Perspectives and Challenges of Microbial Application for Crop Improvement

Teosinte-derived SynCom and precision biofertilization modulate the maize microbiome, enhancing growth, yield, and soil functionality in a Mexican field

Modern agriculture faces the challenge of optimizing fertilization practices while maintaining soil resilience and microbial diversity, both critical for sustainable crop production. We evaluated the effects of multiple fertilization strategies on soil microbial communities and plant performance, comparing conventional methods (urea-based and phosphorus fertilizers applied manually or via drone-assisted precision delivery) with biofertilization using a synthetic microbial consortium (SynCom) derived from teosinte-associated microbes. This SynCom consisted of seven bacterial strains: Serratia nematodiphila EDR2, Klebsiella variicola EChLG19, Bacillus thuringiensis EML22, Pantoea agglomerans EMH25, Bacillus thuringiensis EBG39, Serratia marcescens EPLG52, and Bacillus tropicus EPP72. High-throughput sequencing revealed significant shifts in bacterial and fungal communities across treatments. Untreated soils showed limited diversity, dominated by Enterobacteriaceae (>70%). Conventional fertilization gradually reduced Enterobacteriaceae while increasing Pseudomonas and Lysinibacillus populations. Drone-assisted conventional fertilization notably enhanced Acinetobacter and Rhizobiales growth. Biofertilization treatments produced the most pronounced shifts, reducing Enterobacteriaceae below 50% while significantly increasing beneficial taxa like Bacillus, Pantoea, and Serratia. Network analysis demonstrated that microbial interaction complexity increased across treatments, with Bacillus emerging as a keystone species. Drone-assisted biofertilization fostered particularly intricate microbial networks, enhancing synergistic relationships involved in nutrient cycling and biocontrol, though maintaining the stability of these complex interactions requires careful monitoring. Our findings provide key insights into how precision biofertilization with teosinte-derived microbial consortia can sustainably reshape the maize microbiome, improving crop performance and soil resilience.

3D Mass Spectrometry Imaging as a Novel Screening Method for Evaluating Biocontrol Agents

The aim of this study was to evaluate innovative mass spectrometry imaging (MSI) for determining the metabolic potential of selected soil bacteria from the genera Bacillus and Priestia in the presence of the phytopathogen Fusarium. This research marks the first application of direct 3D MSI that to visualize interactions between potential biocontrol agents and plant pathogens on agar medium. The LARAPPI/CI-3D-MSI (Laser-Assisted Remote Atmospheric Pressure Imaging/Chemical Ionization-3D Mass Spectrometry Imaging) setup provided valuable insights into the compounds produced by the tested microorganisms, revealing their spatial distributions and their ability to diffuse into the agar medium. Subsequently, a Pathway Impact Analysis of Metabolites was conducted. Ion images based on ultrahigh resolution mass spectrometry data were obtained, including for potentially bioactive compounds. Statistical analysis of the entire MS data set showed that the metabolites identified for Bacillus licheniformis samples were distinctly separated from the Priestia megaterium samples and could be helpful tools for screening biocontrol strains. The LARAPPI/CI MSI technique offers significant advantages over existing MSI methods. Further research using this technology could help validate the effectiveness of various biopreparations and contribute to enhancing the quality of biological plant protection products available on the market.

Native Rhizobium biofertilization enhances yield and quality in Solanum lycopersicum under field conditions

In response to growing concerns about the environmental and economic impacts of chemical fertilizers, this study explores the potential of biofertilization using native Rhizobium strains to enhance the growth, yield, and quality of Solanum lycopersicum (tomato) under field conditions. The experiment assessed the effects of Rhizobium biofertilization on plant performance and soil microbial communities by applying R. calliandrae, R. jaguaris, R. mayense, and a bacterial consortium, in comparison to conventional chemical fertilization. Key parameters such as plant height, fruit yield, macronutrient and micronutrient content, and fruit quality (lycopene and β-carotene levels) were measured. Results showed that R. calliandrae and R. jaguaris significantly enhanced fruit yield, nitrogen, potassium, manganese, and boron levels, while also improving fruit quality compared to the control. The impact of strain inoculation on the structure of the microbial community was also examined. Metataxonomic analysis of rhizospheric soils revealed no significant changes in microbial diversity, indicating that biofertilization with Rhizobium strains promotes plant growth without disrupting the composition of the soil microbiome. These findings suggest that Rhizobium biofertilization is a viable and sustainable alternative to chemical fertilizers, providing benefits to both crop productivity and soil health while minimizing the environmental footprint associated with conventional agricultural practices. The study underscores the importance of carefully selecting bacterial species with complementary functions to maximize the effectiveness of biofertilization strategies.

Root colonization dynamics of alginate encapsulated rhizobacteria: implications for Arabidopsis thaliana root growth and durum wheat performance

Bioencapsulation in alginate capsules offers an interesting opportunity for the efficient delivery of microbial inoculants for agricultural purposes. The present study evaluated the ionic gelation technique to prepare beads loaded with two plant growth-promoting bacteria (PGPB), Bacillus thuringiensis strain B25 and Pantoea agglomerans strain Pa in 1% alginate supplemented with 5mM proline as an osmoprotectant. Capsule morphology, survival rate, encapsulation efficiency, and viability during 24 months of storage as well as the stability of PGP activities were studied. Our results indicate that more than 99% of bacteria were effectively trapped in the alginate beads, which successfully released live bacteria after 60 days of storage at room temperature. A considerable survival of B. thuringiensis B25 throughout the storage period was detected, while the inoculated concentration of 8.72 × 109 (±0.04 ×109) CFU/mL was reduced to 99.9% for P. agglomerans Pa after 24 months of storage. Notably, a higher survival of individually encapsulated bacteria was observed compared to their co-inoculation. The colonization capacity of model plant Arabidopsis thaliana roots by free and encapsulated bacteria was detected by the triphenyltetrazolium chloride test. Moreover, both strains effectively colonized the rhizosphere, rhizoplane, and endosphere of durum wheat plants and exerted a remarkable improvement in plant growth, estimated as a significant increase in the quantities of total proteins, sugars, and chlorophyll pigments, besides roots and shoots length. This study demonstrated that alginate-encapsulated B. thuringiensis B25 and P. agglomerans Pa could be used as inoculants in agriculture, as their encapsulation ensures robust protection, maintenance of viability and PGP activity, and controlled bacterial biostimulant release into the rhizosphere.

Dual RNA-seq reveals transcriptome changes during Fusarium virguliforme-Trichoderma afroharzianum interactions

Trichoderma spp. are among the most studied biocontrol agents. While extensive work has been done to understand Trichoderma antagonistic mechanisms, additional research is needed to fully understand how Trichoderma spp. recognize the pathogen-host and the intra-species variability i frequently observed upon interaction with a specific pathogen-host. This study focuses on elucidating the mechanisms underlying observed phenotypic differences among the T. afroharzianum isolates Th19A and Th4 during confrontation with Fusarium virguliforme by investigating differences in their transcriptome at different stages of interaction. In a dual plate assay, Th19A overgrows F. virguliforme, whereas Th4 forms an inhibition zone. Significant differences were observed in the F. virguliforme transcriptome upon interaction with Th19A compared to Th4 and across the different stages of interaction. GO molecular function categories enriched for F. virguliforme genes differed, indicating possible transcriptional plasticity upon interaction with Th19A versus Th4. Significant transcriptome changes were also observed in T. afroharzianum, with several differences in GO-enriched categories between isolates. Several differentially expressed genes-encoding secreted proteins, including CAZymes and CBM1-domain-containing proteins, were up-regulated in Th19A and Th4 upon interaction with the pathogen, even before physical contact, demonstrating possible volatile-mediated recognition of both isolates by F. virguliforme. This study contributes to a better understanding of the interaction between T. afroharzianum and F. virguliforme, which is crucial for developing efficient biological control programs.

Bioprospecting of multi-stress tolerant Pseudomonas sp. antagonistic to Rhizoctonia solani for enhanced wheat growth promotion

Salt affected cotton rhizospheric soil was explored for multi-stress resistance microbes to obtain 46 rhizobacteria. Of these, seven strains strongly inhibited the growth of phytopathogenic fungus Rhizoctonia solani by virtue of antifungal compound 2,4-diacetylphloroglucinol (DAPG) production. These seven strains demonstrated an array of plant growth-promoting activities as follows: (i) production of indole-3-acetic acid, ammonia, siderophore; (ii) solubilisation of phosphate, while two isolates showed Zn solubilisation. The phenetic and 16S ribotyping revealed affiliation of all the isolates to Pseudomonas guariconensis and presence of phlD gene marker for DAPG production. Among the seven isolates, strain VDA8 showed the highest DAPG production (0.16 μg ml-1) in liquid synthetic medium under aerobic conditions at 28 °C. Furthermore, sucrose, peptone, sodium hydrogen phosphate, ZnSO4, pH 8.0, and NaCl (1%) were observed as the best carbon, nitrogen, phosphate, trace element, pH, and salt concentration, respectively for maximum production of DAPG by strain VDA8 (3.62 ± 0.04 μg ml-1). The strain VDA8 was further assessed for wheat (Triticum aestivum) growth promotion by seed biopriming under laboratory (plate assay) and field condition in alkaline saline soil with pH 8.5. The field scale (324 m2) trials demonstrated 28.6% enhanced grain production compared to control demonstrating the newly isolated Pseudomonas sp. as multi-potent bioinoculant.

The Bacterial Biofilms: Formation, Impacts, and Possible Management Targets in the Healthcare System

Introduction: The persistent increase in multidrug-resistant pathogens has catalyzed the creation of novel strategies to address antivirulence and anti-infective elements. Such methodologies aim to diminish the selective pressure exerted on bacterial populations, decreasing the likelihood of resistance emergence. This review explores the role of biofilm formation as a significant virulence factor and its impact on the development of antimicrobial resistance (AMR). Case Presentation: The ability of bacteria to form a superstructure-biofilm-has made resistance cases in the microbial world a big concern to public health and other sectors as it is a crucial virulence factor that causes difficulties in the management of infections, hence enhancing chronic infection occurrence. Biofilm formation dates to about 3.4 billion years when prokaryotes were discovered to be forming them and since then due to evolution and growth in science, they are more understood. Management and Outcome: The unique microenvironments within bacterial biofilms diminish antibiotic effectiveness and help bacteria evade the host immune system. Biofilm production is a widespread capability among diverse bacterial species. Biofilm formation is enhanced by quorum sensing (QS), reduction of nutrients, or harsh environments for the bacteria. Conclusion: The rise of severe, treatment-resistant biofilm infections poses major challenges in medicine and agriculture, yet much about how these biofilms form remains unknown.

The use of phosphate rock and plant growth promoting microorganisms for the management of Urochloa decumbens (Stapf.) R.D. Webster in acidic soils

Background

Forage production in tropical soils is primarily limited by nutrient deficiencies, especially nitrogen (N) and phosphorus (P). The use of phosphate rock by plants is limited by its low and slow P availability and microbial phosphate solubilization is the main mechanism for P bioavailability in the soil-root system. The objectives of this study were (i) select a nitrogen-fixing bacteria which could be used as a co-inoculant with the Penicillium rugulosum IR94MF1 phosphate-solubilizing fungus and (ii) evaluate under field conditions the effect of inoculation combined with phosphate rock (PR) application on yield and nutrient absorption of a Urochloa decumbens pasture which was previously established in a low-fertility, acidic soil.

Methods

Various laboratory and greenhouse tests allowed for the selection of Enterobacter cloacae C17 as the co-inoculant bacteria with the IR94MF1 fungus. Later, under field conditions, a factorial, completely randomized block design was used to evaluate the inoculation with the IR94MF1 fungus, the IR94MF1+C17 co-inoculation, and a non-inoculated control. Two levels of fertilization with PR treatment (0 kg/ha and 200 kg/ha P2O5) were applied to each.

Results

During five consecutive harvests it was observed that the addition of biofertilizers significantly increased (p < 0.05) the herbage mass and N and P assimilation compared to the non-inoculated control. However, no statistically significant differences were observed for the PR application as P source.

Conclusion

P. rugulosum IR94MF1 is capable of solubilizing and accumulating P from the phosphate rock, making it available for plants growing in acid soils with low N content. These inoculants represent a good option as biofertilizers for tropical grasses already established in acidic soils with low N content.

Identification of cadmium-tolerant plant growth-promoting rhizobacteria and characterization of its Cd-biosorption and strengthening effect on phytoremediation: Development of a new amphibious-biocleaner for Cd-contaminated site

The use of plant growth-promoting rhizobacteria (PGPR) in decontaminating cadmium-contaminated soil and water is a sustainable and eco-friendly approach. This study aimed to isolate a PGPR strain from the rhizosphere soil of Solanum nigrum and evaluate its potential and mechanisms in remediating Cd-contaminated environments. The results showed that the isolated strain, Klebsiella sp. AW2, can tolerate 240 mg/L Cd2+. Batch biosorption experiments indicated that the optimal conditions for PGPR biosorption were a pH of 5.0, a biosorbent dosage of 1.0 g/L, and a Cd2+ concentration of 10 mg/L, resulting in a biosorption rate of 40.99%. Model fitting results revealed that the Cd biosorption process followed a uniform surface monolayer chemisorption mechanism, likely involving complexation with functional groups such as -NH, -OH, and -C=O, according to Fourier transform infrared spectrometer and desorption experiments. Furthermore, pot experiments demonstrated that PGPR application significantly enhanced the phytoremediation efficiency of Cd-contaminated soil, increasing the phytoextraction ratio by 32.41%. This improvement was primarily achieved by promoting S. nigrum growth and facilitating Cd horizontal transfer from rhizosphere soil to plants through influencing the rhizosphere soil physicochemical properties and Cd2+ influx in roots. In addition, the copy number of the 16S rRNA gene of the PGPR revealed that the PGPR was predominantly localized in the rhizosphere soil, directly leading to increased availability of Cd for plant uptake. Overall, these findings indicate that Klebsiella sp. AW2 is a promising biocleaner for Cd-contaminated environments and provide valuable insights into the application of biosorbents in phytoremediation efforts.

Fostering climate-resilient agriculture with ACC-deaminase producing rhizobacterial biostimulants from the cold deserts of the Indian Himalayas

Climate change is one of the most significant threats to agricultural productivity, which necessitates a need for more resilient and sustainable farming practices. Rhizobacterial biostimulants that secrete 1-aminocyclopropane-1-carboxylate (ACC) deaminase and enhance crop resilience and yield can serve as a potential sustainable solution. The present study provides a comprehensive analysis of ACC-deaminase producing rhizobacteria (ACCD) isolated from cold deserts of the Indian trans-Himalayas and their efficacy to improve crop resilience and productivity under diverse climatic conditions. Thirty four efficient ACCD showed ACC deaminase activity ranging from 4.9 to 24484.3 nM α-ketobutyrate/h/mg/protein. These strains also exhibited broad-spectrum plant growth promotion (PGP) attributes, including tri-calcium phosphate (TCP) solubilization ranging from 2.4 to 687.5 μg/ml, siderophore production ranging from 62 to 224% and indole-3-acetic acid (IAA)-like auxin production ranging from 0.9 to 88.2 μg/ml. 16S rRNA gene sequencing of efficient strains showed their belonging to 10 genera, including Acinetobacter, Agrobacterium, Arthrobacter, Cellulomonas, Enterobacter, Microbacterium, Neomicrococcus, Priestia, Pseudomonas, and Rhizobium. Among these, Pseudomonas was the dominant genus with high ACC-deaminase activity and multiple PGP traits. These strains also showed growth under various stressed culture conditions, including acidity/alkalinity, different temperatures, desiccation, and salinity. Field applications of 4 efficient and stress-tolerant ACCD, including Pseudomonas geniculata, P. migulae, Priestia aryabhattai, and Rhizobium nepotum with reduced NPK dose under two different temperate climate conditions showed a significant improvement in growth and productivity of crops such as garlic, pea, potato, and wheat in slightly acidic soils and maize in saline-sodic alkaline soils. These findings indicated the broad-spectrum potential of these efficient and stress-tolerant ACCD strains to improve plant growth and productivity across diverse soil types and climatic conditions.

PGPB Isolated from Drought-Tolerant Plants Help Wheat Plants to Overcome Osmotic Stress

The aim of this research was to study the effect of plant-growth-promoting bacteria (PGPB) isolated from the drought-tolerant plants camel thorn (Alhagi pseudoalhagi (M.Bieb.) Fisch) and white pigweed (Chenopodium album L.) on wheat (Triticum aestivum L.) plants cv. Lenigradskaya 6, growing under hydroponic conditions and osmotic stress (generated by 12% polyethylene glycol-6000 (PEG)). Based on the assumption that plants create a unique microbiome that helps them overcome various stresses, we hypothesized that bacteria isolated from drought-tolerant plants may assist cultivated wheat plants in coping with drought stress. PGPB were isolated from seeds and leaves of plants and identified as Bacillus spp. (strains Cap 07D, Cap 09D, and App 11D); Paenibacillus sp. (Cap 286); and Arthrobacter sp. (Cap 03D). All bacteria produced different phytohormones such as indole acetic acid (IAA), abscisic acid (ABA), and gibberellic acid (GAS3) and were capable of stimulating wheat growth under normal and osmotic stress conditions. All PGPB reduced the malondialdehyde (MDA) content, increased the total chlorophyll content by increasing chlorophyll a, and modulated wheat hormone homeostasis and CAT and POX activities under osmotic conditions. Selected strains can be promising candidates for the mitigating of the drought stress of wheat plants.

Isolation and characterization of non-rhizobial bacteria and arbuscular mycorrhizal fungi from legumes

This study investigates non-rhizobial endophytic bacteria in the root nodules of chickpea (Cicer arietinum L), faba bean (Vicia faba), and cowpea (Vigna unguiculata L. Walp), as well as arbuscular mycorrhizal fungi in the rhizospheric soil of chickpea and faba bean. Out of the 34 endophytic bacterial populations examined, 31 strains were identified as non-rhizobial based on nodulation tests. All strains were assessed for their plant growth-promoting (PGP) activities in vitro. The results revealed that most isolates exhibited multiple PGP activities, such as nitrogen fixation, indole-3-acetic acid (IAA) and ammonia (NH3) production, phosphate solubilization, and exopolysaccharide production. The most effective PGP bacteria were selected for 16S rRNA analysis. Additionally, a total of 36 species of native arbuscular mycorrhizal fungi (AMF) were identified. Acaulospora (100%) and Scutellospora (91.66%) were the most prevalent genera in Cicer arietinum L. and Vicia faba L. plants, respectively. Acaulospora also exhibited the highest spore density and relative abundance in both plants. Moreover, the root colonization of Cicer arietinum L. and Vicia faba L. plants by hyphae, vesicles, and arbuscules (HVA) was significant. The findings of this study provide valuable insights into non-rhizobial endophytic bacteria associated with legume root nodules and the diversity of AMF. These organisms have great potential for PGP and can be manipulated by co-inoculation with rhizobia to enhance their biofertilizer effectiveness. This manipulation is crucial for promoting sustainable agriculture, improving crop growth, and advancing biofertilizer technology.

Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture

Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients' cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature's untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security.

Characterization of Bacillus pacificus G124 and Its Promoting Role in Plant Growth and Drought Tolerance

Drought represents a major environmental threat to global agricultural productivity. Employing plant growth-promoting rhizobacteria (PGPR) offers a promising strategy to enhance plant growth and resilience under drought stress. In this study, the strain G124, isolated from the arid region of Qinghai, was characterized at the molecular level, and its ability to enhance plant drought tolerance was validated through pot experiments. The findings revealed that the strain G124 belongs to Bacillus pacificus, with a 99.93% sequence similarity with B. pacificus EB422 and clustered within the same clade. Further analysis indicated that the strain G124 demonstrated a variety of growth-promoting characteristics, including siderophore production, phosphate solubilization, and the synthesis of indole-3-acetic acid (IAA), among others. Moreover, inoculation with B. pacificus G124 resulted in significant enhancements in plant height, leaf area, chlorophyll content, relative water content, and root development in both Arabidopsis thaliana and Medicago sativa seedlings under drought conditions. Additionally, G124 boosted antioxidant enzyme activities and osmolyte accumulation, while reducing malondialdehyde (MDA) and reactive oxygen species (ROS) levels in M. sativa seedlings exposed to drought. These findings suggest that B. pacificus G124 holds significant promise for enhancing plant drought tolerance and could be effectively utilized in crop management strategies under arid conditions.

Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species

Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed.

Unboxing PGPR-mediated management of abiotic stress and environmental cleanup: what lies inside?

Abiotic stresses including heavy metal toxicity, drought, salt and temperature extremes disrupt the plant growth and development and lowers crop output. Presence of environmental pollutants further causes plants suffering and restrict their ability to thrive. Overuse of chemical fertilizers to reduce the negative impact of these stresses is deteriorating the environment and induces various secondary stresses to plants. Therefore, an environmentally friendly strategy like utilizing plant growth-promoting rhizobacteria (PGPR) is a promising way to lessen the negative effects of stressors and to boost plant growth in stressful conditions. These are naturally occurring inhabitants of various environments, an essential component of the natural ecosystem and have remarkable abilities to promote plant growth. Furthermore, multifarious role of PGPR has recently been widely exploited to restore natural soil against a range of contaminants and to mitigate abiotic stress. For instance, PGPR may mitigate metal phytotoxicity by boosting metal translocation inside the plant and changing the metal bioavailability in the soil. PGPR have been also reported to mitigate other abiotic stress and to degrade environmental contaminants remarkably. Nevertheless, despite the substantial quantity of information that has been produced in the meantime, there has not been much advancement in either the knowledge of the processes behind the alleged positive benefits or in effective yield improvements by PGPR inoculation. This review focuses on addressing the progress accomplished in understanding various mechanisms behind the protective benefits of PGPR against a variety of abiotic stressors and in environmental cleanups and identifying the cause of the restricted applicability in real-world.

Cost Reduction in the Production of Green Dwarf Coconut Palm Seedlings Biostimulated with Bacillus cereus

The production of coconut tree seedlings is an important step in the production process, as it substantially affects the productive performance of the adult plant, and the way of obtaining seedlings directly reflects the added costs. To minimize costs, the introduction of biostimulants can be considered a viable and sustainable technology. This study aimed to evaluate the effects of applying Bacillus cereus in promoting growth and reducing the costs of producing Brazilgreen dwarf coconut seedlings. The study has two stages, the first was an experiment carried out in a commercial nursery in the state of Pará-Brazil. The design was completely randomized, with two treatments: control with water (100% mineral fertilization) and B. cereus inoculation (50% mineral fertilization), with 10 replicates each. Biometric parameters and the quality of seedlings were evaluated. In the second stage, the production of stimulated seedlings was compared to that of commercial seedlings, and the effective operating cost (COE) and the total operating cost (TOC) were determined. Biostimulation with B. cereus promotes the growth of coconut tree seedlings, increases seedling quality, and reduces nursery time. In addition, the cost of production is reduced by 10%. Thus, microbial technology is a positive strategy for the production of Brazilian green dwarf coconut seedlings. Using B. cereus can guarantee obtaining seedlings with high performance and at a lower cost. These results may favor obtaining adult plants with high productivity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01163-9.

PGPB Consortium Formulation to Increase Fermentable Sugar in Agave tequilana Weber var. Blue: A Study in the Field

Agave tequilana Weber var. Blue is used as the primary raw material in tequila production due to its fructans (inulin) content. This study evaluates the formulation of a plant-growth-promoting bacteria (PGPB) consortium (Pseudomonas sp. and Shimwellia sp.) to increase sugars in A. tequilana under field conditions. A total of three doses were tested: low (5 L ha-1), medium (10 L ha-1), and high (15 L ha-1), with a cellular density of 1 × 108 CFU mL-1 and one control treatment (without application). Total reducing sugars (TRS), inulin, sucrose, glucose, fructose, and plant growth were measured in agave plants aged 4-5 years at 0 (T0), 3 (T3), 6 (T6), and 12 (T12) months. Yield was recorded at T12. The TRS increased by 3%, and inulin by 5.3% in the high-dose treatment compared to the control at T12. Additionally, a low content of sucrose, glucose, and fructose (approximately 1%) was detected. At T12, the weight of agave heads increased by 31.2% in the medium dose and 22.3% in the high dose compared to the control. The high dose provided a higher inulin content. The A. tequilana plants were five years old and exhibited growth comparable to the standards for 6-7-year-old plants. This study demonstrates a sustainable strategy for tequila production, optimizing the use of natural resources and enhancing industry performance through increased sugar content and yield.

Promoting sustainable agriculture by exploiting plant growth-promoting rhizobacteria (PGPR) to improve maize and cowpea crops

Maize and cowpea are among the staple foods most consumed by most of the African population, and are of significant importance in food security, crop diversification, biodiversity preservation, and livelihoods. In order to satisfy the growing demand for agricultural products, fertilizers and pesticides have been extensively used to increase yields and protect plants against pathogens. However, the excessive use of these chemicals has harmful consequences on the environment and also on public health. These include soil acidification, loss of biodiversity, groundwater pollution, reduced soil fertility, contamination of crops by heavy metals, etc. Therefore, essential to find alternatives to promote sustainable agriculture and ensure the food and well-being of the people. Among these alternatives, agricultural techniques that offer sustainable, environmentally friendly solutions that reduce or eliminate the excessive use of agricultural inputs are increasingly attracting the attention of researchers. One such alternative is the use of beneficial soil microorganisms such as plant growth-promoting rhizobacteria (PGPR). PGPR provides a variety of ecological services and can play an essential role as crop yield enhancers and biological control agents. They can promote root development in plants, increasing their capacity to absorb water and nutrients from the soil, increase stress tolerance, reduce disease and promote root development. Previous research has highlighted the benefits of using PGPRs to increase agricultural productivity. A thorough understanding of the mechanisms of action of PGPRs and their exploitation as biofertilizers would present a promising prospect for increasing agricultural production, particularly in maize and cowpea, and for ensuring sustainable and prosperous agriculture, while contributing to food security and reducing the impact of chemical fertilizers and pesticides on the environment. Looking ahead, PGPR research should continue to deepen our understanding of these microorganisms and their impact on crops, with a view to constantly improving sustainable agricultural practices. On the other hand, farmers and agricultural industry players need to be made aware of the benefits of PGPRs and encouraged to adopt them to promote sustainable agricultural practices.

Investigating the relationship between microbial network features of giant kelp "seedbank" cultures and subsequent farm performance

Microbial inoculants can increase the yield of cultivated crops and are successful in independent trials; however, efficacy drops in large-scale applications due to insufficient consideration of microbial community dynamics. The structure of microbiomes, in addition to the impact of individual taxa, is an important factor to consider when designing growth-promoting inoculants. Here, we investigate the microbial network and community assembly patterns of Macrocystis pyrifera gametophyte germplasm cultures (collectively referred to as a "seedbank") used to cultivate an offshore farm in Santa Barbara, California, and identify network features associated with increased biomass of mature sporophytes. We found that [1] several network features, such as clustering coefficient and edge ratios, significantly vary with biomass outcomes; [2] gametophytes that become low- or high-biomass sporophytes have different hub taxa; and [3] microbial community assembly of gametophyte germplasm cultures is niche-driven. Overall, this study describes microbial community dynamics in M. pyrifera germplasm cultures and ultimately supports the development of early life stage inoculants that can be used on seaweed cultivars to increase biomass yield.

Trichoderma application methods differentially affect the tomato growth, rhizomicrobiome, and rhizosphere soil suppressiveness against Fusarium oxysporum

Trichoderma spp. are widely used to enhance crop growth and suppress diverse diseases. However, inconsistent field efficacy remains a major barrier to their use as a reliable alternative to synthetic pesticides. Various strategies have been investigated to enhance the robustness of their application. Here, we evaluated how T. virens application methods (pre-, at-, and post-transplant) affect the growth of two tomato varieties and their rhizosphere fungal and bacterial communities. Although the greatest rhizosphere abundance of T. virens was observed in the post-transplant application, the at-transplant application promoted tomato growth the most, indicating that greater rhizosphere abundance does not necessarily result in better tomato growth. None of the application methods significantly altered the global rhizosphere fungal and bacterial communities of the tested varieties. Changes in specific microbial genera and guilds may underpin the enhanced tomato growth. We also investigated whether the resulting microbiome changes affect the mycelial growth and conidial germination of Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici, soilborne fungal pathogens of tomato, upon exposure to volatile compounds emitted by culturable rhizosphere microbes and metabolites extracted from the rhizosphere soils after Trichoderma treatments. Volatile compounds produced by cultured rhizosphere microbes after the at-transplant application suppressed the mycelial growth of both pathogens better than those after the other treatments. Similarly, water-soluble metabolites extracted from the rhizosphere soil samples after the at-transplant application most effectively suppressed the germination rate of F. oxysporum spores. Overall, our results suggest that the at-transplant application is most advantageous for promoting the growth of the tested tomato varieties and building soil suppressiveness against the tested fusaria. However, further studies are needed before applying this method to support tomato production. We discuss critical future questions.

Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change

Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.

Efficacy of High-Altitude Biofilm-Forming Novel Bacillus subtilis Species as Plant Growth-Promoting Rhizobacteria on Zea mays L

With the global population explosion, the need for increasing crop productivity is reaching its peak. The significance of organic means of cultivation including biofertilizers and biopesticides is undeniable in this context. Over the last few decades, the use of rhizobacteria to induce crop productivity has gained particular interest of researchers. Of these, several Bacillus spp. have been known for their potential plant growth-promoting and phyto-pathogenic actions. Keeping this background in mind, this study was formulated with an aim to unravel the PGPR and phyto-pathogenic potency of Bacillus sp. isolated from extreme environmental conditions, viz. high-altitude waters of Ganges at Gangotri (Basin Extent Longitude Latitude-73° 2' to 89° 5' E 21° 6' to 31° 21' N). Based on recent studies showing the impact of biofilm on bacterial PGPR potency, three novel strains of Bacillus subtilis were isolated on basis of their extremely high biofilm-producing abilities (BRAM_G1: Accession Number MW006633; BRAM_G2: Accession Numbers MT998278-MT998280; BRAM_G3: Accession Number MT998617), and were tested for their PGPR properties like nutrient sequestration, growth hormone production (IAA, GA3), stress-responsive enzyme production (ACC deaminase) and lignocellulolytic and agriculturally important enzyme productions. The strains were further tested for the plethora of metabolites (liquid and VOCs) exuded by them. Finally, the strains both in individually and in an association, i.e. consortium was tested on a test crop, viz. Zea mays L., and the data were collected at regular intervals and the results were statistically analysed. In the present study, the role of high-altitude novel Bacillus subtilis strains as potent PGPR has been analysed statistically.

Screening of rhizosphere nitrogen fixing, phosphorus and potassium solubilizing bacteria of Malus sieversii (Ldb.) Roem. and the effect on apple growth

Nitrogen, phosphorus and potassium inorganic fertilizers are commonly used when growing apples, but their excessive application has resulted in a decline in soil fertility and therefore an inability to maintain sustainable cultivation systems. It is possible to compensate for this with biofertilizers. Nitrogen-fixing, phosphorus solubilizing, and potassium solubilizing bacteria are biofertilizers with a broad range of possible uses. In this study, beneficial microorganisms were screened from the rhizosphere soil of the apple tree, Malus sieversii (Ldb.) Roem., which is rich in microbial diversity in natural environments. It was essential to investigate their effects on the growth of apple seedlings. Eight populations of organic phosphorus solubilizing bacteria (56), inorganic phosphorus solubilizing bacteria (13), nitrogen-fixing bacteria (22), and potassium solubilizing bacteria (24) were isolated from eight populations of Xinjiang wild apple rhizosphere in Ili by medium culture. Their morphological characteristics were recorded and their activity was determined. The most active strains were Pseudomonas migulae, Pseudomonas poae, and Pseudomonas extremaustralis, which was determined by physiological and biochemical properties and 16S rDNA sequence analysis. The L16 (45) orthogonal experiment, which used the three strains as testing materials, was created to assess the effects of the strains on apple physiological indicators, soil nutrients, leaf nutrients, and biomass, as well as to identify the ideal combination, concentration, timing, and application method. The results indicated that the peroxidase (POD) and catalase (CAT) activities of apple seedlings increased significantly under the 10 treatment, and the (SOD) activities of the 0 (control) and 1 (inorganic fertilizer only) treatments were significantly lower than the other treatments; soluble sugar, soluble protein and chlorophyll contents increased in all treatments compared to 0 and 1, while malondialdehyde and proline contents increased or decreased compared to 0 and 1; apple seedlings in treatment 10 had the highest soil N, P, and K content, leaf N, P, and K content and biomass were also all highest in treatment 10. In summary, the strains screened for the test can be used as biofertilizers and the optimum application was determined for treatment 10, meaning that the results also provide a theoretical basis for their application in artificially grown orchards.

Competition and co-association, but not phosphorous availability, shape the benefits of phosphate-solubilizing root bacteria for maize (Zea mays)

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilizing rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. We used maize-associated rhizobacteria with varying phosphate solubilization ability in experiments in soil, sterilized soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated the intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: the beneficial effects of one Serratia isolate were only detectable when plants were inoculated with a single strain and the beneficial effects of a competition-sensitive Rhizobium was only detectable in sterilized soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilization may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.

Plant Growth-Promoting Soil Bacteria: Nitrogen Fixation, Phosphate Solubilization, Siderophore Production, and Other Biological Activities

This review covers the literature data on plant growth-promoting bacteria in soil, which can fix atmospheric nitrogen, solubilize phosphates, produce and secrete siderophores, and may exhibit several different behaviors simultaneously. We discuss perspectives for creating bacterial consortia and introducing them into the soil to increase crop productivity in agrosystems. The application of rhizosphere bacteria-which are capable of fixing nitrogen, solubilizing organic and inorganic phosphates, and secreting siderophores, as well as their consortia-has been demonstrated to meet the objectives of sustainable agriculture, such as increasing soil fertility and crop yields. The combining of plant growth-promoting bacteria with mineral fertilizers is a crucial trend that allows for a reduction in fertilizer use and is beneficial for crop production.

Promotional Properties of ACC Deaminase-Producing Bacterial Strain DY1-3 and Its Enhancement of Maize Resistance to Salt and Drought Stresses

Salt stress and drought stress can decrease the growth and productivity of agricultural crops. Plant growth-promoting bacteria (PGPB) may protect and promote plant growth at abiotic stress. The aim of this study was to search for bacterial strains that can help crops resist rises in drought and salt stresses, to improve crop seed resistance under drought and salt stresses, and to investigate the effect of bacterial strains that can help crop resist external stresses under different stress conditions. Pseudomonas DY1-3, a strain from the soil under the glacier moss community of Tien Shan No. 1, was selected to investigate its growth-promoting effects. Previous studies have shown that this strain is capable of producing ACC (1-aminocyclopropane-1-carboxylic acid) deaminase. In this experiment, multifunctional biochemical test assays were evaluated to determine their potential as PGPB and their bacterial growth-promoting properties and stress-resistant effects on maize plants were verified through seed germination experiments and pot experiments. The results showed that strain DY1-3 has good salt and drought tolerance, as well as the ability to melt phosphorus, fix nitrogen, and produce iron carriers, IAA, EPS, and other pro-biomasses. This study on the growth-promoting effects of the DY1-3 bacterial strain on maize seeds revealed that the germination rate, primary root length, germ length, number of root meristems, and vigor index of the maize seeds were increased after soaking them in bacterial solution under no-stress, drought-stress, and salt-stress environments. In the potting experiments, seedlings in the experimental group inoculated with DY1-3 showed increased stem thicknesses, primary root length, numbers of root meristems, and plant height compared to control seedlings using sterile water. In the study on the physiological properties of the plants related to resistance to stress, the SOD, POD, CAT, and chlorophyll contents of the seedlings in the experimental group, to which the DY1-3 strain was applied, were higher than those of the control group of seedlings to which the bacterial solution was not applied. The addition of the bacterial solution reduced the content of MDA in the experimental group seedlings, which indicated that DY1-3 could positively affect the promotion of maize seedlings and seeds against abiotic stress. In this study, it was concluded that strain DY1-3 is a valuable strain for application, which can produce a variety of pro-biotic substances to promote plant growth in stress-free environments or to help plants resist abiotic stresses. In addition to this, the strain itself has good salt and drought tolerance, making it an option to help crops grown in saline soils to withstand abiotic stresses, and a promising candidate for future application in agricultural biofertilizers.

Biofilm modifiers: The disparity in paradigm of oral biofilm ecosystem

A biofilm is a population of sessile microorganisms that has a distinct organized structure and characteristics like channels and projections. Good oral hygiene and reduction in the prevalence of periodontal diseases arise from minimal biofilm accumulation in the mouth, however, studies focusing on modifying the ecology of oral biofilms have not yet been consistently effective. The self-produced matrix of extracellular polymeric substances and greater antibiotic resistance make it difficult to target and eliminate biofilm infections, which lead to serious clinical consequences that are often lethal. Therefore, a better understanding is required to target and modify the ecology of biofilms in order to eradicate the infection, not only in instances of oral disorders but also in terms of nosocomial infections. The review focuses on several biofilm ecology modifiers to prevent biofilm infections, as well as the involvement of biofilm in antibiotic resistance, implants or in-dwelling device contamination, dental caries, and other periodontal disorders. It also discusses recent advances in nanotechnology that may lead to novel strategies for preventing and treating infections caused by biofilms as well as a novel outlook to infection control.

Diversity and characteristics of plant immunity-activating bacteria from Brassicaceae plants

BACKGROUND

Microorganisms that activate plant immune responses are useful for application as biocontrol agents in agriculture to minimize crop losses. The present study was conducted to identify and characterize plant immunity-activating microorganisms in Brassicaceae plants.

RESULTS

A total of 25 bacterial strains were isolated from the interior of a Brassicaceae plant, Raphanus sativus var. hortensis. Ten different genera of bacteria were identified: Pseudomonas, Leclercia, Enterobacter, Xanthomonas, Rhizobium, Agrobacterium, Pantoea, Rhodococcus, Microbacterium, and Plantibacter. The isolated strains were analyzed using a method to detect plant immunity-activating microorganisms that involves incubation of the microorganism with tobacco BY-2 cells, followed by treatment with cryptogein, a proteinaceous elicitor of tobacco immune responses. In this method, cryptogein-induced production of reactive oxygen species (ROS) in BY-2 cells serves as a marker of immune activation. Among the 25 strains examined, 6 strains markedly enhanced cryptogein-induced ROS production in BY-2 cells. These 6 strains colonized the interior of Arabidopsis plants, and Pseudomonas sp. RS3R-1 and Rhodococcus sp. RS1R-6 selectively enhanced plant resistance to the bacterial pathogens Pseudomonas syringae pv. tomato DC3000 and Pectobacterium carotovorum subsp. carotovorum NBRC 14082, respectively. In addition, Pseudomonas sp. RS1P-1 effectively enhanced resistance to both pathogens. We also comprehensively investigated the localization (i.e., cellular or extracellular) of the plant immunity-activating components produced by the bacteria derived from R. sativus var. hortensis and the components produced by previously isolated bacteria derived from another Brassicaceae plant species, Brassica rapa var. perviridis. Most gram-negative strains enhanced cryptogein-induced ROS production in BY-2 cells via the presence of cells themselves rather than via extracellular components, whereas many gram-positive strains enhanced ROS production via extracellular components. Comparative genomic analyses supported the hypothesis that the structure of lipopolysaccharides in the outer cell envelope plays an important role in the ROS-enhancing activity of gram-negative Pseudomonas strains.

CONCLUSIONS

The assay method described here based on elicitor-induced ROS production in cultured plant cells enabled the discovery of novel plant immunity-activating bacteria from R. sativus var. hortensis. The results in this study also suggest that components involved in the ROS-enhancing activity of the bacteria may differ depending largely on genus and species.

The Plant Growth-Promoting Potential of Halotolerant Bacteria Is Not Phylogenetically Determined: Evidence from Two Bacillus megaterium Strains Isolated from Saline Soils Used to Grow Wheat

(1) Background: Increasing salinity, further potentiated by climate change and soil degradation, will jeopardize food security even more. Therefore, there is an urgent need for sustainable agricultural practices capable of maintaining high crop yields despite adverse conditions. Here, we tested if wheat, a salt-sensitive crop, could be a good reservoir for halotolerant bacteria with plant growth-promoting (PGP) capabilities. (2) Methods: We used two agricultural soils from Algeria, which differ in salinity but are both used to grow wheat. Soil halotolerant bacterial strains were isolated and screened for 12 PGP traits related to phytohormone production, improved nitrogen and phosphorus availability, nutrient cycling, and plant defence. The four 'most promising' halotolerant PGPB strains were tested hydroponically on wheat by measuring their effect on germination, survival, and biomass along a salinity gradient. (3) Results: Two halotolerant bacterial strains with PGP traits were isolated from the non-saline soil and were identified as Bacillus subtilis and Pseudomonas fluorescens, and another two halotolerant bacterial strains with PGP traits were isolated from the saline soil and identified as B. megaterium. When grown under 250 mM of NaCl, only the inoculated wheat seedlings survived. The halotolerant bacterial strain that displayed all 12 PGP traits and promoted seed germination and plant growth the most was one of the B. megaterium strains isolated from the saline soil. Although they both belonged to the B. megaterium clade and displayed a remarkable halotolerance, the two bacterial strains isolated from the saline soil differed in two PGP traits and had different effects on plant performance, which clearly shows that PGP potential is not phylogenetically determined. (4) Conclusions: Our data highlight that salt-sensitive plants and non-saline soils can be reservoirs for halotolerant microbes with the potential to become effective and sustainable strategies to improve plant tolerance to salinity. However, these strains need to be tested under field conditions and with more crops before being considered biofertilizer candidates.

The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology

Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.

Azospirillum brasilense AbV5/6 encapsulation in dual-crosslinked beads based on cationic starch

The main challenge of agriculture is feeding the growing population and at the same time providing environmental sustainability. Using Azospirillum brasilense as a biofertilizer has proved to be a promising solution. However, its prevalence in soil has not been efficient due to biotic and abiotic stresses. Thus, to overcome this drawback, we encapsulated the A. brasilense AbV5 and AbV6 strains in a dual-crosslinked bead based on cationic starch. The starch was previously modified with ethylenediamine by an alkylation approach. Then, the beads were obtained by a dripping technique, crosslinking sodium tripolyphosphate with a blend containing starch, cationic starch, and chitosan. The AbV5/6 strains were encapsulated into the hydrogel beads by a swelling diffusion method followed by desiccation. Plants treated with encapsulated AbV5/6 cells showed an increase in the root length by 19 %, shoot fresh weight by 17 %, and the content of chlorophyll b by 71 %. The encapsulation of AbV5/6 strains showed to keep A. brasilense viability for at least 60 days and efficiency to promote maize growth.

Ectomycorrhizal fungi, two species of Laccaria, differentially block the migration and accumulation of cadmium and copper in Pinus densiflora

The root tips of host plant species can establish ectomycorrhizae with their fungal partners, thereby altering the responses of the host plants to heavy metal (HM) toxicity. Here, two species of Laccaria, L. bicolor and L. japonica, were investigated in symbiosis with Pinus densiflora to study their potential for promotion of phytoremediation of HM-contaminated soils in pot experiments. The results showed that L. japonica had significantly higher dry biomass than L. bicolor in mycelia grown on modified Melin-Norkrans medium containing elevated levels of cadmium (Cd) or copper (Cu). Meanwhile, the accumulations of Cd or Cu in L. bicolor mycelia were much higher than that in L. japonica at the same level of Cd or Cu. Therefore, L. japonica displayed a stronger tolerance to HM toxicity than L. bicolor in situ. Compared with non-mycorrhizal P. densiflora seedlings, inoculation with two Laccaria species significantly increased the growth of P. densiflora seedlings in absence or presence of HM. The mantle of host roots blocked the uptake and migration of HM, which led to the decrease of Cd and Cu accumulation in the P. densiflora shoots and roots, except for the root Cd accumulation of L. bicolor-mycorrhizal plants when 25 mg kg^-1 Cd exposure. Furthermore, HM distribution in mycelia showed Cd and Cu are mainly retained in the cell walls of mycelia. These results provide strong evidence that the two species of Laccaria in this system may have different strategies to assist host tree against HM toxicity.

Biodiversity and Functional Attributes of Rhizospheric Microbiomes: Potential Tools for Sustainable Agriculture

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.

Comparative study on plant growth-promoting bacterial inoculation by irrigation and spraying for promoting Bidens pilosa L. phytoremediation of cadmium-contaminated soil

A field study was conducted to compare FM-1 inoculation by irrigation and spraying for promoting Bidens pilosa L. phytoremediation of cadmium (Cd)-contaminated soil. Cascading relationships between bacterial inoculation by irrigation and spraying and soil properties, plant growth-promoting traits, plant biomass and Cd concentrations in Bidens pilosa L. were explored based on the partial least squares path model (PLS-PM). The results indicated that inoculation with FM-1 not only improved the rhizosphere soil environment of B. pilosa L. but also increased the Cd extracted from the soil. Moreover, Fe and P in leaves play vital roles in promoting plant growth when FM-1 is inoculated by irrigation, while Fe in leaves and stems plays a vital role in promoting plant growth when FM-1 is inoculated by spraying. In addition, FM-1 inoculation decreased the soil pH by affecting soil dehydrogenase and oxalic acid in cases with irrigation and Fe in roots in cases with spraying. Thus, the soil bioavailable Cd content increased and promoted Cd uptake by Bidens pilosa L. To address Cd-induced oxidative stress, Fe in leaves helped to convert GSH into PCs, which played a vital role in ROS scavenging when FM-1 was inoculated by irrigation. The soil urease content effectively increased the POD and APX activities in the leaves of Bidens pilosa L., which helped alleviate Cd-induced oxidative stress when FM-1 was inoculated by spraying. This study compares and illustrates the potential mechanism by which FM-1 inoculation can improve the phytoremediation of Cd-contaminated soil by Bidens pilosa L., suggesting that FM-1 inoculation by irrigation and spraying is useful in the phytoremediation of Cd-contaminated sites.

Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments

Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.

Decrypting the multi-functional biological activators and inducers of defense responses against biotic stresses in plants

Plant diseases are still the main problem for the reduction in crop yield and a threat to global food security. Additionally, excessive usage of chemical inputs such as pesticides and fungicides to control plant diseases have created another serious problem for human and environmental health. In view of this, the application of plant growth-promoting rhizobacteria (PGPR) for controlling plant disease incidences has been identified as an eco-friendly approach for coping with the food security issue. In this review, we have identified different ways by which PGPRs are capable of reducing phytopathogenic infestations and enhancing crop yield. PGPR suppresses plant diseases, both directly and indirectly, mediated by microbial metabolites and signaling components. Microbial synthesized anti-pathogenic metabolites such as siderophores, antibiotics, lytic enzymes, hydrogen cyanide, and several others act directly on phytopathogens. The indirect mechanisms of reducing plant disease infestation are caused by the stimulation of plant immune responses known as initiation of systemic resistance (ISR) which is mediated by triggering plant immune responses elicited through pathogen-associated molecular patterns (PAMPs). The ISR triggered in the infected region of the plant leads to the development of systemic acquired resistance (SAR) throughout the plant making the plant resistant to a wide range of pathogens. A number of PGPRs including Pseudomonas and Bacillus genera have proven their ability to stimulate ISR. However, there are still some challenges in the large-scale application and acceptance of PGPR for pest and disease management. Further, we discuss the newly formulated PGPR inoculants possessing both plant growth-promoting activities and plant disease suppression ability for a holistic approach to sustaining plant health and enhancing crop productivity.

Temperature-induced modulation of stress-tolerant PGP genes bioprospected from Bacillus sp. IHBT-705 associated with saffron (Crocus sativus) rhizosphere: A natural -treasure trove of microbial biostimulants

There is a renewed interest in sustainable agriculture wherein novel plant growth-promoting rhizobacteria (PGPR) are being explored for developing efficient biostimulants. The key requirement of a microbe to qualify as a good candidate for developing a biostimulant is its intrinsic plant growth-promoting (PGP) characteristics. Though numerous studies have been conducted to assess the beneficial effects of PGPRs on plant growth under normal and stressed conditions but not much information is available on the characterization of intrinsic traits of PGPR under stress. Here, we focused on understanding how temperature stress impacts the functionality of key stress tolerant and PGP genes of Bacillus sp. IHBT-705 isolated from the rhizosphere of saffron (Crocus sativus). To undertake the study, Bacillus sp. IHBT-705 was grown under varied temperature regimes, their PGP traits were assessed from very low to very high-temperature range and the expression trend of targeted stress tolerant and PGP genes were analyzed. The results illustrated that Bacillus sp. IHBT-705 is a stress-tolerant PGPR as it survived and multiplied in temperatures ranging from 4°C-50°C, tolerated a wide pH range (5-11), withstood high salinity (8%) and osmolarity (10% PEG). The PGP traits varied under different temperature regimes indicating that temperature influences the functionality of PGP genes. This was further ascertained through whole genome sequencing followed by gene expression analyses wherein certain genes like cspB, cspD, hslO, grpE, rimM, trpA, trpC, trpE, fhuC, fhuD, acrB5 were found to be temperature sensitive while, cold tolerant (nhaX and cspC), heat tolerant (htpX) phosphate solubilization (pstB1), siderophore production (fhuB and fhuG), and root colonization (xerC1 and xerC2) were found to be highly versatile as they could express well both under low and high temperatures. Further, the biostimulant potential was checked through a pot study on rice (Oryza sativa), wherein the application of Bacillus sp. IHBT-705 improved the length of shoots, roots, and number of roots over control. Based on the genetic makeup, stress tolerance potential, retention of PGP traits under stress, and growth-promoting potential, Bacillus sp. IHBT-705 could be considered a good candidate for developing biostimulants.

Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T

Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant-bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to PGPB, we performed a genome-wide association study (GWAS) using an Arabidopsis thaliana population treated with Azoarcus olearius DQS-4^T. Phenotypically, the 305 Arabidopsis accessions tested responded differently to bacterial treatment by improving, inhibiting, or not affecting root system or shoot traits. GWA mapping analysis identified several predicted loci associated with primary root length or root fresh weight. Two statistical analyses were performed to narrow down potential gene candidates followed by haplotype block analysis, resulting in the identification of 11 loci associated with the responsiveness of Arabidopsis root fresh weight to bacterial inoculation. Our results showed considerable variation in the ability of plants to respond to inoculation by A. olearius DQS-4^T while revealing considerable complexity regarding statistically associated loci with the growth traits measured. This investigation is a promising starting point for sustainable breeding strategies for future cropping practices that may employ beneficial microbes and/or modifications of the root microbiome.

Chemical and Microbial Characterization of Fermented Forest Litters Used as Biofertilizers

The excessive use of chemicals in intensive agriculture has had a negative impact on soil diversity and fertility. A strategy for developing sustainable agriculture could rely on the use of microbial-based fertilizers, known as biofertilizers. An alternative to marketed products could be offered to small farmers if they could produce their own biofertilizers using forest litters, which harbor one of the highest microbial diversities. The aim of this study is to characterize microbial communities of Fermented Forest Litters (FFL), assuming that the fermentation process will change both their abundance and diversity. We investigated two types of differing in the chemical composition of the initial litters used and the climatic context of the forest where they are originated from. The abundance and diversity of bacterial and fungal communities were assessed using quantitative PCR and molecular genotyping techniques. The litter chemical compositions were compared before and after fermentation using Infrared spectrometry. Results obtained showed that fermentation increased the abundance of bacteria but decreased that of fungi. Low pH and change in organic matter composition observed after fermentation also significantly reduced the α-diversity of both bacterial and fungal communities. The higher proportion of aliphatic molecules and lower C/N of the FFLs compared to initial litters indicate that FFLs should be rapidly decomposed once added into the soil. This preliminary study suggests that the agronomic interest of FFLs used as biofertilizers is probably more related to the contribution of nutrients easily assimilated by plants than to the diversity of microorganisms that compose it. Further studies must be conducted with sequencing techniques to identify precisely the microbial species likely to be beneficial to plant growth.

Plant Beneficial Bacteria and Their Potential Applications in Vertical Farming Systems

In this literature review, we discuss the various functions of beneficial plant bacteria in improving plant nutrition, the defense against biotic and abiotic stress, and hormonal regulation. We also review the recent research on rhizophagy, a nutrient scavenging mechanism in which bacteria enter and exit root cells on a cyclical basis. These concepts are covered in the contexts of soil agriculture and controlled environment agriculture, and they are also used in vertical farming systems. Vertical farming-its advantages and disadvantages over soil agriculture, and the various climatic factors in controlled environment agriculture-is also discussed in relation to plant-bacterial relationships. The different factors under grower control, such as choice of substrate, oxygenation rates, temperature, light, and CO₂ supplementation, may influence plant-bacterial interactions in unintended ways. Understanding the specific effects of these environmental factors may inform the best cultural practices and further elucidate the mechanisms by which beneficial bacteria promote plant growth.

Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production

The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.

Characterizing Effects of Microbial Biostimulants and Whole-Soil Inoculums for Native Plant Revegetation

Soil microbes play important roles in plant health and ecosystem functioning, however, they can often be disturbed or depleted in degraded lands. During seed-based revegetation of such sites there is often very low germination and seedling establishment success, with recruitment of beneficial microbes to the rhizosphere one potential contributor to this problem. Here we investigated whether Australian native plant species may benefit from planting seed encapsulated within extruded seed pellets amended with one of two microbe-rich products: a commercial vermicast extract biostimulant or a whole-soil inoculum from a healthy reference site of native vegetation. Two manipulative glasshouse trials assessing the performance of two Australian native plant species (Acacia parramattensis and Indigofera australis) were carried out in both unmodified field-collected soil (trial 1) and in the same soil reduced in nutrients and microbes (trial 2). Seedling emergence and growth were compared between pelleted and bare-seeded controls and analyzed alongside soil nutrient concentrations and culturable microbial community assessments. The addition of microbial amendments maintained, but did not improve upon, high levels of emergence in both plant species relative to unamended pellets. In trial 1, mean time to emergence of Acacia parramattensis seedlings was slightly shorter in both amended pellet types relative to the standard pellets, and in trial 2, whole-soil inoculum pellets showed significantly improved growth metrics. This work shows that there is potential for microbial amendments to positively affect native plant emergence and growth, however exact effects are dependent on the type of amendment, the plant species, and the characteristics of the planting site soil.

Characteristics of rhizosphere and endogenous bacterial community of Ulleung-sanmaneul, an endemic plant in Korea: application for alleviating salt stress

Microbes influence plant growth and fitness. However, the structure and function of microbiomes associated with rare and endemic plants remain underexplored. To investigate the bacterial community structure of Ulleung-sanmaneul (U-SMN), an endemic plant in Korea, samples were collected from natural and cultivated habitats, and their 16S rDNA was sequenced. The root bacterial community structure differed from those of bulk soil and rhizosphere in both habitats. Endogenous bacteria in cultivated plants were less diverse than wild plants, but Luteibacter rhizovicinus, Pseudomonas fulva, and Sphingomonas pruni were shared. Co-inoculation of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 promoted growth and induced salt stress resistance in Arabidopsis and chive. Changes in growth promotion and phenotypes of plants by co-inoculation were mediated by increased auxin production. Each strain colonized the roots without niche competition. The results indicated that host selectivity was influential than environmental factors in formulating endophytic bacterial composition, and domestication simplified the bacterial community diversity. Our results will contribute to the growth and maintenance of endemic U-SMN plants.

Microbiome-based biotechnology for reducing food loss post harvest

Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety.

Maize-soybean relay strip intercropping reshapes the rhizosphere bacterial community and recruits beneficial bacteria to suppress Fusarium root rot of soybean

Rhizosphere microbes play a vital role in plant health and defense against soil-borne diseases. Previous studies showed that maize-soybean relay strip intercropping altered the diversity and composition of pathogenic Fusarium species and biocontrol fungal communities in the soybean rhizosphere, and significantly suppressed soybean root rot. However, whether the rhizosphere bacterial community participates in the regulation of this intercropping on soybean root rot is not clear. In this study, the rhizosphere soil of soybean healthy plants was collected in the continuous cropping of maize-soybean relay strip intercropping and soybean monoculture in the fields, and the integrated methods of microbial profiling, dual culture assays in vitro, and pot experiments were employed to systematically investigate the diversity, composition, and function of rhizosphere bacteria related to soybean root rot in two cropping patterns. We found that intercropping reshaped the rhizosphere bacterial community and increased microbial community diversity, and meanwhile, it also recruited much richer and more diverse species of Pseudomonas sp., Bacillus sp., Streptomyces sp., and Microbacterium sp. in soybean rhizosphere when compared with monoculture. From the intercropping, nine species of rhizosphere bacteria displayed good antagonism against the pathogen Fusarium oxysporum B3S1 of soybean root rot, and among them, IRHB3 (Pseudomonas chlororaphis), IRHB6 (Streptomyces), and IRHB9 (Bacillus) were the dominant bacteria and extraordinarily rich. In contrast, MRHB108 (Streptomyces virginiae) and MRHB205 (Bacillus subtilis) were the only antagonistic bacteria from monoculture, which were relatively poor in abundance. Interestingly, introducing IRHB3 into the cultured substrates not only significantly promoted the growth and development of soybean roots but also improved the survival rate of seedlings that suffered from F. oxysporum infection. Thus, this study proves that maize-soybean relay strip intercropping could help the host resist soil-borne Fusarium root rot by reshaping the rhizosphere bacterial community and driving more beneficial microorganisms to accumulate in the soybean rhizosphere.

Acetic acid alters rhizosphere microbes and metabolic composition to improve willows drought resistance

The adverse effects of drought on plants are gradually exacerbated with global climatic change. Amelioration of the drought stress that is induced by low doses of acetic acid (AA) has been caused great interest in plants. However, whether AA can change soil microbial composition is still unknown. Here, we investigated how exogenous AA regulates the physiology, rhizosphere soil microorganisms and metabolic composition on Salix myrtillacea under drought stress. The physiological results showed that AA could improve the drought tolerance of S. myrtillacea. Azotobacter and Pseudomonas were enriched in the rhizosphere by AA irrigation. AA significantly increased the relative contents of amino acid metabolites (e.g., glycyl-L-tyrosine, l-glutamine and seryl-tryptophan) and decreased the relative contents of phenylpropane metabolites (e.g., fraxetin and sinapyl aldehyde) in soils. The enrichments of Azotobacter and Pseudomonas were significantly correlated with glycyl-L-tyrosine, l-glutamine, seryl-tryptophan, fraxetin and sinapyl aldehyde, which could increase the stress resistance by promoting nitrogen (N) uptake for willows. Furthermore, inoculation with Azotobacter chroococcum and Pseudomonas fluorescens could significantly improve willows drought tolerance. Therefore, our results reveal that the changes of plant physiology, rhizosphere soil microorganisms and metabolic composition induced by AA can improve willows drought resistance by enhancing N uptake.

The Microbiome Structure of the Symbiosis between the Desert Truffle Terfezia boudieri and Its Host Plant Helianthemum sessiliflorum

The desert truffle Terfezia boudieri is an ascomycete fungus that forms ect-endomycorrhiza in the roots of plants belonging to Cistaceae. The fungus forms hypogeous edible fruit bodies, appreciated as gourmet food. Truffles and host plants are colonized by various microbes, which may contribute to their development. However, the diversity and composition of the bacterial community under field conditions in the Negev desert are still unknown. The overall goal of this research was to identify the rhizosphere microbial community supporting the establishment of a symbiotic association between T. boudieri and Helianthemum sessiliflorum. The bacterial community was characterized by fruiting bodies, mycorrhized roots, and rhizosphere soil. Based on next-generation sequencing meta-analyses of the 16S rRNA gene, we discovered diverse bacterial communities of fruit bodies that differed from those found in the roots and rhizosphere. Families of Proteobacteria, Planctomycetes, and Actinobacteria were present in all four samples. Alpha diversity analysis revealed that the rhizosphere and roots contain significantly higher bacterial species numbers compared to the fruit. Additionally, ANOSIM and PCoA provided a comparative analysis of the bacterial taxa associated with fruiting bodies, roots, and rhizosphere. The core microbiome described consists of groups whose biological role triggers important traits supporting plant growth and fruit body development.