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Microbiological Research Jun 2021Microbial co-inoculation strategy utilizes a combination of microbes to stimulate plant growth concomitant with an increased phytopathogen tolerance. In the present...
Chickpea (Cicer arietinum L.) as model legume for decoding the co-existence of Pseudomonas fluorescens and Mesorhizobium sp. as bio-fertilizer under diverse agro-climatic zones.
Microbial co-inoculation strategy utilizes a combination of microbes to stimulate plant growth concomitant with an increased phytopathogen tolerance. In the present study, 15 endophytic bacterial isolates from rhizosphere and roots of wild chickpea accessions (Cicer pinnatifidum, C. judiacum, C. bijugum and C. reticulatum) were characterized for morphological, biochemical and physiological traits. Two promising isolates were identified as Pseudomonas fluorescens strain LRE-2 (KR303708.1) and Pseudomonas argentinensis LPGPR-1 (JX239745.1) based on 16S rRNA gene sequencing. Biocompatibility of selected endophytes with Mesorhizobium sp. CH1233, a standard isolate used as a national check in All India Coordinated Research Project (AICRP) was assessed to develop functional combinations capable of producing Indole acetic acid, gibberellins, siderophores and improving seed vigour (in vitro). In vivo synergistic effect of promising combinations was further evaluated under national AICRP, (Chickpea) at two different agro-climatic zones [North-West plain (Ludhiana and Hisar) and Central zones (Sehore)] for three consecutive Rabi seasons (2015-18) to elucidate their effect on symbiotic, soil quality and yield parameters. On the pooled mean basis across locations over the years, combination of Mrh+LRE-2 significantly enhanced symbiotic, soil quality traits and grain yield over Mrh alone and highly positive correlation was obtained between the nodulation traits and grain yield. Superior B: C ratio (1.12) and additional income of Rs 6,505.18 ha was obtained by application of Mrh+LRE-2 over Mrh alone and un-inoculated control. The results demonstrate that dual combination of Mrh and Pseudomonas sp. from wild Cicer relatives can be exploited as a potential bio-fertilizer for increasing soil fertility and improving chickpea productivity under sustainable agriculture.
Topics: Agriculture; Cicer; Endophytes; Fabaceae; Fertilizers; Indoleacetic Acids; Mesorhizobium; Phylogeny; Plant Development; Plant Roots; Pseudomonas; Pseudomonas fluorescens; RNA, Ribosomal, 16S; Rhizosphere; Seeds; Soil; Soil Microbiology; Symbiosis
PubMed: 33592359
DOI: 10.1016/j.micres.2021.126720 -
FEMS Microbiology Ecology Jan 2018Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal...
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently, we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid. Whereas Pseudomonas fluorescens and Pseudomonas savastanoi stably maintained the plasmid in both environments, the plasmid was highly unstable in Pseudomonas aeruginosa and Pseudomonas putida, where plasmid-free genotypes with Tn5042 captured to the chromosome invaded to higher frequency under mercury selection. These data confirm that plasmid stability is dependent upon the specific genetic interaction of the plasmid and host chromosome rather than being a property of plasmids alone, and moreover imply that MGE dynamics in diverse natural communities are likely to be complex and driven by a subset of species capable of stably maintaining plasmids that would then act as hubs of HGT.
Topics: Conjugation, Genetic; Drug Resistance, Bacterial; Gene Transfer, Horizontal; Interspersed Repetitive Sequences; Mercury; Plasmids; Pseudomonas aeruginosa; Pseudomonas fluorescens; Pseudomonas putida
PubMed: 29228229
DOI: 10.1093/femsec/fix172 -
PLoS Genetics Aug 2021Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is...
Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general predictive models and fundamental biological assumptions. To develop an extended model system for evolutionary forecasting, we used previous data and models of the genotype-to-phenotype map from the wrinkly spreader system in Pseudomonas fluorescens SBW25 to make predictions of evolutionary outcomes on different biological levels for Pseudomonas protegens Pf-5. In addition to sequence divergence (78% amino acid and 81% nucleotide identity) for the genes targeted by mutations, these species also differ in the inability of Pf-5 to make cellulose, which is the main structural basis for the adaptive phenotype in SBW25. The experimental conditions were changed compared to the SBW25 system to test if forecasts were extendable to a non-identical environment. Forty-three mutants with increased ability to colonize the air-liquid interface were isolated, and the majority had reduced motility and was partly dependent on the Pel exopolysaccharide as a structural component. Most (38/43) mutations are expected to disrupt negative regulation of the same three diguanylate cyclases as in SBW25, with a smaller number of mutations in promoter regions, including an uncharacterized polysaccharide synthase operon. A mathematical model developed for SBW25 predicted the order of the three main pathways and the genes targeted by mutations, but differences in fitness between mutants and mutational biases also appear to influence outcomes. Mutated regions in proteins could be predicted in most cases (16/22), but parallelism at the nucleotide level was low and mutational hot spot sites were not conserved. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations and provides testable predictions for evolutionary outcomes in other Pseudomonas species.
Topics: Adaptation, Physiological; Bacterial Adhesion; Biofilms; Biological Evolution; Cellulose; Directed Molecular Evolution; Environment; Evolution, Molecular; Forecasting; Mutation; Operon; Pseudomonas; Pseudomonas fluorescens
PubMed: 34351900
DOI: 10.1371/journal.pgen.1009722 -
International Journal of Molecular... Apr 2019Drought conditions marked by water deficit impede plant growth thus causing recurrent decline in agricultural productivity. Presently, research efforts are focussed... (Review)
Review
Drought conditions marked by water deficit impede plant growth thus causing recurrent decline in agricultural productivity. Presently, research efforts are focussed towards harnessing the potential of microbes to enhance crop production during drought. Microbial communities, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) buddy up with plants to boost crop productivity during drought via microbial induced systemic tolerance (MIST). The present review summarizes MIST mechanisms during drought comprised of modulation in phytohormonal profiles, sturdy antioxidant defence, osmotic grapnel, bacterial exopolysaccharides (EPS) or AMF glomalin production, volatile organic compounds (VOCs), expression of fungal aquaporins and stress responsive genes, which alters various physiological processes such as hydraulic conductance, transpiration rate, stomatal conductivity and photosynthesis in host plants. Molecular studies have revealed microbial induced differential expression of various genes such as (), (ABA-responsive gene) in , (regulates energy and carbohydrate metabolism), (protein kinase), (stress responsive pathway), , and (chaperones in ABA signalling) in treated rice, , (encoding potassium channels) in Lycium, and (IAA biosynthesis) in AMF inoculated , , , , , and (polyamine biosynthesis) in PGPR inoculated , 14-3-3 genes (- genes in ABA signalling pathways) in AMF treated , , (ethylene biosynthesis), jasmonate gene in chick pea, (SA regulated gene), (JA marker genes) and (ethylene-response gene) in treated plants. Moreover, the key role of miRNAs in MIST has also been recorded in RA treated chick pea plants.
Topics: Dehydration; Gene Expression Regulation, Plant; Mycorrhizae; Plant Development; Plant Growth Regulators; Plant Proteins; Pseudomonas fluorescens; Pseudomonas putida; Soil Microbiology
PubMed: 30974865
DOI: 10.3390/ijms20071769 -
International Journal of Molecular... May 2023The search for and characterization of new lipases with excellent properties has always been urgent and is of great importance to meet industrial needs. In this study, a...
The search for and characterization of new lipases with excellent properties has always been urgent and is of great importance to meet industrial needs. In this study, a new lipase, from SBW25, belonging to the lipase subfamily I.3, was cloned and expressed in WB800N. Enzymatic properties studies of recombinant LipB found that it exhibited the highest activity towards -nitrophenyl caprylate at 40 °C and pH 8.0, retaining 73% of its original activity after incubation at 70 °C for 6 h. In addition, Ca, Mg, and Ba strongly enhanced the activity of LipB, while Cu, Zn, Mn, and CTAB showed an inhibiting effect. The LipB also displayed noticeable tolerance to organic solvents, especially acetonitrile, isopropanol, acetone, and DMSO. Moreover, LipB was applied to the enrichment of polyunsaturated fatty acids from fish oil. After hydrolyzing for 24 h, it could increase the contents of polyunsaturated fatty acids from 43.16% to 72.18%, consisting of 5.75% eicosapentaenoic acid, 19.57% docosapentaenoic acid, and 46.86% docosahexaenoic acid, respectively. The properties of LipB render it great potential in industrial applications, especially in health food production.
Topics: Lipase; Pseudomonas fluorescens; Fatty Acids, Unsaturated; Docosahexaenoic Acids; Eicosapentaenoic Acid; Enzyme Stability
PubMed: 37240270
DOI: 10.3390/ijms24108924 -
Journal of Bacteriology Apr 2018spp. are widely used model organisms in different areas of research. Despite the relevance of in many applications, the use of protein depletion tools in this host...
spp. are widely used model organisms in different areas of research. Despite the relevance of in many applications, the use of protein depletion tools in this host remains limited. Here, we developed the CRISPR interference system for gene repression in spp. using a nuclease-null Cas9 variant (dead Cas9, or dCas9). We demonstrate a robust and titratable gene depletion system with up to 100-fold repression in β-galactosidase activity in and 300-fold repression in pyoverdine production in This inducible system enables the study of essential genes, as shown by depletions in , , and that led to phenotypic changes consistent with depletion of the targeted gene. Additionally, we performed the first characterization of protospacer adjacent motif (PAM) site preferences of dCas9 and identified NNGCGA as a functional PAM site that resulted in repression efficiencies comparable to the consensus NNGTGA sequence. This discovery significantly expands the potential genomic targets of dCas9, especially in GC-rich organisms. spp. are prevalent in a variety of environments, such as the soil, on the surface of plants, and in the human body. Although spp. are widely used as model organisms in different areas of research, existing tools to deplete a protein of interest in these organisms remain limited. We have developed a robust and inducible gene repression tool in , , and using the dCas9. This method of protein depletion is superior to existing methods, such as promoter replacements and addition of degradation tags, because it does not involve genomic modifications of the target protein, is titratable, and is capable of repressing multiple genes simultaneously. This gene repression system now enables easy depletion of specific proteins in , accelerating the study and engineering of this widely used model organism.
Topics: CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Expression Regulation, Bacterial; Gene Silencing; Genomics; Pseudomonas; Pseudomonas aeruginosa; Pseudomonas fluorescens; Pseudomonas putida; beta-Galactosidase
PubMed: 29311279
DOI: 10.1128/JB.00575-17 -
BMC Genomics May 2019Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of...
BACKGROUND
Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate into high farming costs and are hazardous to the environment when used excessively. Beneficial free-living soil bacteria that colonize the rhizosphere are known as plant growth-promoting rhizobacteria (PGPR). PGPR affect plant growth in direct or indirect ways and hold great promise for sustainable agriculture.
RESULTS
PGPR of the genera Bacillus and Pseudomonas in banana cv. Williams were evaluated. These plants were produced through in vitro culture and inoculated individually with two rhizobacteria, Bacillus amyloliquefaciens strain Bs006 and Pseudomonas fluorescens strain Ps006. Control plants without microbial inoculum were also evaluated. These plants were kept in a controlled climate growth room with conditions required to favor plant-microorganism interactions. These interactions were evaluated at 1-, 48- and 96-h using transcriptome sequencing after inoculation to establish differentially expressed genes (DEGs) in plants elicited by the interaction with the two rhizobacteria. Additionally, droplet digital PCR was performed at 1, 48, 96 h, and also at 15 and 30 days to validate the expression patterns of selected DEGs. The banana cv. Williams transcriptome reported differential expression in a large number of genes of which 22 were experimentally validated. Genes validated experimentally correspond to growth promotion and regulation of specific functions (flowering, photosynthesis, glucose catabolism and root growth) as well as plant defense genes. This study focused on the analysis of 18 genes involved in growth promotion, defense and response to biotic or abiotic stress.
CONCLUSIONS
Differences in banana gene expression profiles in response to the rhizobacteria evaluated here (Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006) are influenced by separate bacterial colonization processes and levels that stimulate distinct groups of genes at various points in time.
Topics: Bacillus amyloliquefaciens; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Ontology; Musa; Plant Proteins; Pseudomonas fluorescens; Sequence Analysis, RNA; Soil Microbiology; Stress, Physiological
PubMed: 31088352
DOI: 10.1186/s12864-019-5763-5 -
Journal of Dairy Science Feb 2015Pseudomonas spp. are usually associated with spoilage microflora of dairy products due to their proteolytic potential. This is of particular concern for protein-based...
Pseudomonas spp. are usually associated with spoilage microflora of dairy products due to their proteolytic potential. This is of particular concern for protein-based products, such as goat milk cheeses and fermented milks. Therefore, the goal of the present study was to characterize the proteolytic activity of Pseudomonas spp. isolated from goat milk. Goat milk samples (n=61) were obtained directly from bulk tanks on dairy goat farms (n=12), and subjected to a modified International Organization for Standardization (ISO) protocol to determine the number and proteolytic activity of Pseudomonas spp. Isolates (n=82) were obtained, identified by PCR, and subjected to pulsed-field gel electrophoresis with XbaI macro-restriction. Then, the isolates were subjected to PCR to detect the alkaline protease gene (apr), and phenotypic tests were performed to check proteolytic activity at 7°C, 25°C, and 35°C. Mean Pseudomonas spp. counts ranged from 2.9 to 4.8 log cfu/mL, and proteolytic Pseudomonas spp. counts ranged from 1.9 to 4.6 log cfu/mL. All isolates were confirmed to be Pseudomonas spp., and 41 were identified as Pseudomonas fluorescens, which clustered into 5 groups sharing approximately 82% similarity. Thirty-six isolates (46.9%) were positive for the apr gene; and 57 (69.5%) isolates presented proteolytic activity at 7°C, 82 (100%) at 25°C, and 64 (78%) at 35°C. The isolates were distributed ubiquitously in the goat farms, and no relationship among isolates was observed when the goat farms, presence of apr, pulsotypes, and proteolytic activity were taken into account. We demonstrated proteolytic activity of Pseudomonas spp. present in goat milk by phenotypic and genotypic tests and indicated their spoilage potential at distinct temperatures. Based on these findings and the ubiquity of Pseudomonas spp. in goat farm environments, proper monitoring and control of Pseudomonas spp. during production are critical.
Topics: Animals; Cheese; Electrophoresis, Gel, Pulsed-Field; Female; Genetic Variation; Genotype; Goats; Milk; Polymerase Chain Reaction; Proteolysis; Pseudomonas; Pseudomonas fluorescens
PubMed: 25497792
DOI: 10.3168/jds.2014-8747 -
MicrobiologyOpen Nov 2021Interspecific interactions within biofilms determine relative species abundance, growth dynamics, community resilience, and success or failure of invasion by an...
Interspecific interactions within biofilms determine relative species abundance, growth dynamics, community resilience, and success or failure of invasion by an extraneous organism. However, deciphering interspecific interactions and assessing their contribution to biofilm properties and function remain a challenge. Here, we describe the constitution of a model biofilm composed of four bacterial species belonging to four different genera (Rhodocyclus sp., Pseudomonas fluorescens, Kocuria varians, and Bacillus cereus), derived from a biofilm isolated from an industrial milk pasteurization unit. We demonstrate that the growth dynamics and equilibrium composition of this biofilm are highly reproducible. Based on its equilibrium composition, we show that the establishment of this four-species biofilm is highly robust against initial, transient perturbations but less so towards continuous perturbations. By comparing biofilms formed from different numbers and combinations of the constituent species and by fitting a growth model to the experimental data, we reveal a network of dynamic, positive, and negative interactions that determine the final composition of the biofilm. Furthermore, we reveal that the molecular determinant of one negative interaction is the thiocillin I synthesized by the B. cereus strain, and demonstrate its importance for species distribution and its impact on robustness by mutational analysis of the biofilm ecosystem.
Topics: Bacillus cereus; Biofilms; Ecosystem; Microbial Interactions; Microbiota; Micrococcaceae; Peptides; Plankton; Pseudomonas fluorescens; Rhodocyclaceae
PubMed: 34964290
DOI: 10.1002/mbo3.1254 -
Scientific Reports Jan 2024The interactions between microbes and plants are governed by complex chemical signals, which can forcefully affect plant growth and development. Here, to understand how...
The interactions between microbes and plants are governed by complex chemical signals, which can forcefully affect plant growth and development. Here, to understand how microbes influence Houttuynia cordata Thunb. plant growth and its secondary metabolite through chemical signals, we established the interaction between single bacteria and a plant. We inoculated H. cordata seedlings with bacteria isolated from their roots. The results showed that the total fresh weight, the total dry weight, and the number of lateral roots per seedling in the P. fluorescens-inoculated seedlings were 174%, 172% and 227% higher than in the control seedlings. Pseudomonas fluorescens had a significant promotional effect of the volatile contents compared to control, with β-myrcene increasing by 192%, 2-undecanone by 203%, decanol by 304%, β-caryophyllene by 197%, α-pinene by 281%, bornyl acetate by 157%, γ-terpinene by 239% and 3-tetradecane by 328% in P. fluorescens-inoculated H. cordata seedlings. the contents of chlorogenic acid, rutin, quercitin, and afzelin were 284%, 154%, 137%, and 213% higher than in control seedlings, respectively. Our study provided basic data to assess the linkages between endophytic bacteria, plant phenotype and metabolites of H. cordata to provide an insight into P. fluorescens use as biological fertilizer, promoting the synthesis of medicinal plant compounds.
Topics: Houttuynia; Pseudomonas fluorescens; Plant Extracts; Plants, Medicinal; Drugs, Chinese Herbal
PubMed: 38243055
DOI: 10.1038/s41598-024-52070-y