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Frontiers in Microbiology 2022Horizontal gene transfer (HGT) is a major driving force in shaping bacterial communities. Key elements responsible for HGT are conjugation-like events and transmissible... (Review)
Review
Horizontal gene transfer (HGT) is a major driving force in shaping bacterial communities. Key elements responsible for HGT are conjugation-like events and transmissible plasmids. Conjugative plasmids can promote their own transfer as well as that of co-resident plasmids. and relatives harbor a plethora of plasmids, including conjugative plasmids, which are at the heart of the group species differentiation and specification. Since the first report of a conjugation-like event between strains of () 40 years ago, many have studied the potential of plasmid transfer across the group, especially for plasmids encoding major toxins. Over the years, more than 20 plasmids from isolates have been reported as conjugative. However, with the increasing number of genomic data available, analyses indicate that more plasmids from genomes present self-transfer potential. bacteria occupy diverse environmental niches, which were mimicked in laboratory conditions to study conjugation-related mechanisms. Laboratory mating conditions remain nonetheless simplistic compared to the complex interactions occurring in natural environments. Given the health, economic and ecological importance of strains of , it is of prime importance to consider the impact of conjugation within this bacterial group.
PubMed: 36406448
DOI: 10.3389/fmicb.2022.1034440 -
Microbiology Spectrum Sep 2021Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history,...
Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history, a comparative investigation of the species pan-genome and the functional gene categorization of 35 isolates obtained from soil samples from northeastern Poland was performed. The pan-genome of these isolates is composed of 20,175 genes and is characterized by a strong predominance of adaptive genes (∼83%), a significant amount of plasmid genes (∼37%), and a great contribution of prophages and insertion sequences. The pan-genome structure and phylodynamic studies had suggested a wide genomic diversity among the isolates, but no correlation between lineages and the bacillus origin was found. Nevertheless, the two B. mycoides populations, one from Białowieża National Park, the last European natural primeval forest with soil classified as organic, and the second from mineral soil samples taken in a farm in Jasienówka, a place with strong anthropogenic pressure, differ significantly in the frequency of genes encoding proteins enabling bacillus adaptation to specific stress conditions and production of a set of compounds, thus facilitating their colonization of various ecological niches. Furthermore, differences in the prevalence of essential stress sigma factors might be an important trail of this process. Due to these numerous adaptive genes, B. mycoides is able to quickly adapt to changing environmental conditions. This research allows deeper understanding of the genetic organization of natural bacterial populations, specifically, Bacillus mycoides, a psychrotrophic member of the Bacillus cereus group that is widely distributed worldwide, especially in areas with continental cold climates. These thorough analyses made it possible to describe, for the first time, the B. mycoides pan-genome, phylogenetic relationship within this species, and the mechanisms behind the species ecology and evolutionary history. Our study indicates a set of functional properties and adaptive genes, in particular, those encoding sigma factors, associated with B. mycoides acclimatization to specific ecological niches and changing environmental conditions.
Topics: Anthropogenic Effects; Bacillus; Biological Evolution; DNA Transposable Elements; Ecology; Genome, Bacterial; Genomics; High-Throughput Nucleotide Sequencing; Phylogeny; Plasmids; Sigma Factor; Soil; Soil Microbiology; Species Specificity
PubMed: 34287030
DOI: 10.1128/Spectrum.00311-21 -
Life (Basel, Switzerland) Jan 2022Soil salinity is one of the abiotic constraints that imbalance nutrient acquisition, hampers plant growth, and leads to potential loss in agricultural productivity....
Soil salinity is one of the abiotic constraints that imbalance nutrient acquisition, hampers plant growth, and leads to potential loss in agricultural productivity. Salt-tolerant plant growth-promoting rhizobacteria (PGPR) can alleviate the adverse impacts of salt stress by mediating molecular, biochemical, and physiological status. In the present study, the bacterium PM35 showed resistance up to 3 M NaCl stress and exhibited plant growth-promoting features. Under salinity stress, the halo-tolerant bacterium PM35 showed significant plant growth-promoting traits, such as the production of indole acetic acid, siderophore, ACC deaminase, and exopolysaccharides. Inoculation of PM35 alleviated salt stress in plants and enhanced shoot and root length under salinity stress (0, 300, 600, and 900 mM). The PM35 alleviated salinity stress by enhancing the photosynthetic pigments, carotenoids, radical scavenging capacity, soluble sugars, and protein content in inoculated maize plants compared to non-inoculated plants. In addition, PM35 significantly boosted antioxidant activities, relative water content, flavonoid, phenolic content, and osmolytes while reducing electrolyte leakage, HO, and MDA in maize compared to control plants. Genes conferring abiotic stress tolerance ( and genes) were amplified in PM35. Moreover, all reactions are accompanied by the upregulation of stress-related genes (APX and SOD). Our study reveals that PM35 is capable of promoting plant growth and increasing agricultural productivity.
PubMed: 35207506
DOI: 10.3390/life12020219 -
Applied and Environmental Microbiology Mar 2020Changes with time of a population of KBAB4 and AD978 dormant spores into germinated spores and vegetative cells were followed by flow cytometry, at pH ranges of 4.7 to...
Changes with time of a population of KBAB4 and AD978 dormant spores into germinated spores and vegetative cells were followed by flow cytometry, at pH ranges of 4.7 to 7.4 and temperatures of 10°C to 37°C for and 18°C to 59°C for Incubation conditions lower than optimal temperatures or pH led to lower proportions of dormant spores able to germinate and extended time of germination, a lower proportion of germinated spores able to outgrow, an extension of their times of outgrowth, and an increase of the heterogeneity of spore outgrowth time. A model based on the strain growth limits was proposed to quantify the impact of incubation temperature and pH on the passage through each physiological stage. The heat treatment temperature or time acted independently on spore recovery. Indeed, a treatment at 85°C for 12 min or at 95°C for 2 min did not have the same impact on spore germination and outgrowth kinetics of despite the fact that they both led to a 10-fold reduction of the population. Moreover, acidic sporulation pH increased the time of outgrowth 1.2-fold and lowered the proportion of spores able to germinate and outgrow 1.4-fold. Interestingly, we showed by proteomic analysis that some proteins involved in germination and outgrowth were detected at a lower abundance in spores produced at pH 5.5 than in those produced at pH 7.0, maybe at the origin of germination and outgrowth behavior of spores produced at suboptimal pH. Sporulation and incubation conditions have an impact on the numbers of spores able to recover after exposure to sublethal heat treatment. Using flow cytometry, we were able to follow at a single-cell level the changes in the physiological states of heat-stressed spores of spp. and to discriminate between dormant spores, germinated spores, and outgrowing vegetative cells. We developed original mathematical models that describe (i) the changes with time of the proportion of cells in their different states during germination and outgrowth and (ii) the influence of temperature and pH on the kinetics of spore recovery using the growth limits of the tested strains as model parameters. We think that these models better predict spore recovery after a sublethal heat treatment, a common situation in food processing and a concern for food preservation and safety.
Topics: Bacillus; Bacillus licheniformis; Hot Temperature; Models, Theoretical; Spores, Bacterial
PubMed: 31900309
DOI: 10.1128/AEM.02061-19 -
ISME Communications Nov 2023Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus...
Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S rRNA gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification of Bacillus species. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution of Bacillus species in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for the tuf gene were not only specific for the Bacillus genus but also sufficiently discriminated species both in silico and in vitro in a mixture of 11 distinct Bacillus species. Investigating the primers using a natural soil sample, 13 dominant species were detected including Bacillus badius, Bacillus velezensis, and Bacillus mycoides as primary members, neither of which could be distinguished with 16S rRNA sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification of Bacillus species and aids the description of the ecological distribution of Bacilli in various natural environment.
PubMed: 38012258
DOI: 10.1038/s43705-023-00330-9 -
BMC Plant Biology Feb 2024Zinc (Zn) and nickel (Ni) are nutrients that are crucial for plant growth; however, when they are present at higher concentrations, they can cause toxicity in plants....
BACKGROUND
Zinc (Zn) and nickel (Ni) are nutrients that are crucial for plant growth; however, when they are present at higher concentrations, they can cause toxicity in plants. The present study aimed to isolate plant growth promoting endophytic bacteria from Viburnum grandiflorum and assess its plant and defense promoting potential alone and in combination with RP in zinc (Zn) and nickel (Ni) toxic soil. The isolated endophytic bacteria were identified using 16s rRNA gene sequencing. For the experiment, twelve different treatments were applied using Zn, Ni, isolated endophytic Bacillus mycoides (Accession # MW979613), and rock phosphate (RP). The Ni, Zn and RP were used at the rate of (100 mg/kg) and (0.2 g/kg) respectively. A pot experiment with three replicates of each treatment was conducted using a complete randomized design (CRD).
RESULTS
The results indicated that Ni (T5 = seed + 100 mg/kg Ni and T9 = seed + 100 mg/kg Zn) and Zn concentrations inhibited plant growth, but the intensity of growth inhibition was higher in Ni-contaminated soil. Bacillus mycoides and RP at 100 mg/Kg Zn (T12 = inoculated seed + 100 mg/kg Zn + RP0.2 g/kg.) increased the shoot length, leaf width, protein and sugar content by 57%, 13%, 20% and 34%, respectively, compared to the control. The antioxidant enzymes superoxide dismutases (SOD), peroxidase (POD) were decreased in contaminated soil. Furthermore, Ni and Zn accumulation was inhibited in T11 (seed + 100 mg/kg Zn + RP0.2 g/Kg) and T12 (inoculated seed + 100 mg/kg Zn + RP0.2 g/Kg) by 62 and 63% respectively. The Cu, Ca, and K, contents increased by 128, 219 and 85, Mn, Na, and K by 326, 449, and 84% in (T3 = inoculated seed) and (T4 = inoculated seed + RP 0.2 g/Kg) respectively.
CONCLUSIONS
Ni was more toxic to plants than Zn, but endophytic bacteria isolated from Viburnum grandiflorum, helped wheat (Triticum aestivum) plants and reduced the toxic effects of Ni and Zn. The effect of Bacillus mycoides was more prominent in combination with RP which promoted and suppressed heavy-metal toxicity. The reported combination of Bacillus mycoides and RP may be useful for improving plant growth and overcoming metal stress.
Topics: Triticum; Nickel; Phosphates; RNA, Ribosomal, 16S; Metals, Heavy; Zinc; Bacteria; Soil; Soil Pollutants; Bacillus
PubMed: 38373884
DOI: 10.1186/s12870-024-04812-3 -
Frontiers in Microbiology 2019The group comprises genetical closely related species with variable toxigenic characteristics. However, detection and differentiation of the group species in routine...
The group comprises genetical closely related species with variable toxigenic characteristics. However, detection and differentiation of the group species in routine diagnostics can be difficult, expensive and laborious since current species designation is linked to specific phenotypic characteristic or the presence of species-specific genes. Especially the differentiation of and , the identification of psychrotolerant and , as well as the identification of emetic and s, which are both producing highly potent toxins, is of high importance in food microbiology. Thus, we investigated the use of a machine learning approach, based on artificial neural network (ANN) assisted Fourier transform infrared (FTIR) spectroscopy, for discrimination of group members. The deep learning tool box of Matlab was employed to construct a one-level ANN, allowing the discrimination of the aforementioned group members. This model resulted in 100% correct identification for the training set and 99.5% correct identification overall. The established ANN was applied to investigate the composition of group members in soil, as a natural habitat of , and in food samples originating from foodborne outbreaks. These analyses revealed a high complexity of group populations, not only in soil samples but also in the samples from the foodborne outbreaks, highlighting the importance of taking multiple isolates from samples implicated in food poisonings. Notable, in contrast to the soil samples, no bacteria belonging to the psychrotolerant group members were detected in the food samples linked to foodborne outbreaks, while the overall abundancy of did not significantly differ between the sample categories. None of the isolates was classified as , fostering the hypothesis that the latter species is linked to very specific ecological niches. Overall, our work shows that machine learning assisted (FTIR) spectroscopy is suitable for identification of group members in routine diagnostics and outbreak investigations. In addition, it is a promising tool to explore the natural habitats of group, such as soil.
PubMed: 31105681
DOI: 10.3389/fmicb.2019.00902 -
International Journal of Molecular... Aug 2016The objectives of this investigation were to produce a novel chitosanase for application in industries and waste treatment. The transformation of chitinous biowaste into...
The objectives of this investigation were to produce a novel chitosanase for application in industries and waste treatment. The transformation of chitinous biowaste into valuable bioactive chitooligomers (COS) is one of the most exciting applications of chitosanase. An amphiprotic novel chitosanase from Bacillus mycoides TKU038 using squid pen powder (SPP)-containing medium was retrieved from a Taiwan soil sample, which was purified by column chromatography, and characterized by biochemical protocol. Extracellular chitosanase (CS038) was purified to 130-fold with a 35% yield, and its molecular mass was roughly 48 kDa. CS038 was stable over a wide range of pH values (4-10) at 50 °C and exhibited an optimal temperature of 50 °C. Interestingly, the optimum pH values were estimated as 6 and 10, whereas CS038 exhibited chitosan-degrading activity (100% and 94%, respectively). CS038 had Km and Vmax values of 0.098 mg/mL and 1.336 U/min, separately, using different concentrations of water-soluble chitosan. A combination of the high performance liquid chromatography (HPLC) and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometer data revealed that the chitosan oligosaccharides obtained from the hydrolysis of chitosan by CS038 comprise oligomers with multiple degrees of polymerization (DP), varying from 3-9, as well as CS038 in an endolytic fashion. The TKU038 culture supernatant and COS mixture exhibited 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activities. The COS activities were dose dependent and correlated to their DP. The COS with high DP exhibited enhanced DPPH radical scavenging capability compared with COS with low DP. Furthermore, the COS exhibited inhibitory behavior on nitric oxide (NO) production in murine RAW 264.7 macrophage cells, which was induced by Escherichia coli O111 lipopolysaccharide (LPS). The COS with low DP possesses a more potent anti-inflammatory capability to decrease NO production (IC50, 76.27 ± 1.49 µg/mL) than that of COS with high DP (IC50, 82.65 ± 1.18 µg/mL). Given its effectiveness in production and purification, acidophilic and alkalophilic properties, stability over ranges of pH values, ability to generate COS, antioxidant activity, and anti-inflammatory, CS038 has potential applications in SPP waste treatment and industries for COS production as a medical prebiotic.
Topics: Animals; Anti-Inflammatory Agents; Antioxidants; Bacillus; Biphenyl Compounds; Cell Line, Tumor; Cell Proliferation; Chitin; Chitosan; Chromatography, High Pressure Liquid; Electrophoresis, Polyacrylamide Gel; Glycoside Hydrolases; Hep G2 Cells; Humans; Hydrogen-Ion Concentration; Mice; Picrates; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 27517920
DOI: 10.3390/ijms17081302 -
Journal of Food Protection Aug 2022Cereulide-producing Bacillus cereus, which causes foodborne illnesses with vomiting, and psychrotolerant B. cereus group strains such as Bacillus mycoides, which can...
Simultaneous Discrimination of Cereulide-Producing Bacillus cereus and Psychrotolerant B. cereus Group by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry.
ABSTRACT
Cereulide-producing Bacillus cereus, which causes foodborne illnesses with vomiting, and psychrotolerant B. cereus group strains such as Bacillus mycoides, which can grow at ≥7°C and cause spoilage of refrigerated foods, are significant concerns for the food industry. Rapid and simple methods to discriminate the cereulide-producing B. cereus and psychrotolerant B. cereus group strains from other B. cereus group strains are needed. We developed a novel, rapid, and simple method with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) analysis for simultaneous discrimination of these two groups from other B. cereus group strains. A potassium adduct of cereulide was used to detect cereulide-producing B. cereus, and three ribosomal subunit proteins (L30, S16, and S20) were used to detect psychrotolerant B. cereus group. A total of 51 B. cereus group strains were analyzed by MALDI-TOF MS. The biomarkers allowed successful discrimination of 16 cereulide-producing B. cereus and 15 psychrotolerant B. cereus group strains from other B. cereus group strains. The results showed that this MALDI-TOF MS analysis allows simultaneous discrimination of cereulide-producing B. cereus and psychrotolerant B. cereus group strains from other B. cereus group strains. This efficient method has the potential to be a valuable tool for ensuring food safety.
Topics: Bacillus cereus; Depsipeptides; Lasers; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 35687734
DOI: 10.4315/JFP-21-450 -
Current Research in Microbial Sciences Dec 2021Organic farming is an eco-friendly and sustainable farming practice that enhances soil fertility and helps in improving soil quality. But with the commencement of more...
Organic farming is an eco-friendly and sustainable farming practice that enhances soil fertility and helps in improving soil quality. But with the commencement of more sophisticated advances in agricultural techniques, organic farming has gradually become limited in the world. Culture-dependent plant growth-promoting bacterial isolates were isolated from the bulk and rhizospheric soil, of the native high yielding pole type organic pea ( L.) cultivar of Dentam, West Sikkim, India. Based on the 16S rRNA gene sequencing identification of these isolates, it was found that from the bulk soil, Actinobacteria (58%) was the dominant phyla followed by Firmicutes (28%), and Proteobacteria (14%). In the rhizospheric soil it was dominated by Proteobacteria (56%), followed by Firmicutes (33%), and Bacteriodetes (11%). A total of 40 bacterial isolates were initially screened for the plant growth-promoting (PGP) activity and out of them only four bacterial isolates i.e., P8, s DP2, PP3, and PP10 with accession numbers MN589697, MN559516, MN519462 and MN589696 respectively were found to possess higher PGP activity (i.e. phosphorous, potassium solubilization and nitrogen-fixing activity) as compared to the other bacteria present in the soil. Based on the indole-3-acetic acid (IAA) quantitative assay and siderophore production assay, it was found that (MN589697) produced the highest IAA (65.5 µg mL) and siderophore (71%) when compared with the other isolates. The statistical correlation suggests that pH and available phosphorus were the strongest influencing factors for the distribution of Proteobacteria in the rhizospheric soil. The results indicate that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India. To the best of our knowledge the present study is the first report of its kind and showcases significant findings pertaining to the assessment of diversity, isolation and identification of plant growth-promoting rhizobacteria of organic pea grown in Sikkim.
PubMed: 34841358
DOI: 10.1016/j.crmicr.2021.100068