scholarly journals Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

2019 ◽  
Author(s):  
Luz K. Medina-Cordoba ◽  
Aroon T. Chande ◽  
Lavanya Rishishwar ◽  
Leonard W. Mayer ◽  
Lina C. Valderrama-Aguirre ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Nitrogen Fixation ◽  
Plant Growth ◽  
Phosphate Solubilization ◽  
Bacterial Isolates ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
A Genome ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACTPrevious studies have shown that the sugarcane microbiome harbors diverse plant growth promoting (PGP) microorganisms, including nitrogen-fixing bacteria, and the objective of this study was to design a genome-enabled approach to prioritize sugarcane associated nitrogen-fixing bacteria according to their potential as biofertilizers. Using a systematic high throughput approach, 22 pure cultures of nitrogen-fixing bacteria were isolated and tested for diazotrophic potential by PCR amplification of nitrogenase (nifH) genes, common molecular markers for nitrogen fixation capacity. Genome sequencing confirmed the presence of intact nitrogenase nifH genes and operons in the genomes of 18 of the isolates. Isolate genomes also encoded operons for phosphate solubilization, siderophore production operons, and other PGP phenotypes. Klebsiella pneumoniae strains comprised 14 of the 22 nitrogen-fixing isolates, and four others were members of closely related genera to Klebsiella. A computational phenotyping approach was developed to rapidly screen for strains that have high potential for nitrogen fixation and other PGP phenotypes while showing low risk for virulence and antibiotic resistance. The majority of sugarcane isolates were below a genotypic and phenotypic threshold, showing uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six prioritized strains were experimentally evaluated for PGP phenotypes: nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid and indole acetic acid. Results from the biochemical assays were consistent with the computational phenotype predictions for these isolates. Our results indicate that computational phenotyping is a promising tool for the assessment of benefits and risks associated with bacteria commonly detected in agricultural ecosystems.IMPORTANCEA genome-enabled approach was developed for the prioritization of native bacterial isolates with the potential to serve as biofertilizers for sugarcane fields in Colombia’s Cauca Valley. The approach is based on computational phenotyping, which entails predictions related to traits of interest based on bioinformatic analysis of whole genome sequences. Bioinformatic predictions of the presence of plant growth promoting traits were validated with experimental assays and more extensive genome comparisons, thereby demonstrating the utility of computational phenotyping for assessing the benefits and risks posed by bacterial isolates that can be used as biofertilizers. The quantitative approach to computational phenotyping developed here for the discovery of biofertilizers has the potential for use with a broad range of applications in environmental and industrial microbiology, food safety, water quality, and antibiotic resistance studies.

scholarly journals Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luz K. Medina-Cordoba ◽  
Aroon T. Chande ◽  
Lavanya Rishishwar ◽  
Leonard W. Mayer ◽  
Lina C. Valderrama-Aguirre ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Nitrogen Fixation ◽  
Plant Growth ◽  
Phosphate Solubilization ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Promising Tool ◽  
A Genome ◽  
Plant Growth Promoting ◽  
Growth Promoting

AbstractPrevious studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.

scholarly journals Isolation and characterization of plant growth-promoting endophytic bacteria of wild legumes growing on sandy soils of Binh Thuan province, Vietnam

2021 ◽  
Vol 10 (3) ◽  
pp. 246-254
Author(s):  
Dang Thi Ngoc Thanh ◽  
Pham Thi Thu Ly ◽  
Pham Thi Nga ◽  
Pham Van Ngot
Keyword(s):  
Nitrogen Fixation ◽  
Plant Growth ◽  
Endophytic Bacteria ◽  
Phosphate Solubilization ◽  
Sandy Soils ◽  
Legume Species ◽  
Bacterial Isolates ◽  
Isolation And Characterization ◽  
Plant Growth Promoting ◽  
Growth Promoting

The roots of two legume species (Tephrosia purpurea and Tephrosia villosa) that grew wild on dry sandy soils of Binh Thuan province were sources for isolating plant growth-promoting endophytic bacteria. Semi-solid LGI medium was used for the isolation of nitrogen-fixing bacteria from root extracts. All bacterial isolates isolates were evaluated for their ability to solubilize calcium orthophosphate on solid NBRIP medium and their ability to produce IAA in Burk's liquid medium supplemented with 100 mg/L tryptophan. The possibilities of nitrogen fixation, phosphate solubilization and IAA synthesis were all quantitative examined by colorimetric method. Twenty-two bacterial isolates of T. purpurea and 18 isolates of T. villosa were capable of nitrogen fixation in the range of 1.94 to 2.81 mg/L NH4+, whereas only 18 isolates of T. purpurea and 16 isolates of T. villosa showed phosphate solubilization in the range of 12.30 – 48.90 mg/L P2O5, and IAA production in the range of 0.38 – 12.72 mg/L. Sixteen outstanding bacterial isolates of the two legume species were identified by MALDI-TOF technique. The results showed that 13 isolates had high similarity with five bacterial genera including Klebsiella, Cronobacter, Enterobacter, Burkholderia, and Bacillus with score values in the range of 2.070 – 2.411.

Nitrogen-fixing bacteria with multiple plant growth-promoting activities enhance growth of tomato and red pepper

2013 ◽  
Vol 53 (12) ◽  
pp. 1004-1015 ◽  
Author(s):  
Md. Rashedul Islam ◽  
Tahera Sultana ◽  
M. Melvin Joe ◽  
Woojong Yim ◽  
Jang-Cheon Cho ◽  
...  
Keyword(s):  
Plant Growth ◽  
Red Pepper ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Plant Growth Promoting Activities ◽  
Plant Growth Promoting ◽  
Growth Promoting

scholarly journals Characterization of Arsenic-Resistant Endophytic Bacteria From Alfalfa and Chickpea Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Hazhir Tashan ◽  
Behrouz Harighi ◽  
Jalal Rostamzadeh ◽  
Abdolbaset Azizi
Keyword(s):  
Nitrogen Fixation ◽  
Plant Growth ◽  
Endophytic Bacteria ◽  
Phosphate Solubilization ◽  
Lipase Production ◽  
Growth Potential ◽  
Sodium Arsenate ◽  
Plant Growth Promoting ◽  
Growth Promoting

The present investigation was carried out to isolate arsenic (As)-resistant endophytic bacteria from the roots of alfalfa and chickpea plants grown in arsenic-contamination soil, characterize their As tolerance ability, plant growth-promoting characteristics, and their role to induce As resistance by the plant. A total of four root endophytic bacteria were isolated from plants grown in As-contaminated soil (160–260-mg As kg−1 of soil). These isolates were studied for plant growth-promoting (PGP) characteristics through siderophore, phosphate solubilization, nitrogen fixation, protease, and lipase production, and the presence of the arsenate reductase (arsC) gene. Based on 16S rDNA sequence analysis, these isolates belong to the genera Acinetobacter, Pseudomonas, and Rahnella. All isolates were found As tolerant, of which one isolate, Pseudomonas sp. QNC1, showed the highest tolerance up to 350-mM concentration in the LB medium. All isolates exhibited phosphate solubilization activity. Siderophore production activity was shown by only Pseudomonas sp. QNC1, while nitrogen fixation activity was shown by only Rahnella sp. QNC2 isolate. Acinetobacter sp. QNA1, QNA2, and Rahnella sp. QNC2 exhibited lipase production, while only Pseudomonas sp. QNC1 was able to produce protease. The presence of the arsC gene was detected in all isolates. The effect of endophytic bacteria on biomass production of alfalfa and chickpea in five levels of arsenic concentrations (0-, 10-, 50-, 75-, and 100-mg kg−1 soil) was evaluated. The fresh and dry weights of roots of alfalfa and chickpea plants were decreased as the arsenic concentration of the soil was increased. Results indicate that the fresh and dry root weights of alfalfa and chickpea plants were significantly higher in endophytic bacteria-treated plants compared with non-treated plants. Inoculation of chickpea plants with Pseudomonas sp. QNC1 and Rahnella sp. QNC2 induced lower NPR3 gene expression in chickpea roots grown in soil with the final concentration of 100-mg kg−1 sodium arsenate compared with the non-endophyte-treated control. The same results were obtained in Acinetobacter sp. QNA2-treated alfalfa plants grown in the soil plus 50-mg kg−1 sodium arsenate. These results demonstrated that arsenic-resistant endophytic bacteria are potential candidates to enhance plant-growth promotion in As contamination soils. Characterization of bacterial endophytes with plant growth potential can help us apply them to improve plant yield under stress conditions.

scholarly journals Isolation and characterization of salt-tolerant bacteria with plant growth-promoting activities from saline agricultural fields of Haryana, India

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Arti Sharma ◽  
Kamal Dev ◽  
Anuradha Sourirajan ◽  
Madhu Choudhary
Keyword(s):  
Salt Tolerance ◽  
Plant Growth ◽  
Phosphate Solubilization ◽  
Saline Soil ◽  
Plant Growth Promoting Rhizobacteria ◽  
Bacterial Isolates ◽  
Salt Tolerant ◽  
Plant Growth Promoting ◽  
Growth Promoting

Abstract Background Soil salinity has been one of the biggest hurdles in achieving better crop yield and quality. Plant growth-promoting rhizobacteria (PGPR) are the symbiotic heterogeneous bacteria that play an important role in the recycling of plant nutrients through phytostimulation and phytoremediation. In this study, bacterial isolates were isolated from salt-polluted soil of Jhajjar and Panipat districts of Haryana, India. The potential salt-tolerant bacteria were screened for their PGPR activities such as phosphate solubilization, hydrogen cyanide (HCN), indole acetic acid (IAA) and ammonia production. The molecular characterization of potent isolates with salt tolerance and PGPR activity was done by 16S rDNA sequencing. Results Eighteen soil samples from saline soils of Haryana state were screened for salt-tolerant bacteria. The bacterial isolates were analyzed for salt tolerance ranging from 2 to 10%. Thirteen isolates were found salt tolerant at varied salt concentrations. Isolates HB6P2 and HB6J2 showed maximum tolerance to salts at 10% followed by HB4A1, HB4N3 and HB8P1. All the salt-tolerant bacterial isolates showed HCN production with maximum production by HB6J2. Phosphate solubilization was demonstrated by three isolates viz., HB4N3, HB6P2 and HB6J2. IAA production was maximum in HB4A1 (15.89) and HB6P2 (14.01) and least in HB4N3 (8.91). Ammonia production was maximum in HB6P2 (12.3) and least in HB8P1 (6.2). Three isolates HB6J2, HB8P1 and HB4N3 with significant salt tolerance, and PGPR ability were identified through sequencing of amplified 16SrRNA gene and were found to be Bacillus paramycoides, Bacillus amyloliquefaciens and Bacillus pumilus, respectively. Conclusions The salt-tolerant plant growth-promoting rhizobacteria (PGPR) isolated from saline soil can be used to overcome the detrimental effects of salt stress on plants, with beneficial effects of physiological functions of plants such as growth and yield, and overcome disease resistance. Therefore, application of microbial inoculants to alleviate stresses and enhance yield in plants could be a low cost and environmental friendly option for the management of saline soil for better crop productivity.

scholarly journals Use of termitarium soil as a viable source for biofertilizer and biocontrol

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Seun Owolabi Adebajo ◽  
Pius Olugbenga Akintokun ◽  
Emmanuel Ezaka ◽  
Abidemi Esther Ojo ◽  
Donald Uzowulu Olannye ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Plant Growth ◽  
Indole Acetic Acid ◽  
Phosphate Solubilization ◽  
Soil Samples ◽  
Production Test ◽  
Bacterial Isolates ◽  
Acetic Acid Production ◽  
Plant Growth Promoting ◽  
Growth Promoting

Abstract Background Environmental deterioration arising from the misuse of pesticides and chemical fertilizers in agriculture has resulted in the pursuit of eco-friendly means of growing crop. Evidence has shown that biofertilizers and biocontrol can boost soil fertility and suppress soil pathogens without compromising the safety of the environment. Hence, the study investigated the use of termitarium soil as a viable source for biofertilizer and biocontrol. Results Twenty-seven soil samples were collected from nine different mound soil (household, farm and water bodies in a sterile sample bag). Aliquots of serially diluted samples were plated on nutrient agar, plate count agar, eosin methylene blue agar and MacConkey agar plates. Isolates were identified using standard microbiological techniques. Identified isolates were screened for plant growth-promoting properties using phosphate solubilization test, potassium solubilization test and indole acetic acid production test. Activities of the plant growth-promoting bacteria were carried out using antagonism by diffusible substance method and antagonistic activity of cell-free culture filtrate of bacterial isolates against Ralstonia solanacearum and Fusarium oxysporum. Two hundred bacterial isolates were recovered from the 27 soil samples. The most predominant isolate was Bacillus spp. Out of the 200 bacterial isolates, 57 were positive for phosphate solubilization test, potassium solubilization test and indole acetic acid production test. Out of the 57 isolates, six bacterial isolates had antagonistic activities against Fusarium oxysporum, while seven bacterial isolates antagonized Ralstonia solanacearum. Conclusion The result showed that termite mound soil contains some useful bacteria that are capable of solubilizing phosphate and potassium and producing indole acetic acid which are the plant growth-promoting potentials and as well suppressing plant soil pathogen.

scholarly journals Evaluation of Phytase Producing Bacteria for Their Plant Growth Promoting Activities

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Prashant Singh ◽  
Vinod Kumar ◽  
Sanjeev Agrawal
Keyword(s):  
Plant Growth ◽  
Phosphate Solubilization ◽  
Growth Promotion ◽  
Growth Parameters ◽  
Growth Effect ◽  
Bacterial Isolates ◽  
Iaa Production ◽  
Plant Growth Promoting Activities ◽  
Plant Growth Promoting ◽  
Growth Promoting

Bacterial inoculants are known to possess plant growth promoting abilities and have potential as liquid biofertilizer application. Four phytase producing bacterial isolates (phytase activity in the range of 0.076–0.174 U/mL), identified asAdvenellaspecies (PB-05, PB-06, and PB-10) andCellulosimicrobiumsp. PB-09, were analyzed for their plant growth promoting activities like siderophore production, IAA production, HCN production, ammonia production, phosphate solubilization, and antifungal activity. All isolates were positive for the above characteristics except for HCN production. The solubilization index for phosphorus on Pikovskaya agar plates was in the range of 2–4. Significant amount of IAA (7.19 to 35.03 μg/mL) production and solubilized phosphate (189.53 to 746.84 μg/mL) was noticed by these isolates at different time intervals. Besides that, a greenhouse study was also conducted with Indian mustard to evaluate the potential of these isolates to promote plant growth. Effect of seed bacterization on various plant growth parameters and P uptake by plant were used as indicators. The plant growth promoting ability of bacterial isolates in pot experiments was correlated to IAA production, phosphate solubilization, and otherin vitrotests. On the basis of present findings, isolate PB-06 was most promising in plant growth promotion with multiple growth promoting characteristics.

scholarly journals Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs

2018 ◽  
Author(s):  
Lorena Jacqueline Gómez-Godínez ◽  
Ernesto Ormeño-Orrillo ◽  
Esperanza Martínez-Romero
Keyword(s):  
Nitrogen Fixation ◽  
Plant Growth ◽  
Differential Expression Analysis ◽  
Plant Growth Promoting Rhizobacteria ◽  
Single Species ◽  
Microbial Consortia ◽  
Plant Growth Promoting Bacteria ◽  
Nitrogen Fixing ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACTThe free-living soil bacteria that are beneficial for the growth of plants are known as plant growth-promoting rhizobacteria (PGPR). In this work, a multi-species of PGPR bacteria inoculant was designed, which included nitrogen-fixing strains such as Rhizobium phaseoli, Sinorhizobium americanum and Azospirillum brasilense, as well as other plant growth promoting bacteria such as Bacillus subtillis and Methylobacterium extorquens. The multi-species community exerted a beneficial effect on plant seedlings when it was inoculated, greater than the effect observed when inoculating each bacteria individually. Acetylene reduction of maize roots was recorded with the multi-species inoculant, which suggests that nitrogen fixation occurred under these conditions. To analyze the contributions of the different nitrogen-fixing bacteria that were inoculated, a metatranscriptomic analysis was performed. The differential expression analysis revealed that the predominantly nif transcripts of Azospirillum are overexpressed, suggesting that it was responsible for nitrogen fixation in maize. Overall, we analyzed the interaction of a synthetic community, suggesting it as an option, for future formulations of biofertilizers.IMPORTANCEWhile nodulation processes and nitrogen fixation by rhizobia have been well studied, little is known about the interaction between rhizobia and non-leguminous plants such as maize, which is used as a model for this study. Nitrogen fixation in cereals is a long searched goal. Instead of single species inoculants, multi-species inoculation may be more efficient to promote plant growth and fix nitrogen. Metatrascriptomes allowed us to recognize the bacteria responsible for nitrogen fixation in plant rootlets. The study of the function of certain genes may help to understand how microorganisms interact with the root plant, as well as allow a better use of microorganisms for the generation of novel biofertilizers using microbial consortia.

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