The potential of Bacilli rhizobacteria for sustainable crop production and environmental sustainability

Biocontrol potential of Bacillus velezensis HG-8-2 against postharvest anthracnose on chili pepper caused by Colletotrichum scovillei

Anthracnose caused by Colletotrichum scovillei is a significant disease of pepper, including in postharvest stage. Bacillus species represent a potential microbial resource for controlling postharvest plant diseases. Here, a strain HG-8-2 was obtained and identified as Bacillus velezensis through morphological, biochemical, physiological, and molecular analyses. The culture filtrate showed highly antifungal activity against C. scovillei both in vitro and on pepper fruit. Crude lipopeptide extracts, which had excellent stability, could effectively inhibit mycelial growth of C. scovillei with an EC50 value of 28.48 ± 1.45 μg mL-1 and inhibited conidial germination. Pretreatment with the extracts reduced the incidence and lesion size of postharvest anthracnose on pepper fruit. Analysis using propidium iodide staining, malondialdehyde content detection and scanning electron microscope observation suggested that the crude lipopeptide extracts harbored antifungal activity by damaging cell membranes and mycelial structures. The RNA-seq analysis conducted on C. scovillei samples treated with the extracts, as compared to untreated samples, revealed significant alterations in the expression of multiple genes involved in protein biosynthesis. Overall, these results demonstrated that B. velezensis HG-8-2 and its crude lipopeptide extracts exhibit highly antagonistic ability against C. scovillei, thereby offering an effective biological agent for the control of anthracnose in pepper fruit.

Enhancing mango yield and soil health with organic and slow-release fertilizers: A multifaceted evaluation

Excessive utilization of chemical fertilizers in mango orchards not only hampers the attainment of sustainable harvests but also poses significant ecological detriments. This investigation proposes a promising solution by advocating the judicious replacement of chemical fertilizers with organic fertilizer (OF) and slow-release fertilizer (SRF), with potential to bolster soil health and augment crop productivity. In light of the promise held by these alternatives, it is imperative to establish detailed fertilization protocols for enhanced sustainable practices in mango farming. This two-year field study employed a comprehensive suite of seven fertilization strategies, unveiling that a 25 % chemical fertilizers substitution with OF and SRF improved mango yields by 12.5 % and 11.3 %, respectively, over standard practices. Additionally, these approaches substantially augmented the nutritional quality of mangoes, evident from Vitamin C enhancements of 53.9 % to 56.9 %, and improvements in sugar-to-acid ratio (19.2 %-30.3 %) and solid-to-acid ratio (12.1 %-25.3 %). Notably, the application of OF and SRF led to increased leaf nitrogen and phosphorus concentrations, while simultaneously reducing soil phosphorus and potassium levels. Furthermore, these fertilizers fostered the growth of beneficial soil microorganisms, namely Actinobacteria and Proteobacteria, and strengthened the synergy within the soil bacterial community, hence optimizing bacterial competition and nutrient cycling. The study proposes that the adoption of OF or SRF can effectively regulate soil nutrient balance, promote resilient and functional soil bacterial ecosystems, and ultimately improve mango yield and fruit quality. It recommends a fertilization scheme incorporating 25 % organic or slow-release nitrogen to align with ecological sustainability goals, promoting a more vigorous and resilient soil and crop system.

Priestia aryabhattai Improves Soil Environment and Promotes Alfalfa Growth by Enhancing Rhizosphere Microbial Carbon Sequestration Capacity Under Greenhouse Conditions

Plant Growth-Promoting Rhizobacteria (PGPR) are gaining increasing attention, but their interactions with indigenous rhizosphere microbiomes remain unclear. To address this issue, we isolated a strain of Priestia aryabhattai with a growth-promoting effect. Under greenhouse conditions, its growth-promoting effect on alfalfa was evaluated, and amplicon sequencing was used to analyze changes in the rhizosphere microbial community to explore the growth promotion mechanism. Our study shows that inoculation with Priestia aryabhattai increases the α-diversity index of the alfalfa rhizosphere microbiome and enhances the abundance of beneficial bacterial genera. This is likely because inoculation with Priestia aryabhattai increased the abundance of carbon-sequestering genera, particularly Gemmatimonas, thereby improving the soil environment. The increased abundance of beneficial bacteria stimulates root development in alfalfa and enhances nutrient uptake, particularly phosphorus, which in turn boosts photosynthesis and promotes alfalfa growth. In summary, Priestia aryabhattai improves soil environment and promotes alfalfa growth by enhancing the carbon sequestration capacity of the rhizosphere microbial community. This work provides theoretical support and insight for the development of PGPR inoculants and for further research on their mechanisms.

The potential of Burkholderia gladioli KRS027 in plant growth promotion and biocontrol against Verticillium dahliae revealed by dual transcriptome of pathogen and host

Verticillium dahliae is a destructive, soil-borne pathogen that causes significant losses on numerous important dicots. Recently, beneficial microbes inhabiting the rhizosphere have been exploited and used to control plant diseases. In the present study, Burkholderia gladioli KRS027 demonstrated excellent inhibitory effects against Verticillium wilt in cotton seedlings. Plant growth and development was promoted by affecting the biosynthesis and signaling pathways of brassinosteroids (BRs), gibberellins (GAs), and auxins, consequently promoting stem elongation, shoot apical meristem, and root apical tissue division in cotton. Furthermore, based on the host transcriptional response to V. dahliae infection, it was found that KRS027 modulates the plants to maintain cell homeostasis and respond to other pathogen stress. Moreover, KRS027 induced disruption of V. dahliae cellular structures, as evidenced by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses. Based on the comparative transcriptomic analysis between KRS027 treated and control group of V. dahliae, KRS027 induced substantial alterations in the transcriptome, particularly affecting genes encoding secreted proteins, small cysteine-rich proteins (SCRPs), and protein kinases. In addition, KRS027 suppressed the growth of different clonal lineages of V. dahliae strains through metabolites, and volatile organic compounds (VOCs) released by KRS027 inhibited melanin biosynthesis and microsclerotia development. These findings provide valuable insights into an alternative biocontrol strategy for Verticillium wilt, demonstrating that the antagonistic bacterium KRS027 holds promise as a biocontrol agent for promoting plant growth and managing disease occurrence.

Insights into the antifungal mechanism of Bacillus subtilis cyclic lipopeptide iturin A mediated by potassium ion channel

Fungal infections pose severe and potentially lethal threats to plant, animal, and human health. Ergosterol has served as the primary target for developing antifungal medications. However, many antifungal drugs remain highly toxic to humans due to similarity in cell membrane composition between fungal and animal cells. Iturin A, lipopeptide produced by Bacillus subtilis, efficiently inhibit various fungi, but demonstrated safety in oral administration, indicating the existence of targets different from ergosterol. To pinpoint the exact antifungal target of iturin A, we used homologous recombination to knock out and overexpress erg3, a key gene in ergosterol synthesis. Saccharomyces cerevisiae and Aspergillus carbonarius were transformed using the LiAc/SS-DNNPEG and Agrobacterium-mediated transformation (AMT), respectively. Surprisingly, increasing ergosterol content did not augment antifungal activity. Furthermore, iturin A's antifungal activity against S. cerevisiae was reduced while it pre-incubation with voltage-gated potassium (Kv) channel inhibitor, indicating that Kv activation was responsible for cell death. Iturin A was found to activate the Kv protein, stimulating K+ efflux from cell. In vitro tests confirmed interaction between iturin A and Kv protein. This study highlights Kv as one of the precise targets of iturin A in its antifungal activity, offering a novel target for the development of antifungal medications.

Rhizobacterial diversity, community composition, and the influence of keystone taxa on O'Neal blueberry (Vaccinium corymbosum)

Rhizosphere microbiotas play vital roles in resisting environmental stress, transforming soil nutrients, and promoting plant health, growth, and productivity. The effects of rhizosphere microbial community shaping and the characteristics and functions of keystone taxa on blueberries were comprehensively studied by examining the rhizobacteria of healthy old trees (O), young seedlings (OG), and poorly growing seedlings (OB) of O'Neal blueberries. Our results showed that rhizobacterial diversity followed the order OB > > OG > O, and the microbial community of OG was similar to that of O, while that of OB was distinctly different. The predominant rhizobacteria identified included Actinobacteria, Proteobacteria, Firmicutes, Chloroflexi, and Acidobacteria. Firmicutes were highly enriched in healthy blueberries, with Bacillus identified as a key genus that significantly enhanced blueberry growth when inoculated. Bradyrhizobium and Gaiellales were common core bacteria in the blueberry rhizosphere. In contrast, Acidobacteria were the predominant phylum in poorly growing OB, with the specific Vicinamibacterales-related and Latescibacterota-related genera acting as keystone taxa that shaped the microbial community. In addition, bacterial species in Vicinamibacterales might act as a potential pathogen predicted by BugBase. Taken together, these findings provide fundamental insights into the development of the blueberry rhizosphere microbial community and highlight the role of beneficial rhizobacteria, such as Bacillus, in enhancing blueberry growth. This knowledge could contribute to the exploitation of beneficial rhizobacteria and the prevention of pathogens in modern agriculture.

Pseudomonas thivervalensis K321, a promising and effective biocontrol agent for managing apple Valsa canker triggered by Valsa mali

Plant growth-promoting rhizobacteria (PGPR) have been reported to suppress various diseases as potential bioagents. It can inhibit disease occurrence through various means such as directly killing pathogens and inducing systemic plant resistance. In this study, a bacterium isolated from soil showed significant inhibition of Valsa mali. Morphological observations and phylogenetic analysis identified the strain as Pseudomonas thivervalensis, named K321. Plate confrontation assays demonstrated that K321 treatment severely damaged V. mali growth, with scanning electron microscopy (SEM) observations showing severe distortion of hyphae due to K321 treatment. In vitro twigs inoculation experiments indicated that K321 had good preventive and therapeutic effects against apple Valsa canker (AVC). Applying K321 on apples significantly enhanced the apple inducing systemic resistance (ISR), including induced expression of apple ISR-related genes and increased ISR-related enzyme activity. Additionally, applying K321 on apples can activate apple MAPK by enhancing the phosphorylation of MPK3 and MPK6. In addition, K321 can promote plant growth by solubilizing phosphate, producing siderophores, and producing 3-indole-acetic acid (IAA). Application of 0.2% K321 increased tomato plant height by 53.71%, while 0.1% K321 increased tomato fresh weight by 59.55%. Transcriptome analysis revealed that K321 can inhibit the growth of V. mali by disrupting the integrity of its cell membrane through inhibiting the metabolism of essential membrane components (fatty acids) and disrupting carbohydrate metabolism. In addition, transcriptome analysis also showed that K321 can enhance plant resistance to AVC by inducing ISR-related hormones and MAPK signaling, and application of K321 significantly induced the transcription of plant growth-related genes. In summary, an excellent biocontrol strain has been discovered that can prevent AVC by inducing apple ISR and directly killing V. mali. This study indicated the great potential of P. thivervalensis K321 for use as a biological agent for the control of AVC.

Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application

Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant - bacteria) - suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB - suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global "One Health".

Response of sweet potato cultivars to Bacillus velezensis T149-19 and Bacillus safensis T052-76 used as biofertilizers

The global market of sweet potato (Ipomoea batatas (L.) Lam.) is continuously growing and, consequently, demands greater productivity from the agricultural sector. The use of biofertilizers facilitates plant growth by making essential nutrients available to crops or providing resistance against different abiotic and biotic factors. The strains Bacillus safensis T052-76 and Bacillus velezensis T149-19 have previously been inoculated in the sweet potato cultivar Ourinho, showing positive effects on plant shoot growth and inhibiting the phytopathogen Plenodomus destruens. To elucidate the effects of these strains on sweet potato growth, four different cultivars of sweet potato were selected: Capivara, IAPAR 69, Rosinha de Verdan and Roxa. The plants were grown in pots in a greenhouse and inoculated with the combined strains according to a randomized block design. A control (without the inoculation of both strains) was also used. A slight positive effect of the inoculation of the two Bacillus strains was observed on the aerial parts of some of the cultivars. An increase in the fresh weight of the sweet potatoes of the inoculated plants was obtained, varying from 2.7 to 11.4 %. The number of sweet potatoes obtained from the inoculated cultivars IAPAR 69 and Roxa increased 15.2 % and 16.7 %, respectively. The rhizosphere soil of each cultivar was further sampled for DNA extraction, and the 16S rRNA gene metabarcoding technique was used to determine how the introduction of these Bacillus strains influenced the rhizosphere bacterial community. The bacterial communities of the four different cultivars were dominated by Actinobacteria, Proteobacteria and Firmicutes. Nonmetric multidimensional scaling (NMDS) revealed that the rhizosphere bacterial communities of plants inoculated with Bacillus strains were more similar to each other than to the bacterial communities of uninoculated plants. This study highlights the contribution of these Bacillus strains to the promotion of sweet potato growth.

Inoculation with Bacillus megaterium CNPMS B119 and Bacillus subtilis CNPMS B2084 improve P-acquisition and maize yield in Brazil

Phosphorus (P) is a critical nutrient for plant growth, yet its uptake is often hindered by soil factors like clay minerals and metal oxides such as aluminum (Al), iron (Fe), and calcium (Ca), which bind P and limit its availability. Phosphate-solubilizing bacteria (PSB) have the unique ability to convert insoluble P into a soluble form, thereby fostering plant growth. This study aimed to assess the efficacy of inoculation of Bacillus megaterium B119 (rhizospheric) and B. subtilis B2084 (endophytic) via seed treatment in enhancing maize yield, grain P content, and enzyme activities across two distinct soil types in field conditions. Additionally, we investigated various mechanisms contributing to plant growth promotion, compatibility with commercial inoculants, and the maize root adhesion profile of these strains. During five crop seasons in two experimental areas in Brazil, Sete Lagoas-MG and Santo Antônio de Goiás-GO, single inoculations with either B119 or B2084 were implemented in three seasons, while a co-inoculation with both strains was applied in two seasons. All treatments received P fertilizer according to plot recommendations, except for control. Both the Bacillus strains exhibited plant growth-promoting properties relevant to P dynamics, including phosphate solubilization and mineralization, production of indole-3-acetic acid (IAA)-like molecules, siderophores, exopolysaccharides (EPS), biofilms, and phosphatases, with no antagonism observed with Azospirillum and Bradyrizhobium. Strain B2084 displayed superior maize root adhesion compared to B119. In field trials, single inoculations with either B119 or B2084 resulted in increased maize grain yield, with relative average productivities of 22 and 16% in Sete Lagoas and 6 and 3% in Santo Antônio de Goiás, respectively. Co-inoculation proved more effective, with an average yield increase of 24% in Sete Lagoas and 11% in Santo Antônio de Goiás compared to the non-inoculated control. Across all seasons, accumulated grain P content correlated with yield, and soil P availability in the rhizosphere increased after co-inoculation in Santo Antônio de Goiás. These findings complement previous research efforts and have led to the validation and registration of the first Brazilian inoculant formulated with Bacillus strains for maize, effectively enhancing and P grain content.

Effects of returning peach branch waste to fields on soil carbon cycle mediated by soil microbial communities

In recent years, the rise in greenhouse gas emissions from agriculture has worsened climate change. Efficiently utilizing agricultural waste can significantly mitigate these effects. This study investigated the ecological benefits of returning peach branch waste to fields (RPBF) through three innovative strategies: (1) application of peach branch organic fertilizer (OF), (2) mushroom cultivation using peach branches as a substrate (MC), and (3) surface mulching with peach branches (SM). Conducted within a peach orchard ecosystem, our research aimed to assess these resource utilization strategies' effects on soil properties, microbial community, and carbon cycle, thereby contributing to sustainable agricultural practices. Our findings indicated that all RPBF treatments enhance soil nutrient content, enriching beneficial microorganisms, such as Humicola, Rhizobiales, and Bacillus. Moreover, soil AP and AK were observed to regulate the soil carbon cycle by altering the compositions and functions of microbial communities. Notably, OF and MC treatments were found to boost autotrophic microorganism abundance, thereby augmenting the potential for soil carbon sequestration and emission reduction. Interestingly, in peach orchard soil, fungal communities were found to contribute more greatly to SOC content than bacterial communities. However, SM treatment resulted in an increase in the presence of bacterial communities, thereby enhancing carbon emissions. Overall, this study illustrated the fundamental pathways by which RPBF treatment affects the soil carbon cycle, providing novel insights into the rational resource utilization of peach branch waste and the advancement of ecological agriculture.

Composition and diversity of soil microbial communities change by introducing Phallus impudicus into a Gastrodia elata Bl.-based soil

BACKGROUND

The Gastrodia elata Bl. is an orchid, and its growth demands the presence of Armillaria species. The strong competitiveness of Armillaria species has always been a concern of major threat to other soil organisms, thus disrupting the equilibrium of soil biodiversity. Introducing other species to where G. elata was cultivated, could possibly alleviate the problems associated with the disequilibrium of soil microenvironment; however, their impacts on the soil microbial communities and the underlying mechanisms remain unclear. To reveal the changes of microbial groups associated with soil chemical properties responding to different cultivation species, the chemical property measurements coupled with the next-generation pyrosequencing analyses were applied with soil samples collected from fallow land, cultivation of G. elata and Phallus impudicus, respectively.

RESULTS

The cultivation of G. elata induced significant increases (p < 0.05) in soil pH and NO3-N content compared with fallow land, whereas subsequent cultivation of P. impudicus reversed these G. elata-induced increases and was also found to significantly increase (p < 0.05) the content of soil NH4+-N and AP. The alpha diversities of soil microbial communities were significantly increased (p < 0.01) by cultivation of G. elata and P. impudicus as indicated with Chao1 estimator and Shannon index. The structure and composition of soil microbial communities differed responding to different cultivation species. In particular, the relative abundances of Bacillus, norank_o_Gaiellales, Mortierella and unclassified_k_Fungi were significantly increased (p < 0.05), while the abundances of potentially beneficial genera such as Acidibacter, Acidothermus, Cryptococcus, and Penicillium etc., were significantly decreased (p < 0.05) by cultivation of G. elata. It's interesting to find that cultivation of P. impudicus increased the abundances of these genera that G. elata decreased before, which contributed to the difference of composition and structure. The results of CCA and heatmap indicated that the changes of soil microbial communities had strong correlations with soil nutrients. Specifically, among 28 genera presented, 50% and 42.9% demonstrated significant correlations with soil pH and NO3-N in response to cultivation of G. elata and P. impudicus.

CONCLUSIONS

Our findings suggested that the cultivation of P. impudicus might have potential benefits as result of affecting soil microorganisms coupled with changes in soil nutrient profile.

Complete genome sequence of Bacillus velezensis strain Ag109, a biocontrol agent against plant-parasitic nematodes and Sclerotinia sclerotiorum

Soybean is the main oilseed cultivated worldwide. Even though Brazil is the world's largest producer and exporter of soybean, its production is severely limited by biotic factors. Soil borne diseases are the most damaging biotic stressors since they significantly reduce yield and are challenging to manage. In this context, the present study aimed to evaluate the potential of a bacterial strain (Ag109) as a biocontrol agent for different soil pathogens (nematodes and fungi) of soybean. In addition, the genome of Ag109 was wholly sequenced and genes related to secondary metabolite production and plant growth promotion were mined. Ag109 showed nematode control in soybean and controlled 69 and 45% of the populations of Meloidogyne javanica and Pratylenchus brachyurus, respectively. Regarding antifungal activity, these strains showed activity against Macrophomia phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. For S. sclerotiorum, this strain increased the number of healthy plants and root dry mass compared to the control (with inoculation). Based on the average nucleotide identity and digital DNA-DNA hybridization, this strain was identified as Bacillus velezensis. Diverse clusters of specific genes related to secondary metabolite biosynthesis and root growth promotion were identified, highlighting the potential of this strain to be used as a multifunctional microbial inoculant that acts as a biological control agent while promoting plant growth in soybean.

Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Assessing the reclamation of a contaminated site affected by the Fundão dam tailings trough phytoremediation and bioremediation

The rupture of the Fundão dam (Brazil) spread tailings contaminated with sodium and ether-amine into the Doce River Basin. Aiming at rehabilitating a contaminated riparian site, phytoremediation with native species of the Atlantic Forest was performed under four treatments: ES-1: physical remediation (sediment scraping) + chemical remediation (organic matter) + bioremediation (double inoculation with the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis and the plant growth-promoting bacteria Bacillus subtilis); ES-2: chemical remediation + bioremediation; ES-3: physical remediation + chemical remediation; ES-4: chemical remediation. Ether-amine and sodium contents, plant growth and, soil quality parameters were compared among treatments and relative to preserved and degraded sites. Two years after planting, the outstanding plant growth was attributed to the phytoremediation of ether-amine and ammonium, followed by a significant increase in soil microbial biomass (Phospholipid fatty acids-PLFAs), particularly the Gram+ bacteria and total fungi but not AMF, whose response was independent of the inoculation. While sodium and ether-amine declined, soil K, P, NO3- contents, dehydrogenase and acid phosphatase activities, cation exchange capacity (CEC) and soil aggregation increased, especially in ES-1. Thus, such remediation procedures are recommended for the restoration of riparian areas affected by the Fundão tailings, ultimately improving sediment fertility, aggregation and stabilization.

Exploring Bacillus subtilis: Ecology, biotechnological applications, and future prospects

From its early identification by Christian Gottfried Ehrenberg to its current prominence in scientific research, Bacillus subtilis (B. subtilis) has emerged as a foundational model organism in microbiology. This comprehensive review delves deep into its genetic, physiological, and biochemical intricacies, revealing a sophisticated cellular blueprint. With the incorporation of advanced techniques such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 and integrative computational methodologies, the potential applications of B. subtilis span diverse sectors. These encompass its significant contributions to biotechnology, agriculture, and medical fields and its potential for aiding environmental cleanup efforts. Yet, as we move forward, we must grapple with concerns related to safety, ethics, and the practical implementation of our lab findings in everyday scenarios. As our understanding of B. subtilis deepens, it is evident that its contributions will be central to pioneering sustainable solutions for global challenges in the years to come.

Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07

Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as biocontrol biopesticides that promise improved sustainability and ecological safety in agriculture. Here, we present a draft-quality genome sequence for Bacillus velezensis EU07, which shows growth-promotion in tomato plants and biocontrol against Fusarium head blight. We found that the genome of EU07 is almost identical to that of the commercially used strain QST713, but identified 46 single-nucleotide differences that distinguish these strains from each other. The availability of this genome sequence will facilitate future efforts to unravel the genetic and molecular basis for EU07's beneficial properties.

Uncovering the secret weapons of an invasive plant: The endophytic microbes of Anthemis cotula

Understanding plant-microbe interaction can be useful in identifying the microbial drivers of plant invasions. It is in this context that we explored the diversity of endophytic microbes from leaves of Anthemis cotula, an annual plant that is highly invasive in Kashmir Himalaya. We also tried to establish the role of endophytes in the invasiveness of this alien species. We collected and processed leaf samples from three populations at three different sites. A total of 902 endophytic isolates belonging to 4 bacterial and 2 fungal phyla were recovered that belonged to 27 bacterial and 14 fungal genera. Firmicutes (29.1%), Proteobacteria (24.1%), Ascomycota (22.8%) and Actinobacteria (19%) were dominant across all samples. Plant growth promoting traits, such as Ammonia production, Indole Acetic Acid (IAA) production, Phosphate solubilization and biocontrol activity of these endophytes were also studied and most of the isolates (74.68%) were positive for ammonia production. IAA production, phosphate solubilization and biocontrol activity was present in 39.24%, 36.70% and 20.26% isolates, respectively. Furthermore, Botrytis cinerea, a pathogen of A. cotula in its native range, though present in Kashmir Himalaya does not affect A. cotula probably due to the presence of leaf endophytic microbial antagonists. Our results highlight that the beneficial plant growth promoting interactions and enemy suppression by leaf endophytes of A. cotula, may be contributing to its survival and invasion in the Kashmir Himalaya.

Difference in the Effect of Applying Bacillus to Control Tomato Verticillium Wilt in Black and Red Soil

In practical applications, the effectiveness of biological control agents such as Bacillus is often unstable due to different soil environments. Herein, we aimed to explore the control effect and intrinsic mechanism of Bacillus in black soil and red soil in combination with tomato Verticillium wilt. Bacillus application effectively controlled the occurrence of Verticillium wilt in red soil, reducing the incidence by 19.83%, but played a limited role in black soil. Bacillus colonized red soil more efficiently. The Verticillium pathogen decreased by 71.13% and 76.09% after the application of Bacillus combinations in the rhizosphere and bulk of the red soil, respectively, while there was no significant difference in the black soil. Additionally, Bacillus application to red soil significantly promoted phosphorus absorption. Furthermore, it significantly altered the bacterial community in red soil and enriched genes related to pathogen antagonism and phosphorus activation, which jointly participated in soil nutrient activation and disease prevention, promoting tomato plant growth in red soil. This study revealed that the shaping of the bacterial community by native soil may be the key factor affecting the colonization and function of exogenous Bacillus.

Contribution to the characterization of the seed endophyte microbiome of Argania spinosa across geographical locations in Central Morocco using metagenomic approaches

Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree (Argania spinosa) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored. This study aimed to compare the bacterial and fungal endophyte communities associated with argan seeds collected from six sites across Morocco using Illumina MiSeq sequencing of the 16S rRNA gene and ITS regions, respectively. Bacterial DNA was extracted from surface-sterilized seeds and amplified using universal primers, while fungal DNA was isolated directly from seeds. Bioinformatics analysis of sequencing data identified taxonomic profiles at the phylum to genus levels. The results indicated that bacterial communities were dominated by the genus Rhodoligotrophos, while fungal communities exhibited varying degrees of dominance between Ascomycota and Basidiomycota depending on site, with Penicillium being the most abundant overall. Distinct site-specific profiles were observed, with Pseudomonas, Bacillus, and Aspergillus present across multiple locations. Alpha diversity indices revealed variation in endophyte richness between seed sources. In conclusion, this first exploration of the argan seed endophyte microbiome demonstrated environmental influence on community structure. While facing limitations due to small sample sizes and lack of ecological metadata, it provides a foundation for future mechanistic investigations into how specific endophyte-host interactions shape argan adaptation across Morocco's diverse landscapes.

Parameter evaluation for developing phosphate-solubilizing Bacillus inoculants

Bacterial inoculants have been used in agriculture to improve plant performance. However, laboratory and field requirements must be completed before a candidate can be employed as an inoculant. Therefore, this study aimed to evaluate the parameters for inoculant formulation and the potential of Bacillus subtilis (B70) and B. pumilus (B32) to improve phosphorus availability in maize (Zea mays L.) crops. In vitro experiments assessed the bacterial ability to solubilize and mineralize phosphate, their adherence to roots, and shelf life in cassava starch (CS), carboxymethyl cellulose (CMC), peat, and activated charcoal (AC) stored at 4 °C and room temperature for 6 months. A field experiment evaluated the effectiveness of strains to increase the P availability to plants growing with rock phosphate (RP) and a mixture of RP and triple superphosphate (TS) and their contribution to improving maize yield and P accumulation in grains. The B70 was outstanding in solubilizing RP and phytate mineralization and more stable in carriers and storage conditions than B32. However, root adherence was more noticeable in B32. Among carriers, AC was the most effective for preserving viable cell counts, closely similar to those of the initial inoculum of both strains. Maize productivity using the mixture RPTS was similar for B70 and B32. The best combination was B70 with RP, which improved the maize yield (6532 kg ha-1) and P accumulation in grains (15.95 kg ha-1). Our results indicated that the inoculant formulation with AC carrier and B70 is a feasible strategy for improving phosphorus mobilization in the soil and maize productivity.

A Bacillus velezensis strain shows antimicrobial activity against soilborne and foliar fungi and oomycetes

Biological control uses naturally occurring antagonists such as bacteria or fungi for environmentally friendly control of plant pathogens. Bacillus spp. have been used for biocontrol of numerous plant and insect pests and are well-known to synthesize a variety of bioactive secondary metabolites. We hypothesized that bacteria isolated from agricultural soil would be effective antagonists of soilborne fungal pathogens. Here, we show that the Delaware soil isolate Bacillus velezensis strain S4 has in vitro activity against soilborne and foliar plant pathogenic fungi, including two with a large host range, and one oomycete. Further, this strain shows putative protease and cellulase activity, consistent with our prior finding that the genome of this organism is highly enriched in antifungal and antimicrobial biosynthetic gene clusters. We demonstrate that this bacterium causes changes to the fungal and oomycete hyphae at the inhibition zone, with some of the hyphae forming bubble-like structures and irregular branching. We tested strain S4 against Magnaporthe oryzae spores, which typically form germ tubes and penetration structures called appressoria, on the surface of the leaf. Our results suggest that after 12 hours of incubation with the bacterium, fungal spores form germ tubes, but instead of producing appressoria, they appear to form rounded, bubble-like structures. Future work will investigate whether a single antifungal molecule induces all these effects, or if they are the result of a combination of bacterially produced antimicrobials.

Fertilization- and Irrigation-Modified Bacterial Community Composition and Stimulated Enzyme Activity of Eucalyptus Plantations Soil

Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a total of 20 soil samples collected from Eucalyptus plantations were analyzed using high-throughput sequencing. Experimental treatments consisting of control (CK, no irrigation or fertilization), fertilization only (F), irrigation only (W), and irrigation and fertilization (WF). The results showed a positive correlation between soil enzyme activities (urease, cellulase, and chitinase) and fertilization treatments. These enzyme activities were also significantly correlated with the diversity of soil bacterial communities in Eucalyptus plantations.. Bacteria diversity was considerably increased under irrigation and fertilization (W, F, and WF) treatments when compared with the CK treatment. Additionally, the soil bacterial richness was increased in the Eucalyptus plantations soil under irrigation (W and WF) treatments. The Acidobacteria (38.92-47.9%), Proteobacteria (20.50-28.30%), and Chloroflexi (13.88-15.55%) were the predominant phyla found in the Eucalyptus plantations soil. Specifically, compared to the CK treatment, the relative abundance of Proteobacteria was considerably higher under the W, F, and WF treatments, while the relative abundance of Acidobacteria was considerably lower. The contents of total phosphorus, accessible potassium, and organic carbon in the soil were all positively associated with fertilization and irrigation treatments. Under the WF treatment, the abundance of bacteria associated with nitrogen and carbon metabolisms, enzyme activity, and soil nutrient contents showed an increase, indicating the positive impact of irrigation and fertilization on Eucalyptus plantations production. Collectively, these findings provide the scientific and managerial bases for improving the productivity of Eucalyptus plantations.

Application of rhizobacteria to improve microbial community structure and maize (Zea mays L.) growth in saline soil

The utilization of plant growth-promoting rhizobacteria (PGPR) has emerged as a prominent focus in contemporary research on soil microbiology, microecology, and plant stress tolerance. However, how PGPR influence the soil bacterial community and related ecological functions remains unclear. The aim of this study was to investigate the effects of three natural PGPR inoculations (YL07, Planococcus soli WZYH02; YL10, Bacillus atrophaeus WZYH01; YL0710, Planococcus soli WZYH02 and Bacillus atrophaeus WZYH01) on maize (Zea mays L.) growth under two salt stress conditions (S1, ECe = 2.1 ~ 2.5 dS/m; S2, ECe = 5.5 ~ 5.9 dS/m). The results revealed that compared to the control (CK), the average plant height of maize seedlings significantly increased by 27%, 23%, and 29% with YL07, YL10, and YL0710 inoculation under S1 conditions, respectively, and increased by 30%, 20%, and 18% under S2 conditions, respectively. Moreover, PGPR inoculation positively influenced the content of superoxide dismutase, catalase, soluble sugar, and proline in maize under salt stress. Subsequent analysis of alpha diversity indices, relative microbial abundance, principal coordinate analysis, cladograms, and linear discriminant analysis effect size histograms indicated significant alterations in the rhizosphere microbial community due to PGPR inoculation. FAPROTAX analysis demonstrated that YL10 inoculation in S2 rhizosphere soil had a notable impact on carbon cycle functions, specifically chemoheterotrophy, fermentation, and phototrophy. Thus, this study provides evidence that PGPR inoculation improves soil microbial communities and plant indices under salt stress. These findings shed light on the potential of PGPR as a viable approach for enhancing plant stress tolerance and fostering sustainable agricultural practices.

Seed bio-priming enhanced salt stress tolerance of maize (Zea mays L.) seedlings by regulating the antioxidant system and miRNA expression

Maize (Zea mays) is moderately sensitive to salt stress. Therefore, increasing salinity in soil causes the arrestment of physiological processes and retention of growth and development, consequently leading to yield loss. Although many strategies have been launched to improve salt stress tolerance, plant growth-promoting rhizobacteria (PGPR) are considered the most promising approach due to being more environmentally friendly and agronomically sustainable than chemicals. Therefore, this study aims to investigate the potential of Bacillus spp. and the role of microRNA-mediated genetic regulation in maize subjected to seed bio-priming application to mitigate salt stress effects. To this end, maize seeds were bio-primed with the vegetative form of B. pumilus, B. licheniformis, and B. coagulans both individually or combined, subsequently treated to NaCl, and the seedlings were screened morphologically, physiologically, and transcriptionally. The study revealed that seed bio-priming with B. licheniformis reduced the stress effects of maize seedlings by increasing catalase (CAT) and ascorbate peroxidase (APX) activities by 2.5- and 3-fold, respectively, tolerating the decrease in chlorophyll content (CC), upregulating miR160d expression which led to a 36% increase in root fresh weight (RFW) and a 39% increase in shoot fresh weight (SFW). In conclusion, Bacillus spp. successfully alleviated salt stress effects on maize by modulating antioxidant enzymes and miRNA expression.

Pesticide-tolerant microbial consortia: Potential candidates for remediation/clean-up of pesticide-contaminated agricultural soil

Reclamation of pesticide-polluted lands has long been a difficult endeavour. The use of synthetic pesticides could not be restricted due to rising agricultural demand. Pesticide toxicity has become a pressing agronomic problem due to its adverse impact on agroecosystems, agricultural output, and consequently food security and safety. Among different techniques used for the reclamation of pesticide-polluted sites, microbial bioremediation is an eco-friendly approach, which focuses on the application of resilient plant growth promoting rhizobacteria (PGPR) that may transform or degrade chemical pesticides to innocuous forms. Such pesticide-resilient PGPR has demonstrated favourable effects on soil-plant systems, even in pesticide-contaminated environments, by degrading pesticides, providing macro-and micronutrients, and secreting active but variable secondary metabolites like-phytohormones, siderophores, ACC deaminase, etc. This review critically aims to advance mechanistic understanding related to the reduction of phytotoxicity of pesticides via the use of microbe-mediated remediation techniques leading to crop optimization in pesticide-stressed soils. The literature surveyed and data presented herein are extremely useful, offering agronomists-and crop protectionists microbes-assisted remedial strategies for affordably enhancing crop productivity in pesticide-stressed soils.

Evaluation and Genome Mining of Bacillus stercoris Isolate B.PNR1 as Potential Agent for Fusarium Wilt Control and Growth Promotion of Tomato

Recently, strategies for controlling Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol agents. In this study, an analysis of the biocontrol and plant growth promoting (PGP) attributes of 11 isolates of loamy soil Bacillus spp. has been conducted. Among them, the isolates B.PNR1 and B.PNR2 inhibited the mycelial growth of Fol by inducing abnormal fungal cell wall structures and cell wall collapse. Moreover, broad-spectrum activity against four other plant pathogenic fungi, F. oxysporum f. sp. cubense race 1 (Foc), Sclerotium rolfsii, Colletotrichum musae, and C. gloeosporioides were noted for these isolates. These two Bacillus isolates produced indole acetic acid, phosphate solubilization enzymes, and amylolytic and cellulolytic enzymes. In the pot experiment, the culture filtrate from B.PNR1 showed greater inhibition of the fungal pathogens and significantly promoted the growth of tomato plants more than those of the other treatments. Isolate B.PNR1, the best biocontrol and PGP, was identified as Bacillus stercoris by its 16S rRNA gene sequence and whole genome sequencing analysis (WGS). The WGS, through genome mining, confirmed that the B.PNR1 genome contained genes/gene cluster of a nonribosomal peptide synthetase/polyketide synthase, such as fengycin, surfactin, bacillaene, subtilosin A, bacilysin, and bacillibactin, which are involved in antagonistic and PGP activities. Therefore, our finding demonstrates the effectiveness of B. stercoris strain B.PNR1 as an antagonist and for plant growth promotion, highlighting the use of this microorganism as a biocontrol agent against the Fusarium wilt pathogen and PGP abilities in tomatoes.

Molecular Mechanisms Determining the Role of Bacteria from the Genus Azospirillum in Plant Adaptation to Damaging Environmental Factors

Agricultural plants are continuously exposed to environmental stressors, which can lead to a significant reduction in yield and even the death of plants. One of the ways to mitigate stress impacts is the inoculation of plant growth-promoting rhizobacteria (PGPR), including bacteria from the genus Azospirillum, into the rhizosphere of plants. Different representatives of this genus have different sensitivities or resistances to osmotic stress, pesticides, heavy metals, hydrocarbons, and perchlorate and also have the ability to mitigate the consequences of such stresses for plants. Bacteria from the genus Azospirillum contribute to the bioremediation of polluted soils and induce systemic resistance and have a positive effect on plants under stress by synthesizing siderophores and polysaccharides and modulating the levels of phytohormones, osmolytes, and volatile organic compounds in plants, as well as altering the efficiency of photosynthesis and the antioxidant defense system. In this review, we focus on molecular genetic features that provide bacterial resistance to various stress factors as well as on Azospirillum-related pathways for increasing plant resistance to unfavorable anthropogenic and natural factors.

Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds

Helianthus annus (sunflower) is a globally important oilseed crop whose survival is threatened by various pathogenic diseases. Agrochemical products are used to eradicate these diseases; however, due to their unfriendly environmental consequences, characterizing microorganisms for exploration as biocontrol agents are considered better alternatives against the use of synthetic chemicals. The study assessed the oil contents of 20 sunflower seed cultivars using FAMEs-chromatography and characterized the endophytic fungi and bacteria microbiome using Illumina sequencing of fungi ITS 1 and bacteria 16S (V3-V4) regions of the rRNA operon. The oil contents ranged between 41-52.8%, and 23 fatty acid components (in varied amounts) were found in all the cultivars, with linoleic (53%) and oleic (28%) acids as the most abundant. Ascomycota (fungi) and Proteobacteria (bacteria) dominated the cultivars at the phyla level, while Alternaria and Bacillus at the genus level in varying abundance. AGSUN 5102 and AGSUN 5101 (AGSUN 5270 for bacteria) had the highest fungi diversity structure, which may have been contributed by the high relative abundance of linoleic acid in the fatty acid components. Dominant fungi genera such as Alternaria, Aspergillus, Aureobasidium, Alternariaste, Cladosporium, Penicillium, and bacteria including Bacillus, Staphylococcus, and Lactobacillus are established, providing insight into the fungi and bacteria community structures from the seeds of South Africa sunflower.

Bacillus subtilis and Bacillus licheniformis promote tomato growth

Bacillus spp. are widely marketed and used in agricultural systems as antagonists to various phytopathogens, but it can also benefit the plant as plant growth promoters. Therefore, the longer presence of the bacterium in the rhizosphere would result in a prolonged growth-promoting benefit, but little is yet known about its persistence in the rhizosphere after seed coating. The objectives of this study were to evaluate the tomato growth promotion mediated by Bacillus licheniformis FMCH001 and Bacillus subtilis FMCH002 and the survival rate of these bacteria both in shoots and in the rhizosphere. The Bacillus strains used throughout this study were obtained from Quartzo® produced by Chr. Hansen. The application of a mixture of B. subtilis and B. licheniformis (Quartzo®) at concentrations 1 × 108, 1 × 109, and 1 × 1010 CFU mL-1, as well as the application of B. subtilis and B. licheniformis individually at concentration 1 × 108 CFU mL-1, increased fresh and dry masses of shoot and root system, volume of root system, and length of roots of tomato plants when compared to control. Both Bacillus strains produced IAA after 48 h of in vitro. Bacillus colonies obtained from plant sap were morphologically similar to colonies of B. subtilis and B. licheniformis strains and were detected in inoculated on plants and not detected in control ones. A similar pattern was obtained through DNA-based detection (qPCR). Therefore, B. subtilis and B. licheniformis were able to produce auxin, promote tomato growth, and colonize and persist in the rhizosphere.

Bacillus-Loaded Biochar as Soil Amendment for Improved Germination of Maize Seeds

Biochar is considered one of the most promising long-term solutions for soil quality improvement, representing an ideal environment for microorganisms' immobilization. Hence there is a possibility to design microbial products formulated using biochar as a solid carrier. The present study was aimed at development and characterization of Bacillus-loaded biochar to be applied as a soil amendment. The producing microorganism Bacillus sp. BioSol021 was evaluated in terms of plant growth promotion traits, indicating significant potential for production of hydrolytic enzymes, indole acetic acid (IAA) and surfactin and positive tests for ammonia and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production. Soybean biochar was characterised in terms of physicochemical properties to evaluate its suitability for agricultural applications. The experimental plan for Bacillus sp. BioSol021 immobilisation to biochar included variation of biochar concentration in cultivation broth and adhesion time, while the soil amendment effectiveness was evaluated during maize germination. The best results in terms of maize seed germination and seedling growth promotion were achieved by applying 5% of biochar during the 48 h immobilisation procedure. Germination percentage, root and shoot length and seed vigour index were significantly improved when using Bacillus-biochar soil amendment compared to separate treatments including biochar and Bacillus sp. BioSol021 cultivation broth. The results indicated the synergistic effect of producing microorganism and biochar on maize seed germination and seedling growth promotion, pointing out the promising potential of this proposed multi-beneficial solution for application in agricultural practices.

Characterization of the Culturable Sporobiota of Spanish Olive Groves and Its Tolerance toward Environmental Challenges

Olive agriculture presents an integral economic and social pillar of the Mediterranean region with 95% of the world's olive tree population concentrated in this area. A diverse ecosystem consisting of fungi, archaea, viruses, protozoa, and microbial communities-the soil microbiome-plays a central role in maintaining healthy soils while keeping up productivity. Spore-forming organisms (i.e., the sporobiota) have been identified as one of the predominant communities of the soil microbiome and are known for the wide variety of antimicrobial properties and extraordinary resistance. Hence, the aim of this work was to determine the culturable sporobiota of Spanish olive orchards and characterize its phenotypic properties toward common environmental challenges. A collection of 417 heat-resistant bacteria were isolated from five Spanish olive orchards. This collective was termed the "olive sporobiota." Rep-PCR clustering of representative isolates revealed that they all belonged to the group of Bacillus spp., or closely related species, showing a great variety of species and strains. Representative isolates showed susceptibility to common antibiotics, as well as good resistance to heavy metal exposure, with an order of metal tolerance determined as iron > copper > nickel > manganese > zinc > cadmium. Finally, we showed that the application of mineral fertilizer can in several cases enhance bacterial growth and thus potentially increase the relative proportion of the sporobiota in the olive grove ecosystem. In summary, the identification of the culturable olive sporobiota increases our understanding of the microbial diversity in Spanish olive groves, while tolerance and resistance profiles provide important insights into the phenotypic characteristics of the microbial community. IMPORTANCE Microbial communities are a key component of healthy soils. Spore-forming microorganisms represent a large fraction of this community-termed the "sporobiota"-and play a central role in creating a conducive environment for plant growth and food production. In addition, given their unique features, such as extraordinary stability and antimicrobial properties, members of the sporobiota present interesting candidates for biotechnological applications, such as sustainable plant protection products or in a clinical setting. For this, however, more information is needed on the spore-forming community of agricultural installations, ultimately promoting a transition toward a more sustainable agriculture.

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.

The Effect of Cultivation Conditions on Antifungal and Maize Seed Germination Activity of Bacillus-Based Biocontrol Agent

Aflatoxin contamination is a global risk and a concerning problem threatening food safety. The biotechnological answer lies in the production of biocontrol agents that are effective against aflatoxins producers. In addition to their biocontrol effect, microbial-based products are recognized as efficient biosolutions for plant nutrition and growth promotion. The present study addresses the characterization of the representative of Phaseolus vulgaris rhizosphere microbiome, Bacillus sp. BioSol021, regarding plant growth promotion traits, including the activity of protease, cellulase, xylanase, and pectinase with the enzymatic activity index values 1.06, 2.04, 2.41, and 3.51, respectively. The potential for the wider commercialization of this kind of product is determined by the possibility of developing a scalable bioprocess solution suitable for technology transfer to an industrial scale. Therefore, the study addresses one of the most challenging steps in bioprocess development, including the production scale-up from the Erlenmeyer flask to the laboratory bioreactor. The results indicated the influence of the key bioprocess parameters on the dual mechanism of action of biocontrol effects against the aflatoxigenic Aspergillus flavus, as well on maize seed germination activity, pointing out the positive impact of high aeration intensity and agitation rate, resulting in inhibition zone diameters of 60 mm, a root length 96 mm, and a shoot length 27 mm.

Bacillus spp. as Bioagents: Uses and Application for Sustainable Agriculture

Food security will be a substantial issue in the near future due to the expeditiously growing global population. The current trend in the agriculture industry entails the extravagant use of synthesized pesticides and fertilizers, making sustainability a difficult challenge. Land degradation, lower production, and vulnerability to both abiotic and biotic stresses are problems caused by the usage of these pesticides and fertilizers. The major goal of sustainable agriculture is to ameliorate productivity and reduce pests and disease prevalence to such a degree that prevents large-scale damage to crops. Agriculture is a composite interrelation among plants, microbes, and soil. Plant microbes play a major role in growth promotion and improve soil fertility as well. Bacillus spp. produces an extensive range of bio-chemicals that assist in plant disease control, promote plant development, and make them suitable for agricultural uses. Bacillus spp. support plant growth by N fixation, P and K solubilization, and phytohormone synthesis, in addition to being the most propitious biocontrol agent. Moreover, Bacilli excrete extracellular metabolites, including antibiotics, lytic enzymes, and siderophores, and demonstrate antagonistic activity against phytopathogens. Bacillus spp. boosts plant resistance toward pathogens by inducing systemic resistance (ISR). The most effective microbial insecticide against insects and pests in agriculture is Bacillus thuringiensis (Bt). Additionally, the incorporation of toxin genes in genetically modified crops increases resistance to insects and pests. There is a constant increase in the identified Bacillus species as potential biocontrol agents. Moreover, they have been involved in the biosynthesis of metallic nanoparticles. The main objective of this review article is to display the uses and application of Bacillus specie as a promising biopesticide in sustainable agriculture. Bacillus spp. strains that are antagonistic and promote plant yield attributes could be valuable in developing novel formulations to lead the way toward sustainable agriculture.

Coinoculation impact on plant growth promotion: a review and meta-analysis on coinoculation of rhizobia and plant growth-promoting bacilli in grain legumes

Coinoculation of symbiotic N2-fixing rhizobia and plant growth-promoting Bacillus on legume seeds can increase crop productivity. We collected highly resolved data on coinoculation of rhizobia and bacilli on 11 grain legume crops: chickpea, common bean, cowpea, faba bean, groundnut, lentil, mung bean, pea, pigeon pea, soybean, and urad bean to verify the magnitude of additive effects of coinoculation in relation to single inoculation of rhizobia on plant growth and yield of grain legumes. Coinoculation of rhizobia and bacilli on legume seeds and/or soil during sowing significantly increased nodulation, nitrogenase activity, plant N and P contents, and shoot and root biomass, as well as the grain yield of most grain legumes studied. There were however a few instances where coinoculation decreased plant growth parameters. Therefore, coinoculation of rhizobia and Bacillus has the potential to increase the growth and productivity of grain legumes, and can be recommended as an environmental-friendly agricultural practice for increased crop yields.

Bacillus spp.-Mediated Growth Promotion of Rice Seedlings and Suppression of Bacterial Blight Disease under Greenhouse Conditions

Rice (Oryza sativa L.) is a major cereal and staple food crop worldwide, and its growth and production are affected by several fungal and bacterial phytopathogens. Bacterial blight (BB) is one of the world's most devastating rice diseases, caused by Xanthomonas oryzae pv. oryzae (Xoo). In the current study, Bacillus atrophaeus FA12 and B. cabrialesii FA26 were isolated from the rice rhizosphere and characterized as having broad-range antifungal and antibacterial activities against various phytopathogens, including Xoo. In addition, the selected strains were further evaluated for their potent rice growth promotion and suppression efficacy against BB under greenhouse conditions. The result shows that FA12 and FA26, applied as seed inoculants, significantly enhanced the vigor index of rice seedlings by 78.89% and 108.70%, respectively. Suppression efficacy against BB disease by FA12 and FA26 reached up to 59.74% and 54.70%, respectively, in pot experiments. Furthermore, MALDI-TOF MS analysis of selected strains revealed the masses ranged from m/z 1040 to 1540, representing that iturins and fengycin are the major antimicrobial compounds in the crude extracts, which might have beneficial roles in rice defence responses against BB. In conclusion, FA12 and FA26 possess broad-range antagonistic activity and have the capability to promote plant growth traits. More importantly, applying these strains has a high potential for implementing eco-friendly, cost-effective, and sustainable management practices for BB disease.

Bacillus velezensis Strain GUMT319 Reshapes Soil Microbiome Biodiversity and Increases Grape Yields

Bacillus velezensis strain GUMT319 is a rhizobacteria biocontrol agent that can control tobacco black shank disease. We took GUMT319 as a biological fertilizer on Vitis vinifera L. The test group was treated with GUMT319 for one year and the control group had a water treatment. Yields of GUMT319-treated grape groups were significantly increased compared to the controls. The average length and width of single grape fruit, weight of 100 grape fruits, the sugar/acid ratio, and the content of vitamin C were all increased in the GUMT319-treated grape group. The pH of the soil was higher and the contents of alkaline hydrolyzable nitrogen and available potassium were significantly lower in the GUMT319-treated groups than the controls. The soil microbial community composition was evaluated by 16S rDNA high-throughput sequencing, and the Shannon index and Simpson index all showed that soil microbes were more abundant in the GUMT319-treated group. These results indicate that GUMT319 is not only a biocontrol agent, but also a plant growth-promoting rihizobacteria. It can increase the yield of grape by altering the physical and chemical properties and the microbial community composition of the soil.

Integrated organic and inorganic fertilization and reduced irrigation altered prokaryotic microbial community and diversity in different compartments of wheat root zone contributing to improved nitrogen uptake and wheat yield

The effect of long-term water and integrated fertilization on prokaryotic microorganisms and their regulation for crop nutrient uptake remains unknown. Therefore, the impact of soil water and integrated fertilization after eight years on prokaryotic microbial communities in different compartments of root zone and their association with wheat nitrogen (N) absorption and yield were investigated. The results showed that compared with fertilization treatments (F), water regimes (W) more drastically modulated the prokaryotic microbial community structure and diversity in bulk soil, rhizosphere and endosphere. The increase of irrigation improved the prokaryotic diversity in the rhizosphere and endosphere while decreased the diversity in the bulk soil. Application of organic fertilizers significantly improved soil organic matter (SOM) and nutrient contents, increased rhizosphere and endophytic prokaryotic microbial diversity, and elevated the relative abundance of aerobic ammonia oxidation and nitrification-related functional microorganisms in rhizosphere and endosphere. Increasing irrigation elevated the relative abundance of functional microorganisms related to aerobic ammonia oxidation and nitrification in the rhizosphere and endosphere. Soil water content (SWC) and NH₄⁺-N as well as NO₃^--N were key predictors of prokaryotic microbial community composition under W and F treatments, respectively. Appropriate application of irrigation and organic fertilizers increased the relative abundance of some beneficial bacteria such as Flavobacterium. Water and fertilization treatments regulated the prokaryotic microbial communities of bulk soil, rhizosphere and endosphere by altering SWC and SOM, and provided evidence for the modulation of prokaryotic microorganisms to promote nitrogen uptake and wheat yield under long-term irrigation and fertilization. Conclusively, the addition of organic manure (50 %) with inorganic fertilizers (50 %) and reduced amount of irrigation (pre-sowing and jointing-period irrigation) decreased the application amount of chemical fertilizers and water, while increased SOM and nutrient content, improved prokaryotic diversity, and changed prokaryotic microbial community structure in the wheat root zone, resulting in enhanced nutrient uptake and wheat yield.

Identification of the core c-di-GMP turnover proteins responsible for root colonization of Bacillus velezensis

Root colonization by beneficial rhizobacteria determines their plant beneficial effects. The messenger c-di-GMP is involved in the bacterial transition process between motility and biofilm, which are crucial to the colonization ability of the rhizobacteria. In this study, we identified three GGDEF domain-containing proteins (YdaK, YhcK, and YtrP) and two EAL domain-containing proteins (YuxH and YkuI) in beneficial rhizobacterium Bacillus velezensis SQR9. We found that deficiency of ytrP or ykuI in SQR9 led to impaired biofilm formation, while deficiency of yuxH led to weakened motility. Further investigation showed that YtrP, YuxH, and YkuI all contributed to the root colonization of SQR9 on cucumber root. Further bioinformatics analysis showed that YtrP and YuxH are conserved in plant beneficial Bacillus group, while they do not occur in animal pathogenic Bacillus. This research will be useful for enhancing the beneficial function of Bacillus spp. in agricultural application.

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C-di-GMP is involved in root colonization of B. velezensis

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YtrP and YkuI enhance the root colonization by regulating biofilm of B velezensis

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YuxH enhances the root colonization by affecting the motility of B. velezensis

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YtrP and YuxH are conserved in plant beneficial Bacillus group

Characterization of a new Bacillus velezensis as a powerful biocontrol agent against tomato gray mold

Biocontrol microbes are environment-friendly and safe for humans and animals. To seek biocontrol microbes effective in suppressing tomato gray mold is important for tomato production. Therefore, serial experiments were conducted to characterize the antagonism of Bacillus velezensis HY19, a novel self-isolated biocontrol bacterium, against Botrytis cinerea in vitro and the control on tomato gray mold in greenhouse. This bacterium produced extracellular phosphatase, protease, cellulose and siderophores, and considerably inhibited the growth of B. cinerea. A liquid chromatography-mass spectrometry (LC-MS) detected salicylic acid and numerous antifungal substances present in B. velezensis HY19 fermentation liquid (BVFL). When B. cinerea was grown on potato glucose agar, BVFL crude extract remarkably suppressed the fungal growth and reduced protein content and the activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD). Transcriptome studies showed that BVFL crude extract significantly induced different expression of numerous genes in B. cinerea, most of which were down-regulated. Theses differently expressed genes were involved in the biological process, cell compartment, molecular functions, and metabolisms of glycine, serine, threonine, and sulfur in pathogen hyphae. Thus, this biocontrol bacterium antagonized B. cinerea in multiple ways due to the production of numerous antifungal substances that acted on multiple targets in the cells. BVFL significantly increased antioxidant enzyme activities in tomato leaves and decreased the incidence of tomato gray mold, with the control efficacies of 73.12-76.51%. Taken together, B. velezensis HY19 showed a promising use potential as a powerful bioagent against tomato gray mold.

Plant growth-promoting rhizobacterial biofertilizers for crop production: The past, present, and future

Recent decades have witnessed increased agricultural production to match the global demand for food fueled by population increase. Conventional agricultural practices are heavily reliant on artificial fertilizers that have numerous human and environmental health effects. Cognizant of this, sustainability researchers and environmentalists have increased their focus on other crop fertilization mechanisms. Biofertilizers are microbial formulations constituted of indigenous plant growth-promoting rhizobacteria (PGPR) that directly or indirectly promote plant growth through the solubilization of soil nutrients, and the production of plant growth-stimulating hormones and iron-sequestering metabolites called siderophores. Biofertilizers have continually been studied, recommended, and even successfully adopted for the production of many crops in the world. These microbial products hold massive potential as sustainable crop production tools, especially in the wake of climate change that is partly fueled by artificial fertilizers. Despite the growing interest in the technology, its full potential has not yet been achieved and utilization still seems to be in infancy. There is a need to shed light on the past, current, and future prospects of biofertilizers to increase their understanding and utility. This review evaluates the history of PGPR biofertilizers, assesses their present utilization, and critically advocates their future in sustainable crop production. It, therefore, updates our understanding of the evolution of PGPR biofertilizers in crop production. Such information can facilitate the evaluation of their potential and ultimately pave the way for increased exploitation.

Production of extracellular amylase contributes to the colonization of Bacillus cereus 0-9 in wheat roots

Background

Bacteria usually secrete a variety of extracellular enzymes to degrade extracellular macromolecules to meet their nutritional needs and enhance their environmental adaptability. Bacillus cereus 0–9, a biocontrol bacterial strain isolated from wheat roots, has three genes annotated as encoding amylases in the genome, but their functions are unknown, and whether they are involved in the colonization process of the bacterium remains to be further studied.

Methods

Mutant gene strains and fluorescently tagged strains were constructed by homologous recombination, and amylase protein was expressed in the prokaryotic Escherichia coli BL21(DE3) expression system. The iodine staining method was used to measure the activity of amylase proteins. We further observed the colonization abilities of the test strains in wheat roots through frozen section technology.

Results

The results showed that there were three amylase-encoding genes, amyC, amyP and amyS, in the B. cereus 0–9 genome. Among the three amylase encoding genes, only amyS produced extracellular amylase whose secretion was related to signal peptide at position 1–27. The AmyS protein encoded by the amyS gene is an α-amylase. The growth of Rhizoctonia cerealis was inhibited 84.7% by B. cereus 0–9, but the biocontrol ability of the ΔamyS strain decreased to 43.8% and that of ΔamyS/amyS was restored when the amyS gene was complemented. Furthermore, the biocontrol ability of the ΔamySec strain was decreased to 46.8%, almost the same as that of the ΔamyS mutant. Due to the deletion of the amyS gene, the colonization capacities of ΔamyS (RFP) and ΔamySec (RFP) in wheat roots decreased, while that of ΔamyS/amyS (RFP) was restored after the amyS gene was complemented, indicating that the amyS gene influences the colonization of B. cereus 0–9 in wheat roots. In addition, the colonization and biocontrol abilities of the mutant were restored after the addition of sugars, such as glucose and maltose.

Conclusions

B. cereus 0–9 encodes three genes annotated as amylases, amyC, amyP and amyS. Only the deletion of the amyS gene with a signal peptide did not produce extracellular amylase. The AmyS protein encoded by the amyS gene is an α-amylase. Our results indicated that the amyS gene is closely related to the colonization abilities of B. cereus 0–9 in wheat roots and the biocontrol abilities of B. cereus 0–9 to fight against R. cerealis. The extracellular amylase produced by B. cereus 0–9 can hydrolyze starch and use glucose, maltose and other nutrients to meet the needs of bacterial growth. Therefore, it is very possible that the secretion and hydrolytic activities of extracellular amylase can promote the colonization of B. cereus 0–9 in wheat roots and play important roles in the prevention and control of plant diseases. Our results contribute to exploring the mechanisms of microbial colonization in plant roots.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02618-7.

The bacterial world inside the plant

Sustainable agriculture requires the recruitment of bacterial agents to reduce the demand for mineral fertilizers and pesticides such as bacterial endophytes. Bacterial endophytes represent a potential alternative to the widespread use of synthetic fertilizers and pesticides in conventional agriculture practices. Endophytes are formed by complex microbial communities and microorganisms that colonize the plant interior for at least part of their life. Their functions range from mutualism to pathogenicity. Bacterial endophytes colonize plant tissues, and their composition and diversity depend on many factors, including the plant organ, physiological conditions, plant growth stage, and environmental conditions. The presence of endophytes influences several vital activities of the host plant. They can promote plant growth, elicit a defense response against pathogen attack, and lessen abiotic stress. Despite their potential, especially with regard to crop production and environmental sustainability, research remains sparse. This review provides an overview of the current research, including the concept of endophytes, endophytes in plant organs, endophyte colonization, nutrient efficiency use, endophytes and crop nutrition, inoculation with synergistic bacteria, the effect of inoculum concentration on plant root microbiota and synthetic communities. It also examines the practical opportunities and challenges when utilizing endophytes in the field of sustainable agriculture. Finally, it explores the importance of these associations with regard to the future of agriculture and the environment.

Bacillus thuringiensis PM25 ameliorates oxidative damage of salinity stress in maize via regulating growth, leaf pigments, antioxidant defense system, and stress responsive gene expression

Soil salinity is the major abiotic stress that disrupts nutrient uptake, hinders plant growth, and threatens agricultural production. Plant growth-promoting rhizobacteria (PGPR) are the most promising eco-friendly beneficial microorganisms that can be used to improve plant responses against biotic and abiotic stresses. In this study, a previously identified B. thuringiensis PM25 showed tolerance to salinity stress up to 3 M NaCl. The Halo-tolerant Bacillus thuringiensis PM25 demonstrated distinct salinity tolerance and enhance plant growth-promoting activities under salinity stress. Antibiotic-resistant Iturin C (ItuC) and bio-surfactant-producing (sfp and srfAA) genes that confer biotic and abiotic stresses were also amplified in B. thuringiensis PM25. Under salinity stress, the physiological and molecular processes were followed by the over-expression of stress-related genes (APX and SOD) in B. thuringiensis PM25. The results detected that B. thuringiensis PM25 inoculation substantially improved phenotypic traits, chlorophyll content, radical scavenging capability, and relative water content under salinity stress. Under salinity stress, the inoculation of B. thuringiensis PM25 significantly increased antioxidant enzyme levels in inoculated maize as compared to uninoculated plants. In addition, B. thuringiensis PM25-inoculation dramatically increased soluble sugars, proteins, total phenols, and flavonoids in maize as compared to uninoculated plants. The inoculation of B. thuringiensis PM25 significantly reduced oxidative burst in inoculated maize under salinity stress, compared to uninoculated plants. Furthermore, B. thuringiensis PM25-inoculated plants had higher levels of compatible solutes than uninoculated controls. The current results demonstrated that B. thuringiensis PM25 plays an important role in reducing salinity stress by influencing antioxidant defense systems and abiotic stress-related genes. These findings also suggest that multi-stress tolerant B. thuringiensis PM25 could enhance plant growth by mitigating salt stress, which might be used as an innovative tool for enhancing plant yield and productivity.

Emerging Function of Ecotype-Specific Splicing in the Recruitment of Commensal Microbiome

In recent years, host-microbiome interactions in both animals and plants has emerged as a novel research area for studying the relationship between host organisms and their commensal microbial communities. The fitness advantages of this mutualistic interaction can be found in both plant hosts and their associated microbiome, however, the driving forces mediating this beneficial interaction are poorly understood. Alternative splicing (AS), a pivotal post-transcriptional mechanism, has been demonstrated to play a crucial role in plant development and stress responses among diverse plant ecotypes. This natural variation of plants also has an impact on their commensal microbiome. In this article, we review the current progress of plant natural variation on their microbiome community, and discuss knowledge gaps between AS regulation of plants in response to their intimately related microbiota. Through the impact of this article, an avenue could be established to study the biological mechanism of naturally varied splicing isoforms on plant-associated microbiome assembly.

Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere?

Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays, but they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.

Prospecting potential of endophytes for modulation of biosynthesis of therapeutic bioactive secondary metabolites and plant growth promotion of medicinal and aromatic plants

Medicinal and aromatic plants possess pharmacological properties (antidiabetes, anticancer, antihypertension, anticardiovascular, antileprosy, etc.) because of their potential to synthesize a wide range of therapeutic bioactive secondary metabolites. The concentration of bioactive secondry metabolites depends on plant species, local environment, soil type and internal microbiome. The internal microbiome of medicinal plants plays the crucial role in the production of bioactive secondary metabolites, namely alkaloids, steroids, terpenoids, peptides, polyketones, flavonoids, quinols and phenols. In this review, the host specific secondry metabolites produced by endophytes, their therapeutic properties and host-endophytes interaction in relation to production of bioactive secondry metaboloites and the role of endophytes in enhancing the production of bioactive secondry metabolites is discussed. How biological nitrogen fixation, phosphorus solubilization, micronutrient uptake, phytohormone production, disease suppression, etc. can play a vital role in enhacing the plant growth and development.The role of endophytes in enhancing the plant growth and content of bioactive secondary metabolites in medicinal and aromatic plants in a sustainable mode is highlighted.

Current perspectives on the beneficial effects of soybean isoflavones and their metabolites on plants

Soybeans have traditionally been a staple part of the human diet being highly rich in protein and lipid content. In an addition to the high nutritional components, soybeans have several functional components, like isoflavones, saponins, lecithin, and oligosaccharides. Soybeans emerge as a healthy functional food option. Isoflavones are most notable functional component of soybeans, exhibiting antioxidant activity while preventing plant-related diseases (e.g., antimicrobial and antiherbivore activities) and having positive effects on the life quality of plants. Isoflavones are thus sometimes referred to as phytochemicals. The latest research trends evince substantial interest in the biological efficacy of isoflavones in the human body as well as in plants and their related mechanisms. However, there is little information on the relationship between isoflavones and plants than beneficial human effects. This review discusses what is known about the physiological communication (transport and secretion) between isoflavones and plants, especially in soybeans.

Biohardening of Banana cv. Karpooravalli (ABB; Pisang Awak) With Bacillus velezensis YEBBR6 Promotes Plant Growth and Reprograms the Innate Immune Response Against Fusarium oxysporum f.sp. cubense

Induction of innate immune response and growth promotion in banana by B. velezensis against Foc.