Comparative Genomics and In Vitro Plant Growth Promotion and Biocontrol Traits of Lactic Acid Bacteria from the Wheat Rhizosphere

Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects

Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.

The effect of seed germination and Bacillus spp. on the ripening of plant cheese analogs

Consumer demand for plant cheeses is increasing, but challenges of improving both flavor and quality remain. This study investigated the microbiological and physicochemical impact of seed germination and fermentation with Bacillus velezensis and Bacillus amyloliquefaciens on the ripening of plant cheese analogs. Chlorine treatment or addition of Lactiplantibacillus plantarum and Lactococcus lactis controlled microbial growth during seed germination. Lp. plantarum and Lc. lactis also served as starter cultures for the acidification of soy and lupine milk and were subsequently present in the unripened plant cheese as dominant microbes. Acidification also inhibited the growth and metabolic activity of bacilli but Bacillus spores remained viable throughout ripening. During plant cheese ripening, Lc. lactis was inactivated before Lp. plantarum and the presence of bacilli during seed germination delayed Lc. lactis inactivation. Metagenomic sequencing of full-length 16S rRNA gene amplicons confirmed that the relative abundance of the inoculated strains in each ripened cheese sample exceeded 99%. Oligosaccharides including raffinose, stachyose, and verbascose were rapidly depleted in the initial stage of ripening. Both germination and the presence of bacilli during seed germination had impact on polysaccharide hydrolysis during ripening. Bacilli but not seed germination enhanced proteolysis of plant cheese during ripening. In conclusion, the use of germination with lactic acid bacteria in combination with Bacillus spp. exhibited the potential to improve the quality of ripened plant cheeses with a positive effect on the reduction of hygienic risks.

IMPORTANCE

The development of novel plant-based fermented food products for which no traditional templates exist requires the development of starter cultures. Although the principles of microbial flavor formation in plant-based analogs partially overlap with dairy fermentations, the composition of the raw materials and thus likely the selective pressure on the activity of starter cultures differs. Experiments that are described in this study explored the use of seed germination, the use of lactic acid bacteria, and the use of bacilli to reduce hygienic risks, to acidify plant milk, and to generate taste-active compounds through proteolysis and fermentative conversion of carbohydrates. The characterization of fermentation microbiota by culture-dependent and culture-independent methods also confirmed that the starter cultures used were able to control microbial communities throughout 90 d of ripening. Taken together, the results provide novel tools for the development of plant-based analogs of fermented dairy products.

Microbiology of fermented soy foods in Asia: Can we learn lessons for production of plant cheese analogues?

The food industry is facing the challenge of creating innovative, nutritious, and flavored plant-based products, due to consumer's increasing demand for the health and environmental sustainability. Fermentation as a unique and effective tool plays an important role in the innovation of food products. Traditional fermented soy foods are popular in many Asian and African countries as nutritious, digestible and flavorful daily staples or condiments. They are produced by specific microorganisms with the unique fermentation process in which microorganisms convert the ingredients of whole soybean or soybean curd to flavorful and functional molecules. This review provides an overview on traditional fermented food produced from soy, including douchi, natto, tempeh, and sufu as well as stinky tofu, including the background of these products, the manufacturing process, and the microbial diversity involved in fermentation procedures as well as flavor volatiles that were identified in the final products. The contribution of microbes to the quality of these five fermented soy foods is discussed, with the comparison to the role of cheese ripening microorganisms in cheese flavor formation. This communication aims to summarize the microbiology of fermented soy foods in Asia, evoking innovative ideas for the development of new plant-based fermented foods especially plant-based cheese analogues.

Biochemical and pharmaceutical traits of Marrubium vulgare L. plants treated with plant growth-promoting bacteria and elevated CO2

The present research aimed to understand the influence of plant growth-promoting bacteria (PGPB) on various biochemical, nutritional, and pharmaceutical characteristics of Marrubium vulgare plants grown under elevated carbon dioxide (eCO2). To achieve this objective, a pot experiment was carried out, consisting of two treatments, namely: (i) biofertilization (Bf) by a PGPB strain (Micromonospora sp.) and (ii) two different air CO2 levels, including ambient CO2 (aCO2) and eCO2 concentrations (410 and 710 μmol CO2 mol-1, respectively). The improvement in the photosynthesis rate of eCO2 and Bf-treated plants can explain the increase in the production of carbohydrate. This is evidenced by a substantial rise, reaching up to + 75% and 25% in the total sugar and starch content in plants subjected to eCO2 treatment, respectively. Additionally, eCO2-treated plants exhibited a remarkable 102% increase in soluble sugar synthesis, while plants subjected to Bf treatment showed a notable increase of 66%. Such modifications could be the main factor affecting plants carbon and nitrogen metabolism. Although the level of certain amino acids (such as glycine, tyrosine, and phenylalanine) in plants exhibited significant increases in response to eCO2 and Bf, the levels of other amino acids demonstrated enhancements in plants grown under eCO2 (e.g., histidine) or under treatments containing Bf (e.g., alanine and ornithine). Improvements in primary metabolites led to more benefits in plants treated with Bf and CO2 by boosting secondary metabolites accumulation, including phenolics (+ 27-100%), flavonoids (+ 30-92%), and essential oils (up to + 296%), as well as improved antioxidant capacity (FRAP). This remarkable effectiveness was evident in the significant increase in the biomass production, highlighting the synergistic impact of the treatments. Therefore, the interaction of Bf and eCO2 not only induced plant biomass accumulation but also improved the nutritional and pharmaceutical value of M. vulgare plants.

Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family

Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.

Impact of Enterococcus italicus ONU547 on the growth and acclimatization of micropropagated Rubus fruticosus L. and Paulownia tomentosa Steud. plants to ex vitro conditions

Clonal micropropagation is an effective method for plant reproduction, applicable in both scientific and industrial domains. However, a significant number of microclones are lost during the ex vitro acclimatization process. To address this, the introduction of beneficial microorganisms into the rhizosphere of micropropagated plants could have a positive effect on the survival rates and external characteristics of acclimatized plantlets. The aim of this study was to determine the protective and growth-promoting potential of Enterococcus italicus ONU547 and its effect on micropropagated plants during acclimatization. The antagonistic activity of the bacteria was determined using the agar block method. Lepidium sativum L. seeds were inoculated with bacterial suspensions at concentrations of 106, 107, and 108 CFU/ml. Subsequently, the roots of the microclones were treated with suspensions of 106 and 107 CFU/ml, and biometric characteristics were measured. The results demonstrated antagonistic properties against various phytopathogenic fungi, including Aspergillus niger, Cladosporium cladosporioides, Alternaria alternata, Alternaria tenuissima, Rhizoctonia cerealis, Penicillium expansum, and Paecilomyces variotii. Inoculation of L. sativum L. seeds resulted in improved germination rates, increased root numbers, and enhanced root and shoot lengths. Similarly, the effects of the studied bacteria on Rubus fruticosus L. and Paulownia tomentosa Steud. during the acclimatization stage led to higher survival rates, increased shoot lengths, greater node numbers, and larger leaf areas. A concentration of 107 CFU/ml was identified as optimal for inoculating the microclones. The findings indicate that E. italicus ONU547 holds promise for the inoculation of micropropagated plants during the acclimatization process. Further research is recommended to establish the specific interaction mechanisms between these bacteria and plants.

Chromium(VI) Toxicity and Active Tolerance Mechanisms of Wheat Plant Treated with Plant Growth-Promoting Actinobacteria and Olive Solid Waste

The present study aimed to assess the potential of plant growth-promoting Actinobacteria and olive solid waste (OSW) in ameliorating some biochemical and molecular parameters of wheat (Triticum aestivum) plants under the toxicity of high chromium levels in the soil. With this aim, a pot experiment was conducted, where the wheat plants were treated with a consortium of four Actinobacterium sp. (Bf treatment) and/or OSW (4% w/w) under two levels of nonstress and chromium stress [400 mg Cr(VI) per kg of soil] to estimate the photosynthetic traits, antioxidant protection machine, and detoxification activity. Both Bf and OSW treatments improved the levels of chlorophyll a (+47-98%), carotenoid (+324-566%), stomatal conductance (+17-18%), chlorophyll fluorescence (+12-28%), and photorespiratory metabolism (including +44-72% in glycolate oxidase activity, +6-72% in hydroxypyruvate reductase activity, and +5-44% in a glycine to serine ratio) in leaves of stressed plants as compared to those in the stressed control, which resulted in higher photosynthesis capacity (+18-40%) in chromium-stressed plants. These results were associated with an enhancement in the content of antioxidant metabolites (+10-117%), of direct reactive oxygen species-detoxifying enzymes (+49-94%), and of enzymatic (+40-261%) and nonenzymatic (+17-175%) components of the ascorbate-glutathione cycle in Bf- and OSW-treated plants under stress. Moreover, increments in the content of phytochelatins (+38-74%) and metallothioneins (+29-41%), as markers of detoxification activity, were recorded in the plants treated with Bf and OSW under chromium toxicity. In conclusion, this study revealed that the application of beneficial Actinobacteria and OSW as biofertilization/supplementation could represent a worthwhile consequence in improving dry matter production and enhancing plant tolerance and adaptability to chromium toxicity.

Galaxolide-contaminated soil and tolerance strategies in soybean plants using biofertilization and selenium nanoparticle supplementation

The current study aimed to address the response of soybean (Glycine max) plants to biofertilization and selenium supplementation treatments under galaxolide contamination of soil. In this regard, a pot experiment was carried out where the soybean plants were treated with the plant growth-promoting Actinobacteria (Actinobacterium sp.) as a biofertilizer (PGPB treatment) and/or selenium nanoparticles (Se treatment; 25 mg L-1) under two non-polluted and galaxolide-polluted soils (250 mg galaxolide per kg of soil) to assess the modifications in some plant physiological and biochemical traits. Although higher accumulation of oxidative biomarkers, including hydrogen peroxide (+180%), malondialdehyde (+163%), and protein oxidation (+125%), indicating oxidative stress in galaxolide-contaminated plants, an apparent decline in their contents was observed in response to biofertilization/supplementation treatments in contaminated soil, especially. It was mainly related to the higher detoxification of ROS in PGPB- and Se-treated plants under galaxolide-induced oxidative stress, in which the direct ROS-scavenging enzymes (+44 -179%), enzymatic (+34 - 293%) and non-enzymatic (+35 - 98%) components of the ascorbate-glutathione pathway, and antioxidant molecules (+38 - 370%) were more activated than in control plants. In addition, a higher accumulation of detoxification activity markers, including phytochelatins (+32%) and metallothioneins (+79%), were found in the combined treatments (PGPB+Se) under galaxolide contamination. Moreover, combined treatment with PGPB and Se ameliorated the levels of chlorophyll a content (+58%), stomatal conductance (+57%), the maximum efficiency of photosystem II (PSII) (+36%), and photorespiratory metabolism (including +99% in glycolate oxidase and +54% in hydroxypyruvate reductase activity) in leaves under galaxolide contamination, which resulted in higher photosynthesis capacity (+36%) and biomass production (+74%) in galaxolide-stressed plants as compared to control group. In conclusion, the application of beneficial Actinobacteria and selenium nanoparticles as biofertilization/supplementation is expected to be useful for improving plant toleration and adaptation against galaxolide contamination.

Synergistic Impacts of Plant-Growth-Promoting Bacteria and Selenium Nanoparticles on Improving the Nutritional Value and Biological Activities of Three Cultivars of Brassica Sprouts

Due to the growing world population and increasing environmental stress, improving the production, nutritional quality, and pharmaceutical applications of plants have become an urgent need. Therefore, current research was designed to investigate the impact of seed priming using plant-growth-promoting bacteria (PGPB) along with selenium nanoparticles (SeNPs) treatment on chemical and biological properties of three Brassica oleracea cultivars [Southern star (VA1), Prominence (VA2), Monotop (VA3)]. With this aim, one out of five morphologically different strains of bacteria, namely, JM18, which was further identified via 16S rRNA gene sequencing as a Nocardiopsis species with strong plant-growth-promoting traits, isolated from soil, was used. To explore the growth-promoting potential of Nocardiopsis species, seeds of three varieties of B. oleracea were primed with JM18 individually or in combination with SeNP treatment. Seed treatments increased sprout growth (fresh and dry weights) and glucosinolate accumulation. The activity of myrosinase was significantly increased through brassica sprouts and consequently enhanced the amino-acid-derived glucosinolate induction. Notably, a reduction in effective sulforaphane nitrile was detected, being positively correlated with a decrease in epithiospecifier protein (EP). Consequently, the antioxidant activities of VA2 and VA3, determined by the ferric reducing antioxidant power (FRAP) assay, were increased by 74 and 79%, respectively. Additionally, the antibacterial activities of JM18-treated cultivars were improved. However, a decrease was observed in SeNP- and JM18 + SeNP-treated VA2 and VA3 against Serratia marcescens and Candida glabrata and VA1 against S. marcescens. In conclusion, seed priming with the JM18 extract is a promising method to enhance the health-promoting activities of B. oleracea sprouts.

A biochemical analysis of Black Soldier fly (Hermetia illucens) larval frass plant growth promoting activity

Black Soldier fly (Hermetia illucens) larval (BSFL) frass was examined for its nutrient nitrogen, phosphate and potassium (N:P205:K2O), phytohormone and biogenic amine content, its plant growth promoting activity, and screened to test the hypothesis that bacteria characteristic of the genus Enterococcus (present in the biome of decaying catering waste and the larval gut) are excreted by BSFL in their frass. Frass plant growth promoting activity was measured by comparing the growth of winter wheat berry (Triticum aestivum) in frass treated soil to that of untreated (control) soil. The N:P205:K2O percent dry matter average, biogenic amine and phytohormone content of frass was determined by standard soil analysis, HPLC and HPLC/GC-MS methodologies, respectively. All were at too low of concentrations to account for its plant growth promoting activity. Frass added to soil induced a 11% increase in aerial mass and shoot length in treated plants over controls. Numerous colonies of Enterococci growing out on BEA (bile-esculin-agar) plates were detected in frass collected directly from larvae confirming the hypothesis that viable Enteroccoci are passing from the larval gut into their frass. Since a number of rhizobacteria, including Enterococci, have previously been identified as part of the larval gut biome, the passage of Enterococci from the larval gut into frass in the face of only trace N:P205:K2O percent dry matter averages, biogenic amine and phytohormone content is consistent with the hypothesis that Enterococci exhibiting rhizobacterial activity have a role in conferring to frass its plant growth promoting activity.

Interaction between plants and epiphytic lactic acid bacteria that affect plant silage fermentation

Lactic acid bacteria (LAB) have the ability to ferment water-soluble carbohydrates, resulting in the production of significant amounts of lactic acid. When utilized as additives in silage fermentation and feed, they have been shown to enhance the quality of these products. Epiphytic LAB of plants play a major role in the fermentation of silage plants. Plant species in turn affect the community structure of epiphytic LAB. In recent years, an increasing number of studies have suggested that epiphytic LAB are more effective than exogenous LAB when applied to silage. Inoculating silage plants with epiphytic LAB has attracted extensive attention because of the potential to improve the fermentation quality of silages. This review discusses the interaction of epiphytic LAB with plants during silage fermentation and compares the effects of exogenous and epiphytic LAB on plant fermentation. Overall, this review provides insight into the potential benefits of using epiphytic LAB as an inoculant and proposes a theoretical basis for improving silage quality.

Positive biofilms to guide surface microbial ecology in livestock buildings

The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.

Inoculation with carbofuran-degrading rhizobacteria promotes maize growth through production of IAA and regulation of the release of plant-specialized metabolites

Toxic residues of the insecticide carbofuran in farmland is an urgent problem, and high concentrations of carbofuran have been found in the rhizoshperic soil of maize treated with seed coating agents 120-180 days after planting. Using an enrichment co-culture method, we identify a bacterial strain obtained from these carbofuran-contaminated rhizosphere soils as Leclercia adecarboxylata MCH-1. This strain exhibited a significant ability to degrade both carbofuran and 3-keto carbofuran, with total degradation of 55.6 ± 4.6% and 75.7 ± 3.4%, respectively, 24 h following start of co-culture. Further activity screening revealed that the inoculation of maize roots with L. adecarboxylata MCH-1 promoted maize seedling growth. Quantitative analysis demonstrated that this bacterial strain had the ability to synthesize the phytohormone IAA. Simultaneously, the concentration of IAA in the rhizospheric soil increased following inoculation of maize roots with L. adecarboxylata MCH-1. Moreover, the concentrations of plant specialized metabolites, including phenolics, terpenoids, and alkaloids, decreased in maize seedlings and were elevated in the rhizospheric soil after maize roots had been inoculated with the MCH-1 strain. Interestingly, the growth of the strain MCH-1 was improved by co-culture with root exudates obtained from the rhizospheric soil, specifically 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, and zealexin A₁ (ZA₁). Taken together, our results suggest that the carbofuran-degrading rhizobacterium L. adecarboxylata MCH-1 is able to interact with maize plants through the regulation of maize root exudates. Moreover, inoculation with L. adecarboxylata MCH-1 promotes maize growth through the production of IAA and regulation of the release of plant specialized metabolites. Our results provide a new model organism for the remediation of farmland soils from pollution with carbofuran residues.

Application of Lactic Acid Bacteria (LAB) in Sustainable Agriculture: Advantages and Limitations

Lactic acid bacteria (LAB) are significant groups of probiotic organisms in fermented food and are generally considered safe. LAB regulate soil organic matter and the biochemical cycle, detoxify hazardous chemicals, and enhance plant health. They are found in decomposing plants, traditional fermented milk products, and normal human gastrointestinal and vaginal flora. Exploring LAB identified in unknown niches may lead to isolating unique species. However, their classification is quite complex, and they are adapted to high sugar concentrations and acidic environments. LAB strains are considered promising candidates for sustainable agriculture, and they promote soil health and fertility. Therefore, they have received much attention regarding sustainable agriculture. LAB metabolites promote plant growth and stimulate shoot and root growth. As fertilizers, LAB can promote biodegradation, accelerate the soil organic content, and produce organic acid and bacteriocin metabolites. However, LAB show an antagonistic effect against phytopathogens, inhibiting fungal and bacterial populations in the rhizosphere and phyllosphere. Several studies have proposed the LAB bioremediation efficiency and detoxification of heavy metals and mycotoxins. However, LAB genetic manipulation and metabolic engineered tools provide efficient cell factories tailor-made to produce beneficial industrial and agro-products. This review discusses lactic acid bacteria advantages and limitations in sustainable agricultural development.