1-aminocyclopropane-1-carboxylate (ACC) deaminase genes in rhizobia from southern Saskatchewan

Isolation and Characterization of Plant-Growth-Promoting, Drought-Tolerant Rhizobacteria for Improved Maize Productivity

Drought is one of the main abiotic factors affecting global agricultural productivity. However, the application of bioinocula containing plant-growth-promoting rhizobacteria (PGPR) has been seen as a potential environmentally friendly technology for increasing plants' resistance to water stress. In this study, rhizobacteria strains were isolated from maize (Zea mays L.) and subjected to drought tolerance tests at varying concentrations using polyethylene glycol (PEG)-8000 and screened for plant-growth-promoting activities. From this study, 11 bacterial isolates were characterized and identified molecularly, which include Bacillus licheniformis A5-1, Aeromonas caviae A1-2, A. veronii C7_8, B. cereus B8-3, P. endophytica A10-11, B. halotolerans A9-10, B. licheniformis B9-5, B. simplex B15-6, Priestia flexa B12-4, Priestia flexa C6-7, and Priestia aryabhattai C1-9. All isolates were positive for indole-3-acetic acid (IAA), siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, ammonia production, nitrogen fixation, and phosphate solubilization, but negative for hydrogen cyanide production. Aeromonas strains A1-2 and C7_8, showing the highest drought tolerance of 0.71 and 0.77, respectively, were selected for bioinoculation, singularly and combined. An increase in the above- and below-ground biomass of the maize plants at 100, 50, and 25% water-holding capacity (WHC) was recorded. Bacterial inoculants, which showed an increase in the aerial biomass of plants subjected to moderate water deficiency by up to 89%, suggested that they can be suitable candidates to enhance drought tolerance and nutrient acquisition and mitigate the impacts of water stress on plants.

Enhancing Pisum sativum growth and symbiosis under heat stress: the synergistic impact of co-inoculated bacterial consortia and ACC deaminase-lacking Rhizobium

The 1-aminocyclopropane-1-carboxylate (ACC) deaminase is a crucial bacterial trait, yet it is not widely distributed among rhizobia. Hence, employing a co-inoculation approach that combines selected plant growth-promoting bacteria with compatible rhizobial strains, especially those lacking ACC deaminase, presents a practical solution to alleviate the negative effects of diverse abiotic stresses on legume nodulation. Our objective was to explore the efficacy of three non-rhizobial endophytes, Phyllobacterium salinisoli (PH), Starkeya sp. (ST) and Pseudomonas turukhanskensis (PS), isolated from native legumes grown in Tunisian arid regions, in improving the growth of cool-season legume and fostering symbiosis with an ACC deaminase-lacking rhizobial strain under heat stress. Various combinations of these endophytes (ST + PS, ST + PH, PS + PH, and ST + PS + PH) were co-inoculated with Rhizobium leguminosarum 128C53 or its ΔacdS mutant derivative on Pisum sativum plants exposed to a two-week heat stress period.Our findings revealed that the absence of ACC deaminase activity negatively impacted both pea growth and symbiosis under heat stress. Nevertheless, these detrimental effects were successfully mitigated in plants co-inoculated with ΔacdS mutant strain and specific non-rhizobial endophytes consortia. Our results indicated that heat stress significantly altered the phenolic content of pea root exudates. Despite this, there was no impact on IAA production. Interestingly, these changes positively influenced biofilm formation in consortia containing the mutant strain, indicating synergistic bacteria-bacteria interactions. Additionally, no positive effects were observed when these endophytic consortia were combined with the wild-type strain. This study highlights the potential of non-rhizobial endophytes to improve symbiotic performance of rhizobial strains lacking genetic mechanisms to mitigate stress effects on their legume host, holding promising potential to enhance the growth and yield of targeted legumes by boosting symbiosis.

Fertilization of Microbial Composts: A Technology for Improving Stress Resilience in Plants

Microbial compost plays a crucial role in improving soil health, soil fertility, and plant biomass. These biofertilizers, based on microorganisms, offer numerous benefits such as enhanced nutrient acquisition (N, P, and K), production of hydrogen cyanide (HCN), and control of pathogens through induced systematic resistance. Additionally, they promote the production of phytohormones, siderophore, vitamins, protective enzymes, and antibiotics, further contributing to soil sustainability and optimal agricultural productivity. The escalating generation of organic waste from farm operations poses significant threats to the environment and soil fertility. Simultaneously, the excessive utilization of chemical fertilizers to achieve high crop yields results in detrimental impacts on soil structure and fertility. To address these challenges, a sustainable agriculture system that ensures enhanced soil fertility and minimal ecological impact is imperative. Microbial composts, developed by incorporating characterized plant-growth-promoting bacteria or fungal strains into compost derived from agricultural waste, offer a promising solution. These biofertilizers, with selected microbial strains capable of thriving in compost, offer an eco-friendly, cost-effective, and sustainable alternative for agricultural practices. In this review article, we explore the potential of microbial composts as a viable strategy for improving plant growth and environmental safety. By harnessing the benefits of microorganisms in compost, we can pave the way for sustainable agriculture and foster a healthier relationship between soil, plants, and the environment.

Evaluation of the Co-inoculation Effect of Rhizobium and Plant Growth Promoting Non-rhizobial Endophytes on Vigna radiata

A unique feature of leguminous plants is the establishment of symbiotic bacterial genera inside root or stem nodules that is being recently re-evaluated for investigating the micro-flora discrete to nitrogen fixation. The present research was carried out to evaluate non-rhizobial endophytes and Rhizobium from root nodules of Vigna radiata and ascertain their co-inoculation effect in pot and field conditions. Each strain displayed one or more plant growth-promoting behaviors in varying degrees. The ability to fix nitrogen was observed in all strains; however, a noticeable enhancement in nitrogen fixation was observed when all three strains were co-inoculated. All three strains were found to possess the nifH gene, which plays a key role in the nitrogen fixation process. However, only Rhizobium sp. AAU B3 also had the nodD gene present. Furthermore, combinations of all three strains produced the highest levels of phosphate solubilization, potash mobilisation, Indole Acetic Acid (IAA), and the stress-relieving enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Interestingly, the succession of the root nodule formation within root hairs seedlings was observed under a fluorescence microscope and two NRE were found to be located inside the root nodules, indicating that they are endophytic. Additionally, a pot and field investigation revealed that the combination of chosen Rhizobium and NRE strains had a favorable impact on the growth and yield characteristics of a green gram. Selected bio-inoculants can reduce the utilization of synthetic fertilizers by 75%, which might lead to the restoration of the soil's health. Therefore, these bio-inoculants might be explored commercially for sustainable agriculture production.

Biodegradation of monocrotophos by Brucella intermedia Msd2 isolated from cotton plant

Widespread and inadequate use of Monocrotophos has led to several environmental issues. Biodegradation is an ecofriendly method used for detoxification of toxic monocrotophos. In the present study, Msd2 bacterial strain was isolated from the cotton plant growing in contaminated sites of Sahiwal, Pakistan. Msd2 is capable of utilizing the monocrotophos (MCP) organophosphate pesticide as its sole carbon source for growth. Msd2 was identified as Brucella intermedia on the basis of morphology, biochemical characterization and 16S rRNA sequencing. B. intermedia showed tolerance of MCP up to 100 ppm. The presence of opd candidate gene for pesticide degradation, gives credence to B. intermedia as an effective bacterium to degrade MCP. Screening of the B. intermedia strain Msd2 for plant growth promoting activities revealed its ability to produce ammonia, exopolysaccharides, catalase, amylase and ACC-deaminase, and phosphorus, zinc and potassium solubilization. The optimization of the growth parameters (temperatures, shaking rpm, and pH level) of the MCP-degrading isolate was carried out in minimal salt broth supplemented with MCP. The optimal pH, temperature, and rpm for Msd2 growth were observed as pH 6, 35 °C, and 120 rpm, respectively. Based on optimization results, batch degradation experiment was performed. Biodegradation of MCP by B. intermedia was monitored using HPLC and recorded 78% degradation of MCP at 100 ppm concentration within 7 days of incubation. Degradation of MCP by Msd2 followed the first order reaction kinetics. Plant growth promoting and multi-stress tolerance ability of Msd2 was confirmed by molecular analysis. It is concluded that Brucella intermedia strain Msd2 could be beneficial as potential biological agent for an effective bioremediation for polluted environments.

Replacement of water yam (Dioscorea alata L.) indigenous root endophytes and rhizosphere bacterial communities via inoculation with a synthetic bacterial community of dominant nitrogen-fixing bacteria

Biofertilizers containing high-density plant growth-promoting bacteria are gaining interest as a sustainable solution to environmental problems caused by eutrophication. However, owing to the limitations of current investigative techniques, the selected microorganisms are not always preferred by the host plant, preventing recruitment into the native microbiota or failing to induce plant growth-promoting effects. To address this, five nitrogen-fixing bacteria previously isolated from water yam (Dioscorea alata L.) plants and showing dominant abundance of 1% or more in the water yam microbiota were selected for analysis of their plant growth-promoting activities when used as a synthetic bacterial inoculant. Water yam cv. A-19 plants were inoculated twice at 10 and 12 weeks after planting under greenhouse conditions. Bacterial communities in root, rhizosphere, and bulk soil samples were characterized using high-throughput 16S rRNA amplicon sequencing. Compared with non-inoculated plants, all bacterial communities were significantly altered by inoculation, mainly at the genus level. The inoculation effects were apparently found in the root communities at 16 weeks after planting, with all inoculated genera showing dominance (in the top 35 genera) compared with the control samples. However, no significant differences in any of the growth parameters or nitrogen contents were observed between treatments. At 20 weeks after planting, the dominance of Stenotrophomonas in the inoculated roots decreased, indicating a decline in the inoculation effects. Interestingly, only the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade was dominant (>1% relative abundance) across all samples, suggesting that bacteria related to this clade are essential core bacteria for water yam growth. This is the first report on addition of a synthetic nitrogen-fixing bacterial community in water yam plants showing that native bacterial communities can be replaced by a synthetic bacterial community, with declining in the effects of Stenotrophomonas on the modified communities several weeks after inoculation.

Recent Advances in the Bacterial Phytohormone Modulation of Plant Growth

Phytohormones are regulators of plant growth and development, which under different types of stress can play a fundamental role in a plant's adaptation and survival. Some of these phytohormones such as cytokinin, gibberellin, salicylic acid, auxin, and ethylene are also produced by plant growth-promoting bacteria (PGPB). In addition, numerous volatile organic compounds are released by PGPB and, like bacterial phytohormones, modulate plant physiology and genetics. In the present work we review the basic functions of these bacterial phytohormones during their interaction with different plant species. Moreover, we discuss the most recent advances of the beneficial effects on plant growth of the phytohormones produced by PGPB. Finally, we review some aspects of the cross-link between phytohormone production and other plant growth promotion (PGP) mechanisms. This work highlights the most recent advances in the essential functions performed by bacterial phytohormones and their potential application in agricultural production.

Draft Genome Sequence of Aeromonas caviae Strain A1-2, a Potential Plant Growth-Promoting Rhizospheric Bacterium

The genomic analysis of the plant growth-promoting rhizospheric Aeromonas caviae strain A1-2, which was isolated from a maize plant in Northwest Province, South Africa, is presented in this paper. Aeromonas caviae strain A1-2 demonstrates its potential to promote plant growth and enhance the tolerance of maize plants to drought stress.

Ambiguities of PGPR-Induced Plant Signaling and Stress Management

The growth and stress responses developed by the plant in virtue of the action of PGPR are dictated by the changes in hormone levels and related signaling pathways. Each plant possesses its specific type of microbiota that is shaped by the composition of root exudates and the signal molecules produced by the plant and microbes. Plants convey signals through diverse and complex signaling pathways. The signaling pathways are also controlled by phytohormones wherein they regulate and coordinate various defense responses and developmental stages. On account of improved growth and stress tolerance provided by the PGPR to plants, there exist crosstalk of signaling events between phytohormones and other signaling molecules secreted by the plants and the PGPR. This review discusses some of the important aspects related to the ambiguities of signaling events occurring in plants, allowing the interaction of PGPR with plants and providing stress tolerance to the plant.

Evaluation of Symbiotic Association between Various Rhizobia, Capable of Producing Plant-Growth-Promoting Biomolecules, and Mung Bean for Sustainable Production

To feed the increased world population, sustainability in the production of crops is the need of the hour, and exploration of an effective symbiotic association of rhizobia with legumes may serve the purpose. A laboratory-scale experiment was conducted to evaluate the symbiotic effectiveness of twenty wild rhizobial isolates (MR1–MR20) on the growth, physiology, biochemical traits, and nodulation of mung bean to predict better crop production with higher yields. Rhizobial strain MR4 resulted in a 52% increase in shoot length and 49% increase in shoot fresh mass, while MR5 showed a 30% increase in root length, with 67% and 65% improvement in root fresh mass by MR4 and MR5, respectively, compared to uninoculated control. Total dry matter of mung bean was enhanced by 73% and 68% with strains MR4 and MR5 followed by MR1 and MR3 with 60% increase in comparison to control. Rhizobial strain MR5 produced a maximum (25 nodules) number of nodules followed by MR4, MR3, and MR1 which produced 24, 23, and 21 nodules per plant. Results related to physiological parameters showed the best performance of MR4 and MR5 compared to control among all treatments. MR4 strain helped the plants to produce the lowest values of total soluble protein (TSP) (38% less), flavonoids contents (44% less), and malondialdehyde (MDA) contents (52% less) among all treatments compared to uninoculated control plants. Total phenolics contents of mung bean plants also showed significantly variable results, with the highest value of 54.79 mg kg−1 in MR4 inoculated plants, followed by MR5 and MR1 inoculated plants, while the minimum concentration of total phenolics was recorded in uninoculated control plants of mung bean. Based on the results of growth promotion, nodulation ability, and physiological and biochemical characteristics recorded in an experimental trial conducted under gnotobiotic conditions, four rhizobial isolates (MR1, MR3, MR4, and MR5) were selected using cluster and principal component analysis. Selected strains were also tested for a variety of plant-growth-promoting molecules to develop a correlation with the results of plant-based parameters, and it was concluded that these wild rhizobial strains were effective in improving sustainable production of mung bean.

The ACC deaminase-producing plant growth-promoting bacteria: Influences of bacterial strains and ACC deaminase activities in plant tolerance to abiotic stress

Global climate change results in frequent occurrences and/or long durations of abiotic stress. Field grown plants are affected by abiotic stress, and they modulate ethylene in response to abiotic stress exposure and use it as a signaling molecule in stress tolerance mechanisms. However, frequent occurrences and/or long durations of stress conditions can cause plants to induce ethylene levels higher than their thresholds, resulting in a reduction of plant growth and crop productivity. The use of plant growth-promoting bacteria (PGPB) that produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase has increased in various plant species to ameliorate the deleterious effects of stress-induced ethylene and promote plant growth despite abiotic stress conditions. Unfortunately, there are restrictions that limit the use of ACC deaminase-producing PGPB to protect plants from abiotic stresses. This review describes how abiotic stress induces ethylene and how stress-induced ethylene adversely affects plant growth. In addition, this review emphasizes the importance of the compatibility of PGPB strains and specific host plants and ACC deaminase activities in the reduction of stress ethylene and the promotion of plant growth, based on the research published in the last 10 years. Moreover, due to the restrictions in PGPB use, this review highlights the potential generation of transgenic plants expressing the AcdS gene that encodes the ACC deaminase enzyme as a substitute for PGPB in the future to support and uplift agricultural sustainability and food security globally.

Phomopsis liquidambaris reduces ethylene biosynthesis in rice under salt stress via inhibiting the activity of 1-aminocyclopropane-1-carboxylate deaminase

The endophytic fungus Phomopsis liquidambaris is characterized as a plant growth-promoting agent under salt stress, but its mechanism is unknown. Herein, 1-aminocyclopropane-1-carboxylate deaminase (ACCD) from the strain was confirmed that it had the ability of utilizing 1-aminocyclopropane-1-carboxylate as the sole nitrogen source. The full-length ACCD gene was 1152 bp, which encodes a mature protein of 384 amino acids with a molecular mass of 41.53 kDa. The ACCD activity was 3.9-fold in 3 mmol L^-1 ACC by qRT-PCR under salt stress comparing with no salt tress. Ethylene production was increased to 34.55-70.60% and reduced the growth of rice by 23-69.73% under salt stress. Inoculation of P. liquidambaris increased root-shoot length, fresh and dry weight, and overall growth of stressed rice seedlings. ACC accumulation, ACC synthase and ACC oxidase activities increased in salt-treated rice seedlings, while they were significantly reduced when P. liquidambaris was inoculated into rice by qRT-PCR. It therefore can be concluded that P. liquidambaris can be used as a plant growth promoting fungus against salt stress and other biotic or abiotic stresses.

Competency of Rhizobial Inoculation in Sustainable Agricultural Production and Biocontrol of Plant Diseases

The rate of growth of the global population poses a risk to food security, demanding an increase in food production. Much of the world's cultivable soils also do not have ideal farming conditions such as soil health and fertility problem and increased pest attacks, which are challenges of food production. In this perspective, there is a need to increase agricultural production using a more economically and environmentally sustainable approach. As practices of agricultural production and improvement, rhizobial inoculants represent a practically effective, ecologically safe, and economically alternative means of realizing maximum agricultural production. This review addressed how rhizobial inoculation advances agricultural production through improving plant growth, nutrient availability and uptake, and yields by enhancing bio-fixation of atmospheric nitrogen and solubilization of soil nutrients. Besides, rhizobial inoculants offer biocontrol of plant diseases by providing resistance against disease-causing pathogens or suppression of diseases. Mechanisms involved in biocontrol of plant diseases include competition for infection sites and nutrients, activation of induced systemic resistance, and production of substances such as growth hormones, antibiotics, enzymes, siderophores, hydrogen cyanide, and exo-polysaccharides. Consequently, this approach is promising as sustainable agricultural practices have yet to supplement or replace chemical fertilizers, serving as a basis for future research on sustainable agricultural production. Despite the multifunctional benefits of rhizobial inoculation, there is a variation in the implementation of this practice by farmers. Therefore, researchers should work on eradicating farmers' constraints in using rhizobia, and future studies should be concentrated toward the methods of improving inoculant quality and promotion of the technology.

Alleviation of Salt Stress in Wheat Seedlings via Multifunctional Bacillus aryabhattai PM34: An In-Vitro Study

Plant growth-promoting rhizobacteria play a substantial role in plant growth and development under biotic and abiotic stress conditions. However, understanding about the functional role of rhizobacterial strains for wheat growth under salt stress remains largely unknown. Here we investigated the antagonistic bacterial strain Bacillus aryabhattai PM34 inhabiting ACC deaminase and exopolysaccharide producing ability to ameliorate salinity stress in wheat seedlings under in vitro conditions. The strain PM34 was isolated from the potato rhizosphere and screened for different PGP traits comprising nitrogen fixation, potassium, zinc solubilization, indole acetic acid, siderophore, and ammonia production, along with various extracellular enzyme activities. The strain PM34 showed significant tolerance towards both abiotic stresses including salt stress (NaCl 2 M), heavy metal (nickel, 100 ppm, and cadmium, 300 ppm), heat stress (60 °C), and biotic stress through mycelial inhibition of Rhizoctonia solani (43%) and Fusarium solani (41%). The PCR detection of ituC, nifH, and acds genes coding for iturin, nitrogenase, and ACC deaminase enzyme indicated the potential of strain PM34 for plant growth promotion and stress tolerance. In the in vitro experiment, NaCl (2 M) decreased the wheat growth while the inoculation of strain PM34 enhanced the germination% (48%), root length (76%), shoot length (75%), fresh biomass (79%), and dry biomass (87%) over to un-inoculated control under 2M NaCl level. The results of experiments depicted the ability of antagonistic bacterial strain Bacillus aryabhattai PM34 to augment salt stress tolerance when inoculated to wheat plants under saline environment.

ACC deaminase-producing Ensifer adhaerens KS23 enhances proximate nutrient of Pisum sativum L. cultivated in high altitude

A phytohormone producing, N2-fixing and 1-aminocyclopropane-1-carboxylate (ACC) deaminase synthesizing bacterium Ensifer adhaerens KS23 effectively increased the yield and nutritional contents of Pisum sativum var. Arkel. The isolate KS23 showed positive ACC deaminase activity with 174.2 (nmol of α-ketobutyrate/g-1 biomass½ h-1) a 9.7-fold increase in glutathione S-transferase activity. The proximate analysis exhibited an increased yield of protein (21.45%), carbohydrate (38.90%), sulphur (29.94%) starch (27.52%), total ash (35.57%), fat content (27.5%), nitrogen (24.06%) and hydrogen (17.91%) in treated seeds of P. sativum as compared to untreated crop seeds in field trials at Srikot village, Srinagar-246,174 (Garhwal) India. The most desirable essential and non-essential amino-acids content was also enhanced simultaneously by E. adhaerens KS23 as compared to non-treated crop seeds. This study revealed the enhancement of various nutritional contents resulting in quality improvement and an increase in growth productivity of pea. This study provides an encouraging result that may benefit the marginal income of farmers belonging mainly to hilly regions who are dependent on traditional methods of farming and thus improving their economy.

The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea

Since the discovery of the Escherichia coli leucine-responsive regulatory protein (Lrp) almost 50 years ago, hundreds of Lrp homologs have been discovered, occurring in 45% of sequenced bacteria and almost all sequenced archaea. Lrp-like proteins are often referred to as the feast/famine regulatory proteins (FFRPs), reflecting their common regulatory roles. Acting as either global or local transcriptional regulators, FFRPs detect the environmental nutritional status by sensing small effector molecules (usually amino acids) and regulate the expression of genes involved in metabolism, virulence, motility, nutrient transport, stress tolerance, and antibiotic resistance to implement appropriate behaviors for the specific ecological niche of each organism. Despite FFRPs' complexity, a significant role in gene regulation, and prevalence throughout prokaryotes, the last comprehensive review on this family of proteins was published about a decade ago. In this review, we integrate recent notable findings regarding E. coli Lrp and other FFRPs across bacteria and archaea with previous observations to synthesize a more complete view on the mechanistic details and biological roles of this ancient class of transcription factors.

Is phosphate solubilizing ability in plant growth-promoting rhizobacteria isolated from chickpea linked to their ability to produce ACC deaminase?

AIMS

Since most phosphate solubilizing bacteria (PSB) also produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase, we investigated if there was an association between these two plant growth-promoting properties under in vitro conditions.

METHODS AND RESULTS

A total of 841 bacterial isolates were obtained using selective and enrichment isolation methods. ACC deaminase was investigated using in vitro methods and by sequencing the acdS gene. The effect of ACC deaminase on P solubilization was investigated further using five efficient PSB. ACC deaminase production ability was found amongst a wide range of bacteria belonging to the genera Bacillus, Burkholderia, Pseudomonas and Variovorax. The amount of ACC deaminase produced by PSB was significantly associated with the liberation of Pi from Ca-P when ACC was the sole N source. Ca-P solubilization was associated with the degree of acidification of the medium. Additionally, the P solubilization potential of PSB with (NH₄ )₂ SO₄ was determined by the type of carboxylates produced. An in-planta experiment was conducted using Burkholderia sp. 12F on chickpea cv. Genesis-863 in sand : vermiculite (1 : 1 v/v) amended with rock phosphate and inoculation of this efficient PSB significantly increased growth, nodulation and P uptake of chickpea fertilized with rock phosphate.

CONCLUSION

ACC deaminase activity influenced the capacity of PSB to solubilize P from Ca-P when ACC was the sole N source and Burkholderia sp. 12F promoted the chickpea-Mesorhizobium symbiosis.

SIGNIFICANCE AND IMPACT OF THE STUDY

ACC deaminase activity could enhance the P solubilizing activity of rhizobacteria that improve plant growth.

Bacterial endophytes: Molecular interactions with their hosts

Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.

Phosphate solubilization and multiple plant growth promoting properties of Mesorhizobium species nodulating chickpea from acidic soils of Ethiopia

The main purpose of this study was to screen and select strains from seven Mesorhizobium spp. for efficient phosphate solubilizing and other plant growth-promoting traits. Mesorhizobium species were tested for their ability to dissolve inorganic phosphate sources and multiple plant growth-promoting attributes. From a total of 62 Mesorhizobium strains, 47(76%) strains formed clear zones with an average PSI of 1.9-2.7 on Pikovskaya's agar plate. The selected strains also released soluble phosphorus [125-150 P (µgml-1)] from tri-calcium phosphate and low level of phosphorous i.e., 15.4 µg/ml and 14.5 µg/ml from inorganic ferrous and aluminum phosphates, respectively, in a liquid medium after 4 days of incubation. The release of soluble P was significantly (P < 0.01) correlated with a drop in pH of the medium. Moreover, screening for multiple plant growth-promoting attributes showed that 40, 28, 26, 21, and 38% of the strains were capable of producing indole-3-acetic acid, hydrogen cyanide, siderophores, ACC deaminase, and antagonism against Fusarium oxysporum f.sp. ciceris under in vitro conditions. The Mesorhizobium strains were endowed with the presence of ACC deaminase which was rarely reported elsewhere. All taken together, the acidic soils harbor numerous and more diverse phosphate solubilizing and plant growth-promoting Mesorhizobium spp. However, greenhouse and field conditions can be further studied within the context of improving chickpea production in Ethiopia.

1-Aminocyclopropane-1-carboxylate (ACC) Deaminase Gene in Pseudomonas azotoformans Is Associated with the Amelioration of Salinity Stress in Tomato

Although bacteria with 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity have been used to mitigate biotic and abiotic stresses in crops, it is not well known whether the ACC deaminase gene (acdS) in Pseudomonas azotoformans is related to the alleviation of salt stress by the bacterium. This study aimed to evaluate the effects of acdS in P. azotoformans strain CHB 1107 on the nutrient uptake and growth of tomato plants under salt stress. The acdS mutant (CHB 1107 M) of P. azotoformans CHB 1107 was obtained through bacterial conjugation. Wild-type (CHB 1107 WT) and CHB 1107 M were used to inoculate tomato plants grown in a soil or solution with an electrical conductivity of 6 dS/m adjusted by NaCl. CHB 1107 M completely lost the ability to produce ACC deaminase, whereas the complementation of acdS in CHB 1107 M preserved its ACC deaminase activity. CHB 1107 WT significantly reduced the production of ethylene and proline by tomato plants under salt stress, increasing the shoot and root dry weights of tomato plants compared with the noninoculated control and CHB 1107 M. In addition, tomato plants inoculated with CHB 1107 M showed a significant reduction in K (27.5%), Ca (23.0%), and Mn uptake (17.5%) compared with those inoculated with CHB 1107 WT. In contrast, CHB 1107 WT significantly reduced Na uptake by tomato plants in comparison to CHB 1107 M in saline soil conditions. In addition, the inoculation of tomato plants with CHB 1107 WT resulted in a higher K/Na ratio than in those inoculated with CHB 1107 M and the noninoculated control. These findings suggest that acdS in P. azotoformans is associated with the amelioration of salinity stress in tomato. Plant transformation with acdS and the field application of P. azotoformans may be used as potential management tools for crops under salt stress.

Exogenous ACC Deaminase Is Key to Improving the Performance of Pasture Legume-Rhizobial Symbioses in the Presence of a High Manganese Concentration

Manganese (Mn) toxicity is a very common soil stress around the world, which is responsible for low soil fertility. This manuscript evaluates the effect of the endophytic bacterium Pseudomonas sp. Q1 on different rhizobial-legume symbioses in the absence and presence of Mn toxicity. Three legume species, Cicer arietinum (chickpea), Trifolium subterraneum (subterranean clover), and Medicago polymorpha (burr medic) were used. To evaluate the role of 1-aminocyclopropane-1-carboxylate (ACC) deaminase produced by strain Q1 in these interactions, an ACC deaminase knockout mutant of this strain was constructed and used in those trials. The Q1 strain only promoted the symbiotic performance of Rhizobium leguminosarum bv. trifolii ATCC 14480^T and Ensifer meliloti ATCC 9930^T, leading to an increase of the growth of their hosts in both conditions. Notably, the acdS gene disruption of strain Q1 abolished the beneficial effect of this bacterium as well as causing this mutant strain to act deleteriously in those specific symbioses. This study suggests that the addition of non-rhizobia with functional ACC deaminase may be a strategy to improve the pasture legume–rhizobial symbioses, particularly when the use of rhizobial strains alone does not yield the expected results due to their difficulty in competing with native strains or in adapting to inhibitory soil conditions.

Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere

The plant microbiota may differ depending on soil type, but these microbiota probably share the same functions necessary for holobiont fitness. Thus, we tested the hypothesis that phytostimulatory microbial functional groups are likely to co-occur in the rhizosphere, using groups corresponding to nitrogen fixation (nifH) and 1-aminocyclopropane-1-carboxylate deamination (acdS), i.e. two key modes of action in plant-beneficial rhizobacteria. The analysis of three maize fields in two consecutive years showed that quantitative PCR numbers of nifH and of acdS alleles differed according to field site, but a positive correlation was found overall when comparing nifH and acdS numbers. Metabarcoding analyses in the second year indicated that the diversity level of acdS but not nifH rhizobacteria in the rhizosphere differed across fields. Furthermore, between-class analysis showed that the three sites differed from one another based on nifH or acdS sequence data (or rrs data), and the bacterial genera contributing most to field differentiation were not the same for the three bacterial groups. However, co-inertia analysis indicated that the genetic structures of both functional groups and of the whole bacterial community were similar across the three fields. Therefore, results point to co-selection of rhizobacteria harboring nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities.

Salt tolerance enhancement Of wheat (Triticum Asativium L) genotypes by selected plant growth promoting bacteria

The study was conducted at green house and laboratories of Agriculture Botany Department, Faculty of Agriculture, Suez Canal University, Ismailia governorate, Egypt during 2018/2019 to test rhizosphere growth promoting bacteria as known strategy to increase salinity tolerance of six genotypes of wheat namely; Line 404, Line 356, Line 420, Line432, Sakha 93 and Line 380 were grown under 3000 ppm and 5000 ppm of salinity. Four bacterial strains were used namely; Pseudomonas fluorescens NBRC 14160, Serratia liquefaciens ATCC 27592, Bacillus subtilis SBMP4 and Bacillus megaterium NBRC 15308. All the strains could be able to tolerate salinity levels up to 3% NaCl and produced indole acetic acid (IAA). The both strains Pseudomonas fluorescens NBRC 14160 and Bacillus megaterium NBRC 15308 were grow on NA media supplemented with 6% NaCl, and showed 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity and Pseudomonas fluorescens NBRC 14160 strain also fixed nitrogen. PCR results confirmed the previous results for both strains. Pseudomonas fluorescens NBRC 14160 and Bacillus megaterium NBRC 15308 were selected to study their reflection in vivo on wheat plants growth at different levels of salinity. The selected strains were able to improve plants growth under salinity stress conditions when compared with non-inoculated plants for all wheat genotypes especially sakha93 showed the highest mean values over rest genotypes under saline and non-saline conditions. Results of genetic parameters for studied traits showed that values of PCV were higher than GCV values for most studied traits. Germination percentage, shoot length and potassium content had high values of heritability and genetic advance, so these traits might use in selection of plant breeding programs for salinity tolerance.

Secondary Metabolites From Halotolerant Plant Growth Promoting Rhizobacteria for Ameliorating Salinity Stress in Plants

Soil salinization has emerged as one of the prime environmental constraints endangering soil quality and agricultural productivity. Anthropogenic activities coupled with rapid pace of climate change are the key drivers of soil salinity resulting in degradation of agricultural lands. Increasing levels of salt not only impair structure of soil and its microbial activity but also restrict plant growth by causing harmful imbalance and metabolic disorders. Potential of secondary metabolites synthesized by halotolerant plant growth promoting rhizobacteria (HT-PGPR) in the management of salinity stress in crops is gaining importance. A wide array of secondary metabolites such as osmoprotectants/compatible solutes, exopolysaccharides (EPS) and volatile organic compounds (VOCs) from HT-PGPR have been reported to play crucial roles in ameliorating salinity stress in plants and their symbiotic partners. In addition, HT-PGPR and their metabolites also help in prompt buffering of the salt stress and act as biological engineers enhancing the quality and productivity of saline soils. The review documents prominent secondary metabolites from HT-PGPR and their role in modulating responses of plants to salinity stress. The review also highlights the mechanisms involved in the production of secondary metabolites by HT-PGPR in saline conditions. Utilizing the HT-PGPR and their secondary metabolites for the development of novel bioinoculants for the management of saline agro-ecosystems can be an important strategy in the future.

Mediterranean Native Leguminous Plants: A Reservoir of Endophytic Bacteria with Potential to Enhance Chickpea Growth under Stress Conditions

Bacterial endophytes, a subset of a plant’s microbiota, can facilitate plant growth by a number of different mechanisms. The aims of this study were to assess the diversity and functionality of endophytic bacterial strains from internal root tissues of native legume species grown in two distinct sites in South of Portugal and to evaluate their ability to promote plant growth. Here, 122 endophytic bacterial isolates were obtained from 12 different native legume species. Most of these bacteria possess at least one of the plant growth-promoting features tested in vitro, with indole acetic acid production being the most common feature among the isolates followed by the production of siderophores and inorganic phosphate solubilization. The results of in planta experiments revealed that co-inoculation of chickpea plants with specific endophytic bacteria along with N₂-fixing symbionts significantly improved the total biomass of chickpea plants, in particular when these plants were grown under saline conditions. Altogether, this study revealed that Mediterranean native legume species are a reservoir of plant growth-promoting bacteria, that are also tolerant to salinity and to toxic levels of Mn. Thus, these bacterial endophytes are well adapted to common constraints present in soils of this region which constitutes important factors to consider in the development of bacterial inoculants for stressful conditions in the Mediterranean region.

Isolation and characterization of novel soil- and plant-associated bacteria with multiple phytohormone-degrading activities using a targeted methodology

Ethylene (ET), salicylic acid (SA) and indole-3-acetic acid (IAA) are important phytohormones regulating plant growth and development, as well as plant-microbe interactions. Plant growth-promoting bacteria (PGPB) naturally associate with plants and facilitate plant growth through a variety of mechanisms, including the ability to modulate the concentrations of these phytohormones in planta. Importantly, the wide presence of phytohormone degradation mechanisms amongst symbiotic and other soil- and plant-associated bacteria indicates that the ability to modulate phytohormone concentrations plays an important role in bacterial colonization and plant-growth promotion abilities. Obtaining phytohormone-degrading bacteria is therefore key for the development of novel solutions aiming to increase plant growth and protection. In this paper, we report an optimized targeted methodology and the consequent isolation of novel soil- and plant-associated bacteria, including rhizospheric, endophytic and phyllospheric strains, with the ability to degrade the phytohormones, SA and IAA, as well as the ET precursor, 1-aminocyclopropane-1-carboxylic acid (ACC). By using an optimized targeted methodology, we rapidly isolated diverse soil- and plant-associated bacteria presenting phytohormone-degrading abilities from several plants, plant tissues and environments, without the need for prior extensive and laborious isolation and maintenance of large numbers of isolates. The developed methodology facilitates PGPB research, especially in developing countries. Here, we also report, for the first time, the isolation of bacterial strains able to concomitantly catabolize three phytohormones (SA, IAA and ACC). Ultimately, the described targeted methodology and the novel phytohormone-degrading bacteria obtained in this work may be useful tools for future plant-microbe interaction studies, and in the development of new inoculant formulations for agriculture and biotechnology.

Isolation, identification and plant growth promotion ability of endophytic bacteria associated with lupine root nodule grown in Tunisian soil

The present study aims to characterize nodule endophytic bacteria of spontaneous lupine plants regarding their diversity and their plant growth promoting (PGP) traits. The potential of PGPR inoculation was investigated to improve white lupine growth across controlled, semi-natural and field conditions. Lupinus luteus and Lupinus angustifolius nodules were shown inhabited by a large diversity of endophytes. Several endophytes harbor numerous plant growth promotion traits such as phosphates solubilization, siderophores production and 1-aminocyclopropane-1-carboxylate deaminase activity. In vivo analysis confirmed the plant growth promotion ability of two strains (Paenibacillus glycanilyticus LJ121 and Pseudomonas brenneri LJ215) in both sterilized and semi-natural conditions. Under field conditions, the co-inoculation of lupine by these strains increased shoot N content and grain yield by 25% and 36%, respectively. These two strains Paenibacillus glycanilyticus LJ121 and Pseudomonas brenneri LJ215 are effective plant growth-promoting bacteria and they may be used to develop an eco-friendly biofertilizer to boost white lupine productivity.

The Production of ACC Deaminase and Trehalose by the Plant Growth Promoting Bacterium Pseudomonas sp. UW4 Synergistically Protect Tomato Plants Against Salt Stress

Soil salinity is a major problem in agriculture. However, crop growth and productivity can be improved by the inoculation of plants with beneficial bacteria that promote plant growth under stress conditions such as high salinity. Here, we evaluated 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity and trehalose accumulation of the plant growth promoting bacterium Pseudomonas sp. UW4. Mutant strains (mutated at acdS, treS, or both) and a trehalose over-expressing strain (OxtreS) were constructed. The acdS mutant was ACC deaminase minus; the treS^- strain significantly decreased its accumulation of trehalose, and the double mutant was affected in both characteristics. The OxtreS strain accumulated more trehalose than the wild-type strain UW4. Inoculating tomato plants subjected to salt stress with these strains significantly impacted root and shoot length, total dry weight, and chlorophyll content. The evaluated parameters in the single acdS and treS mutants were impaired. The double acdS/treS mutant was negatively affected to a greater extent than the single-gene mutants, suggesting a synergistic action of these activities in the protection of plants against salt stress. Finally, the OxtreS overproducing strain protected tomato plants to a greater extent under stress conditions than the wild-type strain. Taken together, these results are consistent with the synergistic action of ACC deaminase and trehalose in Pseudomonas sp. UW4 in the protection of tomato plants against salt stress.

Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants

The aims of this study were to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) roots grown in different soils. In addition, the effects of rhizobial inoculation, soil and stress on the functionality of those culturable endophytic bacterial communities were also investigated. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that the endophytic bacteria isolated in this work belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, with Enterobacter and Pseudomonas being the most frequently observed genera. Production of indoleacetic acid and ammonia were the most widespread plant growth-promoting features, while antifungal activity was relatively rare among the isolates. Despite the fact that the majority of bacterial endophytes were salt- and Mn-tolerant, the isolates obtained from soil with Mn toxicity were generally more Mn-tolerant than those obtained from the same soil amended with dolomitic limestone. Several associations between an isolate's genus and specific plant growth-promoting mechanisms were observed. The data suggest that soil strongly impacts the Mn tolerance of endophytic bacterial communities present in chickpea roots while rhizobial inoculation induces significant changes in terms of isolates' plant growth-promoting abilities. In addition, this study also revealed chickpea-associated endophytic bacteria that could be exploited as sources with potential application in agriculture.

Bioaccumulation of cadmium by Enterobacter sp. and enhancement of rice seedling growth under cadmium stress

Bacteria-mediated plant growth promotion and bioremediation of heavy metal containing soil is a widely accepted eco-friendly method. The present study is aimed to screen out cadmium resistant bacterial strain from metal contaminated rice rhizosphere and evaluate its effects on the growth of rice seedlings under cadmium stress. Among four different isolates (designated as S1, S2, S3 and S5), the S2 isolate was screened on the basis of different PGP traits and multi heavy metal resistance (minimum inhibitory concentration for cadmium, lead and arsenic were 3500, 2500 and 1050 µg/ml respectively). The selected S2 strain has ability to produce ACC deaminase (236.11 ng α-keto-butyrate/mg protein/h), IAA (726 µg/ml), solubilize phosphate (73.56 ppm) and fix nitrogen (4.4 µg of nitrogen fixed/h/mg protein). The selected strain was identified as Enterobacter sp. on the basis of phenotypic characterization, MALDI-TOF MS analysis of ribosomal proteins, FAME analysis and 16 S rDNA sequence homology. The high cadmium removal efficiency (> 95%) of this strain from the growth medium was measured by Atomic Absorption Spectrophotometer and it was due to intracellular cadmium accumulation evidenced by SEM-EDX-TEM-EDX study. SEM analysis also revealed no distortion of surface morphology of this strain even grown in the presence of high cadmium concentration (3000 µg/ml). Inoculation of this strain with rice seedlings significantly enhanced various morphological, biochemical characters of seedling growth compared with un-inoculated seedlings under Cd stress. The strain also exhibited alleviation of cadmium-induced oxidative stress, reduction of stress ethylene and decreased the accumulation of cadmium in seedlings as well that conferred cadmium tolerance to the plant. Thus the S2 strain could be considered as a potent heavy metal resistant PGPR applicable in heavy metal contaminated agricultural soil for bioremediation and plant growth promotion as well.

MAIN FINDING

A cadmium resistant plant growth promoting Enterobacter sp. was isolated that accumulated cadmium evidenced by SEM-TEM-EDX study. It reduced Cd uptake and enhanced growth in rice seedlings.

Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences

The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants upregulate ethylene production in response to stress, and this hormone triggers defense mechanisms. Due to the pleiotropic effects of ethylene, adjusting stress responses to maximize resistance, while minimizing costs, is a central determinant of plant fitness. Ethylene signaling is influenced by the plant-associated microbiome. We therefore argue that the regulation, physiology, and evolution of the ethylene signaling can best be viewed as the interactive result of plant genotype and associated microbiota. In this article, we summarize the current knowledge on ethylene signaling and recapitulate the multiple ways microorganisms interfere with it. We present ethylene signaling as a model system for holobiont-level evolution of plant phenotype: this cascade is tractable, extremely well studied from both a plant and a microbial perspective, and regulates fundamental components of plant life history. We finally discuss the potential impacts of ethylene modulation microorganisms on plant ecology and evolution. We assert that ethylene signaling cannot be fully appreciated without considering microbiota as integral regulatory actors, and we more generally suggest that plant ecophysiology and evolution can only be fully understood in the light of plant-microbiome interactions.

The expression of an exogenous ACC deaminase by the endophyte Serratia grimesii BXF1 promotes the early nodulation and growth of common bean

Ethylene acts as an inhibitor of the nodulation process of leguminous plants. However, some bacteria can decrease deleterious ethylene levels by the action of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase which degrades ACC, the ethylene precursor in all higher plants. Co-inoculation of rhizobia with endophytes enhances the rhizobial symbiotic efficiency with legumes, improving both nodulation and nitrogen fixation. However, not much is understood about the mechanisms employed by these endophytic bacteria. In this regard, the role of ACC deaminase from endophytic strains in assisting rhizobia in this process has yet to be confirmed. In this study, the role of ACC deaminase in an endophyte's ability to increase Rhizobium tropici nodulation of common bean was evaluated. To assess the effect of ACC deaminase in an endophyte's ability to promote rhizobial nodulation, the endophyte Serratia grimesii BXF1, which does not encode ACC deaminase, was transformed with an exogenous acdS gene. The results obtained indicate that the ACC deaminase-overexpressing transformant strain increased common bean growth, and enhanced the nodulation abilities of R. tropici CIAT899, in both cases compared to the wild-type non-transformed strain. Furthermore, plant inoculation with the ACC deaminase-overproducing strain led to an increased level of plant protection against a seed-borne pathogen.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this work, we studied the effect of ACC deaminase production by the bacterial endophyte Serratia grimesi BXF1, and its impact on the nodulation process of common bean. The results obtained indicate that ACC deaminase is an asset to the synergetic interaction between rhizobia and the endophyte, positively contributing to the overall legume-rhizobia symbiosis by regulating inhibitory ethylene levels that might otherwise inhibit nodulation and overall plant growth. The use of rhizobia together with an ACC deaminase-producing endophyte is, therefore, an important strategy for the development of new bacterial inoculants with increased performance.

Surface display of ACC deaminase on endophytic Enterobacteriaceae strains to increase saline resistance of host rice sprouts by regulating plant ethylene synthesis

Background

Most endophytic bacteria in consortia, which provide robust and broad metabolic capacity, are attractive for applications in plant metabolic engineering. The aim of this study was to investigate the effects of engineered endophytic bacterial strains on rice sprout ethylene level and growth under saline stress. A protocol was developed to synthesize engineered strains by expressing bacterial 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene on cells of endophytic Enterobacter sp. E5 and Kosakonia sp. S1 (denoted as E5P and S1P, respectively).

Results

Results showed that ACC deaminase activities of the engineered strains E5P and S1P were significantly higher than those of the wild strains E5 and S1. About 32–41% deaminase was expressed on the surface of the engineered strains. Compared with the controls without inoculation, inoculation with the wild and engineered strains increased the deaminase activities of sprouts. Inoculation with the engineered strains increased 15–21% more deaminase activities of sprouts than with the wild strains, and reduced the ethylene concentrations of sprouts more significantly than with wild strains (P < 0.05). Inoculation with the wild and engineered strains promoted the growth of sprouts, while the promoting effects were more profound with the engineered strains than with the wild strains. The engineered strains improved saline resistance of sprouts under salt concentrations from 10 to 25 g L⁻¹. The engineered strains promoted longer roots and shoots than the wild strains under the salt stresses, indicating that the ACC deaminases on the endophytic bacterial cells could result in plant-produced ACC degradation and inhibit plant ethylene formation.

Conclusions

The protocols of expressing enzymes on endophytic bacterial cells showed greater potentials than those of plant over-expressed enzymes to increase the efficiency of plant metabolic pathways.

Electronic supplementary material

The online version of this article (10.1186/s12934-017-0831-5) contains supplementary material, which is available to authorized users.

Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene?

Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior.

A Halotolerant Bacterium Bacillus licheniformis HSW-16 Augments Induced Systemic Tolerance to Salt Stress in Wheat Plant (Triticum aestivum)

Certain plant growth promoting bacteria can protect associated plants from harmful effects of salinity. We report the isolation and characterization of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase bacterium Bacillus licheniformis HSW-16 capable of ameliorating salt (NaCl) stress in wheat plants. The bacterium was isolated from the water of Sambhar salt lake, Rajasthan, India. The presence of ACC deaminase activity was confirmed by enzyme assay and analysis of AcdS gene, a structural gene for ACC deaminase. Inoculation of B. licheniformis HSW-16 protected wheat plants from growth inhibition caused by NaCl and increased plant growth (6-38%) in terms of root length, shoot length, fresh weight, and dry weight. Ionic analysis of plant samples showed that the bacterial inoculation decreased the accumulation of Na⁺ content (51%), and increased K⁺ (68%), and Ca²⁺ content (32%) in plants at different concentration of NaCl. It suggested that bacterial inoculation protected plants from the effect of NaCl by decreasing the level of Na⁺ in plants. Production of exopolysaccharide by the B. licheniformis HSW-16 can also protect from Na⁺ by binding this ion. Moreover, application of test isolate resulted in an increase in certain osmolytes such as total soluble sugar, total protein content, and a decrease in malondialdehyde content, illustrating their role in the protection of plants. The ability of B. licheniformis HSW-16 to colonize plant root surface was examined by staining the bacterium with acridine orange followed by fluorescence microscopy and polymerase chain reaction-based DNA finger printing analysis. These results suggested that B. licheniformis HSW-16 could be used as a bioinoculant to improve the productivity of plants growing under salt stress.

Differentiation of 1-aminocyclopropane-1-carboxylate (ACC) deaminase from its homologs is the key for identifying bacteria containing ACC deaminase

1-Aminocyclopropane-1-carboxylate (ACC) deaminase-mediated reduction of ethylene generation in plants under abiotic stresses is a key mechanism by which bacteria can promote plant growth. Misidentification of ACC deaminase and the ACC deaminase structure gene (acdS) can lead to overestimation of the number of bacteria containing ACC deaminase and their function in ecosystems. Previous non-specific amplification of acdS homologs has led to an overestimation of the horizontal transfer of acdS genes. Here, we designed consensus-degenerate hybrid oligonucleotide primers (acdSf3, acdSr3 and acdSr4) based on differentiating the key residues in ACC deaminases from those of homologs for specific amplification of partial acdS genes. PCR amplification, sequencing and phylogenetic analysis identified acdS genes from a wide range of proteobacteria and actinobacteria. PCR amplification and a genomic search did not find the acdS gene in bacteria belonging to Pseudomonas stutzeri or in the genera Enterobacter, Klebsiella or Bacillus. We showed that differentiating the acdS gene and ACC deaminase from their homologs was crucial for the molecular identification of bacteria containing ACC deaminase and for understanding the evolution of the acdS gene. We provide an effective method for screening and identifying bacteria containing ACC deaminase.

Biochemistry and genetics of ACC deaminase: a weapon to "stress ethylene" produced in plants

1-aminocyclopropane-1-carboxylate deaminase (ACCD), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. Owing to ACCD activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of “stress ethylene” which is inhibitory to plant growth. ACCD breaks down ACC, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. ACC deaminase is an inducible enzyme whose synthesis is induced in the presence of its substrate ACC. This enzyme encoded by gene AcdS is under tight regulation and regulated differentially under different environmental conditions. Regulatory elements of gene AcdS are comprised of the regulatory gene encoding LRP protein and other regulatory elements which are activated differentially under aerobic and anaerobic conditions. The role of some additional regulatory genes such as AcdB or LysR may also be required for expression of AcdS. Phylogenetic analysis of AcdS has revealed that distribution of this gene among different bacteria might have resulted from vertical gene transfer with occasional horizontal gene transfer (HGT). Application of bacterial AcdS gene has been extended by developing transgenic plants with ACCD gene which showed increased tolerance to biotic and abiotic stresses in plants. Moreover, distribution of ACCD gene or its homolog's in a wide range of species belonging to all three domains indicate an alternative role of ACCD in the physiology of an organism. Therefore, this review is an attempt to explore current knowledge of bacterial ACC deaminase mediated physiological effects in plants, mode of enzyme action, genetics, distribution among different species, ecological role of ACCD and, future research avenues to develop transgenic plants expressing foreign AcdS gene to cope with biotic and abiotic stressors. Systemic identification of regulatory circuits would be highly valuable to express the gene under diverse environmental conditions.

Bacterial Modulation of Plant Ethylene Levels

A focus on the mechanisms by which ACC deaminase-containing bacteria facilitate plant growth.Bacteria that produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, when present either on the surface of plant roots (rhizospheric) or within plant tissues (endophytic), play an active role in modulating ethylene levels in plants. This enzyme activity facilitates plant growth especially in the presence of various environmental stresses. Thus, plant growth-promoting bacteria that express ACC deaminase activity protect plants from growth inhibition by flooding and anoxia, drought, high salt, the presence of fungal and bacterial pathogens, nematodes, and the presence of metals and organic contaminants. Bacteria that express ACC deaminase activity also decrease the rate of flower wilting, promote the rooting of cuttings, and facilitate the nodulation of legumes. Here, the mechanisms behind bacterial ACC deaminase facilitation of plant growth and development are discussed, and numerous examples of the use of bacteria with this activity are summarized.

Plant growth promoting rhizobia: challenges and opportunities

Modern agriculture faces challenges, such as loss of soil fertility, fluctuating climatic factors and increasing pathogen and pest attacks. Sustainability and environmental safety of agricultural production relies on eco-friendly approaches like biofertilizers, biopesticides and crop residue return. The multiplicity of beneficial effects of microbial inoculants, particularly plant growth promoters (PGP), emphasizes the need for further strengthening the research and their use in modern agriculture. PGP inhabit the rhizosphere for nutrients from plant root exudates. By reaction, they help in (1) increased plant growth through soil nutrient enrichment by nitrogen fixation, phosphate solubilization, siderophore production and phytohormones production (2) increased plant protection by influencing cellulase, protease, lipase and β-1,3 glucanase productions and enhance plant defense by triggering induced systemic resistance through lipopolysaccharides, flagella, homoserine lactones, acetoin and butanediol against pests and pathogens. In addition, the PGP microbes contain useful variation for tolerating abiotic stresses like extremes of temperature, pH, salinity and drought; heavy metal and pesticide pollution. Seeking such tolerant PGP microbes is expected to offer enhanced plant growth and yield even under a combination of stresses. This review summarizes the PGP related research and its benefits, and highlights the benefits of PGP rhizobia belonging to the family Rhizobiaceae, Phyllobacteriaceae and Bradyrhizobiaceae.