisition efficiency, photosynthetic P-use efficiency and P-remobilisation efficiency, and decreasing seed phytate P concentrations. We recommend P-efficient genotypes together with diversified cropping systems involving complementary P-acquisition strategies as well as smart P-fertiliser management to enhance P-use efficiency in agriculture dependent on soil P status. These strategies will reduce P-fertiliser requirements and offsite environmental impacts, while enhancing seed quality for human and livestock nutrition.

Phosphorus Transport in Mycorrhiza: How Far Are We?

Mycorrhizal fungi considerably improve plant nutrition and help them to cope with changing environments. Particularly, these fungi express proteins to transfer inorganic phosphate (P_i) from the soil to colonized roots through symbiotic interfaces. The mechanisms involved in P_i transfer from fungal to plant cells are still largely unknown. Here, we discuss the recent progress made on the description of these mechanisms and we propose the most promising hypotheses and alternative mechanisms for this process. Specifically, we present a phylogenetic survey of candidate P_i transporters of mycorrhizal fungi that might ensure P_i unload into the symbiotic interfaces. Gathering additional knowledge on mycorrhizal P_i transport will improve the P_i-useefficiency in agroecological systems and will guide towards addressing future research challenges.