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Microbial Cell Factories Jul 2023Chemical fertilizers have greatly contributed to the development of agriculture, but alternative fertilizers are needed for the sustainable development of agriculture....
BACKGROUND
Chemical fertilizers have greatly contributed to the development of agriculture, but alternative fertilizers are needed for the sustainable development of agriculture. 2,3-butanediol (2,3-BDO) is a promising biological plant growth promoter.
RESULTS
In this study, we attempted to develop an effective strategy for the biological production of highly pure R,R-2,3-butanediol (R,R-2,3-BDO) by Paenibacillus polymyxa fermentation. First, gamma-ray mutagenesis was performed to obtain P. polymyxa MDBDO, a strain that grew faster than the parent strain and had high production of R,R-2,3-BDO. The activities of R,R-2,3-butanediol dehydrogenase and diacetyl reductase of the mutant strain were increased by 33% and decreased by 60%, respectively. In addition, it was confirmed that the carbon source depletion of the fermentation broth affects the purity of R,R-2,3-BDO through batch fermentation. Fed-batch fermentation using controlled carbon feeding led to production of 77.3 g/L of R,R-2,3-BDO with high optical purity (> 99% of C products) at 48 h. Additionally, fed-batch culture using corn steep liquor as an alternative nitrogen source led to production of 70.3 g/L of R,R-2,3-BDO at 60 h. The fed-batch fermentation broth of P. polymyxa MDBDO, which contained highly pure R,R-2,3-BDO, significantly stimulated the growth of soybean and strawberry seedlings.
CONCLUSIONS
This study suggests that P. polymyxa MDBDO has potential for use in biological plant growth promoting agent applications. In addition, our fermentation strategy demonstrated that high-purity R,R-2,3-BDO can be produced at high concentrations using P. polymyxa.
Topics: Paenibacillus polymyxa; Carbon; Fertilizers; Butylene Glycols; Fermentation; Paenibacillus
PubMed: 37407951
DOI: 10.1186/s12934-023-02133-y -
Microorganisms May 2023is cultivated worldwide. Leaf spot of sorghum, which leads to leaf lesions and yield reduction, is a prevalent and serious disease in Guizhou Province, southwest China....
is cultivated worldwide. Leaf spot of sorghum, which leads to leaf lesions and yield reduction, is a prevalent and serious disease in Guizhou Province, southwest China. In August 2021, new leaf spot symptoms were observed on sorghum leaves. In this study, traditional methods and modern molecular biology techniques were used to isolate and identify the pathogen. Sorghum inoculated with the isolate GY1021 resulted in reddish brown lesion that similar to symptoms observed in the field: the original isolate inoculated was reisolated and Koch's postulates were fulfilled. Based on morphological features and phylogenetic analysis of the internal transcribed spacer (ITS) combined sequence with β-tubulin () and translation elongation factor 1-α () genes, the isolate was identified as (Strain accession: GY 1021; GenBank Accession: ITS (ON882046), -1α (OP096445), and β- (OP096446)). Then, we studied the bioactivity of various natural products and microorganisms against using the dual culture experiment. Carvacrol, 2-allylphenol, honokiol, and cinnamaldehyde showed excellent antifungal activity, with EC values of 24.19, 7.18, 46.18, and 52.81 µg/mL, respectively. The bioactivity of six antagonistic bacteria was measured using a dual culture experiment and the mycelial growth rate method. , and displayed significant antifungal effects against . This study provides a theoretical basis for the green control of leaf spot of sorghum.
PubMed: 37374932
DOI: 10.3390/microorganisms11061431 -
Microbiological Research Sep 2023The bacteriophage phiBP contains a newly discovered putative replisome organizer, a helicase loader, and a beta clamp, which together may serve to replicate its DNA....
The bacteriophage phiBP contains a newly discovered putative replisome organizer, a helicase loader, and a beta clamp, which together may serve to replicate its DNA. Bioinformatics analysis of the phiBP replisome organizer sequence showed that it belongs to a recently identified family of putative initiator proteins. We prepared and isolated a wild type-like recombinant protein, gpRO-HC, and a mutant protein gpRO-HCK8A, containing a lysine to alanine substitution at position 8. gpRO-HC had low ATPase activity regardless of the presence of DNA, while the ATPase activity of the mutant was significantly higher. gpRO-HC bound to both single- and double-stranded DNA substrates. Different methods showed that gpRO-HC forms higher oligomers containing about 12 subunits. This work provides the first information about another group of phage initiator proteins, which trigger DNA replication in phages infecting low GC Gram-positive bacteria.
Topics: Paenibacillus polymyxa; DNA Replication; Bacteriophages; DNA; Adenosine Triphosphatases
PubMed: 37327604
DOI: 10.1016/j.micres.2023.127437 -
Frontiers in Microbiology 2023Pitaya canker, caused by , is one of the most important fungal diseases that cause significant losses in production. To replace chemical pesticides, the use of...
Pitaya canker, caused by , is one of the most important fungal diseases that cause significant losses in production. To replace chemical pesticides, the use of biocontrol strains to manage plant diseases has been the focus of research. In this study, the bacterial strain AF01, identified as , exhibited significant antifungal effects against and four other pitaya fungal pathogens. The strain AF01 produces 13 fusaricidins, which directly inhibit mycelial growth, spore germination and germ tube elongation by causing the membrane integrity and cell ultrastructure to incur irreversible damage. Pot experiment and yield test confirmed that AF01 provided preservative effects by reducing the disease index. In comparison to the untreated control groups, RNA-seq data showed that AF01 selectively blocked some transcription and translation processes and inhibited RNA and DNA structural dynamics, energy production and conversion, and signal transduction, particularly cell wall biosynthesis, changes in membrane permeability, and impairment of protein biosynthesis. Thus, AF01 could be potentially useful as a suitable biocontrol agent for pitaya canker.
PubMed: 37266020
DOI: 10.3389/fmicb.2023.1188722 -
Microbiology Spectrum Jun 2023Through screening of rhizobacteria, species that effectively suppress phytopathogens and/or promote plant growth are found. Genome sequencing is a crucial step in...
Through screening of rhizobacteria, species that effectively suppress phytopathogens and/or promote plant growth are found. Genome sequencing is a crucial step in obtaining a complete characterization of microorganisms for biotechnological applications. This study aimed to sequence the genomes of four rhizobacteria that differ in their inhibition of four root pathogens and in their interaction with chili pepper roots to identify the species and analyze differences in the biosynthetic gene clusters (BGCs) for antibiotic metabolites and to determine possible phenotype-genotype correlations. Results from sequencing and genome alignment identified two bacteria as Paenibacillus polymyxa, one as Kocuria polaris, and one that was previously sequenced as Bacillus velezensis. Analysis with antiSMASH and PRISM tools showed that 2A-2B, the strain with the best performance of referred characteristics, had 13 BGCs, including those related to surfactin, fengycin, and macrolactin, not shared with the other bacteria, whereas 2A-2A and 3A-25AI, with up to 31 BGCs, showed lower pathogen inhibition and plant hostility; showed the least antifungal capacity. and had the highest number of BGCs for nonribosomal peptides and polyketides. In conclusion, the 13 BGCs in the genome of 2A-2B that were not present in the other bacteria could explain its effective antifungal capacity and could also contribute to its friendly interaction with chili pepper roots. The high number of other BGCs for nonribosomal peptides and polyketide shared by the four bacteria contributed much less to phenotypic differences. To advance the characterization of a microorganism as a biocontrol agent against phytopathogens, it is highly recommended to analyze the potential of the profile of secondary metabolites as antibiotics that it produces to counteract pathogens. Some specific metabolites have positive impacts in plants. By analyzing sequenced genomes with bioinformatic tools, such as antiSMASH and PRISM, outstanding bacterial strains with high potential to inhibit phytopathogens and/or promote plant growth can be quickly selected to confirm and expand our knowledge of BGCs of great value in phytopathology.
Topics: Capsicum; Genome, Bacterial; Antifungal Agents; Plant Development; Bacteria; Anti-Bacterial Agents; Multigene Family
PubMed: 37222590
DOI: 10.1128/spectrum.03072-22 -
BioRxiv : the Preprint Server For... May 2023Engaging computational tools for protein design is gaining traction in the enzyme engineering community. However, current design and modeling algorithms have limited...
Engaging computational tools for protein design is gaining traction in the enzyme engineering community. However, current design and modeling algorithms have limited functionality predictive capacities for enzymes due to limitations of the dataset in terms of size and data quality. This study aims to expand training datasets for improved algorithm development with the addition of five rationally designed single-point enzyme variants. β-glucosidase B variants were modeled in Foldit Standalone and then produced and assayed for thermal stability and kinetic parameters. Functional parameters: thermal stability (T ) and Michaelis-Menten constants ( , K , and /K ) of five variants, V311D, Y166H, M221K, F248N, and Y166K, were added into the Design2Data database. As a case study, evaluation of this small mutant set finds mutational effect trends that both corroborate and contradict findings from larger studies examining the entire dataset.
PubMed: 37214998
DOI: 10.1101/2023.05.10.540081 -
Microorganisms Mar 2023Many farmers' incomes in developing countries depend on the cultivation of major crops grown in arid and semi-arid regions. The agricultural productivity of arid and...
Many farmers' incomes in developing countries depend on the cultivation of major crops grown in arid and semi-arid regions. The agricultural productivity of arid and semi-arid areas primarily relies on chemical fertilizers. The effectiveness of chemical fertilizers needs to improve by integration with other sources of nutrients. Plant growth-promoting bacteria can solubilize nutrients, increase plant nutrient uptake, and supplement chemical fertilizers. A pot experiment evaluated the promising plant growth-promoting bacterial strain's effectiveness in promoting cotton growth, antioxidant enzymes, yield, and nutrient uptake. Two phosphate solubilizing bacterial strains ( IA6 and IA7) and two zinc solubilizing bacterial strains ( sp. IA7 and IA20) were coated on cotton seeds in a single as well as co-inoculation treatments. These treatments were compared with uninoculated controls in the presence and absence of recommended chemical fertilizer doses. The results showed the co-inoculation combination of IA7 and IA20 significantly increased the number of bolls, seed cotton yield, lint yield, and antioxidants activities, including superoxide dismutase, guaiacol peroxidase, catalase, and peroxidase. Co-inoculation combination of IA6 and sp. IA16 promoted growth attributes, including shoot length, root length, shoot fresh weight, and root fresh weight. This co-inoculation combination also increased soil nutrient content. At the same time, IA7 + IA20 increased nutrient uptake by plant shoots and roots compared.
PubMed: 37110284
DOI: 10.3390/microorganisms11040861 -
Microorganisms Mar 2023Polymyxin-producing bacteria within the complex have broad-spectrum activities against fungi and bacteria. Their antibacterial activities against soft rot and...
Polymyxin-producing bacteria within the complex have broad-spectrum activities against fungi and bacteria. Their antibacterial activities against soft rot and phytopathogens containing multiple polymyxin-resistant genes were not clear. Here, we selected nine strains within the complex having broad-spectrum antagonistic activities against phytopathogenic fungi and a polymyxin-resistant strain causing stem and root rot disease of sweet potato and did antagonistic assays on nutrient agar and sweet potato tuber slices. These strains within the complex showed clear antagonistic activities against in vitro and in vivo. The most effective antagonistic strain ShX301 showed broad-spectrum antagonistic activities against all the test and strains, completely eliminated from sweet potato seed tubers, and promoted the growth of sweet potato seedlings. Cell-free culture filtrate of ShX301 inhibited growth, swimming motility, and biofilm formation and disrupted plasma membranes, releasing nucleic acids and proteins. Multiple lipopeptides produced by ShX301 may play a major role in the bactericidal and bacteriostatic actions. This study clarifies that the antimicrobial spectrum of polymyxin-producing bacteria within the complex includes the polymyxin-resistant and phytopathogens and strengthens the fact that bacteria within the complex have high probability of being effective biocontrol agents and plant growth promoters.
PubMed: 37110240
DOI: 10.3390/microorganisms11040817 -
Carbohydrate Polymers Jul 2023Paenibacillus polymyxa is a Gram-positive soil bacterium known for producing a wide range of exopolysaccharides. However, due to the biopolymer's complexity, structural...
Paenibacillus polymyxa is a Gram-positive soil bacterium known for producing a wide range of exopolysaccharides. However, due to the biopolymer's complexity, structural elucidation has so far been inconclusive. Combinatorial knock-outs of glycosyltransferases were generated in order to separate distinct polysaccharides produced by P. polymyxa. Using a complementary analytical approach consisting of carbohydrate fingerprints, sequence analysis, methylation analysis as well as NMR spectroscopy, the structure of the repeating units of two additional heteroexopolysaccharides termed paenan I and paenan III were elucidated. Results for paenan I identified a trisaccharide backbone consisting of 1➔4-β-d-Glc, 1➔4-β-d-Man and a 1,3,4-branching β-d-Gal residue with a sidechain comprising of a terminal β-d-Gal and 1➔3-β-d-Glc. For paenan III, results indicated a backbone consisting of 1➔3-β-d-Glc, 1,3,4-linked α-d-Man and 1,3,4-linked α-d-GlcA. NMR analysis indicated monomeric β-d-Glc and α-d-Man sidechains for the branching Man and GlcA residues respectively.
Topics: Humans; Carbohydrate Sequence; Paenibacillus polymyxa; CRISPR-Cas Systems; Polysaccharides; Magnetic Resonance Spectroscopy
PubMed: 37059525
DOI: 10.1016/j.carbpol.2023.120763 -
Archives of Microbiology Apr 2023Concerning the potential application of the optically active isomer (R,R)-2,3-butanediol, and its production by a non-pathogenic bacterium Paenibacillus polymyxa ATCC...
Concerning the potential application of the optically active isomer (R,R)-2,3-butanediol, and its production by a non-pathogenic bacterium Paenibacillus polymyxa ATCC 842, the present study evaluated the use of a commercial crude yeast extract Nucel®, as an organic nitrogen and vitamin source, at different medium composition and two airflows (0.2 or 0.5 vvm). The medium formulated (M4) with crude yeast extract carried out with the airflow of 0.2 vvm (experiment R6) allowed for a reduction in the cultivation time and kept the dissolved oxygen values at low levels until the total glucose consumption. Thus, the experiment R6 led to a fermentation yield of 41% superior when compared to the standard medium (experiment R1), which was conducted at airflow of 0.5 vvm. The maximum specific growth rate at R6 (0.42 h) was lower than R1 (0.60 h), however, the final cell concentration was not affected. Moreover, this condition (medium formulated-M4 and low airflow-0.2 vvm) was a great alternative to produce (R,R)-2,3-BD at fed-batch mode, resulting in 30 g.L of the isomer at 24 h of cultivation, representing the main product in the broth (77%) and with a fermentation yield of 80%. These results showed that both medium composition and oxygen supply have an important role to produce 2,3-BD by P. polymyxa.
Topics: Paenibacillus polymyxa; Acetoin; Fermentation; Butylene Glycols; Paenibacillus; Bioreactors
PubMed: 37017720
DOI: 10.1007/s00203-023-03521-z