Determination of bacterially derived auxins using a microplate method

Unveiling stress-adapted endophytic bacteria: Characterizing plant growth-promoting traits and assessing cross-inoculation effects on Populus deltoides under abiotic stress

In the face of the formidable environmental challenges precipitated by the ongoing climate change, Plant Growth-Promoting Bacteria (PGPB) are gaining widespread acknowledgement for their potential as biofertilizers, biocontrol agents, and microbial inoculants. However, a knowledge gap pertains to the ability of PGPB to improve stress tolerance in forestry species via cross-inoculation. To address this gap, the current investigation centres on PGPBs, namely, Acinetobacter johnsonii, Cronobacter muytjensii, and Priestia endophytica, selected from the phyllosphere of robust and healthy plants thriving in the face of stress-inducing conditions. These strains were selected based on their demonstrated adaptability to saline, arid, and nitrogen-deficient environments. The utilization of PGPB treatment resulted in an improvement of stomatal conductance (gs) and transpiration rate (E) in poplar plants exposed to both salt and drought stress. It also induced an increase in essential biochemical components such as proline (PRO), catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). These reactions were accompanied by a decrease in leaf malonaldehyde (MDA) content and electrolyte leakage (EL). Furthermore, the PGPB treatment demonstrated a notable enhancement in nutrient absorption, particularly nitrogen and carbon, achieved through the solubilization of nutrients. The estimation of canopy temperature via thermal imaging proved to be an efficient method for distinguishing stress reactions in poplar than conventional temperature recording techniques. In summation, the utilization of PGPB especially Cronobacter muytjensii in this study, yielded profound improvements in the stress tolerance of poplar plants, manifesting in reduced membrane lipid peroxidation, enhanced photosynthesis, and bolstered antioxidant capacity within the leaves.

Potential of yeasts as biocontrol agents against Fusarium graminearum in vitro and on corn

AIMS

The antifungal effect of the yeast species Kluyveromyces marxianus, Meyerozyma caribbica, and Wickerhamomyces anomalus was evaluated against two Fusarium graminearum strains (FRS 26 and FSP 27) in vitro and on corn seeds.

METHODS AND RESULTS

The antifungal effect of the yeasts against F. graminearum was evaluated using scanning electron microscopy and extracellular chitinase and glucanase production to further elucidate the biocontrol mode of action. In addition, the germination percentage and vigor test were investigated after applying yeast on corn seeds. All the yeast strains inhibited fungal growth in vitro (57.4%-100.0%) and on corn seeds (18.9%-87.2%). In co-culture with antagonistic yeasts, F. graminearum showed collapsed hyphae and turgidity loss, which could be related to the ability of yeasts to produce chitinases and glucanases. The three yeasts did not affect the seed corn germination, and W. anomalus and M. caribbica increased corn seed growth parameters (germination percentage, shoot and root length, and shoot dry weight).

CONCLUSION

Meyerozyma caribbica and W. anomalus showed satisfactory F. graminearum growth inhibition rates and did not affect seed growth parameters. Further studies are required to evaluate the application of these yeasts to the crop in the field.

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

A high-yielding strain of indole-3-acetic acid isolated from food waste compost: metabolic pathways, optimization of fermentation conditions, and application

Food waste is a potential resource to prepare microbial fertilizer. However, functional microorganisms derived from the food waste compost (FWC) are relatively lacking. We have isolated, identified, characterized and optimized a high-yielding indole-3-acetic acid (IAA) strain from FWC and further evaluated its growth promoting effect on plants. A IAA high-yielding strain, Providencia sp.Y, with an initial IAA yield of 139.98 mg L-1, was obtained through high-throughput screening, and identified by 16S rRNA gene sequence. The novel strain Y may simultaneously involve the following three pathways from L-tryptophan to IAA, which were identified using liquid chromatography-tandem mass spectrometry: (1) L-tryptophan-indole-3-ethanol-indole-3-acetaldehyde-indole-3-acetic acid; (2) L-tryptophan-1-hydroxy-indole-3-ethanol-indole-3-acetic acid; (3) L-tryptophan-indole-3-acetamide-indole-3-acetic acid. The most suitable comprehensive conditions for IAA production, which were optimized by single factor experiment, were: culture time 12 h, inoculation amount 2% (v/v), NaCl concentration 4% (w/v), culture temperature 25℃, initial pH = 5, and L-tryptophan concentration 3.0 g L-1. The yield of IAA after optimization was increased by 590.48%, from 139.98 mg L-1 (before optimization) to 966.54 mg L-1. Diluted 200-fold microbial suspension could significantly improve the growth of pakchoi seedlings. The seedling plant height, root length, leaf width, leaf length, and fresh weight with microbial suspension increased by 17.39%, 107.35%, 77.98%, 37.75%, and 215.38%, respectively, compared with those without microbial suspension. The increase was greater than that of commercial bacterial agents. In conclusion, this isolated strain can be used as an economical microbial inoculant and provides a new germplasm resource for developing microbial fertilizers.

Identification and Characterization of Beneficial Soil Microbial Strains for the Formulation of Biofertilizers Based on Native Plant Growth-Promoting Microorganisms Isolated from Northern Mexico

Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N2-fixation, NH3-, IAA and siderophore production, and antifungal activity against Fusarium oxysporum). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29-176 mg/L), and ammonia production, while fungi for Fusarium growth inhibition (40-69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, p < 0.05) better effects on plants than fungi; treatments improved plant height (23.06-51.32%), leaf diameter (25.43-82.91%), and fresh weight (54.18-85.45%) in both crops. Most potential species belonged to Pseudomonas, Pantoea, Serratia, and Rahnella genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.

Home-based microbial solution to boost crop growth in low-fertility soil

Soil microbial inoculants are expected to boost crop productivity under climate change and soil degradation. However, the efficiency of native vs commercialized microbial inoculants in soils with different fertility and impacts on resident microbial communities remain unclear. We investigated the differential plant growth responses to native synthetic microbial community (SynCom) and commercial plant growth-promoting rhizobacteria (PGPR). We quantified the microbial colonization and dynamic of niche structure to emphasize the home-field advantages for native microbial inoculants. A native SynCom of 21 bacterial strains, originating from three typical agricultural soils, conferred a special advantage in promoting maize growth under low-fertility conditions. The root : shoot ratio of fresh weight increased by 78-121% with SynCom but only 23-86% with PGPRs. This phenotype correlated with the potential robust colonization of SynCom and positive interactions with the resident community. Niche breadth analysis revealed that SynCom inoculation induced a neutral disturbance to the niche structure. However, even PGPRs failed to colonize the natural soil, they decreased niche breadth and increased niche overlap by 59.2-62.4%, exacerbating competition. These results suggest that the home-field advantage of native microbes may serve as a basis for engineering crop microbiomes to support food production in widely distributed poor soils.

Microassay validation for bacterial IAA estimation as a new fine-tuned PGPR screening assay

The detection and quantification of Indole -3 Acetic Acid (IAA) produced by Plant growth promoting rhizobacteria (PGPR) rely on a standard well-documented assay, which remains time-consuming, laborious, and costly. These drawbacks led to sway interest to economic and reliable assays. The aim of this work is to validate and standardize a fast, reliable, and cost-effective microassay to quantify IAA produced by bacteria with an easy microplate method. In order to validate the accuracy of the IAA microplate assay, bacterial samples from different genera were assayed using two methods: the conventional IAA estimation assay and the IAA micro- assay. The microassay shows a prominent reduction in used bacterial supernatant volume as well as Salkowski reagent volume of about 92.5%. It is considerably cheaper than the conventional one of around 56%. The newly performed microplate assay is 23 times faster. The result of IAA quantitative analysis for 13 bacterial strains showed that Bacillus muralis and Bacillus toyonensis produced the highest IAA concentration (23.64±0.003μg/ml and 23.35±0.006μg/ml, respectively). The obtained data from both methods were highly correlated with an R-value of 0.979. The microassay offers the ability to read the optical density of all samples simultaneously since used volumes of bacterial supernatants and Salkowski reagent were minimized to place the mixture in 96-well microplates, which reduces greatly required labor. Furthermore, the application of the IAA micro-plate assay reduces drastically the reagent waste and toxicity hazard of Salkowski reagent in the environment, thus, we can classify it as eco-friendly respecting the Green Chemistry concept according to Environmental Protection Agency (EPA). The IAA microassay is a, reliable, rapid and cost-effective and eco-friendly method to screen plant growth promoting potential of more than 23 bacterial strains by microplate. It could be an alternative for the conventional IAA assay as a routine research tool.

Valorization of spent mushroom substrate in combination with agro-residues to improve the nutrient and phytohormone contents of vermicompost

In recent years, enormous amounts of spent mushroom substrate (SMS) have been generated because of the rapid development of mushroom production. Since the conventional disposal methods of these residues can cause serious environmental problems, alternative waste management techniques are required to ensure sustainable agriculture. However, SMS might be not suitable for vermicomposting when used alone. Therefore, the primary purpose of this study was to investigate the effect of Azolla microphylla (Azolla) biomass, eggshells, fruit peels, and cassava pulp on the biodegradation process of SMS. The results showed the treatments supplemented with cassava pulp and fruit peel waste improved the growth of earthworms, while the carbon-to-nitrogen ratio of these vermicomposts decreased significantly (p < 0.05) due to the improved total nitrogen contents (7.64 g kg^-1 and 6.71 g kg^-1). Concerning the degradation process and the vermicompost quality, the addition of these agro-residues facilitated the enzyme activities (cellulase, urease, and alkaline phosphatase) and increased the total macronutrient (P, K, Mg, and Ca) and phytohormone (fruit peel waste: AA, GA3, and cytokinin; cassava pulp: cytokinin) contents of the final products compared to the control treatment. On the other hand, Azolla had no additional effect on the fecundity and growth of Eudrilus eugenia. Meanwhile, the treatment supplemented with eggshells was high in Mg (7.15 g kg^-1) and Ca (305.6 g kg^-1). Overall, the combined decomposition of SMS-based bedding material with Azolla, eggshells, fruit peel waste, and cassava pulp resulted in mature organic fertilizers with improved chemical properties.

Screening of osmotic stress-tolerant bacteria for plant growth promotion in wheat (Triticum aestivum L.) and brinjal (Solanum melongena L.) under drought conditions

Drought stress adversely affects plant growth and productivity. Therefore, the application of plant growth-promoting bacteria (PGPB) is a viable option for combating drought resistance in crops. In this study, 144 bacteria were isolated from the Kutch desert soil in Gujarat. Based on osmotic stress tolerance and PGP properties, two strains, Bacillus tequilensis (KS5B) and Pseudomonas stutzeri (KS5C) were tested for their effect on wheat (Triticum aestivum L.) and brinjal (Solanum melongena L.) under drought stress conditions. Inoculation with osmotic stress-tolerant bacteria showed 15.15-29.27% enhancement in root length of wheat and 15.27-32.59% in brinjal plants. Similarly, the enhancement of shoot length ranged from 14.72-37.70% for wheat and 59.39-95.94% for brinjal plants. Furthermore, the inoculated plants showed significant improvement in chlorophyll content and antioxidant properties such as proline, peroxidase, and polyphenol oxidase activity compared the control. Therefore, the bacterial strains identified in this study can be used to mitigate drought stress and enhance plant biomass.

Efficiency of Combining Strains Ag87 (Bacillus megaterium) and Ag94 (Lysinibacillus sp.) as Phosphate Solubilizers and Growth Promoters in Maize

Increasing phosphorus (P) use efficiency in agricultural systems is urgent and essential to significantly reduce the global demand for this nutrient. Applying phosphate-solubilizing and plant growth-promoting bacteria in the rhizosphere represents a strategy worthy of attention. In this context, the present work aimed to select and validate bacterial strains capable of solubilizing phosphorous and promoting maize growth, aiming to develop a microbial inoculant to be used in Brazilian agriculture. Bacterial strains from the maize rhizosphere were evaluated based on their ability to solubilize phosphate and produce indole acetic acid. Based on these characteristics, 24 strains were selected to be further evaluated under laboratory, greenhouse, and field conditions. Among the selected strains, four (I04, I12, I13, and I17) showed a high potential to increase maize root growth and shoot P content. Strains I13 (Ag87) and I17 (Ag94) were identified by genomic sequencing as Bacillus megaterium and Lysinibacillus sp., respectively. These strains presented superior yield increments relative to the control treatment with 30% P. In addition, combining Ag87 and Ag94 resulted in even higher yield gains, indicating a synergistic effect that could be harnessed in a commercial inoculant for Brazilian agriculture.

A new endophytic fungus CJAN1179 isolated from the Cholistan desert promotes lateral root growth in Arabidopsis and produces IAA through tryptophan-dependent pathway

Fungi, important for growth of plants in arid lands, are expected to be involved in novel biochemical activities during fungal–plant interactions. We isolated 150 fungi associated with rhizosphere and root endosphere of two perennial grasses, Cymbopogon jwarancusa and Panicum antidotale, from Cholistan desert. The isolates were screened for their impact on plant growth and development using Arabidopsis thaliana (Col-0) as a model system. A root-endophytic fungus CJAN1179 from C. jwarancusa showed the highest plant growth-promoting effects. The most remarkable was enhanced number of lateral roots (3.1-fold). CJAN1179 produced indole-3-acetic acid (IAA) particularly in the presence of tryptophan. ITS sequence and phylogenetic analysis characterisation suggested the fungus to be a new species within Sordariomycetidae. CJAN1179 appears to promote plant growth by secreting IAA using tryptophan as a precursor. This fungus can be further explored for its suitability to promote growth of commercially important crops, particularly in arid regions.

Pseudomonas bijieensis Strain XL17 within the P. corrugata Subgroup Producing 2,4-Diacetylphloroglucinol and Lipopeptides Controls Bacterial Canker and Gray Mold Pathogens of Kiwifruit

Kiwifruit worldwide suffers from the devastating diseases of bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) and gray mold caused by Botrytis cinerea. Here, an endophytic bacterium XL17 isolated from a rape crown gall was screened out for its potent antagonistic activities against Psa and B. cinerea. Strain XL17 and its cell-free culture filtrate (CF) inhibited the growth of Psa and B. cinerea, Psa-associated leaf necrosis, and B. cinerea-associated kiwifruit necrosis. Electron microscopy showed that XL17 CF could damage the cell structures of Psa and B. cinerea. Genome-based taxonomy revealed that strain XL17 belongs to Pseudomonas bijieensis within the P. corrugata subgroup of the P. fluorescens species complex. Among the P. corrugata subgroup containing 31 genomospecies, the presence of the phl operon responsible for the biosynthesis of the phenolic polyketide 2,4-diacetylphloroglucinol (DAPG) and the absence of the lipopeptide/quorum sensing island can serve as the genetic marker for the determination of a plant-protection life style. HPLC detected DAPG in extracts from XL17 CF. MALDI-TOF-MS analysis revealed that strain XL17 produced cyclic lipopeptides of the viscosin family and orfamide family. Together, phenotypic, genomic, and metabolic analyses identified that P. bijieensis XL17 producing DAPG and cyclic lipopeptides can be used to control bacterial canker and gray mold pathogens of kiwifruit.

Pre-Harvest MeJA Application Counteracts the Deleterious Impact of Al and Mn Toxicity in Highbush Blueberry Grown in Acid Soils

Volcanic ash-derived soils are characterized by low pH (pH ≤ 5.5) with increased concentrations of aluminum (Al³⁺) and manganese (Mn²⁺), which decreases plant growth, fruit quality, and yield. Methyl jasmonate (MeJA) improves abiotic stress tolerance. Our work aimed to evaluate the application of MeJA's impact on the growth, antioxidant defense, and fruit quality of highbush blueberry grown under Al and Mn toxicity. A field assay was conducted with four-year-old bushes of highbush blueberry cultivar Legacy under eight treatments (Control, Al (87% of Al saturation), Mn (240 mg kg^-1), and Al-Mn with and without MeJA application). Physiological, biochemical, and fruit quality parameters were measured. Growth rate significantly decreased with Al (20%), Mn (45%), and Al-Mn (40%). MeJA application recovered the growth rate. Photosynthetic parameters were not affected. Antioxidant activity increased under all treatments compared with controls, being higher with MeJA application. Total phenols (TP) were decreased in plants under Al (43%) and Mn (20%) compared with controls. MeJA application increased TP in all treatments. Fruits of bushes under Al and Mn toxicity with MeJA applications exhibited an increase in fruit firmness and weight, maintaining suitable contents of soluble solids. Our results provide insights about the beneficial effect of MeJA application on growth, antioxidant properties, and fruit quality of highbush blueberry plants grown in acid soils under Al and Mn toxicity.

Bioprospecting plant growth-promoting rhizobacteria from rice genotypes and their influence on growth under aerobic conditions

The bacteria that colonize plant roots and enhance plant growth by various mechanisms are known as plant growth-promoting rhizobacteria (PGPR). The functions of rhizobacteria stand substantially unexplored and detailed insights into the aerobic rice ecosystem are yet to be examined. In this study, we have isolated rhizobacteria from rice varieties grown under aerobic conditions. Seed germination test showed that strain Ekn 03 was significantly effective in stimulating germination, enhancing shoot and root length, and increasing dry matter accumulation in treated rice plants as compared to the uninoculated plants. Under greenhouse conditions, strain Ekn 03 treated rice varieties showed an overall increase in plant height by 7.63%, dry matter accumulation by 16.23%, and total chlorophyll content by 76.47%. Soil acetylene reduction assay (ARA) (4.17 nmole ethylene/g soil/h) and in-planta ARA (4.2 × 10^-2  nmole ethylene/mg fresh weight of plant/h) was significantly higher in Ekn 03 treated rice variety PB 1509 under aerobic conditions. Other rice varieties showed comparable performance on inoculation with strain Ekn 03. The endophytic and rhizospheric population of antibiotic tagged Ekn 03 was higher in the roots of PB 1509 (1.02 × 10⁴  cfu/g and 5.8 × 10⁵ cfu/g soil, respectively) compared to other rice varieties. 16S rDNA sequence analysis revealed that strain Ekn 03 was having 100% similarity with Pseudomonas protegens. This study suggests that strain Ekn 03 can be used as a microbial inoculant in rice plants under aerobic system of cultivation. This is the first report on the application of P. protegens as PGPR in rice.

Mutualistic interaction of native Serratia marcescens UENF-22GI with Trichoderma longibrachiatum UENF-F476 boosting seedling growth of tomato and papaya

A plethora of bacteria-fungal interactions occur on the extended fungal hyphae network in soil. The mycosphere of saprophytic fungi can serve as a bacterial niche boosting their survival, dispersion, and activity. Such ecological concepts can be converted to bioproducts for sustainable agriculture. Accordingly, we tested the hypothesis that the well-characterised beneficial bacterium Serratia marcescens UENF-22GI can enhance plant growth-promoting properties when combined with Trichoderma longibrachiatum UENF-F476. The cultural and cell interactions demonstrated S. marcescens and T. longibrachiatum mutual compatibility. Bacteria cells were able to attach, forming aggregates to biofilms and migrating through the fungal hyphae network. Long-distance bacterial migration through growing hyphae was confirmed using a two-compartment Petri dishes assay. Fungal inoculation increased the bacteria survival rates into the vermicompost substrate over the experimental time. Also, in vitro indolic compound, phosphorus, and zinc solubilisation bacteria activities increased in the presence of the fungus. In line with the ecophysiological bacteria fitness, the bacterium-fungal combination boosted tomato and papaya plantlet growth when applied into the plant substrate under nursery conditions. Mutualistic interaction between mycosphere-colonizing bacterium S. marcescens UENF-22GI and the saprotrophic fungi T. longibrachiatum UENF-F467 increased the ecological fitness of the bacteria alongside with beneficial potential for plant growth. A proper combination and delivery of mutual compatible beneficial bacteria-fungal represent an open avenue for microbial-based products for the biological enrichment of plant substrates in agricultural systems.

Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus

Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter by 13,8% and 88,6% respectively, as well as root dry matter by 61,4%, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.

A new pioneer colorimetric micro-plate method for the estimation of ammonia production by plant growth promoting rhizobacteria (PGPR)

The ability of Plant Growth Promoting Rhizobacteria (PGPR) to produce ammonia (NH3) is one of the key mechanisms for the growth and development of plants. Ammonia spectrophotometric quantification assay using Nessler’s reagent remains laborious and seems to be not suitable for large-scale PGP screening assay. Here, we performed a new accurate, easy, and cost-effective micro-plate protocol for large-scale ammonia quantification in bacterial supernatants as an alternative to the spectrophotometric method. In order to validate the accuracy of our innovative microplate assay, 9 bacterial strains were explored for their ability to produce ammonia using both the conventionally described assay and the newly performed micro-plate one. The ammonia 96-well microplate assay was successfully performed by scaling down the spectrophotometric methods to reduce the volume of bacterial supernatant as well as Nessler’s reagent. The reduction was estimated to 90%of the total used volume in comparison to the conventional test. The micro-test is 10-fold cheaper and 26 times faster than the conventional method. All bacterial isolates were positive for ammonia production. Bacillus inaquorsum and Bacillus mojavensis produced the highest ammonia concentration of about 371 and 370μM respectively. Furthermore, the application of the ammonia micro-plate assay reduces drastically the reagent waste and toxicity hazard of K2HgI4 (Nessler’s reagent) in the environment, thus, we can classify it as eco-friendly respecting the Green Chemistry concept according to Environmental Protection Agency (EPA). The statistical data obtained from both assays are significantly correlated (r = 0.985, R squared = 0.9329, and p <  0.001) proving the accuracy of the micro-plate assay. The proposed NH3 micro-assay is a reliable, rapid, eco-friendly, and cost-effective method to screen plant growth-promoting potential of more than 25 bacterial strains in one micro-plate. It could be an alternative for the conventional NH3 assay as a routine research tool.

Rhizospheric Bacillus amyloliquefaciens Protects Capsicum annuum cv. Geumsugangsan From Multiple Abiotic Stresses via Multifarious Plant Growth-Promoting Attributes

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms that can be utilized to improve plant responses against biotic and abiotic stresses. In this study, we investigated whether PGPR (Bacillus amyloliquefaciens) isolated from the endorhizosphere of Sasamorpha borealis have the potential to sustain pepper growth under drought, salinity, and heavy metal stresses. The bacterial strain was determined based on 16S rDNA and gyrB gene sequencing and characterized based on the following biochemical traits: nitrogen fixation; 1-aminocyclopropane-1-carboxylate deaminase activity; indole acetic acid production; inorganic phosphate, potassium, zinc, and silicon solubilization; and siderophore production. Various abiotic stresses were applied to 28-day-old pepper seedlings, and the influence of the PGPR strain on pepper seedling growth under these stress conditions was evaluated. The application of PGPR improved survival of the inoculated pepper plants under stress conditions, which was reflected by higher seedling growth rate and improved physiochemical traits. The PGPR-treated plants maintained high chlorophyll, salicylic acid, sugar, amino acid, and proline contents and showed low lipid metabolism, abscisic acid, protein, hydrogen peroxide contents, and antioxidant activities under stress conditions. Gene expression studies confirmed our physiological and biochemical findings. PGPR inoculation led to enhanced expression of XTH genes and reduced expression of WRKY2, BI-1, PTI1, and binding immunoglobulin protein (BiP) genes. We conclude that the PGPR strain described in this study has great potential for use in the phytoremediation of heavy metals and for enhancing pepper plant productivity under stress conditions, particularly those involving salinity and drought.

The Impact of Growth-Promoting Streptomycetes Isolated from Rhizosphere and Bulk Soil on Oilseed Rape (Brassica napus L.) Growth Parameters

Inoculation of Streptomyces to improve oilseed rape (Brassica napus L.) yields and minimise the use of chemical fertilisers is a promising sustainable strategy. In this study, we isolated 72 actinobacterial strains from rhizosphere of oilseed rape and maize and from bulk soil for screening and characterising their antimicrobial activity. Nine promising strains, identified as Streptomyces sp. by morphology, physiological characteristics, and 16S rRNA gene sequencing, were selected for their plant growth-promoting traits and in planta experiments. The actinobacterial strains were positive for IAA production, siderophore production, and HCN production. In planta experiments were conducted by soaking the oilseed rape seeds in the actinobacterial suspension, followed by plant growth under controlled conditions in a cultivate chamber (22–28 °C, 8 h dark/16 h light, constant humidity 80%). We recorded root and shoot length (cm) and seedling fresh weight (g). For most of the abovementioned parameters, a significant enhancement was observed with strain KmiRC20A118 treatment. The length of the root increased by 53.14%, the shoot length increased by 65.6%, and the weight of the fresh plant by 60% compared to the control. The integrated application of PGPS (Plant Growth Promoting Streptomyces) from the rhizosphere of oilseed rape is a promising strategy to improve the growth of oilseed rape.

Morphological and Metabolite Responses of Potatoes under Various Phosphorus Levels and Their Amelioration by Plant Growth-Promoting Rhizobacteria

Low phosphorus (P) availability is a major limiting factor for potatoes. P fertilizer is applied to enhance P availability; however, it may become toxic when plants accumulate at high concentrations. Therefore, it is necessary to gain more knowledge of the morphological and biochemical processes associated with P deficiency and toxicity for potatoes, as well as to explore an alternative approach to ameliorate the P deficiency condition. A comprehensive study was conducted (I) to assess plant morphology, mineral allocation, and metabolites of potatoes in response to P deficiency and toxicity; and (II) to evaluate the potency of plant growth-promoting rhizobacteria (PGPR) in improving plant biomass, P uptake, and metabolites at low P levels. The results revealed a reduction in plant height and biomass by 60–80% under P deficiency compared to P optimum. P deficiency and toxicity conditions also altered the mineral concentration and allocation in plants due to nutrient imbalance. The stress induced by both P deficiency and toxicity was evident from an accumulation of proline and total free amino acids in young leaves and roots. Furthermore, root metabolite profiling revealed that P deficiency reduced sugars by 50–80% and organic acids by 20–90%, but increased amino acids by 1.5–14.8 times. However, the effect of P toxicity on metabolic changes in roots was less pronounced. Under P deficiency, PGPR significantly improved the root and shoot biomass, total root length, and root surface area by 32–45%. This finding suggests the potency of PGPR inoculation to increase potato plant tolerance under P deficiency.

Diversity and functional characteristics of endophytic bacteria from two grass species growing on an oil-contaminated site in the Yellow River Delta, China

Phragmites australis and Chloris virgata are native, dominant, salt-tolerant grass species that grow in the Yellow River Delta, China, and have potential applications in the phytoremediation of petroleum-polluted saline soil. The characteristics of endophytic bacterial communities of Phragmites australis and Chloris virgata and their functions in hydrocarbon degradation and plant growth promotion have been studied using both high-throughput sequencing and conventional microbial techniques. Through 16S rRNA gene amplicon sequencing, we found five bacterial phyla that were dominant among the endophytic bacterial communities of the two grass species, including Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Tenericutes. The phylum Proteobacteria was common among the endophytic bacterial communities of the two grass species. The diversity in the endophytic bacterial community of Chloris virgata was generally higher than that in the community of Phragmites australis. Thirty-eight hydrocarbon-degrading endophytic bacteria were isolated from the two grasses via culturing techniques. Based on phylogenetic analyses, the bacterial isolates were classified into the phyla Proteobacteria, Firmicutes, and Actinobacteria. The majority of strains belonged to the genera Bacillus and Pseudomonas. More than 70% of the isolates of hydrocarbon-degrading endophytes exhibited the ability to stimulate plant growth. These isolates mainly belonged to Bacillus sp., Pseudomonas sp., Beijerinckia sp., Serratia sp., Acinetobacter sp., Microbacterium sp., and Rhizobium sp. Altogether, the present study revealed that Phragmites australis and Chloris virgata growing on petroleum-polluted saline soil in the Yellow River Delta harbor several diverse species of endophytic bacteria and serve as novel sources of beneficial bacteria and hydrocarbon degradation.

Growth-Promoting Potential of Rhizobacteria Isolated From Sugarcane

The search for plant growth-promoting rhizobacteria (PGPRs) addresses the ongoing need for new bioinoculants to be used on various agricultural crop species, including sugarcane. Bacterial strains were isolated from the rhizosphere of sugarcane plants and identified by sequencing the 16S ribosomal gene. The main indole acetic acid producers were Enterobacter sp. IP11, Enterobacter sp. IP14, and E. asburiae IP24. Achromobacter spanius IP23 presented the highest levels of cellulolytic activity and potassium solubilization. Bacillus thuringiensis IP21 and Staphylococcus saprophyticus IJ8 showed the highest levels of fixed nitrogen. The levels of calcium phosphate and aluminum phosphate in B. thuringiensis IP21 were notable, as this strain solubilized 481.00 and 39.33 mg of phosphorus mL−1, respectively; however, for Araxá apatite, the results for B. anthracis IP17 were notable (622.99 mg phosphorus mL−1), while for iron phosphate solubilization, Enterobacter sp. IP14, which solubilized 105.66 mg phosphorus mL−1 was notable. The B. thuringiensis IP21 and Enterobacter sp. IP11 isolates promoted the growth of the tallest sugarcane plants, inducing increases of 14.1 and 10.4% relative to the control plants, respectively. For shoot dry matter, root dry matter, and total dry matter, plants inoculated with Enterobacter sp. IP14, B. anthracis IP17, and A. spanius IP23 presented higher values than the controls. Furthermore, plants inoculated with B. thuringiensis IP21 presented higher root dry matter and total dry matter values, and those inoculated with Enterobacter sp. IP14 also presented higher total dry matter values. These results indicate that bacteria with the potential for use as future inoculants should be investigated since bacteria with plant growth-related characteristics may not impact growth promotion.

Diversity and Physiological Characteristics of Antarctic Lichens-Associated Bacteria

The diversity of lichen-associated bacteria from lichen taxa Cetraria, Cladonia, Megaspora, Pseudephebe, Psoroma, and Sphaerophorus was investigated by sequencing of 16S rRNA gene amplicons. Physiological characteristics of the cultured bacterial isolates were investigated to understand possible roles in the lichen ecosystem. Proteobacteria (with a relative abundance of 69.7–96.7%) were mostly represented by the order Rhodospirillales. The 117 retrieved isolates were grouped into 35 phylotypes of the phyla Actinobacteria (27), Bacteroidetes (6), Deinococcus-Thermus (1), and Proteobacteria (Alphaproteobacteria (53), Betaproteobacteria (18), and Gammaproteobacteria (12)). Hydrolysis of macromolecules such as skim milk, polymer, and (hypo)xanthine, solubilization of inorganic phosphate, production of phytohormone indole-3-acetic acid, and fixation of atmospheric nitrogen were observed in different taxa. The potential phototrophy of the strains of the genus Polymorphobacter which were cultivated from a lichen for the first time was revealed by the presence of genes involved in photosynthesis. Altogether, the physiological characteristics of diverse bacterial taxa from Antarctic lichens are considered to imply significant roles of lichen-associated bacteria to allow lichens to be tolerant or competitive in the harsh Antarctic environment.

Genome sequencing and analysis of plant growth-promoting attributes from Leclercia adecarboxylata

Plant growth-promoting bacteria are ecological alternatives for fertilization, mainly for gramineous. Since plant x bacteria interaction is genotype and strain dependent, searching for new strains may contribute to the development of new biofertilizers. We aim to characterize plant growth-promoting capacity of Leclercia adecarboxylata strain Palotina, formerly isolated by our group in corn. A single isolated colony was taken and its genome was sequenced using Illumina technology. The whole genome was compared to other Leclercia adecarboxylata strains, and their biological and growth-promoting traits, such as P solubilization and auxin production, were tested. Following that, a 4.8 Mb genome of L. adecarboxylata strain Palotina was assembled and the functional annotation was carried out. This paper is the first to report the genes associated with plant growth promotion demonstrating in vitro indole acid production by this strain. These results project the endophyte as a potential biofertilizer for further commercial exploitation.

Functional Analysis and Genome Mining Reveal High Potential of Biocontrol and Plant Growth Promotion in Nodule-Inhabiting Bacteria Within Paenibacillus polymyxa Complex

Bacteria belonging to the genus Paenibacillus were frequently isolated from legume nodules. The nodule-inhabiting Paenibacillus as a resource of biocontrol and plant growth-promoting endophytes has rarely been explored. This study explored the nodule-inhabiting Paenibacillus' antifungal activities and biocontrol potentials against broad-spectrum important phytopathogenic fungi. We collected strains which were isolated from nodules of Robinia pseudoacacia, Dendrolobium triangulare, Ormosia semicastrata, Cicer arietinum, Acacia crassicarpa, or Acacia implexa and belong to P. peoriae, P. kribbensis, P. endophyticus, P. enshidis, P. puldeungensis, P. taichungensis, or closely related to P. kribbensis, or P. anseongense. These nodule-inhabiting Paenibacillus showed diverse antagonistic activities against five phytopathogenic fungi (Fusarium graminearum, Magnaporthe oryzae, Rhizoctonia solani, Sclerotinia sclerotiorum, and Botrytis cinerea). Six strains within the P. polymyxa complex showed broad-spectrum and potent activities against all the five pathogens, and produced multiple hydrolytic enzymes, siderophores, and lipopeptide fusaricidins. Fusaricidins are likely the key antimicrobials responsible for the broad-spectrum antifungal activities. The nodule-inhabiting strains within the P. polymyxa complex were able to epiphytically and endophytically colonize the non-host wheat plants, produce indole acetic acids (IAA), and dissolve calcium phosphate and calcium phytate. P. peoriae strains RP20, RP51, and RP62 could fix N2. P. peoriae RP51 and Paenibacillus sp. RP31, which showed potent plant colonization and plant growth-promotion competence, effectively control fungal infection in planta. Genome mining revealed that all strains (n = 76) within the P. polymyxa complex contain ipdC gene encoding indole-3-pyruvate decarboxylase for biosynthesis of IAA, 96% (n = 73) contain the fus cluster for biosynthesis of fusaricidins, and 43% (n = 33) contain the nif cluster for nitrogen fixation. Together, our study highlights that endophytic strains within the P. polymyxa complex have a high probability to be effective biocontrol agents and biofertilizers and we propose an effective approach to screen strains within the P. polymyxa complex.

Newly isolated Bacillus sp. PS-6 assisted phytoremediation of heavy metals using Phragmites communis: Potential application in wastewater treatment

This work aimed to study Bacillus sp. PS-6 assisted phytoremediation of metals from pulp and paper industry wastewater as a novel green technique for the removal of metals of wastewater. Results revealed that heavy metal (mg L^-1) contents in wastewater were reduced after in-situ phytoremediation for Fe, Cu, Zn, Cd, Mn, Ni, Pb, and As. Phragmites communis showed higher potential for the enrichment of Fe, Cu, Zn, Cd, Mn, Ni, Pb, and As in its rhizomes, roots, and shoots compared to leaves. The strain produced indole acetic acid, siderophores, and hydrolytic and ligninolytic enzymes, and resulted in nutrients solubilization. Results offer potential basis for the removal of metals from pulp and paper industry wastewater at large scale and prevention of pollution.

Effect of Chemical Fertilization on the Impacts of Plant Growth-Promoting Rhizobacteria in Maize Crops

The use of chemical fertilizers strongly promotes productivity in agricultural crops; therefore, large amounts of chemical fertilizers have been used. The use of plant growth-promoting bacteria may be a strategy to reduce the use of chemical fertilizers; however, little is known about the effect of chemical fertilization on the performance of these bacteria through plant-microbe interactions. The present study aimed to verify the performance of Bacillus subtilis, Azospirillum brasilense, B. pumilus, B. amyloliquefaciens, Herbaspirillum seropedicae, Gluconacetobacter diazotrophicus, and the mixtures A. brasilense + B. subtilis, B. pumilus + B. amyloliquefaciens, and H. seropedicae + G. diazotrophicus on parameters such as nitrogen and phosphorus extraction from soil, the concentrations of these nutrients in maize plants, and plant growth in both fertilized and unfertilized soil. The results showed that H. seropedica increased the nitrogen content by 6.6 g kg^-1 in leaves and 2.2 g kg^-1 in the root when comparing the unfertilized with the fertilized condition. G. diazotrophicus increased the nitrogen content by 3.7 g kg^-1 in leaves and 2.4 g kg^-1 in the root. B. pumilus increased the phosphorous content by 1.7 g kg^-1 in leaves, and B. amyloliquefaciens increased the phosphorous content by 0.61 g kg^-1. The present study showed that even though the bacteria presented good performance related to plant growth under fertilized conditions, H. seropedicae, G. diazotrophicus, B. pumilus, and B. amyloliquefaciens could be used in the maize crop with a reduced chemical fertilization dose.

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum

Studies of the interactions between plants and their microbiome have been conducted worldwide in the search for growth-promoting representative strains for use as biological inputs for agriculture, aiming to achieve more sustainable agriculture practices. With a focus on the isolation of plant growth-promoting (PGP) bacteria with ability to alleviate N stress, representative strains that were found at population densities greater than 10⁴ cells g^-1 and that could grow in N-free semisolid media were isolated from soils under different management conditions and from the roots of tomato (Solanum lycopersicum) and lulo (Solanum quitoense) plants that were grown in those soils. A total of 101 bacterial strains were obtained, after which they were phylogenetically categorized and characterized for their basic PGP mechanisms. All strains belonged to the Proteobacteria phylum in the classes Alphaproteobacteria (61% of isolates), Betaproteobacteria (19% of isolates) and Gammaproteobacteria (20% of isolates), with distribution encompassing nine genera, with the predominant genus being Rhizobium (58.4% of isolates). Strains isolated from conventional horticulture (CH) soil composed three bacterial genera, suggesting a lower diversity for the diazotrophs/N scavenger bacterial community than that observed for soils under organic management (ORG) or secondary forest coverture (SF). Conversely, diazotrophs/N scavenger strains from tomato plants grown in CH soil comprised a higher number of bacterial genera than did strains isolated from tomato plants grown in ORG or SF soils. Furthermore, strains isolated from tomato were phylogenetically more diverse than those from lulo. BOX-PCR fingerprinting of all strains revealed a high genetic diversity for several clonal representatives (four Rhizobium species and one Pseudomonas species). Considering the potential PGP mechanisms, 49 strains (48.5% of the total) produced IAA (2.96–193.97 μg IAA mg protein^-1), 72 strains (71.3%) solubilized FePO₄ (0.40–56.00 mg l^-1), 44 strains (43.5%) solubilized AlPO₄ (0.62–17.05 mg l^-1), and 44 strains produced siderophores (1.06–3.23). Further, 91 isolates (90.1% of total) showed at least one PGP trait, and 68 isolates (67.3%) showed multiple PGP traits. Greenhouse trials using the bacterial collection to inoculate tomato or lulo plants revealed increases in plant biomass (roots, shoots or both plant tissues) elicited by 65 strains (54.5% of the bacterial collection), of which 36 were obtained from the tomato rhizosphere, 15 were obtained from the lulo rhizosphere, and 14 originated from samples of soil that lacked plants. In addition, 18 strains showed positive inoculation effects on both Solanum species, of which 12 were classified as Rhizobium spp. by partial 16S rRNA gene sequencing. Overall, the strategy adopted allowed us to identify the variability in the composition of culturable diazotroph/N-scavenger representatives from soils under different management conditions by using two Solanum species as trap plants. The present results suggest the ability of tomato and lulo plants to enrich their belowground microbiomes with rhizobia representatives and the potential of selected rhizobial strains to promote the growth of Solanum crops under limiting N supply.

Biocontrol and plant growth-promoting ability of plant-associated bacteria from tomato (Lycopersicum esculentum) under field condition

Forty-five bacterial isolates recovered from surface-sterilized root, stem and leaf tissues of tomato were studied for their antifungal activity against phytopathogens, and plant growth-promoting (PGP) and biocontrol traits. Six plant-associated bacteria suppressed all the pathogens tested under in vitro plate assay and also shown PGP and biocontrol traits. The six isolates showing PGP and biocontrol properties were identified as Bacillus spp., based on the microbial identification system (Biolog) and partial sequence analysis of 16S rDNA. Two independent field trials were conducted with biocontrol bacteria along with chemical control (Thiram+Fytolan) and control (Without treatment). The averaged results of two field trails revealed that tomato plants inoculated with BETS11 (11.73 t/ha) and BETR11 (11.24 t/ha) strains showed significantly higher yield and disease reduction on par with chemical control (11.81 t/ha). However, there was an increase in the yield with respect to uninoculated control except the isolate BETS5 (9.09 t/ha). Therefore, the isolates BETS11 and BETR11 may be used as efficient biofertilizer and bio-control agent for tomato production in the Island agricultural ecosystem.

Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress

BACKGROUND

The role of soil microorganisms in plant growth, nutrient utilization, drought tolerance as well as biocontrol activity cannot be over-emphasized, especially in this era when food crisis is a global challenge. This research was therefore designed to gain genomic insights into plant growth promoting (PGP) Rhizobium species capable of enhancing soybean (Glycine max L.) seeds germination under drought condition.

RESULTS

Rhizobium sp. strain R1, Rhizobium tropici strain R2, Rhizobium cellulosilyticum strain R3, Rhizobium taibaishanense strain R4 and Ensifer meliloti strain R5 were found to possess the entire PGP traits tested. Specifically, these rhizobial strains were able to solubilize phosphate, produce exopolysaccharide (EPS), 1-aminocyclopropane-1-carboxylate (ACC), siderophore and indole-acetic-acid (IAA). These strains also survived and grew at a temperature of 45 °C and in an acidic condition with a pH 4. Consequently, all the Rhizobium strains enhanced the germination of soybean seeds (PAN 1532 R) under drought condition imposed by 4% poly-ethylene glycol (PEG); nevertheless, Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 inoculations were able to improve seeds germination more than R2, R4 and R5 strains. Thus, genomic insights into Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 revealed the presence of some genes with their respective proteins involved in symbiotic establishment, nitrogen fixation, drought tolerance and plant growth promotion. In particular, exoX, htrA, Nif, nodA, eptA, IAA and siderophore-producing genes were found in the two rhizobial strains.

CONCLUSIONS

Therefore, the availability of the whole genome sequences of R1 and R3 strains may further be exploited to comprehend the interaction of drought tolerant rhizobia with soybean and other legumes and the PGP ability of these rhizobial strains can also be harnessed for biotechnological application in the field especially in semiarid and arid regions of the globe.

Rhizospheric Microbacterium sp. P27 Showing Potential of Lindane Degradation and Plant Growth Promoting Traits

Lindane is an organochlorine pesticide that is highly persistent in the environment. The amassing of lindane has been identified worldwide and has been found to be very toxic to the environment, human, and animal health. Therefore, urgent consideration and management of the problem is necessary. The current study intends to isolate and identify lindane degrading rhizospheric bacteria from Phragmites karka and to study its degradation kinetics. Also, plant growth promoting potential of the bacterium was evaluated in the presence and absence of studied pesticide. Rhizospheric bacteria were isolated by standard enrichment technique in Mineral Salt Medium. Microbacterium sp. P27 showed the highest degradation percentage, 82.7 ± 1.79% for 50 mg l^-1 lindane, after 15 days. Degradation was also studied at different concentrations of lindane. Maximum degradation was achieved at 10 mg l^-1 followed by 50 mg l^-1 and 100 mg l^-1 lindane. Microbacterium sp. P27 showed positive result for Indole-3-acetic acid production, ammonia production, and 1-aminocyclopropane-1-carboxylate deaminase activity. Presence of lindane revealed a concentration-dependent decrease in plant growth promoting activity. Since the isolated bacterial strain possesses lindane degrading capacity and also other characters that help in plant growth promotion, the isolate can be an important candidate for the progress of bioremediation strategy.

Enterobacter cloacae, an Endophyte That Establishes a Nutrient-Transfer Symbiosis With Banana Plants and Protects Against the Black Sigatoka Pathogen

Banana (Musa spp.) is an important crop worldwide, but black Sigatoka disease caused by the fungus Pseudocercospora fijiensis threatens fruit production. In this work, we examined the potential of the endophytes of banana plants Enterobacter cloacae and Klebsiella pneumoniae, as antagonists of P. fijiensis and support plant growth in nutrient limited soils by N-transfer. The two bacterial isolates were identified by MALDI-TOF mass spectrometry and corroborated by 16S rRNA sequence analysis. Both bacteria were positive for beneficial traits such as N-fixation, indole acetic acid production, phosphate solubilization, negative for 1-aminocyclopropane 1-carboxylic acid deaminase and were antagonistic to P. fijiensis. To measure the effects on plant growth, the two plant bacteria and an E. coli strain (as non-endophyte), were inoculated weekly for 60 days as active cells (AC) and heat-killed cells (HKC) into plant microcosms without nutrients and compared to a water only treatment, and a mineral nutrients solution (MMN) treatment. Bacterial treatments increased growth parameters and prevented accelerated senescence, which was observed for water and mineral nutrients solution (MMN) treatments used as controls. Plants died after the first 20 days of being irrigated with water; irrigation with MMN enabled plants to develop some new leaves, but plants lost weight (−30%) during the same period. Plants treated with bacteria showed good growth, but E. cloacae AC treated plants had significantly greater biomass than the E. cloacae HKC. After 60 days, plants inoculated with E. cloacae AC showed intracellular bacteria within root cells, suggesting that a stable symbiosis was established. To evaluate the transference of organic N from bacteria into the plants, the 3 bacteria were grown with ¹⁵NH₄Cl or Na¹⁵NO₃ as the nitrogen source. The ¹⁵N transferred from bacteria to plant tissues was measured by pheophytin isotopomer abundance. The relative abundance of the isotopomers m/z 872.57, 873.57, 874.57, 875.57, 876.57 unequivocally demonstrated that plants acquired ¹⁵N atoms directly from bacterial cells, using them as a source of N, to support plant growth in restricted nutrient soils. E. cloacae might be a new alternative to promote growth and health of banana crops.

Characterization and Initial Application of Endophytic Bacillus safensis Strain ZY16 for Improving Phytoremediation of Oil-Contaminated Saline Soils

Hydrocarbon-degrading and plant-growth-promoting bacterial endophytes have proven useful for facilitating the phytoremediation of petroleum-contaminated soils with high salinity. In this study, we identified Bacillus safensis strain ZY16 as an endophytic bacterium that can degrade hydrocarbons, produce biosurfactants, tolerate salt, and promote plant growth. The strain was isolated from the root of Chloris virgata Sw., a halotolerant plant collected from the Yellow River Delta. ZY16 survived in Luria-Bertani (LB) broth with 0–16% (w/v) sodium chloride (NaCl) and grew well in LB broth supplemented with 0–8% NaCl, indicating its high salt tolerance. The endophytic strain ZY16 effectively degraded C₁₂–C₃₂n-alkanes of diesel oil effectively, as well as common polycyclic aromatic hydrocarbons under hypersaline conditions. For example, in mineral salts (MS) liquid medium supplemented with 6% NaCl, ZY16 degraded n-undecane, n-hexadecane, n-octacosane, naphthalene, phenanthrene, and pyrene, with degradation percentages of 94.5, 98.2, 64.8, 72.1, 59.4, and 27.6%, respectively. In addition, ZY16 produced biosurfactant, as confirmed by the oil spreading technique, surface tension detection, and emulsification of para-xylene and paraffin. The biosurfactant production ability of ZY16 under hypersaline conditions was also determined. Moreover, ZY16 showed plant-growth-promoting attributes, such as siderophore and indole-3-acetic acid production, as well as phosphate solubilization. To assess the enhanced phytoremediation of saline soils polluted by hydrocarbons and the plant-growth-promotion ability of ZY16, a pot trial with and without inoculation of the endophyte was designed and performed. Inoculated and non-inoculated plantlets of C. virgata Sw. were grown in oil-polluted saline soil, with oil and salt contents of 10462 mg/kg and 0.51%, respectively. After 120 days of growth, significant enhancement of both the aerial and underground biomass of ZY16-inoculated plants was observed. The soil total petroleum hydrocarbon degradation percentage (a metric of phytoremediation) after incubation with ZY16 was 63.2%, representing an elevation of 25.7% over phytoremediation without ZY16 inoculation. Our study should promote the application of endophytic B. safensis ZY16 in phytoremediation by extending our understanding of the mutualistic interactions between endophytes and their host plants.

Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Background

Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil.

Results

Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria.

Conclusions

Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.

Phenotypic, genetic and symbiotic characterization of Erythrina velutina rhizobia from Caatinga dry forest

Erythrina velutina ("mulungu") is a legume tree from Caatinga that associates with rhizobia but the diversity and symbiotic ability of "mulungu" rhizobia are poorly understood. The aim of this study was to characterize "mulungu" rhizobia from Caatinga. Bacteria were obteined from Serra Talhada and Caruaru in Caatinga under natural regeneration. The bacteria were evaluated to the amplification of nifH and nodC and to metabolic characteristics. Ten selected bacteria identified by 16S rRNA sequences. They were tested in vitro to NaCl and temperature tolerance, auxin production and calcium phosphate solubilization. The symbiotic ability were assessed in an greenhouse experiment. A total of 32 bacteria were obtained and 17 amplified both symbiotic genes. The bacteria showed a high variable metabolic profile. Bradyrhizobium (6), Rhizobium (3) and Paraburkholderia (1) were identified, differing from their geographic origin. The isolates grew up to 45°C to 0.51molL-1 of NaCl. Bacteria which produced more auxin in the medium with l-tryptophan and two Rhizobium and one Bradyrhizobium were phosphate solubilizers. All bacteria nodulated and ESA 90 (Rhizobium sp.) plus ESA 96 (Paraburkholderia sp.) were more efficient symbiotically. Diverse and efficient rhizobia inhabit the soils of Caatinga dry forests, with the bacterial differentiation by the sampling sites.

Pseudomonas aeruginosa L10: A Hydrocarbon-Degrading, Biosurfactant-Producing, and Plant-Growth-Promoting Endophytic Bacterium Isolated From a Reed (Phragmites australis)

Bacterial endophytes with the capacity to degrade petroleum hydrocarbons and promote plant growth may facilitate phytoremediation for the removal of petroleum hydrocarbons from contaminated soils. A hydrocarbon-degrading, biosurfactant-producing, and plant-growth-promoting endophytic bacterium, Pseudomonas aeruginosa L10, was isolated from the roots of a reed, Phragmites australis, in the Yellow River Delta, Shandong, China. P. aeruginosa L10 efficiently degraded C₁₀-C₂₆n-alkanes from diesel oil, as well as common polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, and pyrene. In addition, P. aeruginosa L10 could produce biosurfactant, which was confirmed by the oil spreading method, and surface tension determination of inocula. Moreover, P. aeruginosa L10 had plant growth-stimulating attributes, including siderophore and indole-3-acetic acid (IAA) release, along with 1-aminocyclopropane-1-carboxylic (ACC) deaminase activity. To explore the mechanisms underlying the phenotypic traits of endophytic P. aeruginosa L10, we sequenced its complete genome. From the genome, we identified genes related to petroleum hydrocarbon degradation, such as putative genes encoding monooxygenase, dioxygenase, alcohol dehydrogenase, and aldehyde dehydrogenase. Genome annotation revealed that P. aeruginosa L10 contained a gene cluster involved in the biosynthesis of rhamnolipids, rhlABRI, which should be responsible for the observed biosurfactant activity. We also identified two clusters of genes involved in the biosynthesis of siderophore (pvcABCD and pchABCDREFG). The genome also harbored tryptophan biosynthetic genes (trpAB, trpDC, trpE, trpF, and trpG) that are responsible for IAA synthesis. Moreover, the genome contained the ACC deaminase gene essential for ACC deaminase activity. This study will facilitate applications of endophytic P. aeruginosa L10 to phytoremediation by advancing the understanding of hydrocarbon degradation, biosurfactant synthesis, and mutualistic interactions between endophytes and host plants.

Screening of tropically derived, multi-trait plant growth- promoting rhizobacteria and evaluation of corn and soybean colonization ability

The present study assessed the plant growth-promoting (PGP) traits and diversity of culturable rhizobacteria associated with guarana (Paullinia cupana), a typical tropical plant. Ninety-six bacteria were isolated, subjected to biochemical tests, and identified by partial or total 16S rDNA sequencing. Proteobacteria and Firmicutes were the dominant rhizospheric phyla found, and Burkholderia and Bacillus were the most abundant genera. Thirteen strains exhibited the four PGP traits evaluated, and most of them belonged to the genus Burkholderia. Two multi-trait PGP strains, RZ2MS9 (Bacillus sp.) and RZ2MS16 (Burkholderia ambifaria), expressively promoted corn and soybean growth under greenhouse conditions. Compared to the non-inoculated control, increases in corn root dry weight of 247.8 and 136.9% were obtained with RZ2MS9 and RZ2MS16 inoculation, respectively, at 60days after seeding. The dry weights of corn and soybean shoots were significantly higher than those of non-inoculated plants, showing increases of more than 47% for both strains and crops. However, soybean root dry weight did not increased after bacterial inoculation with either strain. The colonization behavior of RZ2MS16 was assessed using GFP-labeling combined with fluorescence microscopy and a cultivation-based approach for quantification. RZ2MS16:gfp was able to colonize the roots and shoots of corn and soybean, revealing an endophytic behavior.

Characterization of culturable bacteria isolated from hot springs for plant growth promoting traits and effect on tomato (Lycopersicon esculentum) seedling

To elucidate the functional diversity of hot spring bacteria, 123 bacteria were isolated and screened for evaluating their multifunctional plant growth promoting (PGP) properties. The antagonistic activity against different phytopathogens showed the presence of a high amount of biocontrol bacteria in the hot springs. During screening for PGP properties, 61.0% isolates showed production of indole acetic acid and 23.6% showed inorganic phosphate solubilization qualitatively. For production of extracellular enzymes, it was found that 61.0% isolates produced lipase, 56.9% produced protease, and 43.9% produced cellulase. In extreme properties, half of the isolates showed tolerance to 5% NaCl (w/v) and 48.8% isolates survived heat shock at 70°C. The identification of 12 multipotential bacteria based on 16S rRNA gene sequencing revealed that the bacteria belonged to Aneurinibacillus aneurinilyticus and Bacillus spp. Bacterization of tomato seeds showed that the hot spring bacteria promoted shoot height, fresh shoot weight, root length, and fresh root weight of tomato seedlings, with values ranging from 3.12% to 74.37%, 33.33% to 350.0%, 16.06% to 130.41%, and 36.36% to 318.18%, respectively, over the control. This research shows that multifunctional bacteria could be isolated from the hot springs. The outcome of this research may have a potential effect on crop production methodologies used in saline and arid environments.

Identification of Genes Involved in Indole-3-Acetic Acid Biosynthesis by Gluconacetobacter diazotrophicus PAL5 Strain Using Transposon Mutagenesis

Gluconacetobacter diazotrophicus is a beneficial nitrogen-fixing endophyte found in association with sugarcane plants and other important crops. Beneficial effects of G. diazotrophicus on sugarcane growth and productivity have been attributed to biological nitrogen fixation process and production of phytohormones especially indole-3-acetic acid (IAA); however, information about the biosynthesis and function of IAA in G. diazotrophicus is still scarce. Therefore, the aim of this work was to identify genes and pathways involved in IAA biosynthesis in this bacterium. In our study, the screening of two independent Tn5 mutant libraries of PAL5^T strain using the Salkowski colorimetric assay revealed two mutants (Gdiaa34 and Gdiaa01), which exhibited 95% less indolic compounds than the parental strain when grown in LGIP medium supplemented with L-tryptophan. HPLC chromatograms of the wild-type strain revealed the presence of IAA and of the biosynthetic intermediates indole-3-pyruvic acid (IPyA) and indole-3-lactate (ILA). In contrast, the HPLC profiles of both mutants showed no IAA but only a large peak of non-metabolized tryptophan and low levels of IPyA and ILA were detected. Molecular characterization revealed that Gdiaa01 and Gdiaa34 mutants had unique Tn5 insertions at different sites within the GDI2456 open read frame, which is predicted to encode a L-amino acid oxidase (LAAO). GDI2456 (lao gene) forms a cluster with GDI2455 and GDI2454 ORFs, which are predicted to encode a cytochrome C and an RidA protein, respectively. RT-qPCR showed that transcript levels of lao. cccA, and ridA genes were reduced in the Gdiaa01 as compared to PAL5^T. In addition, rice plants inoculated with Gdiaa01 showed significantly smaller root development (length, surface area, number of forks and tips) than those plants inoculated with PAL5^T. In conclusion, our study demonstrated that G. diazotrophicus PAL5^T produces IAA via the IPyA pathway in cultures supplemented with tryptophan and provides evidence for the involvement of an L-amino acid oxidase gene cluster in the biosynthesis of IAA. Furthermore, we showed that the mutant strains with reduction in IAA biosynthesis ability, in consequence of the lower transcription levels of genes of the lao cluster, had remarkable effects on development of rice roots.

Potential biocontrol actinobacteria: Rhizospheric isolates from the Argentine Pampas lowlands legumes

Control of fungal plant diseases by using naturally occurring non-pathogenic microorganisms represents a promising approach to biocontrol agents. This study reports the isolation, characterization, and fungal antagonistic activity of actinobacteria from forage soils in the Flooding Pampa, Argentina. A total of 32 saprophytic strains of actinobacteria were obtained by different isolation methods from rhizospheric soil of Lotus tenuis growing in the Salado River Basin. Based on physiological traits, eight isolates were selected for their biocontrol-related activities such as production of lytic extracellular enzymes, siderophores, hydrogen cyanide (HCN), and antagonistic activity against Cercospora sojina, Macrophomia phaseolina, Phomopsis sp., Fusarium oxysporum, and Fusarium verticilloides. These actinobacteria strains were characterized morphologically, physiologically, and identified by using molecular techniques. The characterization of biocontrol-related activities in vitro showed positive results for exoprotease, phospholipase, fungal growth inhibition, and siderophore production. However, none of the strains was positive for the production of hydrogen cyanide (HCN). Streptomyces sp. MM140 presented the highest index for biocontrol, and appear to be promising pathogenic fungi biocontrol agents. These results show the potential capacity of actinobacteria isolated from forage soils in the Argentine Pampas lowlands as promising biocontrol agents, and their future agronomic applications.