Microscopic investigations of the Cr(VI) uptake mechanism of living Ochrobactrum anthropi

A basic understanding related to the immobilization of chromium by bacteria is essential for chromate pollutant remediation in the environment. In this work, we studied the Cr(VI) uptake mechanism of living Ochrobactrum anthropi and the influence of a bacterial culture medium on the Cr-immobilization process. It was found that the Cr-immobilization ratio of bacteria in Tris-HCl buffer is higher than in LB medium. X-ray photoelectron spectroscopy (XPS) and electron paramagnetic resonance (EPR) analysis revealed that the chromium accumulated on bacteria were mostly in Cr(III) states. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) observations showed that noticeable Cr(III) precipitates were accumulated on bacterial surfaces. AFM roughness analysis revealed that the surface roughness of bacteria increased greatly when the bacteria-Cr(VI) interaction was in Tris-HCl buffer rather than in LB solution. Transmission electron microscopy (TEM) thin section analysis coupled with energy-dispersive X-ray spectroscopy showed that Cr(III) is also distributed in bacterial inner portions. A chromium-immobilization mechanism considering the participation of both bacterial inner portions and bacterial surfaces of living Ochrobactrum anthropi was proposed, whereas the bacterial surface was the dominant part of the immobilization of Cr(III). This work also proved that the control of Cr immobilization by living Ochrobactrum anthropi could be achieved via adjusting the bacterial culture medium.     

Cross-species characterisation of abundantly expressed Ochrobactrum anthropi gene products.

The identity of 45 protein spots representing 32 orthologues within the Ochrobactrum anthropi proteome within a gradient of pH 4-7, and mass range 5-90 kDa were determined across species boundaries. These proteins could be classified into 13 functional categories and establish metabolic, regulatory and translatory systems including amino acid biosynthesis, electron transport and the potential for plant symbiosis in a molecularly understudied organism. Amino acid composition and/or peptide mass fingerprinting were employed as a means to search the Swiss-Prot and OWL protein sequence databases for similarity within a broad taxonomic class of bacteria. Candidate matches from database searches could be compared and a simple multiplication matrix based on co-occurrence and rank within the top 96 most similar entries was used to provide statistical confidence. This mathematical matrix was evaluated with respect to the characterisation of O. anthropi, an unsequenced and understudied bacterium, in the light of the recent influx of DNA sequence information.     

Effect of Different Energy Sources on Ochrobactrum anthropi Bacteria Chromium Reduction

Ochrobactrum anthropi CTS-325 isolated from a chromium-contaminated site had better resistance to Cr(Ⅵ) in LB medium under aerobic condition.Meanwhile,it was found that the reduction of Cr(Ⅵ) is not complete during the experimental process.Therefore,a series of small molecule energy sources including nitrogen and carbon sources were added into the LB medium in the bacterial stationary phase to promote the chromium reducibility.The result showed that the bacterial growth was positively correlated with the chromium reduction.SDS-PAGE analysis indicated that the protein groups were changed when the bacteria were stimulated by the chromium.Additionally,it was revealed that O.anthropi CTS-325 could utilize the cheaper alternative of sugar(sucrose residue leaching solution) well for further growth and restart the chromium reduction,which offered a new method for practical appli-cations.     

Proteome analysis demonstrates complex replicon and luteolin interactions in pSyma-cured derivatives of Sinorhizobium meliloti strain 2011

Sinorhizobium meliloti was studied by proteomic analysis to investigate the contribution made by plasmid-encoded functions on the intracellular regulation of this bacterium. Protein profiles of strain 2011 were compared with those from its mutant strains which were either cured of their pRme2011a (also called pSyma) plasmid (strain 818), or contained an extensive deletion of this plasmid (strain SmA146). Plasmid pSyma contains the nodulation and nitrogen fixation genes and is 1.4 Mbp with an estimated coding potential of 1,400 proteins. However, under the growth conditions used we could detect 60 differences between the parent strain and its pSyma-cured derivative, strain 818. While the majority of these differences were due to regulatory changes, such as up- and downregulation, some proteins were totally missing in some strains. These 60 proteins were classified into 21 subgroups, A to U, based on their measured protein levels when the cells were grown in the presence or absence of luteolin. Comparisons were made between the different strains to assess the possible interactions of the different proteins of the subgroups and plasmid pSyma. These results suggest that pSyma has a role in the regulation of the expression of genes from the other replicons (3.5 Mbp chromosome and the 1.7 Mbp pSymB plasmid) present in the S. meliloti cells. Proteome analysis provides a sensitive tool to examine the functional organisation of the S. meliloti genome and the intracellular gene interactions between replicons and will provide a powerful analytical tool to complement the genome sequencing of strain 1021.     

Dynamic kinetic resolution of amino acid amide catalyzed by D-aminopeptidase and alpha-amino-epsilon-caprolactam racemase

Amino acid amide racemizing activity was discovered in alpha-amino-epsilon-caprolactam (ACL) racemase (EC 5. 1. 1. 15) from Achromobacter obae. The enzymatic synthesis of d-alanine from l-alanine amide has been demonstrated by use of d-aminopeptidase (DAP; EC 3. 4. 11. 19) from Ochrobactrum anthropi C1-38 and ACL racemase. The conversion of 45 mM l-alanine amide was carried out at 30 degrees C for 7 h; l-alanine amide was completely converted to d-alanine, and no l-alanine was detected. The result of successive enzymatic reaction shows that the combination of ACL racemase and DAP can be applied for dynamic kinetic resolution of dl-amino acid amides to yield d-amino acids.     

Occurence of subtelomeric rearrangements in the genome of the microsporidian parasite Encephalitozoon cuniculi, as revealed by a new fingerprinting procedure based on two-dimensional pulsed field gel electrophoresis

In Microsporidia, mitochondria-lacking eukaryotic intracellular parasites, genomic comparisons were so far based on molecular karyotyping. The mammal-infecting species Encephalitozoon cuniculi is characterized by a very low haploid genome size (approximately 2.8 Mbp) and rather high karyotype variability. Recently, we developed a two-dimensional pulsed field gel electrophoresis (2-D PFGE) fingerprinting technique useful for constructing a restriction map fo the genome of a mouse E. cuniculi isolate (karyotype variant A). The so-called karyotype and restriction display 2-D PFGE (KARD-PFGE) protocol involved 1-D chromosome separation, digestion with a rare cutter, Klenow radiolabeling of genomic DNA and 2-D separation of restriction fragments followed by autoradiography. In order to assess its suitability for detecting polymorphic loci in E. cuniculi, we applied KARD-PFGE with either BssHII or Mlul digestion to genome analysis of two rabbit isolates representative of two different karyotype variants (A and C). The 2-D spot pattern of the rabbit isolate variant A is identical to the reference mouse isolate but differs greatly from the rabbit isolate variant C. Chromosomal restriction fragment length polymorphisms (RFLPs) provide strong evidence for homologous chromosomes and frequent DNA rearrangements within subtelomeric regions just upstream of the dispersed rDNA units closely associated with each chromosomal end.     

Surface Changes of Ochrobactrum Anthropi in Cr（Ⅵ） Treatment for 1 Hour

Bioremediation has been a considerable method for treating Cr（VI） contamination. Bacterial surface changes of Ochrobactrum anthropi during Cr biosorption was investigated in this study. We found that Cr adsorption capacity increased with the increase of initial Cr（Ⅵ） concentration. Atomic force microscope （AFM） morphologic analysis combined with surface roughness analysis indicated that the bacterial surfaces became rougher during Cr uptake process. X-ray photoelectron spectroscopy （XPS） showed that Cr（Ⅲ） was adsorbed on the bacterial surfaces. Fourier transform infrared （FT-IR） analysis showed that surface functional groups including C-O and C-N might be involved in the Cr biosorption process.     

Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase

Ligilactobacillus equi is common in the horse intestine, alleviates the infection of Salmonella, and regulates intestinal flora. Despite this, there have been no genomic studies on this species. Here, we provide the genomic basis for adaptation to the intestinal habitat of this species. We sequenced the genome of L. equi IMAU81196, compared this with published genome information from three strains in NCBI, and analyzed genome characteristics, phylogenetic relationships, and functional genes. The mean genome size of L. equi strains was 2.08 ± 0.09 Mbp, and the mean GC content was 39.17% ± 0.19%. The genome size of L. equi IMAU81196 was 1.95 Mbp, and the GC content was 39.48%. The phylogenetic tree for L. equi based on 1454 core genes showed that the independent branch of strain IMAU81196 was far from the other three strains. In terms of genomic characteristics, single-nucleotide polymorphism (SNP) sites, rapid annotation using subsystem technology (RAST), carbohydrate activity enzymes (CAZy), and predictions of prophage, we showed that strain L. equi JCM 10991^T and strain DSM 15833^T are not equivalent strains.It is worth mentioning thatthestrain of L. equi has numerous enzymes related to cellulose degradation, and each L. equi strain investigated contained at least one protophage. We speculate that this is the reason why these strains are adapted to the intestinal environment of horses. These results provide new research directions for the future.     

Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin

Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from rice plant as the reference. Re-sequencing results revealed that the genome of strain AU6208 comprised 96 contigs corresponding to a 6.1 Mbp genome of the strain AU6208, with 5322 coding sequences and 68.2 % GC content; this is much larger compared to the genome previously sequenced by us and described by Seo et al (2015), which was reported to be 4.1 Mbp comprising >1200 contigs, 4361 coding sequences, and 67.31 % GC content. Moreover, this updated genome shares >80 % identity to the 7.2 Mbp genome of BGR1, which encodes 6491 coding sequences and has 68.3 % GC content. Further computational analysis revealed that the strain AU6208 encodes several bacteriocin biosynthesis genes, antibiotic, as well as virulent genes such as toxoflavin genes, which included 425 specialty genes and 12 toxoflavin genes. Upon further characterization, 12 toxoflavins (ToxA, B, C, D, E, F, G, H, I, J, TofI, and TofR) were found in AU6208 with 70–100 % sequence, family, and domain similarity with that of BGR1. Upon comparison with BGR1, the structural characterizations of selected toxoflavin genes (ToxB, ToxC, ToxG, H, and TofI) revealed variations in 2D and 3D structures such as differences in α-helix, β-sheets, loops, physiological properties of proteins, RMSD values, etc. These variations may play significant role in different mode of action in different hosts thereby indicating that in addition to their respective hosts, toxoflavins could also contribute to exploit other hosts across the kingdom. In addition to understanding the epidemiology of strain AU6208, this updated genomics data will also unfold the pathogenicity of bacteria in diversity of various hosts and anti-virulence.     

Pulsed-field gel electrophoretic analysis of the genome of Lactobacillus gasseri ATCC33323, and construction of a physical map

Some species of Lactobacillus are of major industrial and health significance as fermenting agents in the manufacturing of food products, as food preservatives, as "probiotic" bacteria or as vaccine delivery vehicles. In spite of their importance, there is a paucity of published information on their genome organization and structure. In this study, a combination of pulsed field gel electrophoresis (PFGE) and hybridization approaches was used to investigate the genome of L. gasseri neotype strain ATCC33323. PFGE analysis of chromosomal DNA (after digestion with the rare-cutting restriction enzymes I-CeuI, CspI, SmaI, ApaI, and SgrAI) allowed the chromosome size of L. gasseri to be estimated at 1.96 Mbp, and also revealed the presence of a linear plasmid of 48.5 kbp. A physical map of the L. gasseri chromosome, containing 6 sites for the enzymes I-CeuI and 12 for CspI, was constructed. Placed on the map were the genes dnaA and gyrB (usually located close to the origin of replication on the bacterial chromosome) and 18 ribosomal RNA (rrn) genes. Mapping analysis also revealed that the chromosome contained six rrn operons, and that one of them was inverted in orientation with respect to the others. Each rrn operon contained a single copy of each of the three rrn genes, 23S rRNA (rrl), 16S rRNA (rrs) and 55 rRNA (rrf) gene. The constructed physical map should be a useful foundation for genomic and genetic studies of the lactobacilli and provides a platform for applied research, such as the engineering of Lactobacillus strains with improved characteristics for industrial and probiotic applications.     

Bacterial adhesion to glass and metal-oxide surfaces

Metal oxides can increase the adhesion of negatively-charged bacteria to surfaces primarily due to their positive charge. However, the hydrophobicity of a metal-oxide surface can also increase adhesion of bacteria. In order to understand the relative contribution of charge and hydrophobicity to bacterial adhesion, we measured the adhesion of 8 strains of bacteria, under conditions of low and high-ionic strength (1 and 100 mM, respectively) to 11 different surfaces and examined adhesion as a function of charge, hydrophobicity (water contact angle) and surface energy. Inorganic surfaces included three uncoated glass surfaces and eight metal-oxide thin films prepared on the upper (non-tin-exposed) side of float glass by chemical vapor deposition. The Gram-negative bacteria differed in lengths of lipopolysaccharides on their outer surface (three Escherichia coli strains), the amounts of exopolysaccharides (two Pseudomonas aeruginosa strains), and their known relative adhesion to sand grains (two Burkholderia cepacia strains). One Gram positive bacterium was also used that had a lower adhesion to glass than these other bacteria (Bacillus subtilis). For all eight bacteria, there was a consistent increase in adhesion between with the type of inorganic surface in the order: float glass exposed to tin (coded here as Si-Sn), glass microscope slide (Si-m), uncoated air-side float glass surface (Si-a), followed by thin films of (Co(1-y-z)Fe(y)Cr(z))3O4, Ti/Fe/O, TiO2, SnO2, SnO2:F, SnO2:Sb, A1(2)O3, and Fe2O3 (the colon indicates metal doping, a slash indicates that the metal is a major component, while the dash is used to distinguish surfaces). Increasing the ionic strength from 1 to 100 mM increased adhesion by a factor of 2.0 +/- 0.6 (73% of the sample results were within the 95% CI) showing electrostatic charge was important in adhesion. However, adhesion was not significantly correlated with bacterial charge and contact angle. Adhesion (A) of the eight strains was significantly (P < 10(-25)) correlated with total adhesion free energy (U) between the bacteria and surface (A = 2162e(-1.8U)).Although the correlation was significant, agreement between the model and data was poor for the low energy surfaces (R2 = 0.68), indicating that better models or additional methods to characterize bacteria and surfaces are still needed to more accurately describe initial bacterial adhesion to inorganic surfaces.     

Pulsed-field gel electrophoresis analysis of a Pseudomonas aeruginosa pathovar.

This paper presents the genome organization and mobility of Pseudomonas aeruginosa strains that had been isolated in half-year intervals from 30 patients with cystic fibrosis since the onset of colonization over a 2- to 8-year period. The chromosomes were digested with DraI or SpeI, separated by pulsed-field gel electrophoresis, blotted and hybridized with probes encoding housekeeping or virulence genes. Strains were differentiated by relatedness of macrorestriction fingerprints. After some turnover of strains during the first two years of colonization, each patient had acquired a set of strains that diversified during the course of the disease. In the majority of patients, two clonal lineages were found to account for colonization in the air passages but each lung habitat was characterized by some specific signature of bands in the macrorestriction fragment pattern.     

The Full Structure of the Carbohydrate Chain of the Lipopolysaccharide of Providencia alcalifaciens O19

An oligosaccharide isolated from the lipopolysaccharide of Providencia alcalifaciens O19 was found to consist of a single O‐antigen repeating unit linked to the core. The full oligosaccharide structure was elucidated by 2D ¹H, ¹³C, and ³¹P NMR spectroscopy. It was shown that the inner core region has the same structure as in other Providencia strains studied, whereas the outer core is structurally diverse between Providencia strains. A pyruvic acid acetal was found in the isolated oligosaccharide and in the long‐chain O‐antigen, whose structure has been established earlier. The biological O‐unit structure was elucidated in the short‐chain lipopolysaccharide.     

Enhanced infrared absorption in a comparative study between multi-sensitive and multiresistant bacteria of the genus Klebsiella sp.

We study the infrared spectral profile of bacteria of the genus Klebsiella sp. with respect to sensitivity and resistance. The differentiation between these organisms can properly guide the therapeutic conduct. We processed the samples obtained from the laboratory of Hospital Santos Dumont in a Mac Conckey culture medium. After that, we processed a micromass to provide a thin film for evaluation by FTIR spectroscopy. The pilot study was performed using glass slides and glass slides coated with a copper sheet of 45 μm thickness as support for the samples. After the bibliographical review, we highlight the relationship between the amino acid serine and bacterial resistance in this type of bacteria, which occurs through plasmids. We collected spectra from 50 bacterial strains divided in two groups: 25 sensitive and 25 resistant strains on glass, and 21 sensitive and 21 resistant strains on the copper sheet. We obtained the composition of the samples by evaluating the spectra with multivariate analysis using the second derivative. We concluded that infrared spectroscopy could also be used to identify multiresistant bacteria of the genus Klebsiella sp. by means of the amino acid serine, which can be considered as a marker of resistance found only in multiresistant forms.     

DEVELOPMENT OF COMMON WHEAT GERM-PLASM RESISTANT TO BARLEY YELLOW DWARF VIRUS BY BIOTECHNOLOGY

Barley yellow dwarf virus (BYDV) is one of the most serious wheat diseases in China. So far no resistance has been described in common wheat. A certain level of BYDV resistance was found in thirteen Triticeae species. Thinopyrum intermedium, two octoploids derived from TH. intermedium/wheat, Zhong 4 awnless and TAF46, and one disomic addition line, L1 derived from TAF46, showed good resistance to BYDV by enzyme linked immunosorbent assay (ELISA). Two wheat/TA. intermedium translocation lines, CPI 119880 and CPI 119899, showing good BYDV resistance were developed from L1 by using both CSph mutant and tissue culture. It is found that their BYDV resistance was controlled by a single dominant gene. Two cDNA probes pEleAcc3 and pPJN8 (E1-T1) were screened for detecting Th. intermedium DNA in wheat background. A specific band for the DNA of Th. intermedium and its derivatives was found in Southern hybridization. It is also possible to determine the size of the alien segment by comparing the relative density o     

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 (Aspergillus niger and Paecilomyces lilacinus) and bacteria (Bacillus sp., Paenibacillus polymyxa and Bacillus amyloliquefaciens) 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.     

A device for extraction, manipulation and stretching of DNA from single human chromosomes

We describe the structure and operation of a micro/nanofluidic device in which individual metaphase chromosomes can be isolated and processed without being displaced during exchange of reagents. The change in chromosome morphology as a result of introducing protease into the device was observed by time-lapse imaging; pressure-driven flow was then used to shunt the chromosomal DNA package into a nanoslit. A long linear DNA strand (>1.3 Mbp) was seen to stretch out from the DNA package and along the length of the nanoslit. Delivery of DNA in its native metaphase chromosome package as well as the microfluidic environment prevented DNA from shearing and will be important for preparing ultra-long lengths of DNA for nanofluidic analysis.     

Isolation and Identification of Pentalenolactone Analogs from Streptomyces sp. NRRL S-4

Terpene synthases are widely distributed in Actinobacteria. Genome sequencing of Streptomyces sp. NRRL S-4 uncovered a biosynthetic gene cluster (BGC) that putatively synthesizes pentalenolactone type terpenes. Guided by genomic information, the S-4 strain was chemically investigated, resulting in the isolation of two new sesquiterpenoids, 1-deoxy-8α-hydroxypentalenic acid (1) and 1-deoxy-9β-hydroxy-11-oxopentalenic acid (2), as shunt metabolites of the pentalenolactone (3) biosynthesis pathway. Their structures and absolute configurations were elucidated by analyses of HRESIMS and NMR spectroscopic data as well as time-dependent density functional theory/electronic circular dichroism (TDDFT/ECD) calculations. Compounds 1 and 2 exhibited moderate antimicrobial activities against Gram-positive and Gram-negative bacteria. These results confirmed that the pentalenolactone pathway was functional in this organism and will facilitate efforts for exploring Actinobacteria using further genome mining strategies.