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Frontiers in Microbiology 2021Eight rhizospheric bacteria were isolated from the organic paddy fields of Sikkim, India, and identified as KSB, SRD, YMA7, SRB, sp. ARA, COW3, PSB2, and PSB1....
Isolation, Characterization, and Evaluation of Native Rhizobacterial Consortia Developed From the Rhizosphere of Rice Grown in Organic State Sikkim, India, and Their Effect on Plant Growth.
Eight rhizospheric bacteria were isolated from the organic paddy fields of Sikkim, India, and identified as KSB, SRD, YMA7, SRB, sp. ARA, COW3, PSB2, and PSB1. They showed plant growth-promoting attributes in rice and have bio-control potential against phytopathogen of large cardamom (). SRD showed production of indole acetic acid and ammonia and solubilization of phosphate and potassium and also possessed nitrogen fixation potential. It showed antagonistic activity against two other plant pathogens of large cardamom, viz., and sp., under conditions. The liquid bacterial consortium was prepared using the bacterial strains SRB, PSB1, and COW3 (Consortia-1); PSB2, SRD, and COW3 (Consortia-2); and COW3, KSB, and YMA7 (Consortia-3) to increase the growth and yield of rice plants under organic farming conditions. Greenhouse and field studies showed that the Consortia-3 had the highest plant growth-promoting activity. Consortia-3 demonstrated better agronomic performance in terms of root length (9.5 cm),number of leaflets per plant (5.3), grains per panicle (110.6), test grain weight (27.4 g), dry root weight per plant (0.73 g), and total dry biomass per plant (8.26 g).
PubMed: 34552571
DOI: 10.3389/fmicb.2021.713660 -
Animal Nutrition (Zhongguo Xu Mu Shou... Sep 2021With the ever-growing strict prohibitions on antibiotic growth promoters (AGP) in animal production, in-feed probiotics are becoming attractive alternatives to...
With the ever-growing strict prohibitions on antibiotic growth promoters (AGP) in animal production, in-feed probiotics are becoming attractive alternatives to antibiotics in the poultry industry. To investigate the effects of 10 and 16 on the growth performance and intestinal health of broilers, 540 male Cobb 500 broilers of 1 d old were randomly divided into 3 groups with 6 replicates per group and 30 chicks per replicate. Broilers were fed with either a basal diet or basal diets supplemented with 1 × 10 colony-forming units (CFU)/kg 10 (BSC10) or 16 (Lac16) for 42 d. Results showed that Lac16 treatment improved ( < 0.05) the growth performance (body weight and feed conversion) of broilers at the starter phase, while BSC10 treatment slightly improved ( > 0.05) the growth performance of the starter phase broilers. The increased villus height ( < 0.05) at d 14, 21 and 42 and villus height to crypt depth ratio ( < 0.05) at d 14 and 21 were observed in the ileum of the 2 probiotic groups. Besides, transmission electron microscopy results showed that the 2 probiotics enhanced the intestinal epithelial barrier. Both probiotic treatments up-regulated ( < 0.05) the mRNA expression of fatty acid binding protein 1 () and sodium-dependent glucose transporters-1 () in the ileal mucosa of broilers at d 21. In addition, BSC10 and Lac16 treatments significantly ( < 0.05) increased the relative abundance of short-chain fatty acids-producing bacteria, such as , , and , and significantly ( < 0.05) decreased the relative abundance of enteric pathogens (, and ). Furthermore, the 2 probiotic treatments also increased the positive connection among the intestinal microbes and the carbohydrate metabolism-related pathways of the intestinal bacteria ( < 0.05), with decreasing ( < 0.05) nucleotides biosynthesis-related pathways of the intestinal bacteria. Overall, these results suggest that the 2 probiotics, especially Lac16, have a potential beneficial effect on the growth performance and intestinal health of starter phase broilers.
PubMed: 34466687
DOI: 10.1016/j.aninu.2021.03.008 -
Molecules (Basel, Switzerland) Aug 2021The main goal of this work was to study the structural transformation of humic acids (HAs) under the influence of selected strains of fungi ( and ) and bacteria ( sp.,...
Chemical Transformation of Humic Acid Molecules under the Influence of Mineral, Fungal and Bacterial Fertilization in the Context of the Agricultural Use of Degraded Soils.
The main goal of this work was to study the structural transformation of humic acids (HAs) under the influence of selected strains of fungi ( and ) and bacteria ( sp., and ) with/without the presence of NPK fertilizers. Two-year experiments were conducted on two different soils and HAs isolated from these soils were examined for structure, humification degree, and quantity using fluorescence and UV-Vis spectroscopy, elemental analysis, and extraction methods. Results showed that the applied additives contributed to the beneficial transformation of HAs, but effects differed for various soils. HAs from silty soil with higher organic carbon content showed simplification of their structure, and decreases in humification, molecular weight, and aromaticity under the influence of fungi and bacteria without NPK, and with NPK alone. With both fungi and NPK, increases in O/H and O/C atomic ratios indicated an increase in the number of O-containing functional groups. HAs from sandy soil did not show as many significant changes as did those from silty soil. Sandy soil exhibited a strong decline in HA content in the second year that was reduced/neutralized by the presence of fungi, bacteria, and NPK. Periodically observed fluorescence at ~300 nm/450 nm reflected formation of low-molecular HAs originating from the activity of microorganisms.
Topics: Agriculture; Bacteria; Fertilizers; Fluorescence; Fungi; Humic Substances; Minerals; Soil; Spectrophotometry, Ultraviolet
PubMed: 34443509
DOI: 10.3390/molecules26164921 -
Frontiers in Microbiology 2021Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium has been widely applied in agriculture and animal husbandry. It...
Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium has been widely applied in agriculture and animal husbandry. It also produces valuable compounds that are used in medicine and industry. Our previous work showed the presence of restriction modification (RM) system in ATCC 842. Here, we further analyzed its genome and methylome by using SMRT sequencing, which revealed the presence of a larger number of genes, as well as a plasmid documented as a genomic region in a previous report. A number of mobile genetic elements (MGEs), including 78 insertion sequences, six genomic islands, and six prophages, were identified in the genome. A putative lysozyme-encoding gene from prophage P6 was shown to express lysin which caused cell lysis. Analysis of the methylome and genome uncovered a pair of reverse-complementary DNA methylation motifs which were widespread in the genome, as well as genes potentially encoding their cognate type I restriction-modification system PpoAI. Further genetic analysis confirmed the function of PpoAI as a RM system in modifying and restricting DNA. The average frequency of the DNA methylation motifs in MGEs was lower than that in the genome, implicating a role of PpoAI in restricting MGEs during genomic evolution of . Finally, comparative analysis of R, M, and S subunits of PpoAI showed that homologs of the PpoAI system were widely distributed in species belonging to other classes of Firmicute, implicating a role of the ancestor of PpoAI in the genomic evolution of species beyond .
PubMed: 34413842
DOI: 10.3389/fmicb.2021.709571 -
Scientific Reports Jul 2021Paenibacillus species are Gram-positive bacteria that have been isolated from a diverse array of plant species and soils, with some species exhibiting plant...
Paenibacillus species are Gram-positive bacteria that have been isolated from a diverse array of plant species and soils, with some species exhibiting plant growth-promoting (PGP) activities. Here we report two strains (S02 and S25) of a novel Paenibacillus sp. that were isolated from perennial ryegrass (Lolium perenne) seeds. Comparative genomics analyses showed this novel species was closely related to P. polymyxa. Genomic analyses revealed that strains S02 and S25 possess PGP genes associated with biological nitrogen fixation, phosphate solubilisation and assimilation, as well as auxin production and transportation. Moreover, secondary metabolite gene cluster analyses identified 13 clusters that are shared by both strains and three clusters unique to S25. In vitro assays demonstrated strong bioprotection activity against phytopathogens (Colletotrichum graminicola and Fusarium verticillioides), particularly for strain S02. A transcriptomics analysis evaluating nitrogen fixation activity showed both strains carry an expressed nif operon, but strain S02 was more active than strain S25 in nitrogen-free media. Another transcriptomics analysis evaluating the interaction of strains with F. verticillioides showed strain S02 had increased expression of core genes of secondary metabolite clusters (fusaricidin, paenilan, tridecaptin and polymyxin) when F. verticillioides was present and absent, compared to S25. Such bioactivities make strain S02 a promising candidate to be developed as a combined biofertiliser/bioprotectant.
Topics: Colletotrichum; Fusarium; Lolium; Paenibacillus; Paenibacillus polymyxa; Transcriptome
PubMed: 34330961
DOI: 10.1038/s41598-021-94820-2 -
Microbial Cell Factories Jul 2021Biological nitrogen fixation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis...
BACKGROUND
Biological nitrogen fixation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis of the cofactors of all nitrogenases. Most diazotrophic Paenibacillus strains have only one nifB gene located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV). But some Paenibacillus strains have multiple nifB genes and their functions are not known.
RESULTS
A total of 138 nifB genes are found in the 116 diazotrophic Paenibacillus strains. Phylogeny analysis shows that these nifB genes fall into 4 classes: nifBI class including the genes (named as nifB1 genes) that are the first gene within the compact nif gene cluster, nifBII class including the genes (named as nifB2 genes) that are adjacent to anf or vnf genes, nifBIII class whose members are designated as nifB3 genes and nifBIV class whose members are named as nifB4 genes are scattered on genomes. Functional analysis by complementation of the ∆nifB mutant of P. polymyxa which has only one nifB gene has shown that both nifB1 and nifB2 are active in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Deletion analysis also has revealed that nifB1 of Paenibacillus sabinae T27 is involved in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Complementation of the P. polymyxa ∆nifBHDK mutant with the four reconstituted operons: nifB1anfHDGK, nifB2anfHDGK, nifB1vnfHDGK and nifB2vnfHDGK, has shown both that nifB1 and nifB2 were able to support synthesis of Fe- or V-nitrogenases. Transcriptional results obtained in the original Paenibacillus strains are consistent with the complementation results.
CONCLUSIONS
The multiple nifB genes of the diazotrophic Paenibacillus strains are divided into 4 classes. The nifB1 located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV) and the nifB2 genes being adjacent to nif or anf or vnf genes are active in synthesis of Mo-, Fe and V-nitrogenases, but nifB3 and nifB4 are not. The reconstituted anf system comprising 8 genes (nifBanfHDGK and nifXhesAnifV) and vnf system comprising 10 genes (nifBvnfHDGKEN and nifXhesAnifV) support synthesis of Fe-nitrogenase and V-nitrogenase in Paenibacillus background, respectively.
Topics: Bacterial Proteins; Gene Expression Regulation, Bacterial; Multigene Family; Nitrogen Fixation; Nitrogenase; Paenibacillus; Phylogeny
PubMed: 34281551
DOI: 10.1186/s12934-021-01629-9 -
Anais Da Academia Brasileira de Ciencias 2021An endophytic bacterium inhibiting pathogenic bacteria was isolated and the strain was genetically identified as Paenibacillus polymyxa. Biochemical characterization of...
An endophytic bacterium inhibiting pathogenic bacteria was isolated and the strain was genetically identified as Paenibacillus polymyxa. Biochemical characterization of fermentation broth indicated the presence of peptidic antimicrobial molecules. Liquid-liquid partition resulted in an organic fraction (OF) and an aqueous fraction (AF). OF presented a broad spectrum of activity against a panel of pathogenic bacteria and a fungus whereas the AF was active only against Gram-negative bacteria. AF was sequentially submitted to ion-exchange, desalting and reverse phase (RP) chromatography. A molecule with an RT of 2.45 min exhibited activity against all Gram-negative pathogenic strains tested beside P. mirabilis. The primary structure of the molecule, named AMP-Pp, was determined as Gly-Glu-Hyp-Gly-Ala by N-terminal sequencing. The molecular mass and amino acid sequence were confirmed by MS/MS. With a molecular mass of 463 Da, AMP-Pp is one of the smallest active natural peptides reported, yet. RP chromatography of OF resulted in four peaks. The first three peaks corresponded to known antimicrobials. MS analysis of peak 4 revealed the presence of an ion with m/z 3,376.4 Da, whose proposed molecular formula is C182H321N29O29. The compound, named polycerradin, showed a spectrum of activity against Gram-positive bacteria, Gram-negative bacteria (beside P. mirabilis) and a fungus.
Topics: Anti-Infective Agents; Gram-Negative Bacteria; Gram-Positive Bacteria; Paenibacillus polymyxa; Tandem Mass Spectrometry
PubMed: 34231758
DOI: 10.1590/0001-3765202120200486 -
PloS One 2021Paenibacillus spp. exopolysaccharides (EPSs) have become a growing interest recently as a source of biomaterials. In this study, we characterized Paenibacillus polymyxa...
Paenibacillus spp. exopolysaccharides (EPSs) have become a growing interest recently as a source of biomaterials. In this study, we characterized Paenibacillus polymyxa 2020 strain, which produces a large quantity of EPS (up to 68 g/L),and was isolated from wasp honeycombs. Here we report its complete genome sequence and full methylome analysis detected by Pacific Biosciences SMRT sequencing. Moreover, bioinformatic analysis identified a putative levan synthetic operon. SacC and sacB genes have been cloned and their products identified as glycoside hydrolase and levansucrase respectively. The Fourier transform infrared (FT-IR) and nuclear magnetic resonance (NMR) spectra demonstrated that the EPS is a linear β-(2→6)-linked fructan (levan). The structure and properties of levan polymer produced from sucrose and molasses were analyzed by FT-IR, NMR, scanning electron microscopy (SEM), high performance size exclusion chromatography (HPSEC), thermogravimetric analysis (TGA), cytotoxicity tests and showed low toxicity and high biocompatibility. Thus, P. polymyxa 2020 could be an exceptional cost-effective source for the industrial production of levan-type EPSs and to obtain functional biomaterials based on it for a broad range of applications, including bioengineering.
Topics: Cloning, Molecular; Epigenome; Magnetic Resonance Spectroscopy; Microscopy, Electron, Scanning; Paenibacillus polymyxa; Polysaccharides, Bacterial; Sequence Analysis, DNA; Spectrometry, X-Ray Emission; Spectroscopy, Fourier Transform Infrared
PubMed: 34228741
DOI: 10.1371/journal.pone.0253482 -
Frontiers in Microbiology 2021Increasing prevalence of antimicrobial resistance (AMR) has posed a major health concern worldwide, and the addition of new antimicrobial agents is diminishing due to...
Increasing prevalence of antimicrobial resistance (AMR) has posed a major health concern worldwide, and the addition of new antimicrobial agents is diminishing due to overexploitation of plants and microbial resources. Inevitably, alternative sources and new strategies are needed to find novel biomolecules to counter AMR and pandemic circumstances. The association of plants with microorganisms is one basic natural interaction that involves the exchange of biomolecules. Such a symbiotic relationship might affect the respective bio-chemical properties and production of secondary metabolites in the host and microbes. Furthermore, the discovery of taxol and taxane from an endophytic fungus, from , has stimulated much research on endophytes from medicinal plants. A gram-positive endophytic bacterium, IBSD35, was isolated from the stem of Benth. It is a rod-shaped, motile, gram-positive, and endospore-forming bacteria. It is neutralophilic as per Joint Genome Institute's (JGI) IMG system analysis. The plant was selected based on its ethnobotany history of traditional uses and highly insecticidal properties. Bioactive molecules were purified from IBSD35 culture broth using 70% ammonium sulfate and column chromatography techniques. The biomolecule was enriched to 151.72-fold and the yield percentage was 0.05. Peoriaerin II, a highly potent and broad-spectrum antimicrobial peptide against ATCC 25923, ATCC 25922, and ATCC 10231 was isolated. LC-MS sequencing revealed that its N-terminal is methionine. It has four negatively charged residues (Asp + Glu) and a total number of two positively charged residues (Arg + Lys). Its molecular weight is 4,685.13 Da. It is linked to an LC-MS/MS inferred biosynthetic gene cluster with accession number A0A2S6P0H9, and blastp has shown it is 82.4% similar to fusaricidin synthetase of SC2. The 3D structure conformation of the BGC and AMP were predicted using SWISS MODEL homology modeling. Therefore, combining both genomic and proteomic results obtained from IBSD35, associated with Benth., will substantially increase the understanding of antimicrobial peptides and assist to uncover novel biological agents.
PubMed: 34149644
DOI: 10.3389/fmicb.2021.656896 -
Frontiers in Microbiology 2021Genome-based identification of new antibiotics is emerging as an alternative to traditional methods. However, uncovering hidden antibiotics under the background of known...
Genome-based identification of new antibiotics is emerging as an alternative to traditional methods. However, uncovering hidden antibiotics under the background of known antibiotics remains a challenge. To over this problem using a quick and effective genetic approach, we developed a multiplex genome editing system using a cytosine base editor (CBE). The CBE system achieved simultaneous double, triple, quadruple, and quintuple gene editing with efficiencies of 100, 100, 83, and 75%, respectively, as well as the 100% editing efficiency of single targets in . Whole-genome sequencing of the edited strains showed that they had an average of 8.5 off-target single-nucleotide variants at gRNA-independent positions. The CBE system was used to simultaneously knockout five known antibiotic biosynthetic gene clusters to leave only an uncharacterized polyketide biosynthetic gene cluster in E681. The polyketide showed antimicrobial activities against gram-positive bacteria, but not gram-negative bacteria and fungi. Therefore, our findings suggested that the CBE system might serve as a powerful tool for multiplex genome editing and greatly accelerating the unraveling of hidden antibiotics in and species.
PubMed: 34122396
DOI: 10.3389/fmicb.2021.691839