Complete genome sequences of Rhizobium sp. strain SL42 and Hydrogenophaga sp. strain SL48, microsymbionts of Amphicarpaea bracteata

This study comprehensively analyzed two distinct rhizobacterial strains, Rhizobium sp. SL42 and Hydrogenophaga sp. SL48, through whole genome de novo sequencing. Isolated from root nodules of Amphicarpaea bracteata, a native legume related to soybean, they were selected to explore beneficial rhizobacteria from native plant relatives. Utilizing Illumina and Nanopore sequencers and MaSuRCA assembly, their complete genetic information was elucidated. Rhizobium sp. SL42 has a 4.06 Mbp circular chromosome and two plasmids with 60% GC content, while Hydrogenophaga sp. SL48 exhibits a 5.43 Mbp circular chromosome with 65% GC content. Genetic analysis identified them as new species, supported by ANI values (77.72% for SL42 and 83.39% for SL48) below the threshold. The genomic analysis unraveled a plethora of genes encoding diverse metabolic functions, secretion systems for substance transport, quorum sensing for coordination, and biosynthetic gene clusters suggesting the production of bioactive compounds. These functional properties contribute to plant growth stimulation, reflecting the symbiotic relationship of rhizobacteria with plants, potentially involving nitrogen fixation and growth-promoting compounds. This research contributes valuable knowledge about plant-microbe interactions and plant growth promotion by these two strains of rhizobacteria

Lipo-chitooligosaccharide and thuricin 17 act as plant growth promoters and alleviate drought stress in Arabidopsis thaliana

Lipo-chito-oligosaccharide (LCO–from Bradyrhizobium japonicum) and thuricin 17 (Th17–from Bacillus thuringiensis) are bacterial signal compounds from the rhizosphere of soybean that have been shown to enhance plant growth in a range of legumes and non-legumes. In this study, an attempt to quantify phytohormones involved in the initial hours after exposure of Arabidopsis thaliana to these compounds was conducted using UPLC-ESI-MS/MS. A petri-plate assay was conducted to screen for drought stress tolerance to PEG 8000 infusion and plant growth was studied 21-days post-stress. Arabidopsis thaliana plants grown in trays with drought stress imposed by water withhold were used for free proline determination, elemental analysis, and untargeted proteomics using LC-MS/MS studies. At 24 h post-exposure to the signal compounds under optimal growth conditions, Arabidopsis thaliana rosettes varied in their responses to the two signals. While LCO-treated rosettes showed a decrease in total IAA, cytokinins, gibberellins, and jasmonic acid, increases in ABA and SA was very clear. Th17-treated rosettes, on the other hand, showed an increase in IAA and SA. Both treatments resulted in decreased JA levels. Under severe drought stress imposed by PEG 8000 infusion, LCO and Th17 treatments were found to significantly increase fresh and dry weight over drought-stressed control plates, indicating that the presence of the signaling compounds decreased the negative effects experienced by the plants. Free proline content increased in LCO- and Th17-treated plants after water-withhold drought stress. Elemental analysis showed a significant increase in carbon percentage at the lower concentration of Th17. Untargeted proteomics revealed changes in the levels of drought-specific ribosomal proteins, glutathione S-transferase, late embryogenesis proteins, vegetative storage proteins 1 and 2, thaumatin-like proteins, and those related to chloroplast and carbon metabolism. The roles of some of these significantly affected proteins detected under drought stress are discussed

Effect of NaCl stress on exoproteome profiles of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H

Salt stress can affect survival, multiplication and ability of plant growth promoting microorganisms to enhance plant growth. Changes in a microbe’s proteome profile is one of the mechanisms employed by PGPM to enhance tolerance of salt stress. This study was focused on understanding changes in the exoproteome profile of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H when exposed to salt stress. The strains were cultured in 100 mL M13 (B. amyloliquefaciens) and 100 mL De man, Rogosa and Sharpe (MRS) (L. helveticus) media, supplemented with 200 and 0 mM NaCl (control), at pH 7.0. The strains were then incubated for 48 h (late exponential growth phase), at 120 rpm and 30 (B. amyloliquefaciens) and 37 (L. helveticus) °C. The microbial cultures were then centrifuged and filtered sterilized, to obtain cell free supernatants whose proteome profiles were studied using LC–MS/MS analysis and quantified using scaffold. Results of the study revealed that treatment with 200 mM NaCl negatively affected the quantity of identified proteins in comparison to the control, for both strains. There was upregulation and downregulation of some proteins, even up to 100%, which resulted in identification of proteins significantly unique between the control or 200 mM NaCl (p ≤ 0.05), for both microbial species. Proteins unique to 200 mM NaCl were mostly those involved in cell wall metabolism, substrate transport, oxidative stress tolerance, gene expression and DNA replication and repair. Some of the identified unique proteins have also been reported to enhance plant growth. In conclusion, based on the results of the work described here, PGPM alter their exoproteome profile when exposed to salt stress, potentially upregulating proteins that enhance their tolerance to this stress

Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture

Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology

Mass spectometry based proteome profiling to understand the effects of Lipo-chito-oligasaccharide and Thuricin 17 in «Arabldopsis thaliana» and «Glycine max» under salt stress

Advances in chemical and bio-technology have helped boost modern agriculture with increased food productivity and consequently, impacted the environment leading to more saline and drought prone arable lands. Mandate of world food security heavily depends on crop improvement and developing strategies to increase abiotic stress tolerance. The use of rhizobacteria and their excreted compounds is a contextually safe and viable option. Lipo-chito-oligosaccharide (LCO) from Bradyrhizobium japonicum 532C and Thuricin 17 (Th17) from Bacillus thuringiensis NEB17 are bacterial signal compounds promoting plant growth in legumes and non-legumes. The effect of these compounds at proteome level under unstressed and salt stressed conditions on Arabidopsis thaliana was studied using root drench method. The phytohormones in Arabidopsis thaliana rosettes were differential expressed at 24 h treatment. At the proteome level, > 2-fold changes in the activation of the carbon and energy metabolism pathway proteins in both LCO and Th17 were observed in comparison to control. At 250 mM NaCl stress, the control plants under osmotic-shock shut down most of the carbon-metabolism and up-regulated the energy-metabolism and antioxidant pathways, while the LCO and Th17 with salt stress retained some of the Light harvesting complex, Photosystem I and II proteins along with the up-regulation of energy and antioxidant pathways suggesting that the rosettes were able to amend the salt stress better when treated with LCO and Th17.Soybean (Absolute RR) germination for salt tolerance suggested that LCO and Th17 helped seeds germinate the best at 100 mM NaCl. The proteome suggested efficient and speedier partitioning of storage proteins, up-regulation of carbon, nitrogen and energy metabolisms in LCO and Th17 seeds in comparison with controls both under optimal and salt stress. These findings suggest that the Arabidopsis rosettes and the soybean germinating seeds alter their proteome based on bacterial signals and on stress. The specificity of this response plays a crucial role in the plants life cycle, and understanding this response is of importance in commercial application.Les progrès de la chimie et de la biotechnologie ont contribué à stimuler l'agriculture moderne et la productivité accrue de nourriture. La conséquence en est l'impact sur l'environnement rendant les terres arables plus sujettes à la salinité et à la sécheresse. La sécurité alimentaire mondiale dépend fortement de l'amélioration des cultures et du développement de stratégies visant à accroître la tolérance aux stress abiotiques. L'utilisation de rhizobactéries et de leurs composés excrétés est dans ce contexte une option sécuritaire et viable.Le lipo-chito-oligosaccharide (LCO) du Bradyrhizobium japonicum 532C et le Thuricin 17 (Th17) du Bacillus thuringiensis NEB17 sont des composés de signaux de bactéries favorisant la croissance des plantes dans les légumineuses et les non-légumineuses. L'effet de ces composés au niveau du protéome d'Arabidopsis thaliana, sans stress et avec le stress du sel, a été étudié en utilisant la méthode par trempage de racine. Les phyto-hormones dans les rosettes d'Arabidopsis thaliana ont été exprimées de manière différentielle lors du traitement de 24h. Au niveau du protéome, des changements 2 fois supérieurs en comparaison au témoin ont été observés dans l'activation des protéines de la voie métabolique énergétique du carbone, pour LCO et pour Th17. Sous un stress produit par 250 mM de NaCl, les plants témoins sous choc osmotique ont diminué la plupart du métabolisme du carbone, et régulé à la hausse les voies du métabolisme énergétique et antioxydant ; tandis que LCO et Th17 sous stress salin ont conservé une partie du complexe de capture de la lumière, les protéines de Photosystem I et II, et régulé positivement les voies énergétiques et antioxydants. Cela suggère que les rosettes furent en mesure de modifier positivement le stress salin lorsque traitées avec LCO et Th17.La germination des graines de soja (Absolute RR) pour la tolérance au sel, a montré que LCO et Th17 aident les graines à germer de manière optimale avec 100 mM de NaCl. Pour les graines avec LCO et Th17 et par rapport aux témoins à la fois sous stress optimal et salin, le protéome suggère: une séparation des protéines de stockage éfficace et plus rapide, et la régulation à la hausse des métabolismes du carbone, de l'azote et énergétiques.Ces résultats démontrent que les rosettes d'Arabidopsis et les graines de soja en germination modifient leur protéome selon les signaux bactériens et le stress. La spécificité de cette réponse joue un rôle crucial dans le cycle de vie des plantes, et la compréhension de cette réponse est d'importance dans son application commerciale

Bacteriocins from the rhizosphere microbiome – from an agriculture perspective

Bacteria produce and excrete a versatile and dynamic suit of compounds to defend against microbial competitors and mediate local population dynamics. These include a wide range of broad-spectrum non-ribosomally synthesized antibiotics, lytic enzymes, metabolic by-products, proteinaceous exotoxins, and ribosomally produced antimicrobial peptides (bacteriocins). Most bacteria produce at least one bacteriocin. Bacteriocins are of interest in the food industry as natural preservatives and in the probiotics industry, leading to extensive studies on lactic acid bacteria (colicin produced by Escherichia coli is a model bacteriocin). Recent studies have projected use of bacteriocins in veterinary medicine and in agriculture, as biostimulants of plant growth and development and as biocontrol agents. For example, bacteriocins such as Cerein 8A, Bac-GM17, putidacin, Bac 14B, amylocyclicin have been studied for their mechanisms of anti-microbial activity. Bac IH7 promotes tomato and musk melon plant growth. Thuricin 17 (Th17) is the only bacteriocin studied extensively for plant growth promotion, including at the molecular level. Th17 functions as a bacterial signal compound, promoting plant growth in legumes and non-legumes. In Arabidopsis thaliana and Glycine max Th17 increased phytohormones IAA and SA at 24 h post treatment. At the proteome level Th17 treatment of 3-week-old A. thaliana rosettes led to >2-fold changes in activation of the carbon and energy metabolism pathway proteins, 24 h post treatment. At 250 mM NaCl stress, the control plants under osmotic-shock shut down most of carbon-metabolism and activated energy-metabolism and antioxidant pathways. Th17 treated plants, at 250 mM NaCl, retained meaningful levels of the light harvesting complex, photosystems I and II proteins and energy and antioxidant pathways were activated, so that rosettes could better withstand the salt stress. In Glycine max, Th17 helped seeds germinate in the presence of NaCl stress, and was most effective at 100 mM NaCl. The 48 h post germination proteome suggested efficient and speedier partitioning of storage proteins, activation of carbon, nitrogen and energy metabolisms in Th17 treated seeds both under optimal and 100 mM NaCl. This review focuses on the bacteriocins produced by plant-rhizosphere colonizers and plant-pathogenic bacteria, that might have uses in agriculture, veterinary, and human medicine

Proteomic Studies on the Effects of Lipo-Chitooligosaccharide and Thuricin 17 under Unstressed and Salt Stressed Conditions in Arabidopsis thaliana

Plants, being sessile organisms, are exposed to widely varying environmental conditions throughout their life cycle. Compatible plant-microbe interactions favor plant growth and development, and help plants deal with these environmental challenges. Microorganisms produce a diverse range of elicitor molecules to establish symbiotic relationships with the plants they associate with, in a given ecological niche. Lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17) are two such compounds shown to positively influence plant growth of both legumes and non-legumes. Arabidopsis thaliana responded positively to treatment with the bacterial signal compounds LCO and Th17 in the presence of salt stress (up to 250 mM NaCl). Shotgun proteomics of unstressed and 250 mM NaCl stressed A. thaliana rosettes (7 days post stress) in combination with the LCO and Th17 revealed many known, putative, hypothetical and unknown proteins. Overall, carbon and energy metabolic pathways were affected under both unstressed and salt stressed conditions when treated with these signals. PEP carboxylase, Rubisco-oxygenase large subunit, pyruvate kinase, and proteins of photosystem I and II were some of the noteworthy proteins enhanced by the signals, along with other stress related proteins. These findings suggest that the proteome of A. thaliana rosettes is altered by the bacterial signals tested, and more so under salt stress, thereby imparting a positive effect on plant growth under high salt stress. The roles of the identified proteins are discussed here in relation to salt stress adaptation, which, when translated to field grown crops can be a crucial component and of significant importance in agriculture and global food production. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD004742

Seed Priming with <i>Devosia</i> sp. Cell-Free Supernatant (CFS) and Citrus Bioflavonoids Enhance Canola and Soybean Seed Germination

Climate change, environmental pollution and associated abiotic stresses are beginning to meaningfully affect agricultural production worldwide. Salt stress is, however, one of the most important threats that significantly impairs plant growth and development. Plants in their early growth stages such as seed germination, seed emergence and early seedling growth are very sensitive to salt stress. Among the range of sustainable techniques adopted to improve seed germination and early plant growth is seed priming; however, with the use of ecofriendly substances, this is one of the most effective and economically viable techniques to improve seed tolerance against such environmental stresses. For instance, priming with appropriate non-synthetic compounds including microbial biostimulants are prominent ways to sustainably address these challenges. Therefore, in this research, by using the “priming technique”, two biostimulants were tested for their potential as sustainable approaches to improve canola and soybean seed germination under salt stress and optimal growth conditions. Canola and soybean seeds were primed with flavonoids extracted from citrus fruits (flavopriming) and cell-free supernatant (CFS; produced by a novel strain of Devosia sp.—SL43), alone and in combination, and exposed to low–higher levels of salt stress and ideal growth conditions. Both biostimulants showed promising effects by significantly improving seed germination of soybean and canola under both ideal and stressful conditions. However, increases in seed germination were greater under salinity stress as flavonoids and CFS with stress amelioration effects showed substantial and statistically significant improvements in seed germination under varying levels of salt stress. In addition, combinations (mixtures) of both biostimulants were tested to determine if their effects might be more additive or multiplicative than the individual applications. However, results suggested incompatibility of both biostimulants as none of the combinations showed better results than that of the individual applications of either flavonoids or CFS. Conceivably, the use of flavonoids and this novel Devosia sp. CFS could be significant plant growth enhancers, perhaps much better than the few other biostimulants and bacterial-based compounds currently in use

Cell-Free Supernatant (CFS) from <i>Bacillus subtilis</i> EB2004S and <i>Lactobacillus helveticus</i> EL2006H Cultured at a Range of pH Levels Modulates Potato Plant Growth under Greenhouse Conditions

Agriculture involving industrial fertilizers is another major human made contributing factor to soil pH variation after natural factors such as soil parent rock, weathering time span, climate, and vegetation. The current study assessed the potential effect of cell-free supernatant (CFS) obtained from Bacillus subtilis EB2004S and Lactobacillus helveticus EL2006H cultured at three pH levels (5, 7, and 8) on potato (var Goldrush) growth enhancement in a greenhouse pot experiment. The results showed that CFSs obtained from B. subtilis EB2004S and L. helveticus EL2006H cultured at pH 5 significantly improved photosynthetic rates, stomatal conductance, root fresh weight, and whole plant fresh weight. interactive effects of pot pH and that of CFSs obtained from pH 5 influenced chlorophyll, plant height, and shoot and whole plant fresh weight. Moreover, treatment 52EB2004S~0.4% initiated early tuberization for potato grown at pH 7 and 8. Potato grown at pH 5, which received a 72EB2004S~0.4% CFS treatment, had greater whole plant fresh and dry weight than that treated with L. helveticus EL2006H CFS and a positive control. Taken together, the findings of this study are unique in that it probed the effect of CFS produced under differing pH conditions which revealed a new possibility to mitigate stresses in plants