Bacillus megaterium strains derived from water and soil exhibit differential responses to the herbicide mesotrione

The intense use of herbicides for weed control in agriculture causes selection pressure on soil microbiota and water ecosystems, possibly resulting in changes to microbial processes, such as biogeochemical cycles. These xenobiotics may increase the production of reactive oxygen species and consequently affect the survival of microorganisms, which need to develop strategies to adapt to these conditions and maintain their ecological functionality. This study analyzed the adaptive responses of bacterial isolates belonging to the same species, originating from two different environments (water and soil), and subjected to selection pressure by herbicides. The effects of herbicide Callisto and its active ingredient, mesotrione, induced different adaptation strategies on the cellular, enzymatic, and structural systems of two Bacillus megaterium isolates obtained from these environments. The lipid saturation patterns observed may have affected membrane permeability in response to this herbicide. Moreover, this may have led to different levels of responses involving superoxide dismutase and catalase activities, and enzyme polymorphisms. Due to these response systems, the strain isolated from water exhibited higher growth rates than did the soil strain, in evaluations made in oligotrophic culture media, which would be more like that found in semi-pristine aquatic environments. The influence of the intracellular oxidizing environments, which changed the mode of degradation of mesotrione in our experimental model and produced different metabolites, can also be observed in soil and water at sites related to agriculture. Since the different metabolites may present different levels of toxicity, we suggest that this fact should be considered in studies on the fate of agrochemicals in different environments.

[Isolation of microorganisms producing enzyme capable of degrading tobacco straw and nicotine]

OBJECTIVE

The aim of this study was to screen tobacco straw and nicotine degrading microorganism.

METHODS

The bacterium was isolated from tobacco field soil using medium containing tobacco straw as the sole carbon and nitrogen source. We identified the bacterium through morphological and physiological characterization combined with the result of 16S rRNA gene sequence and data analysis. We also studied the lignocelluloses degradation and enzyme activities related to the degradation of lignin and cellulose in liquid state fermentation of tobacco stalk.

RESULTS

The bacterium was identified as Bacillus megaterium and we had demonstrated that it has a good ability to degrade lignin in tobacco straw when fermented in liquid state. It showed the highest laccase production of 418. 52 U/L while the highest lignin peroxides and manganese peroxides activity was 19. 71 U/L and 64. 71 U/L. On the other hand, we also found that nicotine in tobacco stem was totally degraded 20 d after inoculation.

CONCLUSION

to the isolated Bacillus megaterium is capable of degrading tobacco straw partially and nicotine totally.

Isolation, identification and characteristics of an endophytic quinclorac degrading bacterium Bacillus megaterium Q3

In this study, we isolated an endophytic quinclorac-degrading bacterium strain Q3 from the root of tobacco grown in quinclorac contaminated soil. Based on morphological characteristics, Biolog identification, and 16S rDNA sequence analysis, we identified strain Q3 as Bacillus megaterium. We investigated the effects of temperature, pH, inoculation size, and initial quinclorac concentration on growth and degrading efficiency of Q3. Under the optimal degrading condition, Q3 could degrade 93% of quinclorac from the initial concentration of 20 mg/L in seven days. We analyzed the degradation products of quinclorac using liquid chromatography–tandem mass spectrometry (LC-MS/MS). The major degradation products by Q3 were different from those of previously identified quinclorac degrading strains, which suggests that Q3 may employ new pathways for quinclorac degradation. Our indoor pot experiments demonstrated that Q3 can effectively alleviate the quinclorac phytotoxicity in tobacco. As the first endophytic microbial that is capable of degrading quinclorac, Q3 can be a good bioremediation bacterium for quinclorac phytotoxicity.

Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319

Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key species and of particular importance in understanding genome evolution, dynamics, and plasticity in the bacilli. B. megaterium is a commercially available, nonpathogenic host for the biotechnological production of several substances, including vitamin B(12), penicillin acylase, and amylases. Here, we report the analysis of the first complete genome sequences of two important B. megaterium strains, the plasmidless strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551 plasmids represent a combined 417 kb and 523 genes, one of the largest plasmid arrays sequenced in a single bacterial strain. We have documented extensive gene transfer between the plasmids and the chromosome. Each strain carries roughly 300 strain-specific chromosomal genes that account for differences in their experimentally confirmed phenotypes. B. megaterium is able to synthesize vitamin B(12) through an oxygen-independent adenosylcobalamin pathway, which together with other key energetic and metabolic pathways has now been fully reconstructed. Other novel genes include a second ftsZ gene, which may be responsible for the large cell size of members of this species, as well as genes for gas vesicles, a second β-galactosidase gene, and most but not all of the genes needed for genetic competence. Comprehensive analyses of the global Bacillus gene pool showed that only an asymmetric region around the origin of replication was syntenic across the genus. This appears to be a characteristic feature of the Bacillus spp. genome architecture and may be key to their sporulating lifestyle.

Identification of key constituents and structure of the extracellular polymeric substances excreted by Bacillus megaterium TF10 for their flocculation capacity

Extracellular polymeric substances (EPS), a complex high-molecular-weight mixture of polymers excreted by microorganisms and produced from cell lysis, may have a high bioflocculation activity. In this work, the EPS excreted from Bacillus megaterium TF10, which was isolated from a soil sample, were systematically characterized to give insights into the relationship between their specific constituents and structure with their flocculation capacity. The results of microscopic observation, zeta potential, and TF10 EPS structure analysis show that the bridging mechanism was mainly responsible for the flocculation of the TF10. The constituents with a large molecular weight (1037-2521 kDA) and functional groups had contributed to the flocculation. GC-MS and NMR analyses demonstrate that the polysaccharides had long chain composed of rhamnose as well as glucose and galactose with uronic acids, acetyl amino sugars, and proteins as the side chains. The proteins in TF10 had no flocculation ability because of their special secondary structure and molecular weight diffusion characters. The EPS from Bacillus megaterium TF10 were found to exhibit a high flocculation activity, and the polysaccharides in EPS, which have the structure of the long backbone with active side chains, were identified as the active constituents for the high flocculation activity.

Bacillus megaterium strain XTBG34 promotes plant growth by producing 2-pentylfuran

Several chemical changes in soil are associated with plant growth-promoting rhizobacteria. An endosporeforming bacterium, strain XTBG34, was isolated from a Xishuangbanna Tropical Botanical Garden soil sample and identified as Bacillus megaterium. The strain's volatiles had remarkable plant growth promotion activity in Arabidopsis thaliana plants; after 15 days treatment, the fresh weight of plants inoculated with XTBG34 was almost 2-fold compared with those inoculated with DH5alpha. Head space volatile compounds produced by XTBG34, trapped with headspace solid phase microextraction and identified by gas chromatography-mass spectrometry, included aldehydes, alkanes, ketones and aroma components. Of the 11 compounds assayed for plant growth promotion activity in divided Petri plates, only 2-pentylfuran increased plant growth. We have therefore identified a new plant growth promotion volatile of B. megaterium XTBG34, which deserves further study in the mechanisms of interaction between plant growth-promoting rhizobacteria and plants.

[Identification, culture optimization and biotransformation of a stevioside-degrading bacterium]

OBJECTIVE

Our study aimed at screening and identifying a specific bacterium capable of degrading stevioside. We also studied the conditions of enzyme production and stevioside conversion.

METHODS

Taxonomic group of the strain was confirmed by physical characterization and phylogenetic analysis by 16S rRNA gene sequence analysis and phylogenetic tree construction of the strain. The optimum conditions of enzyme producing and stevioside degrading were studied by single factor and multi-factor statistical analysis. Degradation product was detected and identified via liquid chromatography-mass spectrometry.

RESULTS

Based on the result of 16S rRNA gene sequence analysis, the strain named J2 shares 100% sequence identity with the sequence of the Bacillus megaterium. The activity of beta-Glucosidase produced by this Bacillus megaterium strain was up to 779.68 U/ml with 4% maize starch, 1% defatted soybean, 0.04% MgSO4 and 0.2% stevioside as culture medium when fermented under the condition of pH 7.0, 37 degrees C, 220 r/min and 10% inoculum for 36 h. The results of conversion showed that 10 mg/ml stevioside can be converted to steviolbioside by 74% after 3 days which has been identified by LC-MS. The ratio of rebaudioside A and stevioside was increased to 0.99 compared to original solution 0.38, which lead to 160.5% increasement of rebaudioside A in the relative amount. Stevioside can be converted completely after 5 days.

CONCLUSION

The isolated strain J2 was identified as Bacillus megaterium. It was a novel and safe strain with high, specific conversion stevioside to steviolbioside ability.

Bacterial degradation and corrosion of naphtha in transporting pipeline

Five naphtha hydrocarbon-degrading bacteria including representative strains of the two classified species (Serratia marcescensAR1, Bacillus pumilusAR2, Bacillus carboniphilus AR3, Bacillus megaterium AR4, and Bacillus cereus AR5) were identified by 16S rDNA gene sequence in a naphtha-transporting pipeline. The naphtha-degrading strains were able to be involved in the corrosion process of API 5LX steel and also utilized the naphtha as the sole carbon source. The biodegradation of naphtha by the bacterial isolates was characterized by gas chromatography-mass spectrometry. Weight-loss measurement on the corrosion of API 5LX steel in the presence/absence of consortia grown in naphtha-water aqueous media was performed. The scanning electron microscope observation showed that the consortia were able to attack the steel API 5LX surface, creating localized corrosion (pit). The biodegradation of naphtha by the strains AR1, AR2, AR3, AR4, and AR5 showed biodegradation efficiency of about 76.21, 67.20, 68.78, 68.78, and 68.15, respectively. The role of degradation on corrosion has been discussed. This basic study will be useful for the development of new approaches for the detection, monitoring, and control of microbial corrosion in a petroleum product pipeline.

Comparative study on central metabolic fluxes of Bacillus megaterium strains in continuous culture using 13C labelled substrates

Fluxes of central carbon metabolism [glycolysis, pentose phosphate pathway (PPP), tricarboxylic acid cycle (TCA cycle), biomass formation] were determined for several Bacillus megaterium strains (DSM319, WH320, WH323, MS941) in C- and N-limited chemostat cultures by (13)C labelling experiments. The labelling patterns of proteinogenic amino acids were analysed by GC/MS and therefrom flux ratios at important nodes within the metabolic network could be calculated. On the basis of a stoichiometric metabolic model flux distributions were estimated for the different B. megaterium strains used at various cultivation conditions. Generally all strains exhibited similar metabolic flux distributions, however, several significant changes were found in (1) the glucose flux entering the PPP via the oxidative branch, (2) the reversibilities within the PPP, (3) the relative fluxes of pyruvate and acetyl-CoA fed to the TCA cycle, (4) the fluxes around the pyruvate node involving a futile cycle.

Isolation of a Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterium from compost, and cloning and characterization of a gene encoding PHB depolymerase ofBacillus megateriumN-18-25-9

A Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterial strain was isolated from compost. This organism, identified as Bacillus megaterium N-18-25-9, produced a clearing zone on opaque NB-PHB agar, indicating the presence of extracellular PHB depolymerase. A PHB depolymerase gene, PhaZ(Bm), of B. megaterium N-18-25-9 was cloned and sequenced, and the recombinant gene product was purified from Escherichia coli. The N-terminal half region of PhaZ(Bm) shared significant homologies with a catalytic domain of other PHB depolymerases. Although the C-terminal half region of PhaZ(Bm) showed no significant similarity with those of other PHB depolymerases, that region was necessary for the PHB depolymerase activity. Therefore, this enzyme's domain structure is unique among extracellular PHB depolymerase domain structures. The addition of PHB to the medium led to a sixfold increase in PhaZ(Bm) mRNA, while the presence of glucose repressed PhaZ(Bm) expression. The maximum activity was observed at pH 9.0 at 65 degrees C.

[New diagnostic methods for bacterial infections after the introduction of increased bioterrorism preparedness]

Bacillus anthracis, Francicella tularensis, Yersinia pestis, Burkholderia pseudomallei and Brucella melitensis are the bacteria most often mentioned in connection with possible biological terrorist acts. It is known that these microorganisms can be cultured and weaponised for such a purpose. This survey provides examples of the use of diagnostic methods for those microorganisms, further detailed in relation to establishing a national center for biological preparedness in Denmark.

Evaluation of microbial strains for linoleic acid hydroxylation and reclassification of strain ALA2

In previous studies, a new microbial strain ALA2 was isolated which produced many new products from linoleic acid [Gardner H.W., Hou C.T., Weisleder D. and Brown W. 2000. Lipids 35: 1055-1060; Hou C.T. 1998. 12,13,17-Trihydroxy-9(Z)-Octodecenoic acid and derivatives and microbial isolate for production of the acid. US Patent No. 5, 852, 196]. Strain ALA2 was preliminary identified as Clavibacter sp. based on its physiological and fatty acid profiles. To determine if strain ALA2 is the optimal strain for industrial applications, other related strains were screened for their abilities to convert linoleic acids. Two strains from Clavibacter and 20 type strains from the phylogenetically related genus Microbacterium were studied. Surprisingly, all of these strains tested showed very little or no activity in converting linoleic acid. On reexamination of the identification of strain ALA2, the sequence of the 16S ribosomal RNA gene of ALA2 was found to be 99% identical to that of Bacillus megaterium and the strain was also found to have 76.3% DNA homology to the B. megaterium type strain. Therefore, strain ALA2 is now reclassified as B. megaterium. Screening of 56 strains of B megaterium strains showed that many of them were able to produce reasonable amounts of hydroxyl fatty acids from linoleic acid, although strain ALA2 possessed the greatest activity.

Pyruvate formation and suppression in recombinant Bacillus megaterium cultivation

A recombinant Bacillus megaterium strain showed the ability to secrete large amounts of pyruvate (up to 27.8 gl( -1)) for growth rates larger than 0.15 h(-1). Cultivation below this growth rate avoids pyruvate formation while minimizing acetate and succinate production. Using exponential feeding, final biomass concentrations of up to 80 g l(-1) were achieved. Overall molar yields for the experiments with pyruvate formation were as high as 0.79 mol mol(-1). Pyruvate formation was caused by the discrepancy between glycolytic and pyruvate dehydrogenase reaction/tricarboxylic acid cycle capacities during glucose excess. High pyruvate resulted in deceleration and subsequent cessation of growth. In addition, this inhibitory effect is likely associated with the phoshoenolpyruvate:glucose phosphotransferase system used by B. megaterium as the main importer for glucose.

Overproduction and secretion of Bacillus circulans endo-beta-1,3-1,4-glucanase gene (bglBC1) in B. subtilis and B. megaterium

A gene coding for endo-beta-1,3-1,4-glucanase (lichenase) containing a recombinant plasmid, pLL200K, was transferred from Bacillus circulans into a new shuttle plasmid, pLLS920, by ligating linearized DNAs of pLL200K and pUB110. B. subtilis RM125 and B. megaterium ATCC14945 transformed with pLLS920 produced the endo-beta-1,3-1,4-glucanase. The enzyme was produced during active growth with maximum activity. The B. subtilis (pLLS920) enzyme was 83 times (8522 mU ml(-1)) more active than that of the gene donor cells (103 mU ml(-1)). The B. megaterium (pLLS920) enzyme was 7 times (735 mU ml(-1)) more active than that of the gene donor cells. While E. coli secreted only about 10% of the produced enzyme, B. subtilis excreted the enzyme completely into the medium and B. megaterium by about 98%. The plasmid pLLS920 was stable in B. megaterium (98%), and in B. subtilis (51%) but not in E. coli (29%).

Nonhemolytic, nonmotile gram-positive rods indicative of Bacillus anthracis

We report a 40-year-old female patient who was admitted to the hospital because of a left ovarian mass torsion. A nonhemolytic, nonmotile Bacillus, suspicious of Bacillus anthracis, was isolated from a blood culture. We discuss the evaluation that led to the final identification of the bacterium as B. megaterium.

Laboratory evolution of a soluble, self-sufficient, highly active alkane hydroxylase

We have converted cytochrome P450 BM-3 from Bacillus megaterium (P450 BM-3), a medium-chain (C12-C18) fatty acid monooxygenase, into a highly efficient catalyst for the conversion of alkanes to alcohols. The evolved P450 BM-3 exhibits higher turnover rates than any reported biocatalyst for the selective oxidation of hydrocarbons of small to medium chain length (C3-C8). Unlike naturally occurring alkane hydroxylases, the best known of which are the large complexes of methane monooxygenase (MMO) and membrane-associated non-heme iron alkane monooxygenase (AlkB), the evolved enzyme is monomeric, soluble, and requires no additional proteins for catalysis. The evolved alkane hydroxylase was found to be even more active on fatty acids than wild-type BM-3, which was already one of the most efficient fatty acid monooxgenases known. A broad range of substrates including the gaseous alkane propane induces the low to high spin shift that activates the enzyme. This catalyst for alkane hydroxylation at room temperature opens new opportunities for clean, selective hydrocarbon activation for chemical synthesis and bioremediation.

[Studies on reduction of Au3+ by bacteria for preparing gold catalyst]

The strain D01, screened from different source bacterial strains, has relatively strong ability of adsorbing Au3+. The strain D01 was identified as Bacillus megatherium D01 and still grew well in the medium containing 600 mg/L Au3+. The results of electrochemical reaction indicated that the strain D01 had a strong ability of reduction. It could reduce the Au3+/alpha-Fe2O3(precursor of the gold catalyst) to highly dispersive Au0/alpha-Fe2O3 catalyst which could catalyze the reaction of CO + O2-->CO2.

Sequencing and phylogenetic analysis of the spoIIA operon from diverse Bacillus and Paenibacillus species

In order to clone the spoIIA operon from three different Bacillus and Paenibacillus species, we designed two sets of PCR primers based on three previously published Bacillus spoIIA sequences. One set of primers corresponded to the C-terminal region of SpoIIAB and a region near the middle of SpoIIAC. These primers were used to amplify the corresponding region of spoIIA from Bacillus stearothermophilus and Paenibacillus polymyxa (previously called Bacillus polymyxa [see Ash, C., Priest, F.G., Collins, M.D., 1993. Molecular identification of ribosomal-RNA group 3 bacilli using a PCR probe test - proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 64, 253-260]. The other set of primers, corresponding to an N-terminal and a C-terminal region of SpoIIAC, was used for B. sphaericus. The PCR products were used as probes for Southern blotting of homologous chromosomal DNA. DNA corresponding to spoIIA from the three organisms was identified by screening chromosomal DNA libraries, and cloned. Sequence analysis showed that all spoIIA sequences were conserved, but conservation was strongest in SpoIIAC and least strong in SpoIIAA. In the promoter the -35 region was conserved well but the -10 region rather poorly. Within the proteins, certain regions were particularly strongly conserved, suggesting that they are essential to the function of the protein. Phylogenetic analysis of spoIIA suggested that B. stearothermophilus is close to B. subtilis and B. licheniformis, but that P. polymyxa and B. sphaericus are remote from B. subtilis.

An assessment of taxonomic congruence between DNA-DNA hybridization and pyrolysis gas-liquid chromatographic classifications

The existence of subgroups within Bacillus megaterium has been reported previously on the basis of DNA-DNA hybridization and DNA base composition studies. In this study the strains used to define these subgroups have been reanalysed by pyrolysis gas-liquid chromatography. The resultant two-group classification of the test strains was directly comparable with that obtained from the previous nucleic acid analyses at the between-group level. However, comparisons of the test strains at the within-group level proved less successful.

Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells

Examination of collections of 16S rRNA sequences revealed sequence domains that were unique to (and invariant within) the three primary lines of cellular descent: the archaebacteria, the eubacteria, and the eucaryotes. Oligodeoxynucleotides complementary to these conserved sequence domains were synthesized and used as hybridization probes. Each of the radiolabeled probes specifically hybridized to nylon membrane-bound 16S rRNA from the targeted kingdom. A probe complementary to a universally conserved sequence in 16S rRNAs was used as a positive control, while its complement provided a negative control for nonspecific binding. The abilities of the probes to bind specifically to whole, fixed cells representing a broad array of phylogenetic diversity were tested in whole-cell dot blot assays. Again, all of the probes specifically bound the targeted groups. By microautoradiography, the method was extended to permit phylogenetic identification of single cells microscopically.

Identification of Bacillus strains using the API system

A system is described for the rapid and accurate identification of Bacillus isolates using a matrix of results from tests in the API 20E and API 50CHB strips and from supplementary tests. API System tests have been shown to be more reproducible than the classical tests. A taxonomy based upon API tests is in good agreement with those obtained by other methods. The results matrix can also be used in computer assisted identification.

Host-range and partial characterization of several new bacteriophages for Bacillus megaterium QM b1551

Several phages infecting Bacillus megaterium QM B1551 have been isolated from the soil and partially characterized. These phages, designated MP9 to MP50, were tested for host-range on several strains of B. megaterium and 13 other Bacillus species. All the phages only infected B. megaterium and on the basis of host-range patterns, 23 groups could be distinguished. The phage patterns also distinguished subgroups of B. megaterium strains within the species and should be useful in phage typing. The phages have varying sensitivities to heat, salts and organic solvents and are all double-stranded DNA phages. Thirty-two have been examined by electron microscopy and are Bradley types A, B and C. This is the first large collection of B. megaterium phages that has been characterized.