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Trends in Microbiology Jun 2023
Topics: Paenibacillus polymyxa
PubMed: 36564337
DOI: 10.1016/j.tim.2022.11.010 -
Planta Aug 2021The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective... (Review)
Review
The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective phytostimulators, biofertilizers, and biocontrol agents. The members of the genera Bacillus and Paenibacillus isolated from several ecological habitats are been thoroughly dissected for their effective application in the development of sustainable and eco-friendly agriculture. Numerous Bacillus and Paenibacillus species are reported as plant growth-promoting bacteria influencing the health and productivity of the food crops. This review narrates the mechanisms utilized by these species to enhance bioavailability and/or facilitate the acquisition of nutrients by the host plant, modulate plant hormones, stimulate host defense and stress resistance mechanisms, exert antagonistic action against soil and airborne pathogens, and alleviate the plant health. The mechanisms employed by Bacillus and Paenibacillus are seldom mutually exclusive. The comprehensive and systematic exploration of the aforementioned mechanisms in conjunction with the field investigations may assist in the exploration and selection of an effective biofertilizer and a biocontrol agent. This review aims to gather and discuss the literature citing the applications of Bacillus and Paenibacillus in the management of sustainable agriculture.
Topics: Agriculture; Bacillus; Crops, Agricultural; Plant Development; Soil Microbiology
PubMed: 34383174
DOI: 10.1007/s00425-021-03695-0 -
Critical Reviews in Biotechnology Dec 2023Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium has been widely applied in: agriculture, medicine, industry, and... (Review)
Review
Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium has been widely applied in: agriculture, medicine, industry, and environmental remediation. species not only accelerate plant growth and degrade toxic substances in wastewater and soil but also produce industrially-relevant enzymes and antimicrobial peptides. Due to a lack of genetic manipulation tools and methods, exploitation of the bioresources of naturally isolated species has long been limited. Genetic manipulation tools and methods continue to improve in , such as shuttle plasmids, promoters, and genetic tools of CRISPR. Furthermore, genetic transformation systems develop gradually, including: penicillin-mediated transformation, electroporation, and magnesium amino acid-mediated transformation. As genetic manipulation methods of homologous recombination and CRISPR-mediated editing system have developed gradually, has come to be regarded as a promising microbial chassis for biomanufacturing, expanding its application scope, such as: industrial enzymes, bioremediation and bioadsorption, surfactants, and antibacterial agents. In this review, we describe the applications of bioproducts, and then discuss recent advances and future challenges in the development of genetic manipulation systems in this genus. This work highlights the potential of as a new microbial chassis for mining bioresources.
PubMed: 38105503
DOI: 10.1080/07388551.2023.2289342 -
Environmental Microbiology Oct 2021The bacterium Paenibacillus polymyxa is found naturally in diverse niches. Microbiome analyses have revealed enrichment in the genus Paenibacillus in soils under... (Review)
Review
The bacterium Paenibacillus polymyxa is found naturally in diverse niches. Microbiome analyses have revealed enrichment in the genus Paenibacillus in soils under different adverse conditions, which is often accompanied by improved growth conditions for residing plants. Furthermore, Paenibacillus is a member of the core microbiome of several agriculturally important crops, making its close association with plants an interesting research topic. This review covers the versatile interaction possibilities of P. polymyxa with plants and its applicability in industry and agriculture. Thanks to its array of produced compounds and traits, P. polymyxa is likely an efficient plant growth-promoting bacterium, with the potential of biofertilization, biocontrol and protection against abiotic stresses. By contrast, cases of phytotoxicity of P. polymyxa have been described as well, in which growth conditions seem to play a key role. Because of its adjustable character, we propose this bacterial species as an outstanding model for future studies on host-microbe communications and on the manner how the environment can influence these interactions.
Topics: Paenibacillus; Paenibacillus polymyxa; Plant Development; Plants
PubMed: 33684235
DOI: 10.1111/1462-2920.15450 -
Applied and Environmental Microbiology Feb 2022Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their...
Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their levoglucosan dehydrogenase (LGDH) activity. On the basis of their 16S rRNA gene sequences, these bacteria represented the diverse genera , , , and Klebsiella. Genomic sequencing of the isolates verified that two isolates represented novel species, MEC069 and MEC087, while the remaining isolates were closely related to Microbacterium lacusdiani or Klebsiella pneumoniae. The genetic sequence of LGDH, , was found in the genomes of these four isolates as well as Pseudarthrobacter phenanthrenivorans Sphe3. The identity of the LGDH was experimentally verified following recombinant expression in Escherichia coli. Comparison of the putative genes surrounding in the isolate genomes indicated that several other gene products facilitate the bacterial catabolism of levoglucosan, including a putative sugar isomerase and several transport proteins. Levoglucosan is the most prevalent soluble carbohydrate remaining after high-temperature pyrolysis of lignocellulosic biomass, but it is not fermented by typical production microbes such as Escherichia coli and Saccharomyces cerevisiae. A few fungi metabolize levoglucosan via the enzyme levoglucosan kinase, while several bacteria metabolize levoglucosan via levoglucosan dehydrogenase. This study describes the isolation and characterization of four bacterial species that degrade levoglucosan. Each isolate is shown to contain several genes within an operon involved in levoglucosan degradation, furthering our understanding of bacteria that metabolize levoglucosan.
Topics: Biomass; Glucose; Paenibacillus; RNA, Ribosomal, 16S
PubMed: 34910566
DOI: 10.1128/AEM.01868-21 -
Archives of Microbiology Dec 2023During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38 and TW40. Both strains...
During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38 and TW40. Both strains were catalase positive and oxidase negative. Strains TW38 and TW40 demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38 and TW40 affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17 (98.6%) and Paenibacillus arachidis E3 (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38, TW40, and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38 and TW40 was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38 and TW40 from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38 and TW40 represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38 (= KCTC 43468 = NBRC 116015) and type strain of Paenibacillus humicola is TW40 (= KCTC 43469 = NBRC 116016).
Topics: Phylogeny; Cardiolipins; Forests; Paenibacillus; DNA
PubMed: 38147140
DOI: 10.1007/s00203-023-03763-x -
International Journal of Biological... Mar 2024Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of... (Review)
Review
Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of many metabolically active substances, including polypeptides, volatile organic compounds, phytohormone, hydrolytic enzymes, exopolysaccharide (EPS), etc. Due to the wide range of compounds that it produces, P. polymyxa has been extensively studied as a plant growth promoting bacterium which provides a direct benefit to plants through the improvement of N fixation from the atmosphere and enhancement of the solubilization of phosphorus and the uptake of iron in the soil, and phytohormones production. Among the metabolites from P. polymyxa, EPS exhibits many activities, for example, antioxidant, immunomodulating, anti-tumor and many others. EPS has various applications in food, agriculture, environmental protection. Particularly, in the field of sustainable agriculture, P. polymyxa EPS can be served as a biofilm to colonize microbes, and also can act as a nutrient sink on the roots of plants in the rhizosphere. Therefore, this paper would provide a comprehensive review of the advancements of diverse aspects of EPS from P. polymyxa, including the production, extraction, structure, biosynthesis, bioactivity and applications, etc. It would provide a direction for future research on P. polymyxa EPS.
Topics: Paenibacillus polymyxa; Paenibacillus; Plant Growth Regulators; Plant Development; Plants
PubMed: 38278396
DOI: 10.1016/j.ijbiomac.2024.129663 -
The Lancet. Microbe Aug 2023Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis,... (Observational Study)
Observational Study
BACKGROUND
Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis, meningitis, and postinfectious hydrocephalus, we aimed to complete three separate studies of Ugandan infants. The first study was on peripartum prevalence of Paenibacillus in mother-newborn pairs. The second study assessed Paenibacillus in blood and cerebrospinal fluid (CSF) from neonates with sepsis. The third study assessed Paenibacillus in CSF from infants with hydrocephalus.
METHODS
In this observational study, we recruited mother-newborn pairs with and without maternal fever (mother-newborn cohort), neonates (aged ≤28 days) with sepsis (sepsis cohort), and infants (aged ≤90 days) with hydrocephalus with and without a history of neonatal sepsis and meningitis (hydrocephalus cohort) from three hospitals in Uganda between Jan 13, 2016 and Oct 2, 2019. We collected maternal blood, vaginal swabs, and placental samples and the cord from the mother-newborn pairs, and blood and CSF from neonates and infants. Bacterial content of infant CSF was characterised by 16S rDNA sequencing. We analysed all samples using quantitative PCR (qPCR) targeting either the Paenibacillus genus or Paenibacillus thiaminolyticus spp. We collected cranial ultrasound and computed tomography images in the subset of participants represented in more than one cohort.
FINDINGS
No Paenibacillus spp were detected in vaginal, maternal blood, placental, or cord blood specimens from the mother-newborn cohort by qPCR. Paenibacillus spp was detected in 6% (37 of 631 neonates) in the sepsis cohort and, of these, 14% (5 of 37 neonates) developed postinfectious hydrocephalus. Paenibacillus was the most enriched bacterial genera in postinfectious hydrocephalus CSF (91 [44%] of 209 patients) from the hydrocephalus cohort, with 16S showing 94% accuracy when validated by qPCR. Imaging showed progression from Paenibacillus spp-related meningitis to postinfectious hydrocephalus over 1-3 months. Patients with postinfectious hydrocephalus with Paenibacillus spp infections were geographically clustered.
INTERPRETATION
Paenibacillus spp causes neonatal sepsis and meningitis in Uganda and is the dominant cause of subsequent postinfectious hydrocephalus. There was no evidence of transplacental transmission, and geographical evidence was consistent with an environmental source of neonatal infection. Further work is needed to identify routes of infection and optimise treatment of neonatal Paenibacillus spp infection to lessen the burden of morbidity and mortality.
FUNDING
National Institutes of Health and Boston Children's Hospital Office of Faculty Development.
Topics: United States; Infant, Newborn; Child; Humans; Infant; Female; Pregnancy; Uganda; Neonatal Sepsis; Placenta; Paenibacillus; Sepsis; Meningitis; Hydrocephalus; Case-Control Studies
PubMed: 37348522
DOI: 10.1016/S2666-5247(23)00106-4 -
International Journal of Systematic and... Dec 2022Members of the genus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated...
Members of the genus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4, JC52 and PR3, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4 exhibited the highest similarity, ANI and digital DDH values with DSM 18201 (99.0/87.5/33.9 %) and DS80 (97.2/-/18.2±1.2 %). Values for JC52 with NBRC 15382 were 96.9, 73.3 and 19.6 %, and with JCM 16352 were 96.1, 72.1 and 19.3 %. Values for PR3 with DCY89 were 98.2, - and 31.8±1.5 %, with ASM318225v1 were 97.8, 83.3 and 26.7 %, and with NBRC 15729 were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4, JC52 and PR3 represent novel species of the genus , with the names sp. nov. (=KACC 19717=JCM 32775), sp. nov. (=KACC 21221=NBRC 113867) and sp. nov. (=KACC 21455=NBRC 114385), respectively.
Topics: Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Rhizosphere; Base Composition; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Paenibacillus
PubMed: 36748605
DOI: 10.1099/ijsem.0.005640 -
Journal of Applied Microbiology Aug 2022Algicidal bacteria can be used for control of harmful algal bloom and extraction of algal bioproducts based on their algae-lysing activities. This work investigated the...
AIMS
Algicidal bacteria can be used for control of harmful algal bloom and extraction of algal bioproducts based on their algae-lysing activities. This work investigated the algae-lysing activity of a newly isolated algicidal bacterium, Paenibacillus polymyxa strain MEZ6 and its possible mechanisms.
METHODS AND RESULTS
Algicidal bacteria were isolated from soil samples collected at the university campus. Co-inoculation tests identified that one isolate, MEZ6, can rapidly kill eukaryotic algae including Chlamydomonas reinhardtii, Tribonema minus, Haematococcus pluvialis, and Chlorella ellipsoidea. The strain was determined as Paenibacillus polymyxa MEZ6 based on 16S rRNA gene sequence and genome comparisons. The algicidal activity was detected in both living cells and cell-free supernatant of spent culture medium, suggesting cell-cell contact is not required for algicidal activity. Strain MEZ6 was less active towards cyanobacterial strains compared to algae. Genomic sequence and comparative proteomic analyses were performed to explore the possible algicidal mechanisms of the strain. Differentially expressed protein analysis identified a number of proteins related to polysaccharides degradation and antimicrobial secondary metabolite biosynthesis that may be involved in the algicidal activity of MEZ6.
CONCLUSION
Paenibacillus polymyxa MEZ6 is a newly discovered gram-positive algicidal bacterial strain with high lytic activity towards several algal species.
SIGNIFICANCE AND IMPACT OF THE STUDY
Our study extends the understanding of the versatile characters of Paenibacillus polymyxa and sheds new insights into its application in algae biotechnology.
Topics: Bacteria; Chlorella; Harmful Algal Bloom; Humans; Microalgae; Paenibacillus; Paenibacillus polymyxa; Proteomics; RNA, Ribosomal, 16S
PubMed: 35462459
DOI: 10.1111/jam.15592