Assessment of Methylobacterium oryzae CBMB20 aggregates for salt tolerance and plant growth promoting characteristics for bio-inoculant development

Biotechnological potential of psychrotolerant methylobacteria isolated from biotopes of Antarctic oases

Ten strains of psychrotolerant methylotrophic bacteria were isolated from the samples collected in Larsemann and Bunger Hills (Antarctica). Most of the isolates are assigned to the genus Pseudomonas, representatives of the genera Janthinobacterium, Massilia, Methylotenera and Flavobacterium were also found. Majority of isolates were able to grow on a wide range of sugars, methylamines and other substrates. Optimal growth temperatures for the isolated strains varied from 6 °C to 28 °C. The optimal concentration of NaCl was 0.5-2.0%. The optimal pH values of the medium were 6-7. It was found that three strains synthesized indole-3-acetic acid on a medium with L-tryptophan reaching 11-12 μg/ml. The values of intracellular carbohydrates in several strains exceeded 50 μg/ml. Presence of calcium-dependent and lanthanum-dependent methanol dehydrogenase have been shown for some isolates. Strains xBan7, xBan20, xBan37, xBan49, xPrg27, xPrg48, xPrg51 showed the presence of free amino acids. Bioprospection of Earth cryosphere for such microorganisms has a potential in biotechnology.

Effects of in situ Fe oxide precipitation on As stabilization and soil ecological resilience under salt stress

Iron (Fe) oxide precipitation is a promising method for stabilizing arsenic (As) in contaminated soils; however, the addition of salts during the process can negatively affect soil functions. This study investigated the effects of in situ Fe oxide precipitation on As stabilization and the impact of salt stress on soil functions and microbial communities. Fe oxide precipitation reduced the concentration of bioaccessible As by 84% in the stabilized soil, resulting in the formation of ferrihydrite and lepidocrocite, as confirmed by XANES. Nevertheless, an increase in salt stress reduced barley development, microbial enzyme activities, and microbial diversity compared to those in the original soil. Despite this, the stabilized soil exhibited natural resilience and potential for enhanced microbial adaptations, with increased retention of salt-tolerant bacteria. Washing the stabilized soil with water restored EC1:5 to the level of the original soil, resulting in increased barley growth rates and enzyme activities after 5-d and 20-week incubation periods, suggesting soil function recovery. 16 S rRNA sequencing revealed the retention of salt-tolerant bacteria in the stabilized soil, while salt-removed soil exhibited an increase in Proteobacteria, which could facilitate ecological functions. Overall, Fe oxide precipitation effectively stabilized soil As and exhibited potential for restoring the natural resilience and ecological functions of soils through microbial adaptations and salt removal.

Beneficial Microorganisms Improve Agricultural Sustainability under Climatic Extremes

The challenging alterations in climate in the last decades have had direct and indirect influences on biotic and abiotic stresses that have led to devastating implications on agricultural crop production and food security. Extreme environmental conditions, such as abiotic stresses, offer great opportunities to study the influence of different microorganisms in plant development and agricultural productivity. The focus of this review is to highlight the mechanisms of plant growth-promoting microorganisms (especially bacteria and fungi) adapted to environmental induced stresses such as drought, salinity, heavy metals, flooding, extreme temperatures, and intense light. The present state of knowledge focuses on the potential, prospective, and biotechnological approaches of plant growth-promoting bacteria and fungi to improve plant nutrition, physio-biochemical attributes, and the fitness of plants under environmental stresses. The current review focuses on the importance of the microbial community in improving sustainable crop production under changing climatic scenarios.

Effects of sublethal stress application on the survival of bacterial inoculants: a systematic review

The use of commercial bacterial inoculants formulated with plant-growth promoting bacteria (PGPB) in agriculture has shown significant prominence in recent years due to growth-promotion benefits provided to plants through different mechanisms. However, the survival and viability of bacterial cells in inoculants are affected during use and may decrease their effectiveness. Physiological adaptation strategies have attracted attention to solve the viability problem. This review aims to provide an overview of research on selecting sublethal stress strategies to increase the effectiveness of bacterial inoculants. The searches were performed in November 2021 using Web of Science, Scopus, PubMed, and Proquest databases. The keywords "nitrogen-fixing bacteria", "plant growth-promoting rhizobacteria", "azospirillum", "pseudomonas", "rhizobium", "stress pre-conditioning", "adaptation", "metabolic physiological adaptation", "cellular adaptation", "increasing survival", "protective agent" and "protective strategy" were used in the searches. A total of 2573 publications were found, and 34 studies were selected for a deeper study of the subject. Based on the studies analysis, gaps and potential applications related to sublethal stress were identified. The most used strategies included osmotic, thermal, oxidative, and nutritional stress, and the primary cell response mechanism to stress was the accumulation of osmolytes, phytohormones, and exopolysaccharides (EPS). Under sublethal stress, the inoculant survival showed positive increments after lyophilization, desiccation, and long-term storage processes. The effectiveness of inoculant-plants interaction also had positive increments after sublethal stress, improving plant development, disease control, and tolerance to environmental stresses compared to unappealed inoculants.

Secondary metabolites from methylotrophic bacteria: their role in improving plant growth under a stressed environment

Climate change is considered a natural disaster that causes the ecosystem to fluctuate and increase temperature, as well as the amount of UV radiation (UV-A and UV-B) on the Earth's surface. Consequently, greenhouse gases such as chlorofluorocarbons, methane, nitrogen oxide, and carbon dioxide have become obstacles to the development of sustainable agriculture. To overcome environmental stress such as phytopathogens, drought, salinity, heavy metals, and high-low temperatures, the utilization of microorganisms is a viable option. The synthesis of secondary metabolites by methylotrophic bacteria improves plant metabolism, enhances tolerance, and facilitates growth. The genus Methylobacterium is a pink-pigmented facultative methylotrophs which abundantly colonizes plants, especially young leaves, owing to the availability of methanol. Secondary metabolites such as amino acids, carotenoids, hormones, antimicrobial compounds, and other compounds produced by methylotrophic bacteria enhance plant metabolism under stress conditions. Therefore, in this review, we discuss the role of secondary metabolites produced by methylotrophic bacteria and their role in promoting plant growth under stress.

Effect of Burkholderia ambifaria LK-P4 inoculation on the plant growth characteristics, metabolism, and pharmacological activity of Anoectochilus roxburghii

BACKGROUND

Plant growth-promoting bacteria (PGPB) represents a common biological fertilizer with remarkable effect in improving crop production and environmental friendliness.

METHODS

In the present work, we presented a detailed characterization of plant morphology and physiology, metabolism, and pharmacological activity of A. roxburghii between Burkholderia ambifaria LK-P4 inoculation and un-inoculation (CK) treatment by routine analytical techniques (include microscopy and enzymatic activity assays and so on) coupled with metabolomics approaches.

RESULTS

Morphological and physiological results showedthat the P4 bacteria could significantly increase plant stomatal density, freshweight, survival rate,and the content of total flavonoids in leaves but reducethe amount of free amino acid. Furthermore, metabolite data showed that fatty acids (linoleic acid, linolenic acid, stearic acid) and active substance (kyotorphin and piceatannol) were specifically up-regulated in P4 inoculation. It was also demonstrated that the differential metabolites were involved in citrate cycle, glyoxylate and dicarboxylate metabolism, and biosynthesis of unsaturated fatty acids pathway. In addition, pharmacological efficacy found that A. roxburghii under P4 inoculation can significantly decrease (p < 0.05) blood glucose levels and protect the organs of mice with similar effect of Glibenclamide tablets.

CONLUSION

Overall, it can be seen that the exogenous P4 bacteria can promote the growth and increase content of special metabolites in A. roxburghii. This study provided theoretical basis and supported for the high-yield and high-quality bionic cultivation of A. roxburghii.

Development of ACCd producer A. brasilense mutant and the effect of inoculation on red pepper plants

Azospirillum is a plant-growth-promoting bacterium capable of colonizing and promoting growth in numerous crops of agronomic and horticultural significance. The objective of the present study is to develop Azospirillum brasilense CW903-acdS flocculating cells and to test their performance in promoting the growth of red pepper plants grown under salt stress. The flocculating CW903-acdS recorded 12.6, 37.3 and 91.6% higher ACCd activity at 50, 100 and 150 mM NaCl concentrations, respectively, compared to non-flocculating (normal) CW903-acdS cells. The flocculating CW903-acdS recorded 29.8 and 24.5% higher specific growth rates compared to non-flocculating CW903-acdS cells at 100 and 150 mM NaCl concentration, respectively. The flocculating CW903-acdS recorded 29.7 and 24.5% higher production of IAA-like molecule compared to the non-flocculating CW903-acdS at 100 and 150 mM NaCl concentration, respectively. Similarly, 27.5 and 25.7% higher ARA activity was observed with the flocculating CW903-acdS compared to the non-flocculating CW903-acdS type cells at 100 and 150 mM NaCl concentration, respectively. In the pot culture experiment at 50 and 100 mM NaCl concentration, CW903-acdS inoculated pepper plants recorded 9.4 and 4.7% less ethylene emission, when compared to plants inoculated with non-flocculating CW903-acdS cells. At 100 mM NaCl concentration, plants inoculated with flocculating CW903-acdS recorded 27.5% higher dry weight compared to plants inoculated with non-flocculating CW903-acdS cells. This study implied the significance of flocculating CW903-acdS with better stress amelioration and plant growth promotion in red pepper plants grown under salt-affected conditions due to the positive influence of ACCd activity.

Co-inoculation of halotolerant potassium solubilizing Bacillus licheniformis and Aspergillus violaceofuscus improves tomato growth and potassium uptake in different soil types under salinity

Soil salinity is an important stress that negatively affects crop growth and productivity, causing extensive agricultural losses, worldwide. Potassium (K) solubilizing microorganisms (KSMs) can impart abiotic stress tolerance in plants in addition to nutrient solubilization. In this study, the salinity tolerance of KSMs Bacillus licheniformis and Aspergillus violaceofuscus originating from saxicolous habitats was examined using different concentrations of NaCl (0, 25, 50, 75, 100, and 125 mM) under in vitro conditions. The results indicated that both KSMs were capable of tolerating salinity. As B. licheniformis had a maximum growth in 100 mM NaCl at 37 °C, A. violaceofuscus had the maximum biomass and catalase (CAT) activity at 75 mM NaCl. However, maximum proline content was detected at 100 mM NaCl in both KSMs. Further, the ability of these KSMs to promote tomato growth individually and in combination with the presence or absence of mica was also examined in unsterilized or sterilized Alfisol and Vertisol soils under induced salinity in greenhouse conditions. The results of the greenhouse study revealed that inoculation of KSMs along with/without mica amendment significantly improved the morphological and physiological characteristics of tomato plants under salinity. Plant height, leaf area, biomass, relative water content, proline content, and CAT activity of dual inoculated plants were significantly higher than non-inoculated plants. Significant correlations existed between various soil, plant growth, soil pH and available K. From the results, it could be concluded that B. licheniformis and A. violaceofuscus are potential candidates for improving crop production in saline-stressed soils.

Salt Stress Tolerance-Promoting Proteins and Metabolites under Plant-Bacteria-Salt Stress Tripartite Interactions

The rapid increase in soil salinization has impacted agricultural output and poses a threat to food security. There is an urgent need to focus on improving soil fertility and agricultural yield, both of which are severely influenced by abiotic variables such as soil salinity and sodicity. Abiotic forces have rendered one-third of the overall land unproductive. Microbes are the primary answer to the majority of agricultural production’s above- and below-ground problems. In stressful conditions, proper communication between plants and beneficial microbes is critical for avoiding plant cell damage. Many chemical substances such as proteins and metabolites synthesized by bacteria and plants mediate communication and stress reduction. Metabolites such as amino acids, fatty acids, carbohydrates, vitamins, and lipids as well as proteins such as aquaporins and antioxidant enzymes play important roles in plant stress tolerance. Plant beneficial bacteria have an important role in stress reduction through protein and metabolite synthesis under salt stress. Proper genomic, proteomic and metabolomics characterization of proteins and metabolites’ roles in salt stress mitigation aids scientists in discovering a profitable avenue for increasing crop output. This review critically examines recent findings on proteins and metabolites produced during plant-bacteria interaction essential for the development of plant salt stress tolerance.

A survey of Methylobacterium species and strains reveals widespread production and varying profiles of cytokinin phytohormones

Background

Symbiotic Methylobacterium strains comprise a significant part of plant microbiomes. Their presence enhances plant productivity and stress resistance, prompting classification of these strains as plant growth-promoting bacteria (PGPB). Methylobacteria can synthesize unusually high levels of plant hormones, called cytokinins (CKs), including the most active form, trans-Zeatin (tZ).

Results

This study provides a comprehensive inventory of 46 representatives of Methylobacterium genus with respect to phytohormone production in vitro, including 16 CK forms, abscisic acid (ABA) and indole-3-acetic acid (IAA). High performance-liquid chromatography—tandem mass spectrometry (HPLC–MS/MS) analyses revealed varying abilities of Methylobacterium strains to secrete phytohormones that ranged from 5.09 to 191.47 pmol mL⁻¹ for total CKs, and 0.46 to 82.16 pmol mL⁻¹ for tZ. Results indicate that reduced methanol availability, the sole carbon source for bacteria in the medium, stimulates CK secretion by Methylobacterium. Additionally, select strains were able to transform L-tryptophan into IAA while no ABA production was detected.

Conclusions

To better understand features of CKs in plants, this study uncovers CK profiles of Methylobacterium that are instrumental in microbe selection for effective biofertilizer formulations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02454-9.

ACC deaminase and indole acetic acid producing endophytic bacterial co-inoculation improves physiological traits of red pepper (Capsicum annum L.) under salt stress

Salinity induces myriad of physiological and biochemical perturbations in plants and its amelioration can be attained by the use of potential bacterial synthetic communities. The use of microbial consortia in contrast to single bacterial inoculation can additively enhance stress tolerance and productivity of agricultural crops. In this study, co-inoculation of Pseudomonas koreensis S2CB45 and Microbacterium hydrothermale IC37-36 isolated from arbuscular mycorrhizal fungi (AMF) spore and rice seed endosphere, respectively, were used to evaluate the physiological and biochemical effects on red pepper at two salt concentrations (75 mM and 150 mM). Plant growth promoting characteristics particularly 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole acetic acid (IAA) and cytokinin production were higher during co-culturing compared to the individual bacterial culture. The higher ACC deaminase activity had resulted in 20% and 22% decrease in stress ethylene emission compared to the non-inoculated plants at 75 mM and 150 mM salt stress, respectively. The decline in ethylene emission had eventually reduced ROS accumulation, and the co-inoculated plants had also harbored enhanced antioxidant enzyme activities and higher sugar accumulation compared to the other treatments suggesting enhanced tolerance to salinity. Collectively, these results put forward a novel consortium of bacterial strains that can be used for sustainable agricultural practices against salinity.

Plant growth promoting bacteria for combating salinity stress in plants - Recent developments and prospects: A review

Soil salinity has emerged as a great threat to the agricultural ecosystems throughout the globe. Many continents of the globe are affected by salinity and crop productivity is severely affected. Anthropogenic activities leading to the degradation of agricultural land have also accelerated the rate of salinization in arid and semi-arid regions. Several approaches are being evaluated for remediating saline soil and restoring their productivity. Amongst these, utilization of plant growth promoting bacteria (PGPB) has been marked as a promising tool. This greener approach is suitable for simultaneous reclamation of saline soil and improving the productivity. Salt-tolerant PGPB utilize numerous mechanisms that affect physiological, biochemical, and molecular responses in plants to cope with salt stress. These mechanisms include osmotic adjustment by ion homeostasis and osmolyte accumulation, protection from free radicals by the formation of free radicals scavenging enzymes, oxidative stress responses and maintenance of growth parameters by the synthesis of phytohormones and other metabolites. As salt-tolerant PGPB elicit better plant survival under salinity, they are the potential candidates for enhancing agricultural productivity. The present review focuses on the various mechanisms used by PGPB to improve plant health under salinity. Recent developments and prospects to facilitate better understanding on the functioning of PGPB for ameliorating salt stress in plants are emphasized.

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

Dominance of Gas-Eating, Biofilm-Forming Methylobacterium Species in the Evaporator Cores of Automobile Air-Conditioning Systems

Air-conditioning systems (ACS) are indispensable for human daily life; however, microbial community analysis in automobile ACS has yet to be comprehensively investigated. A bacterial community analysis of 24 heat exchanger fins from five countries (South Korea, China, the United States, India, and the United Arab Emirates [UAE]) revealed that Methylobacterium species are some of the dominant bacteria in automobile ACS. Furthermore, we suggested that the predominance of Methylobacterium species in automobile ACS is due to the utilization of mixed volatile organic compounds and their great ability for aggregation and biofilm formation.

Microbial communities in the evaporator core (EC) of automobile air-conditioning systems have a large impact on indoor air quality, such as malodor and allergenicity. DNA-based microbial population analysis of the ECs collected from South Korea, China, the United States, India, and the United Arab Emirates revealed the extraordinary dominance of Methylobacterium species in EC biofilms. Mixed-volatile organic compound (VOC) utilization and biofilm-forming capabilities were evaluated to explain the dominance of Methylobacterium species in the ECs. The superior growth of all Methylobacterium species could be possible under mixed-VOC conditions. Interestingly, two lifestyle groups of Methylobacterium species could be categorized as the aggregator group, which sticks together but forms a small amount of biofilm, and the biofilm-forming group, which forms a large amount of biofilm, and their genomes along with phenotypic assays were analyzed. Pili are some of the major contributors to the aggregator lifestyle, and succinoglycan exopolysaccharide production may be responsible for the biofilm formation. However, the coexistence of these two lifestyle Methylobacterium groups enhanced their biofilm formation compared to that with each single culture.

IMPORTANCE Air-conditioning systems (ACS) are indispensable for human daily life; however, microbial community analysis in automobile ACS has yet to be comprehensively investigated. A bacterial community analysis of 24 heat exchanger fins from five countries (South Korea, China, the United States, India, and the United Arab Emirates [UAE]) revealed that Methylobacterium species are some of the dominant bacteria in automobile ACS. Furthermore, we suggested that the predominance of Methylobacterium species in automobile ACS is due to the utilization of mixed volatile organic compounds and their great ability for aggregation and biofilm formation.

Physiological response of tomato plant to chitosan-immobilized aggregated Methylobacterium oryzae CBMB20 inoculation under salinity stress

The use of plant growth promoting bacteria as bioinoculant to alleviate salt stress is a sustainable and eco-friendly approach in agriculture. However, the maintenance of the bacterial population in the soil for longer period is a major concern. In the present study, chitosan-immobilized aggregated Methylobacterium oryzae CBMB20 was used as a bioinoculant to improve tomato plant (Solanum lycopersicum Mill.) growth under salt stress. The chitosan-immobilized aggregated M. oryzae CBMB20 was able to enhance plant dry weight, nutrient uptake (N, P, K and Mg²⁺), photosynthetic efficiency and decrease electrolyte leakage under salt stress conditions. The oxidative stress exerted by elevated levels of salt stress was also alleviated by the formulated bioinoculant, as it up-regulated the antioxidant enzyme activities and enhanced the accumulation of proline which acts as an osmolyte. The chitosan-immobilized aggregated M. oryzae CBMB20 was able to decrease the excess Na⁺ influx into the plant cells and subsequently decreasing the Na⁺/K⁺ ratio to improve tomato plant growth under salt stress conditions. Therefore, it is proposed that the chitosan-immobilized aggregated M. oryzae CBMB20 could be used as a bioinoculant to promote the plant growth under salt stress conditions.

Identification of Klebsiella Variicola T29A Genes Involved In Tolerance To Desiccation

Introduction:

Several plant-beneficial bacteria have the capability to promote the growth of plants through different mechanisms. The survival of such bacteria could be affected by environmental abiotic factors compromising their capabilities of phytostimulation. One of the limiting abiotic factors is low water availability.

Materials and Methods:

In extreme cases, bacterial cells can suffer desiccation, which triggers harmful effects on cells. Bacteria tolerant to desiccation have developed different strategies to cope with these conditions; however, the genes involved in these processes have not been sufficiently explored.Klebsiella variicolaT29A is a beneficial bacterial strain that promotes the growth of corn plants and is highly tolerant to desiccation. In the present work, we investigated genes involved in desiccation tolerance.

Results & Discussion:

As a result, a library of 8974 mutants of this bacterial strain was generated by random mutagenesis with mini-Tn5 transposon, and mutants that lost the capability to tolerate desiccation were selected. We found 14 sensitive mutants; those with the lowest bacterial survival rate contained mini-Tn5 transposon inserted into genes encoding a protein domain related to BetR, putative secretion ATPase and dihydroorotase. The mutant in the betR gene had the lowest survival; therefore, the mutagenized gene was validated using specific amplification and sequencing.

Conclusion:

Trans complementation with the wild-type gene improved the survival of the mutant under desiccation conditions, showing that this gene is a determinant for the survival ofK. variicolaT29A under desiccation conditions.

Development of low-cost formulations of plant growth-promoting bacteria to be used as inoculants in beneficial agricultural technologies

Phosphorus is one of the main macronutrients for plant development. Despite its large deposits in soils, it is scarcely available for plants. Phosphate-solubilizing bacteria, belonging to the group of plant growth-promoting rhizobacteria (PGPR), are capable of mobilizing deposits of insoluble phosphates in the soil. The use of PGPR as inoculants provides an environmentally sustainable approach to increase crop production. The effectiveness of inoculants depends on their proper production, formulation and storage in order to ensure the application of the required number of viable microbial cells. In order to develop inexpensive technology, low-cost compounds for biomass production and protection should be used. After the biomass production process, the product should be formulated in a liquid or a solid form, taking into account required storage time, use of protectors/carriers, storage conditions (temperature, humidity, etc.), ease of application and maintenance of beneficial effects on crops. Careful determination of these optimal conditions would ensure a low-cost efficient inoculant that would promote the growth and yield of various crops.