Plant Associated Rhizobacteria for Biocontrol and Plant Growth Enhancement

Unveiling the secrets of abiotic stress tolerance in plants through molecular and hormonal insights

Phytohormones are signaling substances that control essential elements of growth, development, and reactions to environmental stress. Drought, salt, heat, cold, and floods are a few examples of abiotic factors that have a significant impact on plant development and survival. Complex sensing, signaling, and stress response systems are needed for adaptation and tolerance to such pressures. Abscisic acid (ABA) is a key phytohormone that regulates stress responses. It interacts with the jasmonic acid (JA) and salicylic acid (SA) signaling pathways to direct resources toward reducing the impacts of abiotic stressors rather than fighting against pathogens. Under exposure to nanoparticles, the plant growth hormones also function as molecules that regulate stress and are known to be involved in a variety of signaling cascades. Reactive oxygen species (ROS) are detected in excess while under stress, and nanoparticles can control their formation. Understanding the way these many signaling pathways interact in plants will tremendously help breeders create food crops that can survive in deteriorating environmental circumstances brought on by climate change and that can sustain or even improve crop production. Recent studies have demonstrated that phytohormones, such as the traditional auxins, cytokinins, ethylene, and gibberellins, as well as more recent members like brassinosteroids, jasmonates, and strigolactones, may prove to be significant metabolic engineering targets for creating crop plants that are resistant to abiotic stress. In this review, we address recent developments in current understanding regarding the way various plant hormones regulate plant responses to abiotic stress and highlight instances of hormonal communication between plants during abiotic stress signaling. We also discuss new insights into plant gene and growth regulation mechanisms during stress, phytohormone engineering, nanotechnological crosstalk of phytohormones, and Plant Growth-Promoting Rhizobacteria's Regulatory Powers (PGPR) via the involvement of phytohormones.

Multi-omics analysis of Streptomyces djakartensis strain MEPS155 reveal a molecular response strategy combating Ceratocystis fimbriata causing sweet potato black rot

To investigate the potential antifungal mechanisms of rhizosphere Actinobacteria against Ceratocystis fimbriata in sweet potato, a comprehensive approach combining biochemical analyses and multi-omics techniques was employed in this study. A total of 163 bacterial strains were isolated from the rhizosphere soil of sweet potato. Among them, strain MEPS155, identified as Streptomyces djakartensis, exhibited robust and consistent inhibition of C. fimbriata mycelial growth in in vitro dual culture assays, attributed to both cell-free supernatant and volatile organic compounds. Moreover, strain MEPS155 demonstrated diverse plant growth-promoting attributes, including the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, phosphorus solubilization, nitrogen fixation, and enzymatic activities such as cellulase, chitinase, and protease. Notably, strain MEPS155 exhibited efficacy against various sweet potato pathogenic fungi. Following the inoculation of strain MEPS155, a significant reduction (P < 0.05) in malondialdehyde content was observed in sweet potato slices, indicating a potential protective effect. The whole genome of MEPS155 was characterized by a size of 8,030,375 bp, encompassing 7234 coding DNA sequences and 32 secondary metabolite biosynthetic gene clusters. Transcriptomic analysis revealed 1869 differentially expressed genes in the treated group that cultured with C. fimbriata, notably influencing pathways associated with porphyrin metabolism, fatty acid biosynthesis, and biosynthesis of type II polyketide products. These alterations in gene expression are hypothesized to be linked to the production of secondary metabolites contributing to the inhibition of C. fimbriata. Metabolomic analysis identified 1469 potential differently accumulated metabolites (PDAMs) when comparing MEPS155 and the control group. The up-regulated PDAMs were predominantly associated with the biosynthesis of various secondary metabolites, including vanillin, myristic acid, and protocatechuic acid, suggesting potential inhibitory effects on plant pathogenic fungi. Our study underscores the ability of strain S. djakartensis MEPS155 to inhibit C. fimbriata growth through the production of secretory enzymes or secondary metabolites. The findings contribute to a theoretical foundation for future investigations into the role of MEPS155 in postharvest black rot prevention in sweet potato.

Harnessing rhizobacteria: Isolation, identification, and antifungal potential against soil pathogens

Rhizobacteria play a crucial role in plant health by providing natural antagonism against soil-borne fungi. The use of rhizobacteria has been viewed as an alternative to the use of chemicals that could be useful for the integrated management of plant diseases and also increase yield in an environmentally friendly manner. However, there is limited understanding of the specific mechanisms by which rhizobacteria inhibit these pathogens and the diversity of rhizobacterial species involved. This study aims to isolate, identify, and characterize rhizobacteria with antagonistic activities against soil-borne fungi. Laboratory tests were carried out on isolated rhizobacteria to evaluate their inhibitory activity against Rhizoctonia solani, Pythium aphanidermatum and Macrophomina phaseolina. The selected bacteria were identified using the Vitek 2 compact system and 16S rRNA genes. Experiments were carried out to evaluate the plant growth promotion and biocontrol ability of these selected isolates. Out of 324 rhizobacteria isolates obtained from various plant species, twelve were chosen due to their strong (>50 %) wide-ranging antifungal activity against three significant phytopathogenic fungi species. According to the identification results, they belong to the following species: Aeribacillus pallidus ECC4, Alloiococcus otitis BRE6, Aneurinibacillus thermoaerophilus ECL1, A. thermoaerophilus SDV1, Bacillus halotolerans DMC8, B. megaterium SKE2, B. megaterium TNK1, B. subtilis NAS1, Enterobacter cloacae complex BZD3, Leclercia adecarboxylata DKS3, Paenibacillus polymyxa TRS4, and Staphylococcus lentus BZD2. Eleven isolates produced protease, six isolates produced chitinase, and seven isolates were highly effective in producing hydrogen cyanide. Ten isolates could fix nitrogen, while all isolates could produce potassium, indole-3-acetic acid, siderophore, and ammonia. These findings enhance our understanding of rhizobacterial biodiversity and their potential as biocontrol agents in sustainable agriculture.

Bio-perfume guns: Antifungal volatile activity of Bacillus sp. LNXM12 against postharvest pathogen Botrytis cinerea in tomato and strawberry

Gray mold disease, caused by Botrytis cinerea is a major postharvest disease impacting fruits such as strawberries and tomatoes. This study explores the use of volatile organic compounds (VOCs) produced by Bacillus spp. as eco-friendly biocontrol agents against B. cinerea. In vitro experiments demonstrated that VOCs from Bacillus sp. LNXM12, B. thuringiensis GBAC46, and B. zhanghouensis LLTC93-VOCs inhibited fungal growth by 61.2%, 40.5%, and 21.6%, respectively, compared to the control. LNXM12 was selected for further experiments due to its highest control efficacy of 58.3% and 76.6% on tomato and strawberry fruits, respectively. The LNXM12 VOCs were identified through gas chromatography-mass spectrometry (GC-MS) analysis, and 22 VOCs were identified. Synthetic VOCs with the highest probability percentage, namely ethyloctynol, 3-methyl-2-pentanone (3M2P), 1,3-butadiene-N, N-dimethylformamide (DMF), and squalene were used in experiments. The results showed that the synthetic VOCs ethyloctynol and 3M2P were highly effective, with an inhibition rate of 56.8 and 57.1% against fungal mycelium radial growth at 120 μg/mL on agar plates. Trypan blue staining revealed strongly disrupted, deeper blue, and lysed mycelium in VOC-treated B. cinerea. The scanning and transmission electron microscope (SEM and TEM) results showed that fungal mycelium was smaller, irregular, and shrunken after synthetic VOC treatments. Furthermore, the synthetic VOCs Ethyloctynol and 3M2P revealed high control efficacy on tomatoes and strawberries infected by B. cinerea. The control efficacy on leaves was 67.2%, 66.1% and 64.5%, 78.4% respectively. Similarly, the control efficiency on fruits was 45.5%, 67.3% and 46.3% 65.1%. The expression of virulence genes in B. cinerea was analyzed, and the results revealed that selected genes BcSpl1, BcXyn11A, BcPG2, BcNoxB, BcNoxR, and BcPG1 were downregulated after VOCs treatment. The overall result revealed novel mechanisms by which Bacillus sp. volatiles control postharvest gray mold disease.

Identification of non-canonical antagonistic bacteria via interspecies contact-dependent killing

BACKGROUND

Canonical biocontrol bacteria were considered to inhibit pathogenic bacteria mainly by secreting antibiotic metabolites or enzymes. Recent studies revealed that some biocontrol bacteria can inhibit pathogenic bacteria through contact-dependent killing (CDK) mediated by contact-dependent secretion systems. The CDK was independent of antibiotic metabolites and often ignored in normal biocontrol activity assay.

RESULTS

In this study, we aimed to use a pathogen enrichment strategy to isolate non-canonical bacteria with CDK ability. Rhizosphere soil samples from Chinese cabbage showing soft rot symptom were collected and Pectobacterium carotovorum subsp. carotovorum (Pcc), the pathogen of cabbage soft rot, were added into these samples to enrich bacteria which attached on Pcc cells. By co-culture with Pcc, four bacteria strains (named as PcE1, PcE8, PcE12 and PcE13) showing antibacterial activity were isolated from Chinese cabbage rhizosphere. These four bacteria strains showed CDK abilities to different pathogenic bacteria of horticultural plants. Among them, PcE1 was identified as Chryseobacterium cucumeris. Genome sequencing showed that PcE1 genome encoded a type VI secretion system (T6SS) gene cluster. By heterologous expression, four predicted T6SS effectors of PcE1 showed antibacterial activity to Escherichia coli.

CONCLUSION

Overall, this study isolated four bacteria strains with CDK activity to various horticultural plant pathogens, and revealed possible involvement of T6SS of Chryseobacterium cucumeris in antibacterial activity. These results provide valuable insight for potential application of CDK activity in biocontrol bacteria. © 2024 Society of Chemical Industry.

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.

Antagonistic potential and biological control mechanisms of Pseudomonas strains against banded leaf and sheath blight disease of maize

Rhizoctonia solani, the causal agent of banded leaf and sheath blight (BL&SB), poses a significant threat to maize and various crops globally. The increasing concerns surrounding the environmental and health impacts of chemical fungicides have encouraged intensified concern in the development of biological control agents (BCAs) as eco-friendly alternatives. In this study, we explored the potential of 22 rhizobacteria strains (AS1-AS22) isolates, recovered from the grasslands of the Pithoragarh region in the Central Himalayas, as effective BCAs against BL&SB disease. Among these strains, two Pseudomonas isolates, AS19 and AS21, exhibited pronounced inhibition of fungal mycelium growth in vitro, with respective inhibition rates of 57.04% and 54.15% in cell cultures and 66.56% and 65.60% in cell-free culture filtrates. Additionally, both strains demonstrated effective suppression of sclerotium growth. The strains AS19 and AS21 were identified as Pseudomonas sp. by 16S rDNA phylogeny and deposited under accession numbers NAIMCC-B-02303 and NAIMCC-B-02304, respectively. Further investigations revealed the mechanisms of action of AS19 and AS21, demonstrating their ability to induce systemic resistance (ISR) and exhibit broad-spectrum antifungal activity against Alternaria triticina, Bipolaris sorokiniana, Rhizoctonia maydis, and Fusarium oxysporum f. sp. lentis. Pot trials demonstrated significant reductions in BL&SB disease incidence (DI) following foliar applications of AS19 and AS21, with reductions ranging from 25 to 38.33% compared to control treatments. Scanning electron microscopy revealed substantial degradation of fungal mycelium by the strains, accompanied by the production of hydrolytic enzymes. These findings suggest the potential of Pseudomonas strains AS19 and AS21 as promising BCAs against BL&SB and other fungal pathogens. However, further field trials are warranted to validate their efficacy under natural conditions and elucidate the specific bacterial metabolites responsible for inducing systemic resistance. This study contributes to the advancement of sustainable disease management strategies and emphasizes the potential of Pseudomonas strains AS19 and AS21 in combating BL&SB and other fungal diseases affecting agricultural crops.

Unleashing Bacillus species as versatile antagonists: Harnessing the biocontrol potentials of the plant growth-promoting rhizobacteria to combat Macrophomina phaseolina infection in Gloriosa superba

Charcoal rot caused by Macrophomina phaseolina is one of the most devastating diseases that cause severe yield loss in Gloriosa superba cultivation. Plant growth-promoting rhizobacteria (PGPR) are extensively harnessed as biocontrol agents due to their effectiveness in combating a wide array of plant pathogens through a multifaceted approach. The present study delved into the mechanisms underlying its ability to inhibit root rot pathogen and its capacity to promote plant growth in G. superba, commonly known as glory lily. PGPR isolated from the rhizosphere of glory lily were subjected to in vitro assessments using the dual plate technique. The isolated Bacillus subtilis BGS-10 and B. velezensis BGS-21 showed higher mycelial inhibition (61%) against M. phaseolina. These strains also promote plant growth by producing indole-3-acetic acid, siderophore, ammonia, amylase, cellulase, pectinase, xylanase, and lipase chemicals. Genome screening of BGS-10 and BGS-21 revealed the presence of antimicrobial peptide genes such as Iturin (ituD gene), surfactin (srfA and sfp genes) along with the mycolytic enzyme β-1,3-glucanase. Further, the presence of secondary metabolites in the bacterial secretome was identified through gas chromatography-mass spectrometry (GC/MS) analysis. Notably, pyrrolo[1,2-a] pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl), 9 H-pyrido[3,4-b] indole and L-leucyl-D-leucine exhibited the highest docking score against enzymes responsible for pathogen growth and plant cell wall degradation. Under glasshouse conditions, tuber treatment and soil application of talc-based formulation of B. subtilis BGS-10 and B. velezensis BGS-21 suppress the root rot incidence with a minimal disease incidence of 27.78% over untreated control. Concurrently, there was a notable induction of defense-related enzymes, including peroxidase (PO), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL), in glory lily. Therefore, it can be concluded that plant growth-promoting Bacillus strains play a significant role in fortifying the plant's defense mechanisms against the root rot pathogen.

Exploring Sustainable Agriculture with Nitrogen-Fixing Cyanobacteria and Nanotechnology

The symbiotic relationship between nitrogen-fixing cyanobacteria and plants offers a promising avenue for sustainable agricultural practices and environmental remediation. This review paper explores the molecular interactions between nitrogen-fixing cyanobacteria and nanoparticles, shedding light on their potential synergies in agricultural nanotechnology. Delving into the evolutionary history and specialized adaptations of cyanobacteria, this paper highlights their pivotal role in fixing atmospheric nitrogen, which is crucial for ecosystem productivity. The review discusses the unique characteristics of metal nanoparticles and their emerging applications in agriculture, including improved nutrient delivery, stress tolerance, and disease resistance. It delves into the complex mechanisms of nanoparticle entry into plant cells, intracellular transport, and localization, uncovering the impact on root-shoot translocation and systemic distribution. Furthermore, the paper elucidates cellular responses to nanoparticle exposure, emphasizing oxidative stress, signaling pathways, and enhanced nutrient uptake. The potential of metal nanoparticles as carriers of essential nutrients and their implications for nutrient-use efficiency and crop yield are also explored. Insights into the modulation of plant stress responses, disease resistance, and phytoremediation strategies demonstrate the multifaceted benefits of nanoparticles in agriculture. Current trends, prospects, and challenges in agricultural nanotechnology are discussed, underscoring the need for responsible and safe nanoparticle utilization. By harnessing the power of nitrogen-fixing cyanobacteria and leveraging the unique attributes of nanoparticles, this review paves the way for innovative, sustainable, and efficient agricultural practices.

MAPK Cascades in Plant Microbiota Structure and Functioning

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health

Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.

Screening of rhizobacteria for multi-trait plant growth-promoting ability and antagonism against B. fabae, the causative agent of chocolate spot disease of faba bean

This study aimed to isolate and characterize plant growth-promoting rhizobacteria from the faba bean rhizosphere for future inoculum production. For this purpose,127 dissimilar rhizobacterial colonies were isolated. All isolated colonies were tested for plant growth-promoting traits. Based on their multiple plant growth-promoting traits, eight potential isolates were selected and identified GY01, GY03, and GY08 are affiliated with Acinetobacter sp. GY04 and GY05 are affiliated with Chryseobacterium sp. GY06 and GY07 are affiliated with Pseudomonas costantinii and Pseudomonas chlororaphis, respectively; and GY02 is affiliated with the Bacterium strain. All eight isolates were evaluated for their effects on seed germination and vigor index and potential antagonism against Botrytis fabae. Selected isolates showed positive effects on seed germination and vigor index with different potentials. Isolate GY04 resulted in the highest vigor index (501), while isolate GY08 achieved the lowest (218). B. fabae radial growth inhibition was found in all eight isolates. The isolates inhibited the radial growth of the test pathogen with an inhibition efficacy of 72.38 % in GY04 to 25.57 % in GY-03. Generally, the results of this study indicated the potential of these isolates as a microbial inoculant with multiple functions for faba beans.

Photo-addressable microwell devices for rapid functional screening and isolation of pathogen inhibitors from bacterial strain libraries

Discovery of new strains of bacteria that inhibit pathogen growth can facilitate improvements in biocontrol and probiotic strategies. Traditional, plate-based co-culture approaches that probe microbial interactions can impede this discovery as these methods are inherently low-throughput, labor-intensive, and qualitative. We report a second-generation, photo-addressable microwell device, developed to iteratively screen interactions between candidate biocontrol agents existing in bacterial strain libraries and pathogens under increasing pathogen pressure. Microwells (0.6 pl volume) provide unique co-culture sites between library strains and pathogens at controlled cellular ratios. During sequential screening iterations, library strains are challenged against increasing numbers of pathogens to quantitatively identify microwells containing strains inhibiting the highest numbers of pathogens. Ring-patterned 365 nm light is then used to ablate a photodegradable hydrogel membrane and sequentially release inhibitory strains from the device for recovery. Pathogen inhibition with each recovered strain is validated, followed by whole genome sequencing. To demonstrate the rapid nature of this approach, the device was used to screen a 293-membered biovar 1 agrobacterial strain library for strains inhibitory to the plant pathogen Agrobacterium tumefaciens sp. 15955. One iterative screen revealed nine new inhibitory strains. For comparison, plate-based methods did not uncover any inhibitory strains from the library (n = 30 plates). The novel pathogen-challenge screening mode developed here enables rapid selection and recovery of strains that effectively suppress pathogen growth from bacterial strain libraries, expanding this microwell technology platform toward rapid, cost-effective, and scalable screening for probiotics, biocontrol agents, and inhibitory molecules that can protect against known or emerging pathogens.

Decolorization, degradation and detoxification of mutagenic dye Methyl orange by novel biofilm producing plant growth-promoting rhizobacteria

Discharge of untreated dyeing wastewater nearby water-bodies is one of major causes of water pollution. Generally, bacterial strains isolated from industrial effluents and/or contaminated soils are used for the bioremediation of Methyl orange (MO), a mutagenic recalcitrant mono-azo dye, used in textiles and biomedical. However, MO degradation by biofilm producing plant growth-promoting rhizobacteria (BPPGPR) was not studied yet. In this study, 19 out of 21 BPPGPR strains decolorized 96.3-99.9% and 89.5-96.3% MO under microaerophilic and aerobic conditions, respectively from Luria-Bertani broth (LBB) followed by yeast-extract peptone and salt-optimized broth plus glycerol media within 120 h of incubation at 28 °C. Only selected BPPGPR including Pseudomonas fluorescens ESR7, P. veronii ESR13, Stenotrophomonas maltophilia ESR20, Staphylococcus saprophyticus ESD8, and P. parafulva ESB18 were examined for process optimization of MO decolorization using a single factor optimization method. This study showed that under optimal conditions (e.g., LBB, 100 mg L-1 MO, pH 7, incubation of 96 h, 28 °C), these strains could remove 99.1-99.8% and 97.6-99.5% MO under microaerophilic and aerobic conditions, respectively. Total azoreductase and laccase activities responsible for biodegradation were also remarkably activated in the biodegraded samples under optimal conditions, while these activities were repressed under unfavorable conditions (e.g., 40 °C and 7.5% NaCl). This study confirmed that MO was degraded and detoxified by these bacterial strains through breakage of azo bond. So far, this is the first report on bioremediation of MO by the BPPGPR strains. These BPPGPR strains are highly promising to be utilized for the bioremediation of dyeing wastewater in future.

Taxonomical, functional, and cytopathological characterization of Bacillus spp. from Lake Magadi, Kenya, against Rhizoctonia solani Kühn in Phaseolus vulgaris L

A decline in common bean production and the ineffectiveness of synthetic chemical products in managing plant pathogens has led to exploiting Kenyan soda lakes as an alternative search for biocontrol agents. This study aimed to identify phylogenetically Bacillus spp. from Lake Magadi and their antagonistic activity against Rhizoctonia solani under in vitro and in vivo conditions. The 16 S ribosomal RNA (rRNA) subunit sequences of six bacterial strains isolated from Lake Magadi showed diversity similar to the Bacillus genus; Bacillus velezensis, Bacillus subtilis, and Bacillus pumilus. In vitro, antagonism showed varied mycelium inhibition rates of fungi in the coculture method. Enzymatic assays showed the varied ability of isolates to produce phosphatase, pectinase, chitinase, protease, indole-3-acetic acid (IAA), and hydrogen cyanide (HCD). The in vivo assay showed M09 (B. velezensis) with the lowest root mortality and incidence of postemergence wilt. Pre-emergence wilt incidence was recorded as lowest in M10 (B. subtilis). Isolate M10 had the highest phenylalanine ammonia-lyase (PAL) for defense enzymes, while polyphenol oxidase (PPO) and peroxidase were recorded as highest in M09. For the phenolic content, M10 recorded the highest phenolic content. In conclusion, Lake Magadi harbors Bacillus spp, which can be used as a potential biocontrol of R. solani.

An Innovative Approach for Biocontrol of Meloidogyne incognita in Ginger Using Potential Bacteria Isolated from Indian Himalayas

The prevalence of Meloidogyne incognita, a severe root-knot nematode, is alarmingly high in the production of ginger-a main cash crop of Himachal Pradesh, a Himalayan state of India. In order to control this through natural means, the nematicidal potential of plant growth-promoting rhizobacteria (PGPR) against M. incognita was analyzed. This is an effective alternative solution to manage nematode incidence as compared to hazardous chemicals under protected and field cultivation of ginger. In the present study an attempt has been made to isolate, characterize, and identify potential rhizobacteria associated with ginger rhizosphere and endosphere. In total, 169 bacterial isolates were isolated from ginger (Zingiber officinale) rhizosphere and endosphere of 4 different sites of Sirmaur district, screened out for multifarious PGP traits showing positive results. The combined cluster analysis and 16S rRNA genotypic analysis of selected bacterial isolates revealed that Serratia marcescens FS-23, Pseudochrobacter sp. GS-15, Stonotrophomonas pavanii HER-9, Pseudomonas brassicacearum HER-20 and Serratia marcescens IS-2 exhibited highest PGP traits. All tested bacterial isolates were capable of exerting a significant effect on mortality of juvenile M. incognita ranging upto 40-90% in laboratory experiments. Further a consortium of these screened isolates showed 86.67% reduction in gall formation by M. incognita in lab conditions. The remarkable increase to 93.24% with 138.73 q/ha with application of charcoal based bio-formulation of consortium without adding any chemical fertilizer was observed in field trials of Nohradhar of Sirmaur district. An alternative choice as a biocontrol agent as well as for PGP activities, the novel and most robust isolate Serratia marcescens IS-2 had revealed to have a variety of bioactive metabolic products with abilities against nematodes, bacteria, and fungi.

Differential plant cell responses to Acidovorax citrulli T3SS and T6SS reveal an effective strategy for controlling plant-associated pathogens

Acidovorax citrulli is a gram-negative plant pathogen that employs the type Ⅲ secretion system (T3SS) to infect cucurbit crops and cause bacterial fruit blotch. This bacterium also possesses an active type Ⅵ secretion system (T6SS) with strong antibacterial and antifungal activities. However, how plant cells respond to these two secretion systems and whether there is any cross talk between T3SS and T6SS during infection remain unknown. Here, we employ transcriptomic analysis to compare cellular responses to the T3SS and the T6SS during in planta infection and report distinctive effects on multiple pathways. The T3SS-mediated differentially expressed genes were enriched in the pathways of phenylpropanoid biosynthesis, plant-pathogen interaction, MAPK signaling pathway, and glutathione metabolism, while the T6SS uniquely affected genes were related to photosynthesis. The T6SS does not contribute to the in planta virulence of A. citrulli but is critical for the survival of the bacterium when mixed with watermelon phyllosphere bacteria. In addition, T3SS-mediated virulence is independent of the T6SS, and the inactivation of the T3SS does not affect the T6SS-mediated competition against a diverse set of bacterial pathogens that commonly contaminate edible plants or directly infect plants. A T6SS-active T3SS-null mutant (Acav) could inhibit the growth of Xanthomonas oryzae pv. oryzae significantly both in vitro and in vivo and also reduce symptoms of rice bacterial blight. In conclusion, our data demonstrate the T6SS in A. citrulli is nonpathogenic to the plant host and can be harnessed as a pathogen killer against plant-associated bacteria. IMPORTANCE Chemical pesticides are widely used to protect crops from various pathogens. Still, their extensive use has led to severe consequences, including drug resistance and environmental contamination. Here, we show that an engineered T6SS-active, but avirulent mutant of Acidovorax citrulli has strong inhibition capabilities against several pathogenic bacteria, demonstrating an effective strategy that is an alternative to chemical pesticides for sustainable agricultural practices.

Genome Resource of Streptomyces atratus PY-1, a Broad-Spectrum Antimicrobial Strain in Particular Antagonistic Against Plasmopara viticola

Streptomyces atratus PY-1 exhibited promising antimicrobial properties; in particular, it is highly inhibitory to Plasmopara viticola, which causes downy mildew of grape. It is very necessary to carry out systematic and in-depth research on the PY-1 strain for the improvement, application, and promotion of biocontrol agents. The PY-1 genome was fully sequenced and assembled. We present the draft genome sequence of PY-1, with a size of 9, 254, and 781 bp. Preliminary analysis on the PY-1 genome sequence shows that at least 35 gene clusters are involved in the biosynthesis of polyketides, terpenes, and nonribosomally synthesized peptides.

Acinetobacter oleivorans IRS14 alleviates cold stress in wheat by regulating physiological and biochemical factors

AIMS

Climate change is responsible for extreme cold winters, causing a significant loss in crop yield and productivity due to chilling stress. This study aims to investigate the potential of psychrotrophic plant growth-promoting rhizobacteria (PGPR) strain to promote wheat growth under cold stress and explore the adaptive responses of wheat.

METHODS AND RESULTS

Wheat seeds and seedlings were inoculated with the psychrotrophic strain IRS14 and the plants were cultivated for five weeks at 6°C ± 2°C. The genetic, biochemical, physiological, and molecular analysis of the bacterium and plant was done to evaluate the effect of the PGPR strain in alleviating chilling stress. IRS14 possesses antioxidant activity and produced multiple phytohormones, which enhanced seed germination (∼50%) and plant growth (∼50%) during chilling stress.

CONCLUSIONS

Here, we reported that the application of IRS14 helps to regulate the biochemical and metabolic pathways in wheat plants. It alleviates chilling stress and increases plant growth rate and biomass. Strain IRS14 in wheat effectively increased chlorophyll content, antioxidants, carotenoid, proline, and endogenous phytohormones compared with untreated wheat.

MarR Family Transcriptional Regulators and Their Roles in Plant-Interacting Bacteria

The relationship between plants and associated soil microorganisms plays a major role in ecosystem functioning. Plant-bacteria interactions involve complex signaling pathways regulating various processes required by bacteria to adapt to their fluctuating environment. The establishment and maintenance of these interactions rely on the ability of the bacteria to sense and respond to biotic and abiotic environmental signals. In this context, MarR family transcriptional regulators can use these signals for transcriptional regulation, which is required to establish adapted responses. MarR-like transcriptional regulators are essential for the regulation of the specialized functions involved in plant-bacteria interactions in response to a wide range of molecules associated with the plant host. The conversion of environmental signals into changes in bacterial physiology and behavior allows the bacteria to colonize the plant and ensure a successful interaction. This review focuses on the mechanisms of plant-signal perception by MarR-like regulators, namely how they (i) allow bacteria to cope with the rhizosphere and plant endosphere, (ii) regulate the beneficial functions of Plant-Growth-Promoting Bacteria and (iii) regulate the virulence of phytopathogenic bacteria.

The utilization of microbes for sustainable food production

As the global human population continues to grow, the demand for food rises accordingly. Unfortunately, anthropogenic activities, climate change, and the release of gases from the utilization of synthetic fertilizers and pesticides are causing detrimental effects on sustainable food production and agroecosystems. Despite these challenges, there remain underutilized opportunities for sustainable food production. This review discusses the advantages and benefits of utilizing microbes in food production. Microbes can be used as alternative food sources to directly supply nutrients for both humans and livestock. Additionally, microbes offer higher flexibility and diversity in facilitating crop productivity and agri-food production. Microbes function as natural nitrogen fixators, mineral solubilizers, nano-mineral synthesizers, and plant growth regulator inducers, all of which promote plant growth. They are also active organisms in degrading organic materials and remediating heavy metals and pollution in soils, as well as soil-water binders. In addition, microbes that occupy the plant rhizosphere release biochemicals that have nontoxic effects on the host and the environment. These biochemicals could act as biocides in controlling agricultural pests, pathogens, and diseases. Therefore, it is important to consider the use of microbes for sustainable food production.

Mechanisms associated with the synergistic induction of resistance to tobacco black shank in tobacco by arbuscular mycorrhizal fungi and β-aminobutyric acid

Tobacco black shank (TBS), caused by Phytophthora nicotianae, is one of the most harmful diseases of tobacco. There are many studies have examined the mechanism underlying the induction of disease resistance by arbuscular mycorrhizal fungi (AMF) and β-aminobutyric acid (BABA) alone, but the synergistic effects of AMF and BABA on disease resistance have not yet been studied. This study examined the synergistic effects of BABA application and AMF inoculation on the immune response to TBS in tobacco. The results showed that spraying BABA on leaves could increase the colonization rate of AMF, the disease index of tobacco infected by P.nicotianae treated with AMF and BABA was lower than that of P.nicotianae alone. The control effect of AMF and BABA on tobacco infected by P.nicotianae was higher than that of AMF or BABA and P.nicotianae alone. Joint application of AMF and BABA significantly increased the content of N, P, and K in the leaves and roots, in the joint AMF and BABA treatment than in the sole P. nicotianae treatment. The dry weight of plants treated with AMF and BABA was 22.3% higher than that treated with P.nicotianae alone. In comparison to P. nicotianae alone, the combination treatment with AMF and BABA had increased Pn, Gs, Tr, and root activity, while P. nicotianae alone had reduced Ci, H₂O₂ content, and MDA levels. SOD, POD, CAT, APX, and Ph activity and expression levels were increased under the combined treatment of AMF and BABA than in P.nicotianae alone. In comparison to the treatment of P.nicotianae alone, the combined use of AMF and BABA increased the accumulation of GSH, proline, total phenols, and flavonoids. Therefore, the joint application of AMF and BABA can enhance the TBS resistance of tobacco plants to a greater degree than the application of either AMF or BABA alone. In summary, the application of defense-related amino acids, combined with inoculation with AMF, significantly promoted immune responses in tobacco. Our findings provide new insights that will aid the development and use of green disease control agents.

Screening microbial inoculants and their interventions for cross-kingdom management of wilt disease of solanaceous crops- a step toward sustainable agriculture

Microbial inoculants may be called magical bullets because they are small in size but have a huge impact on plant life and humans. The screening of these beneficial microbes will give us an evergreen technology to manage harmful diseases of cross-kingdom crops. The production of these crops is reducing as a result of multiple biotic factors and among them the bacterial wilt disease triggered by Ralstonia solanacearum is the most important in solanaceous crops. The examination of the diversity of bioinoculants has shown that more microbial species have biocontrol activity against soil-borne pathogens. Reduced crop output, lower yields, and greater cost of cultivation are among the major issues caused by diseases in agriculture around the world. It is universally true that soil-borne disease epidemics pose a greater threat to crops. These necessitate the use of eco-friendly microbial bioinoculants. This review article provides an overview of plant growth-promoting microorganisms bioinoculants, their various characteristics, biochemical and molecular screening insights, and modes of action and interaction. The discussion is concluded with a brief overview of potential future possibilities for the sustainable development of agriculture. This review will be useful for students and researchers to obtain existing knowledge of microbial inoculants, their activities, and their mechanisms, which will facilitate the development of environmentally friendly management strategies for cross-kingdom plant diseases.

Copper and iron metal resistant rhizospheric bacteria boost the plant growth and bacoside A content in Bacopa monnieri under stress conditions

Bacteria that enhance plant growth and development and are found in the vicinity of roots are referred to as plant growth-promoting rhizobacteria. Some beneficial bacteria help plant tolerance to many hazardous chemical elements. In this context, Cupriavidus basilensis , Novosphingobium humi , Bacillus zanthoxyli , Bacillus sp., Paenibacillus alvei , Ancylobacter aquaticus and Ralstonia syzygii metal-tolerant rhizospheric bacteria were isolated from rhizospheric soil associated with Bacopa monnieri . The beneficial effects of rhizospheric bacteria on B. monnieri plant physiology and biochemical responses were investigated under pot conditions at two levels (100μM and 500μM) of CuSO4 or FeCl3 . N. humi , A. aquaticus and R. syzygii bacterial strains were associated with significantly increased height and biomass under normal and stress conditions. An assay for indole acetic acid in isolated rhizospheric bacteria found differential secretion except Bacillus zanthoxyli . Bacoside A is a major phytocompound in B. monnieri with medicinal value; maximum induction was observed in the R. syzygii treatment. High concentration of copper and iron salts negatively influenced height, biomass and photosynthetic pigments; however N. humi , A. aquaticus , Bacilllus sp. and R. syzygii beneficial bacterial helped plants under stress conditions. Moreover, a significant enhancement in chlorophyll a and b was noticed in C. basilensis , B. zanthoxyli , Bacilllus sp., P. alvei and R. syzygii treatments, without much influence on carotenoid levels. Therefore, the present study emphasises the importance of isolating plant growth-promoting rhizobacteria for use in bacopa plants exposed to metals such as copper and iron in soil.

Regenerative agriculture augments bacterial community structure for a healthier soil and agriculture

Introduction

Use of chemical fertilization and pesticides not only harm the environment but also have detrimental consequences on human health. In recent years, there has been a major emphasis worldwide on natural agriculture methods. Regenerative agriculture is known across the world as a combination of nature-friendly farming practices such as no-till, cover cropping, crop-rotation, agroforestry and use of organic home-based/farm-based ingredients to revive soil health. In India, a number of farmers are slowly adopting these practices using home-based mixtures and farmyard manure for soil rejuvenation and pest management. In order to evaluate the efficacy of the regenerative agriculture practices, this study compared conventional and regenerative agriculture plots for their soil bacterial and nutrient profiles.

Methods

Two crops - ragi (Finger millet, an old world cereal eaten in India) and vegetable (tomato/beans), and different lengths (≤3 and >5 years) of regenerative practices were additional metrics considered to understand variabilities due to crop-type and period of application. The common regenerative agriculture practices used by farmers in this study included a mix of practices such as mulching, minimal-till, inter-cropping, crop-rotation, along with application of farmyard manure and other home-based concoctions rich in nutrients and microbes for enriching the soil.

Results

We found that all regenerative practices were effective in bringing about an enrichment for soil bacteria with a more heterogeneous composition. Additionally, in regenerative vegetable (RV) versus conventional vegetable (CV) and barren land (BL) plots the relative percentage abundance of Actinobacteriota (RV-7.47%/ CV-6.24%/BL -7.02%) and Chloroflexi (RV-9.37%/ CV-6.63%/BL-8.75%) was slightly higher. In contrast, levels of Acidobacteriota (RV-8.1%/ CV-9.88%/BL-9.62%) was significantly lower. Similarly, regenerative ragi (RR) in comparison with conventional ragi (CR) and barren land (BL) plots saw higher representation of Firmicutes (RR-5.45%/ CR-2.38%/BL-1.45%) and Actinobacteriota (RR-11.53%/ CR-7.08%/BL-7.15%) and a concurrent reduction in Acidobacteriota (RR-6.91%/CR-7.39%/ BL-9.79%). The RV plots were found to be enriched for Plant Growth Promoting Rhizobacteria (PGPRs) - Pseudomonas sp. (RV-0.51%/CV-0.01%/BL-0.21%), and RR plots were enriched for Bacillus sp. (RR-1.35%/CR-0.95%/BL-0.61%), and Mesorhizobium sp. (0.30%/0.12%/0.21%), which are known to play significant roles in vegetable and ragi growth respectively.

Discussion

Interestingly, long-term regenerative agriculture was able to support good nutrient composition while enhancing Soil Organic Carbon (SOC) levels. In all, the regenerative agriculture practices were found to be effective in improving bacterial community structure and simultaneously improving soil health. We found that BL soil with eucalyptus plantation showed among the least bacterial diversity suggesting detrimental impact on soil health.

Rhizobacteria control damping-off and promote growth of lima bean with and without co-inoculation with Rhizobium tropici CIAT899

Rhizoctonia solani compromises the production of lima bean, an alternative and low-input food source in many tropical regions. Inoculation of bacterial strains has been used, but research on their biocontrol and growth promotion potential on lima bean is scarce. The objective of this study was to evaluate the effects of inoculation with rhizobacterial strains of the genera Bacillus, Brevibacillus, Paenibacillus, Burkholderia, Pseudomonas, and Rhizobium in combination or not with N₂-fixing Rhizobium tropici on the control of damping-off disease and growth promotion in lima bean plants. Greenhouse experiments were conducted to evaluate the inoculation with bacterial strains with biocontrol potential in combination or not with R. tropici in substrate infected with R. solani CML 1846. Growth promotion of these strains was also assessed. Strains of Brevibacillus (UFLA 02-286), Pseudomonas (UFLA 02-281 and UFLA 04-885), Rhizobium (UFLA 04-195), and Burkholderia (UFLA 04-227) co-inoculated with the strain CIAT 899 (Rhizobium tropici) were the most effective in controlling R. solani, reducing the disease incidence in 47-60% on lima bean. The promising strains used in the biocontrol assays were also responsive in promoting growth of lima bean under disease and sterile conditions. A positive synergistic effect of co-inoculation of different genera contributed to plant growth, and these outcomes are important first steps to improve lima bean production.

Screening for Multifarious Plant Growth Promoting and Biocontrol Attributes in Bacillus Strains Isolated from Indo Gangetic Soil for Enhancing Growth of Rice Crops

Multifarious plant growth-promoting Bacillus strains recovered from rhizospheric soils of the Indo Gangetic plains (IGPs) were identified as Bacillus licheniformis MNNITSR2 and Bacillus velezensis MNNITSR18 based on their biochemical characteristics and 16S rDNA gene analysis. Both strains exhibited the ability to produce IAA, siderophores, ammonia, lytic enzymes, HCN production, and phosphate solubilization capability and strongly inhibited the growth of phytopathogens such as Rhizoctonia solani and Fusariun oxysporum in vitro. In addition, these strains are also able to grow at a high temperature of 50 °C and tolerate up to 10-15% NaCl and 25% PEG 6000. The results of the pot experiment showed that individual seed inoculation and the coinoculation of multifarious plant growth promoting (PGP) Bacillus strains (SR2 and SR18) in rice fields significantly enhanced plant height, root length volume, tiller numbers, dry weight, and yield compared to the untreated control. This indicates that these strains are potential candidates for use as PGP inoculants/biofertilizers to increase rice productivity under field conditions for IGPs in Uttar Pradesh, India.

A Culturomics-Based Bacterial Synthetic Community for Improving Resilience towards Arsenic and Heavy Metals in the Nutraceutical Plant Mesembryanthemum crystallinum

Plant-growth-promoting bacteria (PGPB) help plants thrive in polluted environments and increase crops yield using fewer inputs. Therefore, the design of tailored biofertilizers is of the utmost importance. The purpose of this work was to test two different bacterial synthetic communities (SynComs) from the microbiome of Mesembryanthemum crystallinum, a moderate halophyte with cosmetic, pharmaceutical, and nutraceutical applications. The SynComs were composed of specific metal-resistant plant-growth-promoting rhizobacteria and endophytes. In addition, the possibility of modulating the accumulation of nutraceutical substances by the synergetic effect of metal stress and inoculation with selected bacteria was tested. One of the SynComs was isolated on standard tryptone soy agar (TSA), whereas the other was isolated following a culturomics approach. For that, a culture medium based on M. crystallinum biomass, called Mesem Agar (MA), was elaborated. Bacteria of three compartments (rhizosphere soil, root endophytes, and shoot endophytes) were isolated on standard TSA and MA media, stablishing two independent collections. All bacteria were tested for PGP properties, secreted enzymatic activities, and resistance towards As, Cd, Cu, and Zn. The three best bacteria from each collection were selected in order to produce two different consortiums (denominated TSA- and MA-SynComs, respectively), whose effect on plant growth and physiology, metal accumulation, and metabolomics was evaluated. Both SynComs, particularly MA, improved plant growth and physiological parameters under stress by a mixture of As, Cd, Cu, and Zn. Regarding metal accumulation, the concentrations of all metals/metalloids in plant tissues were below the threshold for plant metal toxicity, indicating that this plant is able to thrive in polluted soils when assisted by metal/metalloid-resistant SynComs and could be safely used for pharmaceutical purposes. Initial metabolomics analyses depict changes in plant metabolome upon exposure to metal stress and inoculation, suggesting the possibility of modulating the concentration of high-value metabolites. In addition, the usefulness of both SynComs was tested in a crop plant, namely Medicago sativa (alfalfa). The results demonstrate the effectiveness of these biofertilizers in alfalfa, improving plant growth, physiology, and metal accumulation.

The microbiome of cereal plants: The current state of knowledge and the potential for future applications

The plant microbiota fulfils various crucial functions related to host health, fitness, and productivity. Over the past years, the number of plant microbiome studies continued to steadily increase. Technological advancements not only allow us to produce constantly increasing datasets, but also to extract more information from them in order to advance our understanding of plant-microbe interactions. The growing knowledge base has an enormous potential to improve microbiome-based, sustainable agricultural practices, which are currently poorly understood and have yet to be further developed. Cereal plants are staple foods for a large proportion of the world's population and are therefore often implemented in microbiome studies. In the present review, we conducted extensive literature research to reflect the current state of knowledge in terms of the microbiome of the four most commonly cultivated cereal plants. We found that currently the majority of available studies are targeting the wheat microbiome, which is closely followed by studies on maize and rice. There is a substantial gap, in terms of published studies, addressing the barley microbiome. Overall, the focus of most microbiome studies on cereal plants is on the below-ground microbial communities, and there is more research on bacteria than on fungi and archaea. A meta-analysis conducted in the frame of this review highlights microbiome similarities across different cereal plants. Our review also provides an outlook on how the plant microbiota could be harnessed to improve sustainability of cereal crop production.

Cell-free supernatant of Devosia sp. (strain SL43) mitigates the adverse effects of salt stress on soybean (Glycine max L.) seed vigor index

Soil salinity is a major constraint for soybean production worldwide, and the exploitation of plant growth-promoting bacteria (PGPB) and their bioactive metabolite(s) can improve plant salinity tolerance. With this objective, two experiments were performed, aiming to test 4 culture media (YEM(A), TYE(A), TS(A), and LB(A)) for growing a novel Devosia sp. (strain SL43), and then evaluating cell-free supernatants (CFS) from the Devosia sp. on germination of soybean (Glycine max L.) seeds under salinity stress. Soybean seeds were subjected to three salinity levels (0, 100, and 125 mM NaCl) and 6 levels of Devosia sp. CFS dilution (0, 1:1, 1:100, 1:250, 1:500, 1:1000). The results indicated that 125 mM NaCl concentration caused the greatest reduction in the total number of germinated seeds (15%), germination rate (43.6%), root length (55.2%), root weight (39.3%), and seed vigor (68%), and it also increased mean germination time by 71.9%. However, Devosia-CFS improved soybean germination, and the greatest effect was obtained at 1:1 dilution. Under the highest salinity level, application of CFS at 1:1 dilution increased final germination (17.6%), germination rate (18.6%), root length (162.2%), root weight (239.4%), seed vigor index (318.7%), and also shortening mean germination time by 19.2%. The results indicated that seed vigor index was positively correlated with other traits except for mean germination time. Our study suggested that the highest productivity of Devoisa sp. was obtained from the YEM medium. Results also suggested that CFS produced by the novel Devosia sp. (SL43 strain) can successfully alleviate salt stress effects on soybean seed germination and manipulating the chemical composition of the growth medium can influence the effectiveness of these bioactive metabolites.

Genotyping-driven diversity assessment of biocontrol potent Bacillus spp. strain collection as a potential method for the development of strain-specific biomarkers

Bacillus species are among the most researched and frequently applied biocontrol agents. To estimate their potential as environmentally friendly microbial-based products, reliable and rapid plant colonization monitoring methods are essential. We evaluated repetitive element-based (rep) and Random Amplified Polymorphic DNA (RAPD) PCR (Polymerase Chain Reaction) genotyping in a diversity assessment of 251 strains from bulk soil, straw, and manure samples across Serbia, highlighting their discriminative force and the presence of unique bands. RAPD 272, OPG 5, and (GTG)₅ primers were most potent in revealing the high diversity of a sizable environmental Bacillus spp. collection. RAPD 272 also amplified a unique band for a proven biocontrol strain, opening the possibility of Sequence Characterized Amplified Region (SCAR) marker design. That will enable colonization studies using the SCAR marker for its specific detection. This study provides a guide for primer selection for diversity and monitoring studies of environmental Bacillus spp. isolates.

Suppression of Fusarium Wilt in Watermelon by Bacillus amyloliquefaciens DHA55 through Extracellular Production of Antifungal Lipopeptides

Fusarium wilt caused by Fusarium oxysporum f. sp. niveum is one of the most devastating fungal diseases affecting watermelon (Citrullus lanatus L.). The present study aimed to identify potent antagonistic bacterial strains with substantial antifungal activity against F. oxysporum f. sp. niveum and to explore their potential for biocontrol of Fusarium wilt in watermelon. Out of 77 isolates from watermelon rhizosphere, six bacterial strains—namely, DHA4, DHA6, DHA10, DHA12, DHA41, and DHA55—exhibited significant antifungal activity against F. oxysporum f. sp. niveum, as well as other phytopathogenic fungi, including Didymella bryoniae, Sclerotinia sclerotiorum, Fusarium graminearum, and Rhizoctonia solani. These Gram-positive, rod-shaped, antagonistic bacterial strains were able to produce exo-enzymes (e.g., catalase, protease, and cellulase), siderophore, and indole-3-acetic acid and had the ability to solubilize phosphate. In greenhouse experiments, these antagonistic bacterial strains not only promoted plant growth but also suppressed Fusarium wilt in watermelon. Among these strains, DHA55 was the most effective, achieving the highest disease suppression of 74.9%. Strain DHA55 was identified as Bacillus amyloliquefaciens based on physiological, biochemical, and molecular characterization. B. amyloliquefaciens DHA55 produced various antifungal lipopeptides, including iturin, surfactin, and fengycin, that showed significant antifungal activities against F. oxysporum f. sp. niveum. Microscopic observations revealed that B. amyloliquefaciens DHA55 exhibited an inhibitory effect against F. oxysporum f. sp. niveum on the root surface of watermelon plants. These results demonstrate that B. amyloliquefaciens DHA55 can effectively promote plant growth and suppress the development of watermelon Fusarium wilt, providing a promising agent for the biocontrol of Fusarium wilt in watermelon.

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.

The Pythium periplocum elicitin PpEli2 confers broad-spectrum disease resistance by triggering a novel receptor-dependent immune pathway in plants

Elicitins are microbe-associated molecular patterns produced by oomycetes to elicit plant defense. It is still unclear whether elicitins derived from non-pathogenic oomycetes can be used as bioactive molecules for disease control. Here, for the first time we identify and characterize an elicitin named PpEli2 from the soil-borne oomycete Pythium periplocum, which is a non-pathogenic mycoparasite colonizing the root ecosystem of diverse plant species. Perceived by a novel cell surface receptor-like protein, REli, that is conserved in various plants (e.g. tomato, pepper, soybean), PpEli2 can induce hypersensitive response cell death and an immunity response in Nicotiana benthamiana. Meanwhile, PpEli2 enhances the interaction between REli and its co-receptor BAK1. The receptor-dependent immune response triggered by PpEli2 is able to protect various plant species against Phytophthora and fungal infections. Collectively, our work reveals the potential agricultural application of non-pathogenic elicitins and their receptors in conferring broad-spectrum resistance for plant protection.

Biocontrol and plant growth promoting traits of two avocado rhizobacteria are orchestrated by the emission of diffusible and volatile compounds

Avocado (Persea americana Mill.) is a tree crop of great social and economic importance. However, the crop productivity is hindered by fast-spreading diseases, which calls for the search of new biocontrol alternatives to mitigate the impact of avocado phytopathogens. Our objectives were to evaluate the antimicrobial activity of diffusible and volatile organic compounds (VOCs) produced by two avocado rhizobacteria (Bacillus A8a and HA) against phytopathogens Fusarium solani, Fusarium kuroshium, and Phytophthora cinnamomi, and assess their plant growth promoting effect in Arabidopsis thaliana. We found that, in vitro, VOCs emitted by both bacterial strains inhibited mycelial growth of the tested pathogens by at least 20%. Identification of bacterial VOCs by gas chromatography coupled to mass spectrometry (GC-MS) showed a predominance of ketones, alcohols and nitrogenous compounds, previously reported for their antimicrobial activity. Bacterial organic extracts obtained with ethyl acetate significantly reduced mycelial growth of F. solani, F. kuroshium, and P. cinnamomi, the highest inhibition being displayed by those from strain A8a (32, 77, and 100% inhibition, respectively). Tentative identifications carried out by liquid chromatography coupled to accurate mass spectrometry of diffusible metabolites in the bacterial extracts, evidenced the presence of some polyketides such as macrolactins and difficidin, hybrid peptides including bacillaene, and non-ribosomal peptides such as bacilysin, which have also been described in Bacillus spp. for antimicrobial activities. The plant growth regulator indole-3-acetic acid was also identified in the bacterial extracts. In vitro assays showed that VOCs from strain HA and diffusible compounds from strain A8a modified root development and increased fresh weight of A. thaliana. These compounds differentially activated several hormonal signaling pathways involved in development and defense responses in A. thaliana, such as auxin, jasmonic acid (JA) and salicylic acid (SA); genetic analyses suggested that developmental stimulation of the root system architecture by strain A8a was mediated by the auxin signaling pathway. Furthermore, both strains were able to enhance plant growth and decreased the symptoms of Fusarium wilt in A. thaliana when soil-inoculated. Collectively, our results evidence the potential of these two rhizobacterial strains and their metabolites as biocontrol agents of avocado pathogens and as biofertilizers.

SCAR marker: A potential tool for authentication of agriculturally important microorganisms

Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.

Plant growth promoting bacteria drive food security

The essence of food security centers on ensuring availability and accessibility of foods in adequate amounts and quality for all populations at all times for an active and healthy life. Microorganisms are tiny bioreactors, which represent sustainable resources and promising approaches to bridging the gap between food production and consumption globally via various biotechnological applications. This review focuses on plant-growth promoting bacteria (PGPB) which exert their potential impacts on increasing soil fertility, plant growth, and productivity through a variety of processes, including direct, indirect, and synergistic mechanisms. PGPB plays a substantial role in accelerating nutrients' availability such as (N, P), producing phytohormones such as gibberellins, IAA, and bioactive compounds against biotic and abiotic stressors. Recent advances in PGPB will be addressed as a sustainable approach to satisfy global food demand.

Sustainable strategies for management of the "false root-knot nematode" Nacobbus spp

The genus Nacobbus, known as the false root-knot nematode, is native to the American continent and comprises polyphagous species adapted to a wide range of climatic conditions. Alone or in combination with other biotic and abiotic factors, Nacobbus spp. can cause significant economic yield losses on main food crops such as potato, sugar beet, tomato, pepper and bean, in South and North America. Although the genus distribution is restricted to the American continent, it has quarantine importance and is subject to international legislation to prevent its spread to other regions, such as the European Union. The management of Nacobbus spp. remains unsatisfactory due to the lack of information related to different aspects of its life cycle, survival stages in the soil and in plant material, a rapid and reliable diagnostic method for its detection and the insufficient source of resistant plant genotypes. Due to the high toxicity of chemical nematicides, the search for alternatives has been intensified. Therefore, this review reports findings on the application of environmentally benign treatments to manage Nacobbus spp. Biological control strategies, such as the use of different organisms (mainly bacteria, fungi and entomopathogenic nematodes) and other eco-compatible approaches (such as metabolites, essential oils, plant extracts, phytohormones and amendments), either alone or as part of a combined control strategy, are discussed. Knowledge of potential sources of resistance for genetic improvement for crops susceptible to Nacobbus spp. are also reported. The sustainable strategies outlined here offer immediate benefits, not only to counter the pathogen, but also as good alternatives to improve crop health and growth.

Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum

Introduction

Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

Methods

In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

Results

The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

Discussion

This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.

Application of Bacterial Endophytes to Control Bacterial Leaf Blight Disease and Promote Rice Growth

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight (BLB) disease in rice (Oryza sativa L.) and it is among the most destructive pathogen responsible for severe yield losses. Potential bacterial biocontrol agents (BCAs) with plant growth promotion (PGP) abilities can be applied to better manage the BLB disease and increase crop yield, compared to current conventional practices. Thus, this study aimed to isolate, screen, and identify potential BCAs with PGP abilities. Isolation of the BCAs was performed from internal plant tissues and rhizosphere soil of healthy and Xoo-infected rice. A total of 18 bacterial strains were successfully screened for in vitro antagonistic ability against Xoo, siderophore production and PGP potentials. Among the bacterial strains, 3 endophytes, Bacillus sp. strain USML8, Bacillus sp. strain USML9, and Bacillus sp. strain USMR1 which were isolated from diseased plants harbored the BCA traits and significantly reduced leaf blight severity of rice. Simultaneously, the endophytic BCAs also possessed plant growth promoting traits and were able to enhance rice growth. Application of the selected endophytes (BCAs-PGP) at the early growth stage of rice exhibited potential in suppressing BLB disease and promoting rice growth.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Contrasting genome patterns of two pseudomonas strains isolated from the date palm rhizosphere to assess survival in a hot arid environment

The plant growth-promoting rhizobacteria (PGPRs) improve plant growth and fitness by multiple direct (nitrogen fixation and phosphate solubilization) and indirect (inducing systematic resistance against phytopathogens, soil nutrient stabilization, and maintenance) mechanisms. Nevertheless, the mechanisms by which PGPRs promote plant growth in hot and arid environments remain poorly recorded. In this study, a comparative genome analysis of two phosphate solubilizing bacteria, Pseudomonas atacamensis SM1 and Pseudomonas toyotomiensis SM2, isolated from the rhizosphere of date palm was performed. The abundance of genes conferring stress tolerance (chaperones, heat shock genes, and chemotaxis) and supporting plant growth (plant growth hormone, root colonization, nitrogen fixation, and phosphate solubilization) were compared among the two isolates. This study further evaluated their functions, metabolic pathways, and evolutionary relationship. Results show that both bacterial strains have gene clusters required for plant growth promotion (phosphate solubilization and root colonization), but it is more abundant in P. atacamensis SM1 than in P. toyotomiensis SM2. Genes involved in stress tolerance (mcp, rbs, wsp, and mot), heat shock, and chaperones (hslJ and hslR) were also more common in P. atacamensis SM1. These findings suggest that P. atacamensis SM1could have better adaptability to the hot and arid environment owing to a higher abundance of chaperone genes and heat shock proteins. It may promote plant growth owing to a higher load of root colonization and phosphate solubilization genes and warrants further in vitro study.

The Improved Biocontrol Agent, F1-35, Protects Watermelon against Fusarium Wilt by Triggering Jasmonic Acid and Ethylene Pathways

Watermelon Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (FON), is one of the most important diseases, and has become a major limiting factor to watermelon production worldwide. Previous research has found that the improved biocontrol agent, F1-35, had a high control efficiency to watermelon Fusarium wilt. In this study, the control efficiency of F1-35 to watermelon Fusarium wilt was firstly tested, and the control efficiency was 61.7%. Then, we investigated the mode of action of F1-35 in controlling watermelon Fusarium wilt. Using a pairing assay, we found that F1-35 did not inhibit the normal growth of FON. To know more about the interaction between F1-35 and watermelon root, the protein expressions of roots after 12, 24, and 48 h post-inoculation were examined. A total of 1109 differentially expressed proteins were obtained. KEGG analysis found that the most differentially expressed proteins occurred in alpha-linolenic acid metabolism, cysteine and methionine metabolism, plant–pathogen interaction, and the MAPK signaling pathway to the plant. A further analysis of differentially expressed proteins showed that F1-35 triggered the jasmonic acid and ethylene pathways in watermelon. To validate our results, the qRT-PCR was used to analyze the gene expression levels of PAL, LOX1, and CTR1. The gene expression results showed that those genes, which were positive correlated with the JA pathway, were up-expressed, including PAL and LOX1, and the negative associated gene, CTR1, was down-expressed. In conclusion, the improved biocontrol agent, F1-35, improves the resistance of watermelons to FON by triggering the JA and ET pathways.

Induction of Systemic Resistance to Tobacco mosaic virus in Tomato through Foliar Application of Bacillus amyloliquefaciens Strain TBorg1 Culture Filtrate

The application of microbe-derived products as natural biocontrol agents to boost systemic disease resistance to virus infections in plants is a prospective strategy to make agriculture more sustainable and environmentally friendly. In the current study, the rhizobacterium Bacillus amyloliquefaciens strain TBorg1 was identified based on 16S rRNA, rpoB, and gyrA gene sequences, and evaluated for its efficiency in conferring protection of tomato from infection by Tobacco mosaic virus (TMV). Under greenhouse circumstances, foliar sprays of TBorg1 culture filtrate (TBorg1-CF) promoted tomato growth, lowered disease severity, and significantly decreased TMV accumulation in systemically infected leaves of treated plants relative to untreated controls. TMV accumulation was reduced by 90% following the dual treatment, applied 24 h before and after TMV infection. Significant increases in levels of total soluble carbohydrates, proteins, and ascorbic acid were also found. In addition, a significant rise in activities of enzymes capable of scavenging reactive oxygen species (PPO and POX), as well as decreased levels of non-enzymatic oxidative stress markers (H₂O₂ and MDA) were observed, compared to untreated plants. Enhanced systemic resistance to TMV was indicated by significantly increased transcript accumulation of polyphenolic pathway (C4H, HCT, and CHI) and pathogenesis-related (PR-1 and PR-5) genes. Out of the 15 compounds identified in the GC-MS analysis, 1,2-benzenedicarboxylic acid mono(2-ethylhexyl) ester and phenol, 2,4-bis(1,1-dimethylethyl), as well as L-proline, N-valeryl-, and heptadecyl ester were present in the highest concentrations in the ethyl acetate extract of TBorg1-CF. In addition, significant amounts of n-hexadecanoic acid, pyrrolo [1,2-a] pyrazine-1,4-dione hexahydro-3-(2-methylpropyl)-, nonane, 5-butyl-, and eicosane were also detected. These compounds may act as inducers of systemic resistance to viral infection. Our findings indicate that the newly isolated B. amyloliquefaciens strain TBorg1 could be a potentially useful rhizobacterium for promoting plant growth and a possible source of biocontrol agents for combating plant virus infections.

Phytostimulants in sustainable agriculture

The consistent use of synthetic fertilizers and chemicals in traditional agriculture has not only compromised the fragile agroecosystems but has also adversely affected human, aquatic, and terrestrial life. The use of phytostimulants is an alternative eco-friendly approach that eliminates ecosystem disruption while maintaining agricultural productivity. Phytostimulants include living entities and materials, such as microorganisms and nanomaterials, which when applied to plants or to the rhizosphere, stimulate plant growth and induce tolerance to plants against biotic and abiotic stresses. In this review, we focus on plant growth-promoting rhizobacteria (PGPR), beneficial fungi, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting fungi (PGPF), actinomycetes, cyanobacteria, azolla, and lichens, and their potential benefits in the crop improvement, and mitigation of abiotic and biotic stresses either alone or in combination. PGPR, AMF, and PGPF are plant beneficial microbes that can release phytohormones, such as indole acetic acid (IAA), gibberellic acid (GA), and cytokinins, promoting plant growth and improving soil health, and in addition, they also produce many secondary metabolites, antibiotics, and antioxidant compounds and help to combat biotic and abiotic stresses. Their ability to act as phytostimulator and a supplement of inorganic fertilizers is considered promising in practicing sustainable agriculture and organic farming. Glomalin is a proteinaceous product, produced by AMF, involved in soil aggregation and elevation of soil water holding capacity under stressed and unstressed conditions. The negative effects of continuous cropping can be mitigated by AMF biofertilization. The synergistic effects of PGPR and PGPF may be more effective. The mechanisms of control exercised by PGPF either direct or indirect to suppress plant diseases viz. by competing for space and nutrients, mycoparasitism, antibiosis, mycovirus-mediated cross-protection, and induced systemic resistance (ISR) have been discussed. The emerging role of cyanobacterial metabolites and the implication of nanofertilizers have been highlighted in sustainable agriculture.

Protective and Curative Activities of Paenibacillus polymyxa against Zucchini yellow mosaic virus Infestation in Squash Plants

The use of microbial products as natural biocontrol agents to increase a plant's systemic resistance to viral infections is a promising way to make agriculture more sustainable and less harmful to the environment. The rhizobacterium Paenibacillus polymyxa has been shown to have strong biocontrol action against plant diseases, but its antiviral activity has been little investigated. Here, the efficiency of the culture filtrate of the P. polymyxa strain SZYM (Acc# ON149452) to protect squash (Cucurbita pepo L.) plants against a Zucchini yellow mosaic virus (ZYMV, Acc# ON159933) infection was evaluated. Under greenhouse conditions, the foliar application of the culture filtrate of SZYM either in protective or curative treatment conditions enhanced squash growth, reduced disease severity, and decreased ZYMV accumulation levels in the treated plants when compared to the non-treated plants. The protective treatment group exhibited the highest inhibitory effect (80%), with significant increases in their total soluble carbohydrates, total soluble protein content, ascorbic acid content, and free radical scavenging activity. Furthermore, a considerable increase in the activities of reactive oxygen species scavenging enzymes (superoxide dismutase, polyphenol oxidase, and peroxidase) were also found. In addition, the induction of systemic resistance with a significant elevation in the transcriptional levels of polyphenolic pathway genes (CHS, PAL, and C3H) and pathogenesis-related genes (PR-1 and PR-3) was observed. Out of the 14 detected compounds in the GC-MS analysis, propanoic acid, benzenedicarboxylic acid, tetradecanoic acid, and their derivatives, as well as pyrrolo [1,2-a] pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl) were the primary ingredient compounds in the ethyl acetate extract of the SZYM-culture filtrate. Such compounds may act as elicitor molecules that induce systemic resistance against viral infection. Consequently, P. polymyxa can be considered a powerful plant growth-promoting bacterium (PGPB) in agricultural applications as well as a source of bioactive compounds for sustainable disease management. As far as we know, this is the first time that P. polymyxa has been shown to fight viruses in plants.

Bio-Priming of Soybean with Bradyrhizobium japonicum and Bacillus megaterium: Strategy to Improve Seed Germination and the Initial Seedling Growth

Bio-priming is a new technique of seed treatment that improves seed germination, vigor, crop growth and yield. The objective of this study was to evaluate the effectiveness of Bradyrhizobium japonicum (commercial strains) and Bacillus megaterium (newly isolated strains) as a single inoculant and co-inoculant during seed bio-priming to improve seed germination and initial seedling growth of two soybean cultivars. The treated seeds were subjected to germination test (GT), cold test (CT) and accelerated aging test (AAT). B. megaterium significantly improved all parameters in GT and CT; final germination, shoot length, root length, root dry weight, and seedling vigor index in AAT, as compared to control. In addition, co-inoculation significantly increased all parameters except shoot dry weight in GT; all parameters in CT; germination energy, shoot length, root length, and seedling vigor index in AAT, in comparison to the control. Moreover, Br. japonicum significantly improved the germination energy, shoot length, shoot dry weight, root dry weight, and seedling vigor index in GT; all parameters in CT; shoot length, root length, and seedling vigor index in AAT, compared with non-primed seeds. Thus, B. megaterium strains could be used in soybean bio-priming as a potential single inoculant and co-inoculant, following proper field evaluation.

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.

Linking Reactive Oxygen Species (ROS) to Abiotic and Biotic Feedbacks in Plant Microbiomes: The Dose Makes the Poison

In nature, plants develop in complex, adaptive environments. Plants must therefore respond efficiently to environmental stressors to maintain homeostasis and enhance their fitness. Although many coordinated processes remain integral for achieving homeostasis and driving plant development, reactive oxygen species (ROS) function as critical, fast-acting orchestrators that link abiotic and biotic responses to plant homeostasis and development. In addition to the suite of enzymatic and non-enzymatic ROS processing pathways that plants possess, they also rely on their microbiota to buffer and maintain the oxidative window needed to balance anabolic and catabolic processes. Strong evidence has been communicated recently that links ROS regulation to the aggregated function(s) of commensal microbiota and plant-growth-promoting microbes. To date, many reports have put forth insightful syntheses that either detail ROS regulation across plant development (independent of plant microbiota) or examine abiotic–biotic feedbacks in plant microbiomes (independent of clear emphases on ROS regulation). Here we provide a novel synthesis that incorporates recent findings regarding ROS and plant development in the context of both microbiota regulation and plant-associated microbes. Specifically, we discuss various roles of ROS across plant development to strengthen the links between plant microbiome functioning and ROS regulation for both basic and applied research aims.