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Background: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices. Results: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%. Conclusions: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance. [ABSTRACT FROM AUTHOR]

This study employs a cellular automata (CA) model to investigate the colonization process of Paraburkholderia phytofirmans (PsJN) in the rhizosphere, a complex ecological environment critical to plant–microbe interactions. The proposed CA model simulates bacterial population dynamics, comparing the behavior of the wild-type strain (PsJN WT) with a mutant strain (PsJN-BpI.1) that exhibits impaired quorum sensing (QS), affecting its motility and communication. The model uses a grid where each cell can either be empty or occupied by bacteria. The spread of bacterial colonies is influenced by the state of neighboring cells, with a circular neighborhood used to simulate colony formation. The transition function incorporates both bacterial motility and population control, two critical factors in rhizospheric colonization. Simulation results show that the wild-type strain demonstrates a higher concentration of colonies near the roots, while the mutant strain exhibits reduced growth in these regions. Comparing the simulations with real rhizosphere colonization images confirms the model’s accuracy and highlights the importance of carefully selecting parameters for reliable outcomes. This CA model successfully captures the colonization behavior of PsJN strains in the rhizosphere, providing valuable insights into bacterial ecology and plant–microbe interactions. [ABSTRACT FROM AUTHOR]

The ability of bacteria to colonize diverse environmental niches is often linked to their competence in biofilm formation. It depends on the individual characteristics of a strain, the nature of the colonized surface (abiotic or biotic), or the availability of certain nutrients. Pseudomonas donghuensis P482 efficiently colonizes the rhizosphere of various plant hosts, but a connection between plant tissue colonization and the biofilm formation ability of this strain has not yet been established. We demonstrate here that the potential of P482 to form biofilms on abiotic surfaces and the structural characteristics of the biofilm are influenced by the carbon source available to the bacterium, with glycerol promoting the process. Also, the type of substratum, polystyrene or glass, impacts the ability of P482 to attach to the surface. Moreover, P482 mutants in genes associated with motility or chemotaxis, the synthesis of polysaccharides, and encoding proteases or regulatory factors, which affect biofilm formation on glass, were fully capable of colonizing the root tissue of both tomato and maize hosts. Investigating the role of cellular factors in biofilm formation using these plant-associated bacteria shows that the ability of bacteria to form biofilm on abiotic surfaces does not necessarily mirror its ability to colonize plant tissues. Our research provides a broader perspective on the adaptation of these bacteria to various environments. [ABSTRACT FROM AUTHOR]

Sustainable food production, among other non-intensive production systems, involves the important interactions of myriads of plant growth-promoting microorganisms, plant, soil, soil fauna, and production of utilizable carbon in the rhizosphere capable of enhancing soil health, plant growth, and protection that lead to increased crop productivity. Plant growth-promoting rhizobacteria (PGPR) including symbiotic rhizobia and free-living rhizobacteria possess traits that help to enhance plant growth due to their many modes of action that start with the ability to colonize both the intracellular and extracellular rhizosphere niche in their search for a carbon source and reduction in the free use and quantity of agrochemicals. In the past few decades, the focus on developing biosafety agro-products has shifted from agrochemical-based applications to a more sustainable system without posing negative impacts on the soil microflora or fauna. The present review focuses on the application of PGPR inoculants on soils and seeds to improve biological nitrogen fixation, solubilization of phosphate, and secretion of phytohormones required for growth, especially application in a pressured environment. We discuss how PGPR enhances nutritional regulation and hormonal balance in plants, bacterial taxa enrichment, and improvement of carbon sources utilization beneficial for plant growth. We highlight the antagonistic and synergistic interactions with microorganisms within the rhizosphere and beyond in bulk soil which indirectly boosts plant growth rate and induces resistance against phytopathogens. While soil-borne pathogens continually oppose the functions of these microorganisms, PGPR has improved diverse strategies in the form of agro-compatibility, root colonization, nutrient, iron, and space competition, systemic resistance, antibiotics synthesis, lytic acid, hydrogen cyanide, and siderophore production for advanced food production. Finally, we highlighted the roles of PGPR in phytoremediation, techniques of applying microbial inoculants to enhance plant growth and commercialization of PGPR products and the challenges developing countries have to defeat.

Background and Aims: Intensifying chemotactic rhizocompetence is an effective approach to improving PGPR colonization in the plant rhizosphere and promoting plant growth. Whether increasing the efficient adaptational methylation modification of chemoreceptors enhances chemotactic rhizocompetence is unknown. Pseudomonas sp. UW4 is a typical PGPR, and 1-aminocyclopropane-1-carboxylic acid (ACC) is the strong chemoattractant that directs it to the rhizosphere. Methods: The chemoreceptor pentapeptide involved in UW4 chemotaxis were identified through molecular docking and methylation reactions in vitro. The pentapeptide was identified as PEKPR residing in the C-terminus of the chemoreceptor Mcp14 and shows no sequence conservation with that of other bacteria. Two chemoreceptor mutants were constructed: in one, the pentapeptide was additionally grafted to the ACC chemoreceptor McpACC (UW4-1); in the other, the pentapeptide was transferred to McpACC (UW4-2). Results: UW4-1 and UW4-2 showed unchanged chemotactic responses to arginine and succinic acid compared to UW4, whereas the chemotactic responses of UW4-1 to ACC were 36.0% and 17.2% higher than those of UW4 and UW4-2, respectively. Wheat rhizosphere colonization by UW4-1 in nonaxenic pot trials was 62.0% and 14.3% higher than rhizosphere colonization by UW4 and UW4-2, respectively, and the root and shoot dry weights of wheat inoculated with UW4-1 were 10.3% and 5.5% and 16.5% and 13.2% higher, respectively, than those of wheat inoculated with UW4 and UW4-2. Conclusion: Grafting the pentapeptide to the chemoreceptor corresponding to the strong rhizosphere chemoattractant for PGPR increases PGPR chemotactic response to the strong rhizosphere chemoattractant, increases plant rhizosphere colonization, and leads to higher plant growth promotion. [ABSTRACT FROM AUTHOR]

Among the key diseases affecting the asparagus crop (Asparagus officinalis L.), vascular wilting of asparagus caused by Fusarium oxysporum f. sp. asparagi stands out worldwide. This disease significantly shortens the longevity of the crop and limits economic production. Traditional control measures have been largely ineffective, and chemical control methods are difficult to apply, making biological control approaches, specifically the use of Trichoderma, an economical, effective, and risk-free alternative. This study aimed to identify the main factors that affect the efficacy of biopesticides studied as Biological Control Agents (BCAs) against Fusarium wilt in asparagus and to assess the efficacy of Trichoderma-based biopesticides under greenhouse and semi-field conditions. We evaluated the response of three Trichoderma spp. (T. atroviride, T. asperellum, and T. saturnisporum) to environmental variables, such as temperature and water activity, and their antagonistic capacity against Fusarium oxysporum f. sp. asparagi. All three Trichoderma species inhibited the growth of the pathogen in vitro. A decrease in water activity led to a greater reduction in the growth rate. The efficacy of the three biological control agents decreased with higher temperatures, resulting in minimal inhibition, particularly under conditions of restricted available water in the environment. The effect of the fungal inoculum density was also analyzed at two different temperatures. A direct correlation between the amount of inoculum and the score on the Disease Severity Index (DSI) was observed. A notable reduction in DSI was evident in treatments with high inoculum density (106 conidium/mL) for all three species of Trichoderma tested at both temperatures. In greenhouse and semi-field tests, we observed less disease control than expected, although T. asperellum and T. atroviride showed lower disease severity indices and increased the dry weight of seedlings and crowns, whereas T. saturnisporum resulted in the highest disease rate and lowest dry weight. This work highlights that the efficacy of Trichoderma as BCAs is influenced by various factors, including the quantity of soil inocula, and environmental conditions. The study findings have strong implications for selecting appropriate Trichoderma species for controlling specific pathogens under specific environmental conditions. [ABSTRACT FROM AUTHOR]

Among the key diseases affecting the asparagus crop (Asparagus officinalis L.), vascular wilting of asparagus caused by Fusarium oxysporum f. sp. asparagi stands out worldwide. This disease significantly shortens the longevity of the crop and limits economic production. Traditional control measures have been largely ineffective, and chemical control methods are difficult to apply, making biological control approaches, specifically the use of Trichoderma, an economical, effective, and risk-free alternative. This study aimed to identify the main factors that affect the efficacy of biopesticides studied as Biological Control Agents (BCAs) against Fusarium wilt in asparagus and to assess the efficacy of Trichoderma-based biopesticides under greenhouse and semi-field conditions. We evaluated the response of three Trichoderma spp. (T. atroviride, T. asperellum, and T. saturnisporum) to environmental variables, such as temperature and water activity, and their antagonistic capacity against Fusarium oxysporum f. sp. asparagi. All three Trichoderma species inhibited the growth of the pathogen in vitro. A decrease in water activity led to a greater reduction in the growth rate. The efficacy of the three biological control agents decreased with higher temperatures, resulting in minimal inhibition, particularly under conditions of restricted available water in the environment. The effect of the fungal inoculum density was also analyzed at two different temperatures. A direct correlation between the amount of inoculum and the score on the Disease Severity Index (DSI) was observed. A notable reduction in DSI was evident in treatments with high inoculum density (106 conidium/mL) for all three species of Trichoderma tested at both temperatures. In greenhouse and semi-field tests, we observed less disease control than expected, although T. asperellum and T. atroviride showed lower disease severity indices and increased the dry weight of seedlings and crowns, whereas T. saturnisporum resulted in the highest disease rate and lowest dry weight. This work highlights that the efficacy of Trichoderma as BCAs is influenced by various factors, including the quantity of soil inocula, and environmental conditions. The study findings have strong implications for selecting appropriate Trichoderma species for controlling specific pathogens under specific environmental conditions.

Bacilli are used as biocontrol agents (BCAs) against phytopathogens and most of them can produce poly-γ-glutamic acid (γ-PGA) as one of the major extracellular polymeric substances (EPSs). However, the role of γ-PGA in plant biocontrol is still unclear. In this study, Bacillus atrophaeus NX-12 (γ-PGA yield: 16.8g/l) was screened, which formed a strong biofilm and has been proved to be a promising BCA against Cucumber Fusarium wilt. Then, the γ-PGA synthesis gene cluster pgsBCA was knocked out by CRISPR-Cas9n. Interestingly, the antifungal ability of γ-PGA synthetase-deficient strain NX-12Δpgs (γ-PGA yield: 1.65g/l) was improved in vitro, while the biocontrol ability of NX-12Δpgs was greatly diminished in situ. Data proved that γ-PGA produced by NX-12 contributes to the biofilm formation and rhizosphere colonization, which effectively improved biocontrol capability. Taken together, these findings prove that the mechanism of γ-PGA promotes the colonization of NX-12 and thus assists in controlling plant diseases, which highlight the key role of γ-PGA produced by BCA in biocontrol. [ABSTRACT FROM AUTHOR]

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• FO12 did not exert any evident pathogenic effects on eight herbaceous hosts. • FO12 promoted plant growth in cotton, cucumber, pepper, sunflower, and wheat. • FO12 colonized the root and stem tissues of all herbaceous hosts as an endophyte. • Confocal laser scanning microscopy imaging showed that FO12 root colorization progressed. The nonpathogenic strain Fusarium oxysporum FO12 has been characterized as an effective biological control agent against Verticillium dahliae in olive. Nevertheless, the endophytic role of FO12 in herbaceous hosts is still uncertain. Thus, the aim of this study was to demonstrate the nonpathogenic character of FO12 in eight V. dahliae -susceptible herbaceous hosts and to evaluate its ability to promote plant growth. To this end, plants of each host were grown in pots filled with sterile peat moss and inoculated by irrigation with a conidial suspension of FO12 (106 conidia ml−1) two times—at sowing and at the emergence of the first true leaves. Many plants irrigated with sterile distilled water were included as controls. Sampling was conducted at 7, 14, 21, and 28 days after the second inoculation. The fresh weight and length of the aerial parts, roots, and whole plants were determined at each sampling time. Fungal colonization was assessed via quantitative and qualitative methods, including microbiological isolation from roots and stems and confocal laser scanning microscopy (CLSM) imaging at each sampling time. FO12 exhibited the ability to endophytically colonize the roots and stems of the inoculated plants. However, the effect on growth and the degree of colonization varied depending on the host. FO12 did not exert any evident pathogenic effects or negative effects on plant growth or development. The growth of the eggplant, lettuce, and tomato plants in the FO12 treatment group was similar to that in the control group, whereas the relative area under the growth progress curve was significantly greater than that in the control group for plant length in cotton and cucumber; for root fresh weight in pepper, sunflower, and wheat; and for plant fresh weight in sunflower and wheat. These results highlight the need to continue researching the interaction between FO12 and V. dahliae in a wider range of plant species of agronomic interest. [Display omitted] [ABSTRACT FROM AUTHOR]

Azospirillum sp. is a plant growth-promoting rhizobacteria largely recognized for its potential to increase the yield of different important crops. In this work, we present a thorough genomic and phenotypic analysis of A. argentinense Az39T to provide new insights into the beneficial mechanisms of this microorganism. Phenotypic analyses revealed the following in vitro abilities: growth at 20–38 °C (optimum, 28 °C), pH 6.0–8.0 (optimum, pH 6.8), and in the presence of 1% (w/v) NaCl; production of variable amounts of PHB as intracellular granules; nitrogen fixation under microaerophilic conditions; IAA synthesis in the presence of L-tryptophan. Through biochemical (API 20NE) and carbon utilization profiling (Biolog) assays, we proved that A. argentinense Az39T is able to use 15 substrates and metabolize 19 different carbon substrates. Lipid composition indicated a predominance of medium and long-chain saturated fatty acids. A total of 6 replicons classified as one main chromosome, three chromids, and two plasmids, according to their tRNA and core essential genes contents, were identified. Az39T genome includes genes associated with multiple plant growth-promoting (PGP) traits such as nitrogen fixation and production of auxins, cytokinin, abscisic acid, ethylene, and polyamines. In addition, Az39T genome harbor genetic elements associated with physiological features that facilitate its survival in the soil and competence for rhizospheric colonization; this includes motility, secretion system, and quorum sensing genetic determinants. A metadata analysis of Az39T agronomic performance in the pampas region, Argentina, demonstrated significant grain yield increases in wheat and maize, proving its potential to provide better growth conditions for dryland cereals. In conclusion, our data provide a detailed insight into the metabolic profile of A. argentinense Az39T, the strain most widely used to formulate non-legume inoculants in Argentina, and allow a better understanding of the mechanisms behind its field performance. [ABSTRACT FROM AUTHOR]

Salinity is among the major environmental factors affecting the performance of both crop plants and soil bacterial inoculants beneficial to plant growth. Based on previous screening studies, a novel halotolerant biofilm-forming PGPR strain, namely Pantoea agglomerans -FAP10, was studied for its potential to protect wheat (Triticum aestivum ; var. 343) against salinity stress. The ability of this strain to produce biofilms on glass surfaces, 96 well microtiter plates, and seedling roots was characterized qualitatively and quantitatively using light and scanning electron microscopy (SEM). The FAP10 strain was tested for performance by inoculating wheat in a pot-soil system under varied salinity stresses (75, 125, 250, and 500 mM NaCl). The FAP10 strain exhibited discrete and multifarious plant growth-promoting traits as well as efficient rhizosphere and root colonization which could sustain wheat growth under salinity stress. The FAP10-induced modifications conferred enhanced plant salinity tolerance by regulating photosynthetic attributes (gs, Ci, E, iWUE, P N , PSII, and Rubisco enzyme activity), antioxidant system (SOD, CAT, GR, APX, GSH, MDA, and proline), and sulfur metabolism (sulfur and cysteine content, ATP-S, and SAT activity), and also sustained soil physicochemical characteristics and hydrolytic enzymes including urease, protease, DHA, ALP, ACP and β glucosidase. The findings of the current study can support future efforts to improve plant salinity tolerance by engineering rhizobacterial biofilms and exploiting the potential of native strains for agricultural applications in stressed environments. • Pantoea agglomerans FAP10 a novel biofilm forming and salt tolerant PGPR strain protects inoculated wheat plants against salinity stress • The impact of treatment of FAP10 on wheat plant showed restoration of physiological attributes to normal level from the salinity stress level. • Role of biofilm in effective rhizoplane and rhizosphere colonization by FAP10 strain further supported protection mechanisms against salinity stress and improved soil hydrolytic enzymes • Findings of this study strongly support future efforts in the management of plant salinity stress with the development of effective bioinoculant for agricultural use. [ABSTRACT FROM AUTHOR]

Plants can recruit beneficial microbes to help improve their fitness under abiotic or biotic stress. Our previous studies found that Panax notoginseng could enrich beneficial Burkholderia sp. B36 in the rhizosphere soil under autotoxic ginsenoside stress. Here, we clarified that ginsenoside stress activated the phenylpropanoid biosynthesis and α-linolenic acid metabolism pathways of roots to increase the secretion of cinnamic acid, 2-dodecenoic acid, and 12-oxo-phytodienoic acid. These metabolites could promote the growth of B36. Importantly, cinnamic acid could simultaneously promote the chemotaxis and growth of B36, enhance the colonization of B36 in the rhizosphere, and eventually increase the survival rate of P. notoginseng . Overall, the plants could promote the growth and colonization of beneficial bacteria through key metabolites in root exudates under autotoxin stress. This finding will facilitate the practical application of beneficial bacteria in agricultural production and lead to successful and reproducible biocontrol efficacy by the exogenous addition of key metabolites.