scholarly journals Metagenomic Insights and Genomic Analysis of Phosphogypsum and Its Associated Plant Endophytic Microbiomes Reveals Valuable Actors for Waste Bioremediation

2019 ◽  
Vol 7 (10) ◽  
pp. 382
Author(s):  
Ben Mefteh ◽  
Bouket ◽  
Daoud ◽  
Luptakova ◽  
Alenezi ◽  
...  
Keyword(s):  
Plant Growth ◽  
Stress Tolerance ◽  
Growth Promotion ◽  
Genome Mining ◽  
Environmental Pollutants ◽  
Genomic Analysis ◽  
Amplicon Sequencing ◽  
Waste Remediation ◽  
Plant Growth Promoting ◽  
Pgp Activities

The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. Results highlight a more diverse community of phosphogypsum than plants associated endophytic communities. Additionally, the bacterial culturable communities of phosphogypsum and associated plant endophytes were isolated and their plant-growth promotion capabilities, bioremediation potential and stress tolerance studied. Most of plant endophytes were endowed with plant growth-promoting (PGP) activities and phosphogypsum communities and associated plants endophytes proved highly resistant to salt, metal and antibiotic stress. They also proved very active in bioremediation of phosphogypsum and other organic and inorganic environmental pollutants. Genome sequencing of five members of the phosphogypsum endogenous community showed that they belong to the recently described species Bacillus albus (BA). Genome mining of BA allowed the description of pollutant degradation and stress tolerance mechanisms. Prevalence of this tool box in the core, accessory and unique genome allowed to conclude that accessory and unique genomes are critical for the dynamics of strain acquisition of bioremediation abilities. Additionally, secondary metabolites (SM) active in bioremediation such as petrobactin have been characterized. Taken together, our results reveal hidden untapped valuable bacterial actors for waste remediation.

scholarly journals Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257863
Author(s):  
Nazia R. Zaman ◽  
Umar F. Chowdhury ◽  
Rifath N. Reza ◽  
Farhana T. Chowdhury ◽  
Mrinmoy Sarker ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Genome Mining ◽  
Gene Clusters ◽  
Macrophomina Phaseolina ◽  
Melanin Synthesis ◽  
Burkholderia Contaminans ◽  
Plant Growth Promoting ◽  
Growth Promoting

The endophytic bacterium Burkholderia contaminans NZ was isolated from jute, which is an important fiber-producing plant. This bacterium exhibits significant growth promotion activity in in vivo pot experiments, and like other plant growth-promoting (PGP) bacteria fixes nitrogen, produces indole acetic acid (IAA), siderophore, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. B. contaminans NZ is considered to exert a promising growth inhibitory effect on Macrophomina phaseolina, a phytopathogen responsible for infecting hundreds of crops worldwide. This study aimed to identify the possibility of B. contaminans NZ as a safe biocontrol agent and assess its effectiveness in suppressing phytopathogenic fungi, especially M. phaseolina. Co-culture of M. phaseolina with B. contaminans NZ on both solid and liquid media revealed appreciable growth suppression of M. phaseolina and its chromogenic aberration in liquid culture. Genome mining of B. contaminans NZ using NaPDoS and antiSMASH revealed gene clusters that displayed 100% similarity for cytotoxic and antifungal substances, such as pyrrolnitrin. GC-MS analysis of B. contaminans NZ culture extracts revealed various bioactive compounds, including catechol; 9,10-dihydro-12’-hydroxy-2’-methyl-5’-(phenylmethyl)- ergotaman 3’,6’,18-trione; 2,3-dihydro-3,5- dihydroxy-6-methyl-4H-pyran-4-one; 1-(1,6-Dioxooctadecyl)- pyrrolidine; 9-Octadecenamide; and 2- methoxy- phenol. These compounds reportedly exhibit tyrosinase inhibitory, antifungal, and antibiotic activities. Using a more targeted approach, an RP-HPLC purified fraction was analyzed by LC-MS, confirming the existence of pyrrolnitrin in the B. contaminans NZ extract. Secondary metabolites, such as catechol and ergotaman, have been predicted to inhibit melanin synthesis in M. phaseolina. Thus, B. contaminans NZ appears to inhibit phytopathogens by apparently impairing melanin synthesis and other potential biochemical pathways, exhibiting considerable fungistatic activity.

scholarly journals Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics

2020 ◽  
Vol 8 (5) ◽  
pp. 725 ◽  
Author(s):  
Eiko E. Kuramae ◽  
Stan Derksen ◽  
Thiago R. Schlemper ◽  
Maurício R. Dimitrov ◽  
Ohana Y. A. Costa ◽  
...  
Keyword(s):  
Plant Growth ◽  
Sorghum Bicolor ◽  
Plant Biomass ◽  
Growth Promotion ◽  
Genomic Analysis ◽  
Shoot Biomass ◽  
Plant Growth Promoting ◽  
Plant Hormone Signaling ◽  
Underlying Mechanisms ◽  
High Degree

Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.

scholarly journals Comparative Genomic Understanding of Gram-Positive Plant Growth Promoting Leifsonia

2021 ◽  
Author(s):  
Nathan P Nordstedt ◽  
Veronica Roman-Reyna ◽  
Jonathan Michael Jacobs ◽  
Michelle Lyn Jones
Keyword(s):  
Plant Growth ◽  
Stress Tolerance ◽  
Growth Promotion ◽  
In Vitro Assays ◽  
Comparative Genomic ◽  
Beneficial Bacteria ◽  
Water Stress Tolerance ◽  
Vitamin B9 ◽  
Plant Growth Promoting ◽  
Growth Promoting

Root-associated bacteria play critical roles in shaping plant health for abiotic and biotic stress tolerance. The Leifsonia genus includes pathogenic and beneficial bacteria, but limited research is available comparatively across species regarding association with plants. We recently identified the plant growth-promoting Leifsonia sp. C5G2 isolated from the rhizosphere of Plectranthus scutellarioides (coleus) that increased stress tolerance and quality of water-stressed greenhouse ornamentals. Using this beneficial strain as a model, we performed comparative genomics with beneficial, commensal, and pathogenic Leifsonia species to better understand plant association and growth promotion under abiotic stress. Comparative phylogenetic analyses showed that beneficial and commensal Leifsonia spp. clustered separately from pathogenic Leifsonia xyli subsp. xyli. In addition, the beneficial/commensal strains share biosynthetic gene and orthologous protein clusters that are not shared with known phytopathogens in our analysis. The phytopathogenic Leifsonia strains also share noticeably higher percent homology with plant-associated virulence factors in closely-related Clavibacter spp. than the beneficial/commensal strains. Genome analysis supplemented with in vitro assays validated the findings that our model growth-promoting Leifsonia sp. strain C5G2 was highly prolific on diverse carbon sources. This is unlike known fastidious growth behaviors of phytopathogenic Leifsonia. Beneficial Leifsonia sp. C5G2 imparts water stress tolerance in plants, and multiple genes were identified in the genomes of beneficial Leifsonia strains that are potentially involved in bacterial osmotic stress and the production of osmoprotectants and vitamin B9. This work sheds light on the diversity of the genus Leifsonia with a better understanding of potential mechanisms employed by poorly understood beneficial bacteria.

scholarly journals Genomic analysis and plant growth-promoting potential of a Serratia marcescens isolated from food

2022 ◽  
Vol 11 (1) ◽  
pp. e29611124799
Author(s):  
Cristiane Rodrigues Silva ◽  
Rafael Monção Miller ◽  
Bárbara Costa Pereira ◽  
Lílian Aveleda ◽  
Victor Augustus Marin
Keyword(s):  
Plant Growth ◽  
Serratia Marcescens ◽  
Plant Growth Promotion ◽  
Potential Application ◽  
Growth Promotion ◽  
Genomic Analysis ◽  
Genes Encoding ◽  
Plant Growth Promoting ◽  
Genomic Studies ◽  
Promote Plant Growth

A genomic analysis of the potential application of a Serratia marcescens strain in the plant-growth promotion. We performed whole-genome sequencing of Serratia marcescens isolated from a Minas Frescal Cheese. The genomic repertoire revealed a bacterium of agricultural and biotechnological interest. In the plant-growth promotion traits, we highlight genes encoding proteins possibly responsible for the biosynthesis of phytohormone indole acetic acid, organic compounds that act in iron uptake, and the Phosphate solubilization system. Genes encoding for enzymes like the versatile L-asparaginase stimulates the development of seeds and grains and can benefit the food industry due to a mitigation effect on acrylamide and notably, has medical applications as a chemotherapeutic agent or is applicable by its antimicrobial and anti-inflammatory properties. Moreover, functional diversity of genes encoding for resistance to different metals and metabolism of xenobiotics genes can be found in this strain, reinforcing its biotechnological potential. The versatile enzymes that can be produced by S. marcescens benefit the food, pharmaceutical, textile, agronomic, and cosmetic industries. The relevant genetic systems of S. marcescens described here may be used to promote plant growth and health and improve the environment. To the best of our knowledge, this is the first genome sequence report on S. marcescens isolated from cheese, with potential application as promoting plant growth and providing a baseline for future genomic studies on the development of this species.

scholarly journals Identification of Plant Growth Promoting Rhizobacteria That Improve the Performance of Greenhouse-Grown Petunias under Low Fertility Conditions

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1410
Author(s):  
Kaylee A. South ◽  
Nathan P. Nordstedt ◽  
Michelle L. Jones
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Genomic Analysis ◽  
Dry Weight ◽  
Plant Growth Promoting Rhizobacteria ◽  
Low Fertility ◽  
Plant Performance ◽  
Flower Bud ◽  
Plant Growth Promoting ◽  
Growth Promoting

The production of greenhouse ornamentals relies on high fertilizer inputs to meet scheduling deadlines and quality standards, but overfertilization has negative environmental impacts. The goals of this study were to identify plant-growth-promoting rhizobacteria (PGPR) that can improve greenhouse ornamental crop performance with reduced fertilizer inputs, and to identify the best measurements of plant performance for assessing the beneficial impact of PGPR on ornamentals. A high-throughput greenhouse trial was used to identify 14 PGPR isolates that improved the flower/bud number and shoot dry weight of Petunia × hybrida ‘Picobella Blue’ grown under low fertility conditions in peat-based media. These 14 PGPR were then applied to petunias grown under low fertility conditions (25 mg L−1 N). PGPR-treated plants were compared to negative (untreated at 25 mg L−1 N) and positive (untreated at 50, 75, 100, and 150 mg L−1 N) controls. Multiple parameters were measured in the categories of flowering, vegetative growth, and vegetative quality to determine the best measurements to assess improvements in ornamental plant performance. Caballeronia zhejiangensis C7B12-treated plants performed better in almost all parameters and were comparable to untreated plants fertilized with 50 mg L−1 N. Genomic analysis identified genes that were potentially involved in plant growth promotion. Our study identified potential PGPR that can be used as biostimulants to produce high-quality greenhouse ornamentals with lower fertilizer inputs.

scholarly journals Evaluation of plant growth promotion properties and induction of antioxidative defense mechanism by tea rhizobacteria of Darjeeling, India

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Chandrima Bhattacharyya ◽  
Srimoyee Banerjee ◽  
Udita Acharya ◽  
Aroni Mitra ◽  
Ivy Mallick ◽  
...  
Keyword(s):  
Plant Growth ◽  
Biotic Stress ◽  
Defense Mechanism ◽  
Growth Promotion ◽  
Rrna Gene ◽  
Functional Screening ◽  
Antioxidative Defense ◽  
Plant Growth Promoting ◽  
Pgp Activities ◽  
Growth Promoting

Abstract A total of 120 rhizobacteria were isolated from seven different tea estates of Darjeeling, West Bengal, India. Based on a functional screening of in vitro plant growth-promoting (PGP) activities, thirty potential rhizobacterial isolates were selected for in-planta evaluation of PGP activities in rice and maize crops. All the thirty rhizobacterial isolates were identified using partial 16S rRNA gene sequencing. Out of thirty rhizobacteria, sixteen (53.3%) isolates belong to genus Bacillus, five (16.6%) represent genus Staphylococcus, three (10%) represent genus Ochrobactrum, and one (3.3%) isolate each belongs to genera Pseudomonas, Lysinibacillus, Micrococcus, Leifsonia, Exiguobacterium, and Arthrobacter. Treatment of rice and maize seedlings with these thirty rhizobacterial isolates resulted in growth promotion. Besides, rhizobacterial treatment in rice triggered enzymatic [ascorbate peroxidase (APX), catalase (CAT), chitinase, and phenylalanine ammonia-lyase (PAL)], and non-enzymatic [proline and polyphenolics] antioxidative defense reactions indicating their possible role in the reduction of reactive oxygen species (ROS) burden and thereby priming of plants towards stress mitigation. To understand such a possibility, we tested the effect of rhizobacterial consortia on biotic stress tolerance of rice against necrotrophic fungi, Rhizoctonia solani AG1-IA. Our results indicated that the pretreatment with rhizobacterial consortia increased resistance of the rice plants towards the common foliar pathogen like R. solani AG1-IA. This study supports the idea of the application of plant growth-promoting rhizobacterial consortia in sustainable crop practice through the management of biotic stress under field conditions.

scholarly journals Isolation of Endophytic Salt-Tolerant Plant Growth-Promoting Rhizobacteria From Oryza sativa and Evaluation of Their Plant Growth-Promoting Traits Under Salinity Stress Condition

2021 ◽  
Vol 5 ◽  
Author(s):  
Tania Akter Jhuma ◽  
Jannatul Rafeya ◽  
Shahnaz Sultana ◽  
Mohammad Tariqur Rahman ◽  
Muhammad Manjurul Karim
Keyword(s):  
Oryza Sativa ◽  
Plant Growth ◽  
Salinity Stress ◽  
Growth Promotion ◽  
Restriction Analysis ◽  
Plant Growth Promoting Rhizobacteria ◽  
Microtiter Plate Assay ◽  
Plant Growth Promoting ◽  
Pgp Activities ◽  
Growth Promoting

The application of plant growth-promoting rhizobacteria (PGPR) as vital components for plant growth promotion against biotic and abiotic stresses could be a promising strategy to improve crop production in areas vulnerable to increasing salinity. Here, we isolated Seventy-five endophytic bacteria from roots of healthy Oryza sativa grown in a saline environment of the southern coastal region of Bangladesh. The endophytes in a culture of ~108 CFU/ml showed arrays of plant growth-promoting (PGP) activities: phytohormone (Indole acetic acid) production (1.20–60.13 μg/ ml), nutrient (phosphate) solubilization (0.02–1.81 μg/ml) and nitrogen fixation (70.24–198.70 μg/ml). Four genomically diverse groups were identified namely, Enterobacter, Achromobacter, Bacillus, and Stenotrophomonas using amplified ribosomal DNA restriction analysis followed by their respective 16S rDNA sequence analyses with that of the data available in NCBI GenBank. These four specific isolates showed tolerance to NaCl ranging from 1.37 to 2.57 mol/L in the nutrient agar medium. Under a 200 mmol/L salt stress in vitro, the bacteria in a culture of 108 CFU/ml exhibited competitive exopolysaccharide (EPS) production: Stenotrophomonas (65 μg/ml) and Bacillus (28 μg/ml), when compared to the positive control, Pseudomonas spp. (23.65 μg/ml), a phenomenon ably supported by their strong biofilm-producing abilities both in a microtiter plate assay, and in soil condition; and demonstrated by images of the scanning electron microscope (SEM). Overall, the isolated endophytic microorganisms revealed potential PGP activities that could be supported by their biofilm-forming ability under salinity stress, thereby building up a sustainable solution for ensuring food security in coastal agriculture under changing climate conditions.

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 C4 Bacterial Volatiles Improve Plant Health

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 682
Author(s):  
Bruno Henrique Silva Dias ◽  
Sung-Hee Jung ◽  
Juliana Velasco de Castro Oliveira ◽  
Choong-Min Ryu
Keyword(s):  
Plant Growth ◽  
Volatile Compounds ◽  
Large Scale ◽  
Growth Promotion ◽  
Plant Growth Promoting Rhizobacteria ◽  
Plant Health ◽  
Systemic Resistance ◽  
Potential Applications ◽  
Plant Growth Promoting ◽  
Bacterial Volatiles

Plant growth-promoting rhizobacteria (PGPR) associated with plant roots can trigger plant growth promotion and induced systemic resistance. Several bacterial determinants including cell-wall components and secreted compounds have been identified to date. Here, we review a group of low-molecular-weight volatile compounds released by PGPR, which improve plant health, mostly by protecting plants against pathogen attack under greenhouse and field conditions. We particularly focus on C4 bacterial volatile compounds (BVCs), such as 2,3-butanediol and acetoin, which have been shown to activate the plant immune response and to promote plant growth at the molecular level as well as in large-scale field applications. We also disc/ uss the potential applications, metabolic engineering, and large-scale fermentation of C4 BVCs. The C4 bacterial volatiles act as airborne signals and therefore represent a new type of biocontrol agent. Further advances in the encapsulation procedure, together with the development of standards and guidelines, will promote the application of C4 volatiles in the field.

Genomic analysis of a Pseudomonas strain with multiple plant growth promoting properties

Rhizosphere ◽  
2021 ◽  
pp. 100342
Author(s):  
Olubukola Oluranti Babalola ◽  
Oluwaseun Adeyinka Fasusi ◽  
Adenike Eunice Amoo ◽  
Ayansina Segun Ayangbenro
Keyword(s):  
Plant Growth ◽  
Genomic Analysis ◽  
Plant Growth Promoting ◽  
Growth Promoting
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