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

2021 ◽  
Vol 11 ◽  
Author(s):  
Md. Arshad Ali ◽  
Yang Lou ◽  
Rahila Hafeez ◽  
Xuqing Li ◽  
Afsana Hossain ◽  
...  
Keyword(s):  
Plant Growth ◽  
Broad Spectrum ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Genome Mining ◽  
Hydrolytic Enzymes ◽  
Phytopathogenic Fungi ◽  
Plant Colonization ◽  
In Planta ◽  
Antifungal Activities

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.

scholarly journals Genome Mining and Evaluation of the Biocontrol Potential of Pseudomonas fluorescens BRZ63, a New Endophyte of Oilseed Rape (Brassica napus L.) against Fungal Pathogens

2020 ◽  
Vol 21 (22) ◽  
pp. 8740
Author(s):  
Daria Chlebek ◽  
Artur Pinski ◽  
Joanna Żur ◽  
Justyna Michalska ◽  
Katarzyna Hupert-Kocurek
Keyword(s):  
Brassica Napus ◽  
Plant Growth ◽  
Pseudomonas Fluorescens ◽  
Oilseed Rape ◽  
Plant Growth Promotion ◽  
Fungal Pathogens ◽  
Growth Promotion ◽  
Genome Mining ◽  
Plant Colonization ◽  
Brassica Napus L

Endophytic bacteria hold tremendous potential for use as biocontrol agents. Our study aimed to investigate the biocontrol activity of Pseudomonas fluorescens BRZ63, a new endophyte of oilseed rape (Brassica napus L.) against Rhizoctonia solani W70, Colletotrichum dematium K, Sclerotinia sclerotiorum K2291, and Fusarium avenaceum. In addition, features crucial for biocontrol, plant growth promotion, and colonization were assessed and linked with the genome sequences. The in vitro tests showed that BRZ63 significantly inhibited the mycelium growth of all tested pathogens and stimulated germination and growth of oilseed rape seedlings treated with fungal pathogens. The BRZ63 strain can benefit plants by producing biosurfactants, siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia as well as phosphate solubilization. The abilities of exopolysaccharide production, autoaggregation, and biofilm formation additionally underline its potential to plant colonization and hence biocontrol. The effective colonization properties of the BRZ63 strain were confirmed by microscopy observations of EGFP-expressing cells colonizing the root surface and epidermal cells of Arabidopsis thaliana Col-0. Genome mining identified many genes related to the biocontrol process, such as transporters, siderophores, and other secondary metabolites. All analyses revealed that the BRZ63 strain is an excellent endophytic candidate for biocontrol of various plant pathogens and plant growth promotion.

scholarly journals Perception of Biocontrol Potential of Bacillusinaquosorum KR2-7 against Tomato Fusarium Wilt through Merging Genome Mining with Chemical Analysis

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 137
Author(s):  
Maedeh Kamali ◽  
Dianjing Guo ◽  
Shahram Naeimi ◽  
Jafar Ahmadi
Keyword(s):  
Chemical Analysis ◽  
Plant Growth ◽  
Fusarium Wilt ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Genome Mining ◽  
Gene Clusters ◽  
Systemic Resistance ◽  
Plant Colonization ◽  
Biocontrol Potential

Tomato Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), is a destructive disease that threatens the agricultural production of tomatoes. In the present study, the biocontrol potential of strain KR2-7 against Fol was investigated through integrated genome mining and chemical analysis. Strain KR2-7 was identified as B. inaquosorum based on phylogenetic analysis. Through the genome mining of strain KR2-7, we identified nine antifungal and antibacterial compound biosynthetic gene clusters (BGCs) including fengycin, surfactin and Bacillomycin F, bacillaene, macrolactin, sporulation killing factor (skf), subtilosin A, bacilysin, and bacillibactin. The corresponding compounds were confirmed through MALDI-TOF-MS chemical analysis. The gene/gene clusters involved in plant colonization, plant growth promotion, and induced systemic resistance were also identified in the KR2-7 genome, and their related secondary metabolites were detected. In light of these results, the biocontrol potential of strain KR2-7 against tomato Fusarium wilt was identified. This study highlights the potential to use strain KR2-7 as a plant-growth promotion agent.

scholarly journals Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance

2021 ◽  
Vol 12 ◽  
Author(s):  
Kristina Ulrich ◽  
Michael Kube ◽  
Regina Becker ◽  
Volker Schneck ◽  
Andreas Ulrich
Keyword(s):  
Plant Growth ◽  
Stress Tolerance ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Whole Genome Sequence ◽  
Plant Colonization ◽  
Rrna Gene ◽  
Promote Plant Growth ◽  
Physiological Tests

Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.

scholarly journals Connecting the Lab and the Field: Genome Analysis of Phyllobacterium and Rhizobium Strains and Field Performance on Two Vegetable Crops

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1124
Author(s):  
José David Flores-Félix ◽  
Encarna Velázquez ◽  
Eustoquio Martínez-Molina ◽  
Fernando González-Andrés ◽  
Andrea Squartini ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Genome Mining ◽  
Field Performance ◽  
In Silico Analysis ◽  
Homoserine Lactone ◽  
Plant Colonization ◽  
Vegetable Crops ◽  
Bacterial Strains ◽  
Acetic Acid Production

The legume nodules are a rich source not only of rhizobia but also of endophytic bacteria exhibiting plant growth-promoting mechanisms with potential as plant biostimulants. In this work we analyzed the genomes of Phyllobacterium endophyticum PEPV15 and Rhizobium laguerreae PEPV16 strains, both isolated from Phaseolus vulgaris nodules. In silico analysis showed that the genomes of these two strains contain genes related to N-acyl-homoserine lactone (AHL) and cellulose biosynthesis, involved in quorum sensing and biofilm formation, which are essential for plant colonization. Several genes involved in plant growth promotion such as those related to phosphate solubilization, indole acetic acid production, siderophore biosynthesis and nitrogen fixation were also located in both genomes. When strains PEPV15 and PEPV16 were inoculated in lettuce and carrot in field assays, we found that both significantly increased the yield of lettuce shoots and carrot roots by more than 20% and 10%, respectively. The results of this work confirmed that the genome mining of genes involved in plant colonization and growth promotion is a good strategy for predicting the potential of bacterial strains as crops inoculants, opening new horizons for the selection of bacterial strains with which to design new, effective bacteria-based plant biostimulants.

scholarly journals Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts

2020 ◽  
Author(s):  
Shawn M. Higdon ◽  
Tania Pozzo ◽  
Emily J. Tibbett ◽  
Colleen Chiu ◽  
Richard Jeannotte ◽  
...  
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Marker Genes ◽  
Diazotrophic Bacteria ◽  
In Planta ◽  
Pgp Traits

AbstractSierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic bacteria isolated from Sierra Mixe maize mucilage and sequenced their genomes. Comparative genomic analysis demonstrated that isolates represented diverse genera and possessed multiple marker genes for mechanisms of direct plant growth promotion (PGP). In addition to nitrogen fixation, we examined deamination of 1-amino-1-cyclopropanecarboxylic acid, biosynthesis of indole-3-acetic acid, and phosphate solubilization. Implementing in vitro colorimetric assays revealed each isolate’s potential to confer the alternative PGP activities that corroborated genotype and pathway content. We examined the ability of mucilage diazotrophs to confer PGP by direct inoculation of clonally propagated potato plants in planta, which led to the identification of bio-stimulant candidates that were tested for PGP by inoculating a conventional maize variety. The results indicate that, while many diazotrophic isolates from Sierra Mixe maize possessed genotypes and in vitro phenotypes for targeted PGP traits, a subset of these organisms promoted the growth of potato and conventional maize using multiple promotion mechanisms.

scholarly journals Draft Genome Sequence of Micromonospora sp. Strain MW-13, a Bacterial Strain with Antibacterial Properties and Plant Growth Promotion Potential Isolated from the Rhizosphere of Wheat in Iran

2019 ◽  
Vol 8 (2) ◽  
Author(s):  
Ghazaleh Jahanshah ◽  
Henrike Miess ◽  
Tobias Busche ◽  
Christian Rückert ◽  
Jörn Kalinowski ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Plant Growth ◽  
Broad Spectrum ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Draft Genome ◽  
Antibacterial Properties ◽  
Production Capacity ◽  
Gram Negative ◽  
Insight Into

Strain MW13 exhibited broad-spectrum antibacterial activity toward Gram-positive and Gram-negative pathogens. The 7.1-Mb draft genome gives insight into the complete secondary metabolite production capacity and reveals genes putatively responsible for its antibacterial activity, as well as genes which contribute to plant growth promotion.

scholarly journals Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 601 ◽  
Author(s):  
Johanna Nelkner ◽  
Gonzalo Torres Tejerizo ◽  
Julia Hassa ◽  
Timo Wentong Lin ◽  
Julian Witte ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Genome Mining ◽  
Gene Clusters ◽  
Disease Suppression ◽  
Biocontrol Agents ◽  
Circular Chromosome ◽  
Pseudomonas Brassicacearum

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

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