Biodegradation of selected aminophosphonates by the bacterial isolate Ochrobactrum sp. BTU1

Aminophosphonates, like glyphosate (GS) or metal chelators such as ethylenediaminetetra(methylenephosphonic acid) (EDTMP), are released on a large scale worldwide. Here, we have characterized a bacterial strain capable of degrading synthetic aminophosphonates. The strain was isolated from LC/MS standard solution. Genome sequencing indicated that the strain belongs to the genus Ochrobactrum. Whole-genome classification using pyANI software to compute a pairwise ANI and other metrics between Brucella assemblies and Ochrobactrum contigs revealed that the bacterial strain is designated as Ochrobactrum sp. BTU1. Degradation batch tests with Ochrobactrum sp. BTU1 and the selected aminophosphonates GS, EDTMP, aminomethylphosphonic acid (AMPA), iminodi(methylene-phosphonic) (IDMP) and ethylaminobis(methylenephosphonic) acid (EABMP) showed that the strain can use all phosphonates as sole phosphorus source during phosphorus starvation. The highest growth rate was achieved with AMPA, while EDTMP and GS were least supportive for growth. Proteome analysis revealed that GS degradation is promoted by C-P lyase via the sarcosine pathway, i.e., initial cleavage at the C-P bond. We also identified C-P lyase to be responsible for degradation of EDTMP, EABMP, IDMP and AMPA. However, the identification of the metabolite ethylenediaminetri(methylenephosphonic acid) via LC/MS analysis in the test medium during EDTMP degradation indicates a different initial cleavage step as compared to GS. For EDTMP, it is evident that the initial cleavage occurs at the C-N bond. The detection of different key enzymes at regulated levels, form the bacterial proteoms during EDTMP exposure, further supports this finding. This study illustrates that widely used and structurally more complex aminophosphonates can be degraded by Ochrobactrum sp. BTU1 via the well-known degradation pathways but with different initial cleavage strategy compared to GS.

A new OCH β-lactamase from a Brucella pseudintermedia (Ochrobactrum pseudintermedium) strain isolated from Zophobas morio larvae

OBJECTIVES

OCH class C β-lactamases have been reported in several species belonging to the Brucella genus that were formerly known as Ochrobactrum. Moreover, only one complete genome of Brucella pseudintermedia has been published. In this work, we describe the genome of a B. pseudintermedia strain possessing a new blaOCH gene that was isolated from Zophobas morio larvae.

METHODS

Hybrid whole-genome sequencing analysis (Illumina and Nanopore) was used to identify and characterise the strain (Ops-OCH-23). Phylogenetic analyses based on the 16S rRNA gene sequence and a core-genome alignment were performed to study the relationships among Ops-OCH-23 and deposited genomes. Moreover, all deposited blaOCH genes were compared to the one found in Ops-OCH-23.

RESULTS

Ops-OCH-23 showed a susceptibility profile consistent with the production of AmpC β-lactamase(s). Its genome consisted of two chromosomes, of which one carried the blaOCH gene. Such gene encoded a new class C OCH β-lactamase among the fifteen so far reported. Two plasmids (120-Kb and 59-Kb) without any associated antimicrobial resistance genes were also found. Analysis of 16S rRNA revealed that Ops-OCH-23 shared 100% homology with four deposited B. pseudintermedia strains. Moreover, the core-genome analysis indicated that the closest match (279 ΔSNVs) to Ops-OCH-23 was strain CTOTU49018 isolated from an urban environment in Germany in 2013.

CONCLUSION

We described the second complete genome of a B. pseudintermedia that also encoded a new OCH β-lactamase variant. Overall, this report expands our knowledge regarding this rarely isolated Brucella species that have been reported so far only a few times in human sources.

Ochrobactrum chromiisoli sp. nov., Isolated from Chromium-Contaminated Soil

A Gram-stain-negative, non-spore-forming, flagellated, motile, aerobic, rod-shaped bacteria strain, designated YY2XT, was isolated from chromium-contaminated soil. Phylogenetic analysis based on 16S rRNA gene, recA gene, and whole genome indicated that the strain represented a new member of the genus Ochrobactrum, family Brucellaceae, class Alphaproteobacteria. The phylogenetic trees based on 16 s rRNA gene, revealed that Falsochrobactrum ovis DSM26720T (96.7%), Ochrobactrum gallinifaecis DSM15295T (96.2%), and Pseudochrobactrum asaccharolyticum DSM25619T (96.2%) are the most closely related phylogenetic neighbors of strain YY2XT. The draft genome of YY2XT was approximately 4,650,646 bp in size with a G + C content of 53.0 mol%. Average nucleotide identity and digital DNA-DNA hybridization values among strain YY2XT and the selected Brucellaceae species were 71.4-83.1% and 13.5-42.7%, which are below the recommended cut-off values for species delineation. Growth of strain YY2XT occurred within pH 5-10 (optimum, pH 7-8), 4 ℃-42 °C (optimum, 30 °C), and NaCl concentrations of 0.0-6.0% (optimum, 1.0%). Major quinone system was ubiquinone 10, the major fatty acids were C16:0, C18:1ω7c, and C16:1ω7c and the major polyamines were spermidine and putrescine. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, and four undefined lipids. On the basis of the phenotypic, genotypic and chemotaxonomic traits, strain YY2XT was considered to represent a novel species of the genus Ochrobactrum, for which the name Ochrobactrum chromiisoli sp. nov. is proposed. The type strain is YY2XT (= CCTCC AB 2023035T = JCM 36000T).

If You're Not Confused, You're Not Paying Attention: Ochrobactrum Is Not Brucella

Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.

Biodegradation characteristics and mechanism of quinoline by Ochrobactrum sp. strain C2

A quinoline-degrading strain, C2, which could completely degrade 250 mg/L of quinoline within 24 h, was isolated from coking wastewater. Strain C2 was identified as Ochrobactrum sp. on the basis of 16S rDNA sequence analysis According to 16S rDNA gene sequence analysis, Strain C2 was identified as Ochrobactrum sp. Strain C2 could utilize quinoline as the sole carbon sources and nitrogen sources to grow and degrade quinoline well under acidic conditions. The optimum inoculum concentration, temperature and shaking speed for quinoline degradation were 10%, 30 °C and 150 r/min, respectively. The degradation of quinoline at low concentration by the strain followed the first-order kinetic model. The growth process of strain C2 was more consistent with the Haldane model than the Monod model, and the kinetic parameters were: Vmax = 0.08 h^-1, Ks = 131.5 mg/L, Ki = 183.1 mg/L. Compared with suspended strains, strain C2 immobilized by sodium alginate had better degradation efficiency of quinoline and COD. The metabolic pathway of quinoline by Strain C2 was tentatively proposed, quinoline was firstly converted into 2(1H) quinolone, then the benzene ring was opened with the action of catechol 1,2-dioxygenase and subsequently transformed into benzaldehyde, 2-pentanone, hydroxyphenyl propionic acid and others.

Efficient gene targeting in soybean using Ochrobactrum haywardense-mediated delivery of a marker-free donor template

Gene targeting (GT) for precise gene insertion or swap into pre-defined genomic location has been a bottleneck for expedited soybean precision breeding. We report a robust selectable marker-free GT system in soybean, one of the most economically important crops. An efficient Oh H1-8 (Ochrobactrum haywardense H1-8)-mediated embryonic axis transformation method was used for the delivery of CRISPR-Cas9 components and donor template to regenerate T0 plants 6-8 weeks after transformation. This approach generated up to 3.4% targeted insertion of the donor sequence into the target locus in T0 plants, with ∼ 90% mutation rate observed at the genomic target site. The GT was demonstrated in two genomic sites using two different donor DNA templates without the need for a selectable marker within the template. High-resolution Southern-by-Sequencing analysis identified T1 plants with precise targeted insertion and without unintended plasmid DNA. Unlike previous low-frequency GT reports in soybean that involved particle bombardment-mediated delivery and extensive selection, the method described here is fast, efficient, reproducible, does not require a selectable marker within the donor DNA, and generates nonchimeric plants with heritable GT.

Development of an efficient marker-free soybean transformation method using the novel bacterium Ochrobactrum haywardense H1

We have discovered a novel bacterium, Ochrobactrum haywardense H1 (Oh H1), which is capable of efficient plant transformation. Ochrobactrum is a new host for Agrobacterium-derived vir and T-DNA-mediated transformation. Oh H1 is a unique, non-phytopathogenic species, categorized as a BSL-1 organism. We engineered Oh H1 with repurposed Agrobacterium virulence machinery and demonstrated Oh H1 can transform numerous dicot species and at least one monocot, sorghum. We generated a cysteine auxotrophic Oh H1-8 strain containing a binary vector system. Oh H1-8 produced transgenic soybean plants with an efficiency 1.6 times that of Agrobacterium strain AGL1 and 2.9 times that of LBA4404Thy-. Oh H1-8 successfully transformed several elite Corteva soybean varieties with T0 transformation frequency up to 35%. In addition to higher transformation efficiencies, Oh H1-8 generated high-quality, transgenic events with single-copy, plasmid backbone-free insertion at frequencies higher than AGL1. The SpcN selectable marker gene is excised using a heat shock-inducible excision system resulting in marker-free transgenic events. Approximately, 24.5% of the regenerated plants contained only a single copy of the transgene and contained no vector backbone. There were no statistically significant differences in yield comparing T3 null-segregant lines to wild-type controls. We have demonstrated that Oh H1-8, combined with spectinomycin selection, is an efficient, rapid, marker-free and yield-neutral transformation system for elite soybean.

Enzyme-catalyzed biodegradation of penicillin fermentation residues by β-lactamase OtLac from Ochrobactrum tritici

BACKGROUND

Biodegradation of antibiotics is a promising method for the large-scale removal of antibiotic residues in the environment. However, the enzyme that is involved in the biodegradation process is the key information to be revealed.

RESULTS

In this study, the beta-lactamase from Ochrobactrum tritici that mediates the biodegradation of penicillin V was identified and characterized. When searching the proteins of Ochrobactrum tritici, the β-lactamase (OtLac) was identified. OtLac consists of 347 amino acids, and predicted isoelectric point is 7.0. It is a class C β-lactamase according to BLAST analysis. The coding gene of OtLac was amplified from the genomic DNA of Ochrobactrum tritici. The OtLac was overexpressed in E. coli BL21 (DE3) and purified with Ni2+ column affinity chromatography. The biodegradation ability of penicillin V by OtLac was identified in an in vitro study and analyzed by HPLC. The optimal temperature for OtLac is 32 ℃ and the optimal pH is 7.0. Steady-state kinetics showed that OtLac was highly active against penicillin V with a Km value of 17.86 μM and a kcat value of 25.28 s-1 respectively.

CONCLUSIONS

OtLac demonstrated biodegradation activity towards penicillin V potassium, indicating that OtLac is expected to degrade penicillin V in the future.

A comparative analysis of heavy metal bioaccumulation and functional gene annotation towards multiple metal resistant potential by Ochrobactrum intermedium BPS-20 and Ochrobactrum ciceri BPS-26

The present study describes the heavy metal bioaccumulation potential of Ochrobactrum intermedium BPS-20 and Ochrobactrum ciceri BPS-26. A total of 27 isolates were retrieved from the soils of industrial areas and these two were selected based on their maximum metal tolerance. They can resist up to 2400 mg/L and 2000 mg/L of Lead and 850 mg/L and 1200 mg/L of Nickel respectively. The atomic absorption spectroscopic analysis showed considerably good bioaccumulation by O. intermedium BPS-20 (85.34% and 74.87%) and O. ciceri BPS-26 (71.20% and 88.48%) for Lead and Nickel respectively. The growth rate studies also demonstrated no inhibitory effects of heavy metals in the medium. Further the SEM analysis showed the presence of extracellular polymeric substances around bacterial cells. Moreover, the functional gene annotation confirmed the presence of ATPase, ABC, and HoxN/HupN/NixA families of transporters. Thus, both the isolates provide a better solution for the removal of metal pollutants.

Characterization of novel thorium tolerant Ochrobactrum intermedium AM7 in consort with assessing its EPS-Thorium binding

Currently, radioactive waste is disposed primarily by burial in a deep geological repository. Microorganisms thriving in such contaminated environment show tolerance to radionuclides. In the present study the bacterial flora, from soil sample collected from an area around atomic power station exposed to radionuclides and heavy metals, was cultivated and assessed for thorium (Th) tolerance. Of all the isolates, strain AM7 identified as O. intermedium was selected since it could thrive at high levels of Th (1000 mg L^-1). AM7 was characterized physico-chemically and its culture medium was optimized using central composite design of response surface methodology for assessing its growth properties in presence of Th. The strain also showed exceptional exopolysaccharide (EPS) production and its yield was further analyzed using one factor study to investigate the influence of each medium component. On supplementing the EPS medium with Th, no significant decrease in yield was observed. FTIR spectroscopy revealed the functional groups of EPS involved in EPS-Th binding. To the best of our knowledge, this is the first report showing exceptional Th-tolerance by any bacteria. Such study will help other researchers to strategize an environment-friendly way of radwaste disposal.

Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp

The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.

Ochrobactrum cytisi IPA7.2 promotes growth of potato microplants and is resistant to abiotic stress

Bacteria in natural associations with agricultural crops are promising for use in the improvement of clonal micropropagation of plants. We clarified the taxonomic position of Ochrobactrum cytisi strain IPA7.2 and investigated its tolerance for salinity, high temperature, and glyphosate pollution. We also tested the strain's potential to promote the growth of potato (Solanum tuberosum L.) microplants. Using the IPA7.2 draft genome (no. NZ_MOEC00000000), we searched for housekeeping genes and also for the target genes encoding glyphosate tolerance and plant-growth-promoting ability. A multilocus sequence analysis of the gap, rpoB, dnaK, trpE, aroC, and recA housekeeping genes led us to identify isolate IPA7.2 as O. cytisi. The strain tolerated temperatures up to 50 °C and NaCl concentrations up to 3-4%, and it produced 8 µg ml-1 of indole-3-acetic acid. It also tolerated 6 mM glyphosate owing to the presence of type II 5-enolpyruvylshikimate-3-phosphate synthase. Finally, it was able to colonize the roots and tissues of potato microplants, an ability preserved by several generations after subculturing. We identified the development phase of potato microplants that was optimal for inoculation with O. cytisi IPA7.2. Inoculation of in vitro-grown 15-day-old microplants increased the mitotic index of root meristem cells (by 50%), the length of shoots (by 34%), the number of leaves (by 7%), and the number of roots (by 16%). Under ex vitro conditions, the inoculated plants had a greater leaf area (by 77%) and greater shoot and root dry weight (by 84 and 61%, respectively) than did the control plants. We recommend O. cytisi IPA 7.2 for use in the growing of potato microplants to improve the production of elite seed material.

Biodegradation of bispyribac sodium by a novel bacterial consortium BDAM: Optimization of degradation conditions using response surface methodology

Bispyribac sodium (BS), is a selective, systemic and post emergent herbicide used to eradicate grasses and broad leaf weeds. Extensive use of this herbicide has engendered serious environmental concerns. Hence it is important to develop strategies for bioremediation of BS in a cost effective and environment friendly way. In this study a bacterial consortium named BDAM, comprising three novel isolates Achromobacter xylosoxidans (BD1), Achromobacter pulmonis (BA2), and Ochrobactrum intermedium (BM2), was developed by virtue of its potential for degradation of BS. Different culture conditions (temperature, pH and inoculum size) were optimized for degradation of BS by the consortium BDAM and the mutual interactions of these parameters were analysed using a 2³ full factorial central composite design (CCD) based on Response Surface Methodology (RSM). The optimal values for temperature, pH and inoculum size were found to be 40 °C, 8 and 0.4 g/L respectively to achieve maximum degradation of BS (85.6%). Moreover, the interactive effects of these parameters were investigated using three dimensional surface plots in terms of maximum fitness function. Importantly, it was concluded that the newly developed consortium is a potential candidate for biodegradation of BS in a safe, cost-effective and environmentally friendly manner.

Identification and analysis of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene from glyphosate-resistant Ochrobactrum intermedium Sq20

BACKGROUND

Glyphosate is a herbicide that acts by inhibition of the enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), involved in the catalysis of an essential step in the biosynthesis of aromatic amino acids. The objective of this study was the isolation of glyphosate-resistant bacterial strains and subsequent characterization of the gene(s) encoding glyphosate resistance in these isolates. Using an enrichment culture technique, a glyphosate-resistant bacterium, Ochrobactrum intermedium Sq20 was isolated from glyphosate-contaminated indigenous soil and characterized.

RESULTS

An open reading frame (ORF) comprising of 1353 bp potentially encoding aroAO. intermediumSq20 was amplified from O. intermedium Sq20. It showed 97% homology with aroA genes from other Ochrobactrum spp. Physicochemical characterization revealed that aroAO. intermediumSq20 encodes a polypeptide of 450 amino acids with a calculated molecular mass of 48.9782 kDa and an isoelectric point of 5.21. Secondary structure prediction of AroAO. intermediumSq20 demonstrated a high percentage of random coils and α helices. Methodical optimization and validation of the protein structure helped to build a reliable protein model indicating the presence of 91.8% amino acid residues in most favoured regions. In addition, strain Sq20 was found to be capable of complete degradation of glyphosate at 500 mg L-1 initial concentration as the sole carbon and energy source within 4 days.

CONCLUSION

A glyphosate-resistant bacterial strain O. intermedium Sq20 was discovered. Sequence analysis and structure modelling demonstrated that AroAO. intermediumSq20 closely resembles class II EPSPS and possesses high glyphosate resistance. This provides a good foundation for functional analysis of experimentally derived crystal structures. The cloning and characterization of AroAO. intermediumSq20 will further help in understanding its role at the molecular level and its potential use in the production of glyphosate-resistant transgenic crops. © 2017 Society of Chemical Industry.

Alleviation of drought stress in pulse crops with ACC deaminase producing rhizobacteria isolated from acidic soil of Northeast India

The agricultural crops are often affected by the scarcity of fresh water. Seasonal drought is a major constraint on Northeast Indian agriculture. Almost 80% of the agricultural land in this region is acidic and facing severe drought during the winter period. Apart from classical breeding and transgenic approaches, the application of plant-growth-promoting bacteria (PGPB) is an alternative strategy for improving plant fitness under stressful conditions. The 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing PGPB offer drought stress tolerance by regulating plant ethylene levels. The aim of the present study was to evaluate the consortium effect of three ACC-deaminase producing rhizobacteria - Ochrobactrum pseudogrignonenseRJ12, Pseudomonas sp.RJ15 and Bacillus subtilisRJ46 on drought stress alleviation in Vigna mungo L. and Pisum sativum L. Consortium treatment significantly increase seed germination percentage, root length, shoot length, and dry weight of treated plants. An elevated production of reactive oxygen species scavenging enzymes and cellular osmolytes; higher leaf chlorophyll content; increase in relative water content and root recovery intension were observed after consortium treatment in comparison with the uninoculated plants under drought conditions. The consortium treatment decreased the ACC accumulation and down-regulated ACC-oxidase gene expression. This consortium could be an effective bio-formulator for crop health improvement in drought-affected acidic agricultural fields.

Characterization and genome functional analysis of the DDT-degrading bacterium Ochrobactrum sp. DDT-2

A strain of Ochrobactrum sp. DDT-2 that was capable of degrading DDT as the sole carbon and energy source was isolated and sequenced, and its biodegradation characteristics and metabolism mechanism were examined. The genome sequence of the isolate DDT-2 was composed of 4,630,303bp with a GC content of 55.99% and 4454 coding genes. The degradation rate of DDT by the isolate DDT-2 increased with the increasing substrate concentration (0.1-10mg/l) and temperature (20-40°C). The degradation half-life of DDT in the presence of the isolate DDT-2 at pH7.0 was obviously shorter than those at pH5.0 and 9.0. Potential DDT degradation genes were found in the isolate DDT-2 genome by a BLASTx search against a DDT degradation genes (DDGs) database. A common biodegradation pathway of DDT was proposed based on the combined analysis of genome annotation and mass spectrometry. DDT was initially dechlorinated to form DDD and DDE. Then, it was transformed into DDMU and DDA via dechlorination and carboxylation, and it may ultimately be mineralized to carbon dioxide. The results suggested that the isolate DDT-2 could be useful for the bioremediation of DDT and its metabolite residues.

Genomic and transcriptomic analyses of Agrobacterium tumefaciens S33 reveal the molecular mechanism of a novel hybrid nicotine-degrading pathway

Agrobacterium tumefaciens S33 is able to degrade nicotine via a novel hybrid of the pyridine and pyrrolidine pathways. It can be utilized to remove nicotine from tobacco wastes and transform nicotine into important functionalized pyridine precursors for some valuable drugs and insecticides. However, the molecular mechanism of the hybrid pathway is still not completely clear. Here we report the genome analysis of strain S33 and its transcriptomes grown in glucose-ammonium medium and nicotine medium. The complete gene cluster involved in nicotine catabolism was found to be located on a genomic island composed of genes functionally similar but not in sequences to those of the pyridine and pyrrolidine pathways, as well as genes encoding plasmid partitioning and replication initiation proteins, conjugal transfer proteins and transposases. This suggests that the evolution of this hybrid pathway is not a simple fusion of the genes involved in the two pathways, but the result of a complicated lateral gene transfer. In addition, other genes potentially involved in the hybrid pathway could include those responsible for substrate sensing and transport, transcription regulation and electron transfer during nicotine degradation. This study provides new insights into the molecular mechanism of the novel hybrid pathway for nicotine degradation.

The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs

The genus Brucella comprises various species of both veterinary and human medical importance. All species are genetically highly related to each other, sharing intra-species average nucleotide identities (ANI) of > 99%. Infections occur among various warm-blooded animal species, marine mammals, and humans. Until recently, amphibians had not been recognized as a host for Brucella. In this study, however, we show that novel Brucella species are distributed among exotic frogs worldwide. Comparative recA gene analysis of 36 frog isolates from various continents and different frog species revealed an unexpected high genetic diversity, not observed among classical Brucella species. In phylogenetic reconstructions the isolates consequently formed various clusters and grouped together with atypical more distantly related brucellae, like B. inopinata, strain BO2, and Australian isolates from rodents, some of which were isolated as human pathogens. Of one frog isolate (10RB9215) the genome sequence was determined. Comparative genome analysis of this isolate and the classical Brucella species revealed additional genetic material, absent from classical Brucella species but present in Ochrobactrum, the closest genetic neighbor of Brucella, and in other soil associated genera of the Alphaproteobacteria. The presence of gene clusters encoding for additional metabolic functions, flanked by tRNAs and mobile genetic elements, as well as by bacteriophages is suggestive for a different ecology compared to classical Brucella species. Furthermore it suggests that amphibian isolates may represent a link between free living soil saprophytes and the pathogenic Brucella with a preferred intracellular habitat. We therefore assume that brucellae from frogs have a reservoir in soil and, in contrast to classical brucellae, undergo extensive horizontal gene transfer.

Microbial degradation of endosulfan in contaminated soil with the elution of surfactants

In this work, an endosulfan-degrading strain was isolated from the aged soil contaminated by endosulfan, and identified as Ochrobactrum sp. EB-4 by 16S rDNA sequence analysis. The microbial degradation characteristics of endosulfan in three eluents (Tween 80 + SDS, Tween 80 + Na2SiO3, Tween 80 + SDS + Na2SiO3) were investigated. The results showed that the degradation percents of α-, β-endosulfan in the three eluents were 86.83 %∼92.91 % and 88.90 %∼93.94 % in 15 days, respectively. The degradation process can be well described by the first-order kinetic model, and the half-times of α-endosulfan in eluent 1∼eluent 3 were 3.83, 5.29, and 4.53 days, while those of β-endosulfan were 3.35, 4.50 and 3.79 days, respectively. The endosulfan diol and endosulfan sulfate as main metabolites were detected, and the former can be further degraded by this strain, which revealed that the simultaneously happened hydrolysis and oxidation reactions were the main degradation processes, and dominated by hydrolysis reaction. After 5 days of washing with the eluents, 56.00∼84.33 % of α-endosulfan, and 46.49∼68.56 % of β-endosulfan in soil were eluted, respectively, and can be entirely biodegraded in 12 days, which indicated that the microbial degradation was the rate-determining step.

Biodegradation of chlorpyrifos and its hydrolysis product 3,5,6-trichloro-2-pyridinol using a novel bacterium Ochrobactrum sp. JAS2: A proposal of its metabolic pathway

Biodegradation of chlorpyrifos and its major metabolite 3,5,6-trichloro-2-pyridinol (TCP) were studied with a novel bacterial strain JAS2 isolated from paddy rhizosphere soil. The molecular characterization based on 16S rRNA gene sequence homology confirmed its identity as Ochrobactrum sp. JAS2. The JAS2 strain degraded 300mgl(-1) of chlorpyrifos within 12h of incubation in the aqueous medium and it produced the TCP metabolite. However, after 72h of incubation TCP was also completely degraded by the JAS2 strain. A tentative degradation pathway of chlorpyrifos by Ochrobactrum sp. JAS2 has been proposed on basis of GC-MS analysis. The complete degradation of chlorpyrifos occurred within 24h in the soil spiked with and without addition of nutrients inoculated with Ochrobactrum sp. JAS2. TCP was obtained in both the studies which was degraded completely by 96h in the soil spiked with nutrients and whereas 120h in absence of nutrients in the soil. The mpd gene which is responsible for organophosphorus hydrolase production was identified. The isolates Ochrobactrum sp. JAS2 also exhibited a time dependent increase in the amount of tricalcium phosphate solubilization in Pikovskaya's medium. Further screening of the strain JAS2 for auxiliary plant growth promoting activities revealed its remarkable capability of producing the indole acetic acid (IAA), hydrogen cyanide (HCN) and ammonia.

Molybdenum-containing nicotine hydroxylase genes in a nicotine degradation pathway that is a variant of the pyridine and pyrrolidine pathways

Ochrobactrum sp. strain SJY1 utilizes nicotine as a sole source of carbon, nitrogen, and energy via a variant of the pyridine and pyrrolidine pathways (the VPP pathway). Several strains and genes involved in the VPP pathway have recently been reported; however, the first catalyzing step for enzymatic turnover of nicotine is still unclear. In this study, a nicotine hydroxylase for the initial hydroxylation step of nicotine degradation was identified and characterized. The nicotine hydroxylase (VppA), which converts nicotine to 6-hydroxynicotine in the strain SJY1, is encoded by two open reading frames (vppAS and vppAL [subunits S and L, respectively]). The vppA genes were heterologously expressed in the non-nicotine-degrading strains Escherichia coli DH5α and Pseudomonas putida KT2440; only the Pseudomonas strain acquired the ability to degrade nicotine. The small subunit of VppA contained a [2Fe-2S] cluster-binding domain, and the large subunit of VppA contained a molybdenum cofactor-binding domain; however, an FAD-binding domain was not found in VppA. Resting cells cultivated in a molybdenum-deficient medium had low nicotine transformation activity, and excess molybdenum was detected in the purified VppA by inductively coupled plasma-mass spectrometry analysis. Thus, it is demonstrated that VppA is a two-component molybdenum-containing hydroxylase.

Ochrobactrum endophyticum sp. nov., isolated from roots of Glycyrrhiza uralensis

A novel Gram-staining negative, motile, rod-shaped and aerobic bacterial strain, designated EGI 60010(T), was isolated from healthy roots of Glycyrrhiza uralensis F. collected from Yili County, Xinjiang Province, North-West China. The 16S rRNA gene sequence of strain EGI 60010(T) showed 97.2 % sequence similarities with Ochrobactrum anthropi ATCC 49188(T) and Ochrobactrum cytisi ESC1(T), and 97.1 % with Ochrobactrum lupini LUP21(T). The phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate clustered with members of the genera Ochrobactrum, and formed a distinct clade in the neighbour-joining tree. Q-10 was identified as the respiratory quinone for strain EGI 60010(T). The major fatty acids were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), C19:0 cyclo ω8c, summed feature 4 (C17:1 iso I/anteiso B) and C16:0. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C content of strain EGI 60010(T) was determined to be 60.4 mol%. The genomic DNA relatedness values determined between strain EGI 60010(T) and the closely related strains O. anthropi JCM 21032(T), O. cytisi CCTCC AB2014258(T) and O. lupini NBRC 102587(T) were 50.3, 50.0 and 41.6 %, respectively. Based on the results of the molecular studies supported by its differentiating phenotypic characteristics, strain EGI 60010(T) was considered to represent a novel species within the genus Ochrobactrum, for which the name Ochrobactrum endophyticum sp. nov., is proposed. The type strain is EGI 60010(T) (=CGMCC 1.15082(T) = KCTC 42485(T) = DSM 29930(T)).

Hyper Accumulation of Arsenic in Mutants of Ochrobactrum tritici Silenced for Arsenite Efflux Pumps

Ochrobactrum tritici SCII24T is a highly As-resistant bacterium, with two previously described arsenic resistance operons, ars1 and ars2. Among a large number of genes, these operons contain the arsB and Acr3 genes that encode the arsenite efflux pumps responsible for arsenic resistance. Exploring the genome of O. tritici SCII24T, an additional putative operon (ars3) was identified and revealed the presence of the Acr3_2 gene that encodes for an arsenite efflux protein but which came to prove to not be required for full As resistance. The genes encoding for arsenite efflux pumps, identified in this strain, were inactivated to develop microbial accumulators of arsenic as new tools for bioremediation. Six different mutants were produced, studied and three were more useful as biotools. O. tritici wild type and the Acr3-mutants showed the highest resistance to As(III), being able to grow up to 50 mM of arsenite. On the other hand, arsB-mutants were not able to grow at concentrations higher than 1 mM As(III), and were the most As(III) sensitive mutants. In the presence of 1 mM As(III), the strain with arsB and Acr3_1 mutated showed the highest intracellular arsenic concentration (up to 17 ng(As)/mg protein), while in assays with 5 mM As(III), the single arsB-mutant was able to accumulate the highest concentration of arsenic (up to 10 ng(As)/mg protein). Therefore, arsB is the main gene responsible for arsenite resistance in O. tritici. However, both genes arsB and Acr3_1 play a crucial role in the resistance mechanism, depending on the arsenite concentration in the medium. In conclusion, at moderate arsenite concentrations, the double arsB- and Acr3_1-mutant exhibited a great ability to accumulate arsenite and can be seen as a promising bioremediation tool for environmental arsenic detoxification.

Antibacterial properties of silver nanoparticles synthesized by marine Ochrobactrum sp

Metal nanoparticle synthesis is an interesting area in nanotechnology due to their remarkable optical, magnetic, electrical, catalytic and biomedical properties, but there needs to develop clean, non-toxic and environmental friendly methods for the synthesis and assembly of nanoparticles. Biological agents in the form of microbes have emerged up as efficient candidates for nanoparticle synthesis due to their extreme versatility to synthesize diverse nanoparticles with varying size and shape. In the present study, an eco favorable method for the biosynthesis of silver nanoparticles using marine bacterial isolate has been attempted. Very interestingly, molecular identification proved it as a strain of Ochrobactrum anhtropi. In addition, the isolate was found to have the potential to form silver nanoparticles intracellularly at room temperature within 24 h. The biosynthesized silver nanoparticles were characterized by UV-Vis spectroscopy, transmission electron microscope (TEM) and scanning electron microscope (SEM). The UV-visible spectrum of the aqueous medium containing silver nanoparticles showed a peak at 450 nm corresponding to the plasmon absorbance of silver nanoparticles. The SEM and TEM micrographs revealed that the synthesized silver nanoparticles were spherical in shape with a size range from 38 nm - 85 nm. The silver nanoparticles synthesized by the isolate were also used to explore its antibacterial potential against pathogens like Salmonella Typhi, Salmonella Paratyphi, Vibrio cholerae and Staphylococcus aureus.

Characteristics of a microcystin-LR biodegrading bacterial isolate: Ochrobactrum sp. FDT5

Mass growth of blue-green algae in eutrophic water bodies leads to a large amount of toxins, e.g. microcystins (MCs). How to remove MCs from water bodies is an environmental problem. In this study, an algicidal bacterium Ochrobactrum sp. FDT5 was isolated and found to have microcystin-LR (MC-LR) degradation capacity, which could be enhanced by a domestication process. The FDT5 cell density, MC-LR initial concentration, temperature, and pH on the degradation of MC-LR were investigated. The results indicated that the initial cell density of FDT5 and the initial concentration of MC-LR could influence MC-LR degradation. The optimum conditions were under the temperature of 35°C with pH of 7.0. After FDT5 was exposed to MC-LR for 2 days, FDT5 cells produced active cellular components that degraded MC-LR. These cellular components were heat-inactivated and removed when FDT5 cells were removed by filtration.

Microbial degradation of acetamiprid by Ochrobactrum sp. D-12 isolated from contaminated soil

Neonicotinoid insecticides are one of the most important commercial insecticides used worldwide. The potential toxicity of the residues present in environment to humans has received considerable attention. In this study, a novel Ochrobactrum sp. strain D-12 capable of using acetamiprid as the sole carbon source as well as energy, nitrogen source for growth was isolated and identified from polluted agricultural soil. Strain D-12 was able to completely degrade acetamiprid with initial concentrations of 0–3000 mg·L⁻¹ within 48 h. Haldane inhibition model was used to fit the special degradation rate at different initial concentrations, and the parameters q_max, K_s and K_i were determined to be 0.6394 (6 h)⁻¹, 50.96 mg·L⁻¹ and 1879 mg·L⁻¹, respectively. The strain was found highly effective in degrading acetamiprid over a wide range of temperatures (25–35°C) and pH (6–8). The effects of co-substrates on the degradation efficiency of acetamiprid were investigated. The results indicated that exogenously supplied glucose and ammonium chloride could slightly enhance the biodegradation efficiency, but even more addition of glucose or ammonium chloride delayed the biodegradation. In addition, one metabolic intermediate identified as N-methyl-(6-chloro-3-pyridyl)methylamine formed during the degradation of acetamiprid mediated by strain D-12 was captured by LC-MS, allowing a degradation pathway for acetamiprid to be proposed. This study suggests the bacterium could be a promising candidate for remediation of environments affected by acetamiprid.

Identification and characterization of the transcriptional regulator ChrB in the chromate resistance determinant of Ochrobactrum tritici 5bvl1

Ochrobactrum tritici 5bvl1 is able to resist to high concentrations of chromate through the expression of an inducible chromate-resistant determinant, found in a mobile element (TnOtChr), which carries the genes, chrB, chrA, chrC and chrF. The regulation of chr operon present in TnOtChr, which is controlled by a transcriptional regulator, ChrB, was characterized in the current work. Fusions of chr promoter, or chr promoter and chrB gene, upstream of a gfp reporter gene, identified the most probable promoter sequence within the tnpR-chrB intergenic region. This region contains an AT-rich imperfect inverted repeat sequence, which overlaps a part of the −10 sequence. The results of the in vitro DNA-binding assays with purified ChrB (His- or no-tagged) showed that the protein binds directly to the chr promoter region. In order to identify the ChrB functional domain for sensing chromate stress and for DNA-binding, site-directed mutagenesis of ChrB was performed. Among several single amino acid mutants, three mutants (R180; R187 and H229) prevented chromate induction without any modification to the protein’s stability. Interestingly, two ChrB mutants (R18 and R23) were constitutively active, regardless of chromate stress conditions, indicating that the residues most probably belong to the protein-DNA binding site. As such, the ChrB was classified as a transcriptional regulator that recognizes a specific DNA sequence, regulating the expression of a chromate resistance determinant.

Highly sensitive, highly specific whole-cell bioreporters for the detection of chromate in environmental samples

Microbial bioreporters offer excellent potentialities for the detection of the bioavailable portion of pollutants in contaminated environments, which currently cannot be easily measured. This paper describes the construction and evaluation of two microbial bioreporters designed to detect the bioavailable chromate in contaminated water samples. The developed bioreporters are based on the expression of gfp under the control of the chr promoter and the chrB regulator gene of TnOtChr determinant from Ochrobactrum tritici 5bvl1. pCHRGFP1 Escherichia coli reporter proved to be specific and sensitive, with minimum detectable concentration of 100 nM chromate and did not react with other heavy metals or chemical compounds analysed. In order to have a bioreporter able to be used under different environmental toxics, O. tritici type strain was also engineered to fluoresce in the presence of micromolar levels of chromate and showed to be as specific as the first reporter. Their applicability on environmental samples (spiked Portuguese river water) was also demonstrated using either freshly grown or cryo-preserved cells, a treatment which constitutes an operational advantage. These reporter strains can provide on-demand usability in the field and in a near future may become a powerful tool in identification of chromate-contaminated sites.

New bacterial strain of the genus Ochrobactrum with glyphosate-degrading activity

Thirty bacterial strains with various abilities to utilize glyphosate as the sole phosphorus source were isolated from farm soils using the glyphosate enrichment cultivation technique. Among them, a strain showing a remarkable glyphosate-degrading activity was identified by biochemical features and 16S rRNA sequence analysis as Ochrobactrum sp. (GDOS). Herbicide (3 mM) degradation was induced by phosphate starvation, and was completed within 60 h. Aminomethylphosphonic acid was detected in the exhausted medium, suggesting glyphosate oxidoreductase as the enzyme responsible for herbicide breakdown. As it grew even in the presence of glyphosate concentrations as high as 200 mM, Ochrobactrum sp. could be used for bioremediation purposes and treatment of heavily contaminated soils.

One-step process for debromination and aerobic mineralization of tetrabromobisphenol-A by a novel Ochrobactrum sp. T isolated from an e-waste recycling site

A novel bacterium, Ochrobactrum sp. T, capable of simultaneous debromination and aerobic mineralization of tetrabromobisphenol-A (TBBPA), was isolated from a sludge sample collected from an electronic-waste recycling site. The bacterium exhibited maximal debrominase activity at pH 6.5, 35 °C, and 200 rpm in Luria-Bertani culture medium. Initial TBBPA concentration and pH had more significant effects on degradation efficiency than those of temperature and inoculum size. Degradation and debromination efficiencies of 91.8% and 86.7%, respectively, were achieved within 72 h under optimized conditions of 35 °C, pH 7.0, inoculum volume of 25 mL, and TBBPA concentration of 3 mg L⁻¹. In addition, a 35.6% decrease in total organic carbon was observed after the degradation of 5 mg L⁻¹ TBBPA for 120 h. Eight metabolic intermediates were identified during the biodegradation of TBBPA. This study is the first report to propose a one-step process for TBBPA debromination and mineralization by a single bacterial strain.

Isolation and characterization of lead-tolerant Ochrobactrum intermedium and its role in enhancing lead accumulation by Eucalyptus camaldulensis

In this study, the potential of rhizospheric bacteria in promoting the growth and Pb accumulation by the woody plant Eucalyptus camaldulensis under hydroponic conditions was investigated for the first time. Three Pb-tolerant bacteria were isolated from the rhizosphere of E. camaldulensis grown in Pb-contaminated soils in the Bo Ngam Pb mine, Thailand. Based on analysis of partial 16S rRNA gene sequence, the three isolates were identified as Microbacterium paraoxydans BN-2, Ochrobactrum intermedium BN-3, and Bacillus fusiformis BN-4. Among these strains, O. intermedium BN-3 showed the highest tolerance to not only Pb but also Cd and Zn. After growth in the presence of Pb, the membranes of O. intermedium BN-3 cells exhibited an increase in unsaturated fatty acid levels but a decrease in fluidity. In hydroponic studies, inoculation of O. intermedium BN-3 significantly increased the biomass and Pb accumulation by E. camaldulensis compared to the uninoculated control. The results suggested the role of the natural rhizospheric bacteria localized to the root surface of E. camaldulensis in promoting Pb accumulation and plant growth. Our results indicate that O. intermedium BN-3 and other indigenous rhizospheric bacteria have the potential to improve the efficiency of phytoremediation of Pb-contaminated sites.

Biodegradation of polycyclic aromatic hydrocarbons by a halotolerant bacterial strain Ochrobactrum sp. VA1

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants in the environment and are derived from both man-made and natural resources. The present study is focused on the degradation of PAHs by a halotolerant bacterial strain under saline conditions. The bacterial strain VA1 was isolated from a PAH-degrading consortium that was enriched from marine water samples that were collected from different sites at Chennai, India. In the present study, a clearing zone formed on PAH-amended mineral salt agar media confirmed the utilization of PAH by the bacterial strain VA1. The results show that the strain VA1 was able to degrade anthracene (88%), phenanthrene (98%), naphthalene (90%), fluorene (97%), pyrene (84%), benzo(k)fluoranthene (57%) and benzo(e)pyrene (50%) at a 30 g/L NaCl concentration. The present study reveals that the VA1 strain was able to degrade PAHs in petroleum wastewater under saline conditions. The promising PAH-degrading halotolerant bacterial strain, VA1, was identified as Ochrobactrum sp. using biochemical and molecular techniques.

Degradation of di-n-butyl phthalate by newly isolated Ochrobactrum sp

A gram negative isolate designated JDC-41 was obtained from river sludge using mixtures of phthalate esters as the sole source and energy. The isolate was identified as Ochrobactrum sp. based on its 16S rRNA gene sequence. Over 87% of supplied di-n-butyl phthalate (DBP) was degraded by JDC-41 in a pH neutral mineral salts medium at 30 degrees C within 48 h. Increased DBP (50-500 mg/L) in the culture correspondingly increased degradation half-life from 3.83 to 18.12 h. DBP induced cells more rapidly degraded DBP.

Electrochemical activation of nitrate reduction to nitrogen by Ochrobactrum sp. G3-1 using a noncompartmented electrochemical bioreactor

A denitrification bacterium was isolated from riverbed soil and identified as Ochrobactrum sp., whose specific enzymes for denitrification metabolism were biochemically assayed or confirmed with specific coding genes. The denitrification activity of strain G3-1 was proportional to glucose/nitrate balance, which was consistent with the theoretical balance (0.5). The modified graphite felt cathode with neutral red, which functions as a solid electron mediator, enhanced the electron transfer from electrode to bacterial cell. The porous carbon anode was coated with a ceramic membrane and cellulose acetate film in order to permit the penetration of water molecules from the catholyte to the outside through anode, which functions as an air anode. A non-compartmented electrochemical bioreactor (NCEB) comprised of a solid electron mediator and an air anode was employed for cultivation of G3-1 cells. The intact G3-1 cells were immobilized in the solid electron mediator, by which denitrification activity was greatly increased at the lower glucose/nitrate balance than the theoretical balance (0.5). Metabolic stability of the intact G3-1 cells immobilized in the solid electron mediator was extended to 20 days, even at a glucose/nitrate balance of 0.1.

Isolation of marine benzo[a]pyrene-degrading Ochrobactrum sp. BAP5 and proteins characterization

A bacterial strain BAP5 with a relatively high degradation ability of benzo[a]pyrene (BaP) was isolated from marine sediments of Xiamen Western Sea, China and identified as Ochrobactrum sp. according to 16S rRNA gene sequence as well as Biolog microbial identification system. Strain BAP5 could grow in mineral salt medium with 50 mg/L of BaP and degrade about 20% BaP after 30 d of incubation. Ochrobactrum sp. BAP5 was able to utilize other polycyclic aromatic hydrocarbons (PAHs) (such as phenanthrene, pyrene and fluoranthene) as the sole carbon source and energy source, suggesting its potential application in PAHs bioremediation. The profile of total soluble protein from Ochrobactrum sp. BAP5 was also investigated. Some over- and special-expressed proteins of strain BAP5 when incubated with the presence of BaP were detected by two-dimensional polyacrylamide gel electrophoresis, and found to be related with PAHs metabolism, DNA translation, and energy production based on peptide fingerprint analysis through matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

Specific detection and differentiation of Ochrobactrum anthropi, Ochrobactrum intermedium and Brucella spp. by a multi-primer PCR that targets the recA gene

Ochrobactrum anthropi, Ochrobactrum intermedium and Brucella spp. are phenotypically and genetically closely related pathogens that may cause disease with similar clinical presentation. Consequently, difficulties in their identification and differentiation have been reported. In this study, a sensitive recA gene-based multi-primer single-target PCR (MP-ST-PCR) was developed that allowed the specific detection and differentiation of these clinically relevant pathogens. The specificity of the assay was evaluated using a representative panel of 50 O. anthropi and 16 O. intermedium strains and the type strains of all Brucella spp. Detection limits for purified DNA from O. anthropi, O. intermedium and Brucella melitensis were 100, 10 and 100 fg, respectively. Brucella DNA was also successfully detected in various clinical specimens from a human patient with culture-proven brucellosis and from a Brucella-infected sheep and its aborted fetuses. The sensitivity of the MP-ST-PCR was comparable to that of an evaluated in-house Brucella real-time PCR assay. The developed assay closes a diagnostic gap and provides a simple but robust tool for the sensitive detection and correct identification of O. anthropi, O. intermedium and Brucella spp.

Isolation of urease-positive Ochrobactrum intermedium in the stomach of a non-ulcer dyspeptic patient from north India

Ochrobactrum intermedium is an opportunistic human pathogen found in immunocompromised individuals. We report the case of a north Indian patient with non-ulcer dyspepsia whose gastric biopsy revealed the presence of O. intermedium, along with Helicobacter pylori. Further description of O. intermedium was performed with 16S rRNA (1500 nucleotides) and RecA (1065 nucleotides) gene sequencing, and the identity and phylogenetic affiliation of the isolate was confirmed by 100% nucleotide similarity with O. intermedium LMG3301. Further investigation is required in order to evaluate the link between H. pylori and O. intermedium in the gastric niche.

Removal of methyl parathion from artificial off-gas using a bioreactor containing a constructed microbial consortium

Methyl parathion (MP), a highly toxic organophosphorus pesticide, was widely used for agriculture crop protection. During the production of MP and the process of MP-containing wastewater treatment, MP can release into the atmosphere and will do great harm to adjacent communities. A consortium comprised of an engineered microorganism and a natural p-nitrophenol (PNP) degrader was assembled for complete mineralization of MP. We genetically engineered Escherichia coli BL21 (DE3) enabling the overexpression of methyl parathion hydrolase (MPH). In addition, we isolated Ochrobactrum sp. strain LL-1 that utilized PNP, a product of MP hydrolysis, as the sole carbon, nitrogen, and energy source. The coculture effectively hydrolyzed 0.2 mM MP and prevented the accumulation of PNP in suspended culture. A laboratory-scale bioreactor containing the dual-species consortium was developed for the treatment of artificial off-gas containing MP. The bioreactor maintained over 98% of average MP removal efficiency over a 75 day period, and PNP produced from hydrolysis of MP was degraded completely, indicating that complete mineralization of MP was achieved. The strategy of linking degrading consortium to a bioreactor may provide an alternative to physicochemical abatement technologies for the treatment of waste-gas streams containing MP as well as other PNP-substituted organophosphates.

[Genotypic and phenotypic similarity between bacteria of Brucella genus and Rhizobiaceae family as a basis for reconsideration of Brucella taxonomy]

Accumulated data on assessment of genome of bacteria from Brucella genus and Rhizobiaceae family (results of sequencing, DNA-rRNA hybridization, 16S rRNA gene sequencing etc.) as well as their phenotypic characteristics (first of all, composition of cell fatty acids) were summarized. Data point to phylogenetic proximity of these bacteria and possibility to unite them in one Rhizobiaceae family together with the closest relatives of Brucella--first of all, with bacteria from Ochrobactrum genus). This seems to be more objective than recreation of Brucellaceae family (Rhizobiales order) with genera Brucella, Ochrobactrum and, possibly, others.

Novel Brucella strain (BO1) associated with a prosthetic breast implant infection

We report the microbiological, biochemical, and molecular characterization of an unusual Brucella strain (BO1) isolated from a breast implant wound in a 71-year-old woman with clinical symptoms consistent with brucellosis. Initial phenotypic analysis, including biochemical and antimicrobial susceptibility testing, cellular fatty acid analysis, and molecular analysis based on DNA-DNA reassociation and the presence of multiple copies of IS711 element suggested that the isolate was a Brucella-like organism, but species determination using microbiological algorithms was unsuccessful. Furthermore, molecular data based on 16S rRNA gene sequencing and multilocus sequence analysis demonstrated that BO1 was an unusual Brucella strain and not closely related to any currently described Brucella species. However, comparison with equivalent sequences in Ochrobactrum spp. confirms that the isolate is much more closely related to Brucella than to Ochrobactrum spp., and thus the isolate likely represents an atypical and novel strain within the genus Brucella.

Degradation of aromatic compounds and degradative pathway of 4-nitrocatechol by Ochrobactrum sp. B2

The potential capacity of a soil methyl parathion-degrading bacterium strain, Ochrobactrum sp. B2, for degrading various aromatic compounds were investigated. The results showed B2 was capable of degrading diverse aromatic compounds, but amino-substituted benzene compounds, at a concentration up to 100 mg L(-1) in 4 days. B2 could use 4-nitrocatechol (4-NC) as a sole carbon and energy source with release of nitrite ion. The pathway for 4-NC degradation via 1,2,4-benzenetriol (BT) and hydroquinone (HQ) formation in B2 was proposed based on the identification and quantification of intermediates by gas chromatography-mass spectrometry (GC-MS), and high performance liquid chromatography (HPLC). Degradation studies carried out on a plasmid-cured derivative showed that the genes for 4-NC degradative pathway was plasmid-borne in B2, suggesting that B2 degrades both p-nitrophenol and 4-NC by enzymes encoded by genes on the same plasmid.

Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain

Two strains named ESC1(T) and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 99.9 % similarity to the respective type strains. Despite this high similarity, the results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum. The DNA-DNA hybridization values were respectively 70, 66 and 55 % with respect to O. lupini LUP21(T), O. anthropi DSM 6882(T) and Ochrobactrum tritici DSM 13340(T). The predominant fatty acids were C(18 : 1)omega7c and C(18 : 1) 2-OH. Strains ESC1(T) and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced beta-galactosidase and beta-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1(T) was 56.4 mol%. Both strains ESC1(T) and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1(T) (=LMG 22713(T)=CECT 7172(T)).

Selection and characterization of aerobic bacteria capable of degrading commercial mixtures of low-ethoxylated nonylphenols

AIMS

Isolation and characterization of new bacterial strains capable of degrading nonylphenol ethoxylates (NPnEO) with a low ethoxylation degree, which are particularly recalcitrant to biodegradation.

METHODS AND RESULTS

Seven aerobic bacterial strains were isolated from activated sludges derived from an Italian plant receiving NPnEO-contaminated wastewaters after enrichment with a low-ethoxylated NPnEO mixture. On the basis of 16S rDNA sequence, the strains were positioned into five genera: Ochrobactrum, Castellaniella, Variovorax, Pseudomonas and Psychrobacter. Their degradation capabilities have been evaluated on two commercial mixtures, i.e. Igepal CO-210 and Igepal CO-520, the former rich in low ethoxylated congeners and the latter containing a broader spectrum of NPnEO, and on 4-n-nonylphenol (NP). The strains degraded Igepal CO-210, Igepal CO-520 and 4-n-NP all applied at the initial concentration of 100 mg l(-1), by 35-75%, 35-90% and 15-25%, respectively, after 25 days of incubation.

CONCLUSIONS

Some of the isolated strains, in particular the Pseudomonas strains BCb12/1 and BCb12/3, showed interesting degradation capabilities towards low ethoxylated NPnEO congeners maintaining high cell vitality.

SIGNIFICANCE AND IMPACT OF THE STUDY

Increased knowledge of bacteria involved in NPnEO degradation and the possibility of using the isolated strains in tailored process for a tertiary biological treatment of effluents of wastewater treatment plants.

Reduction of toxic hexavalent chromium by Ochrobactrum intermedium strain SDCr-5 stimulated by heavy metals

A Cr(VI) resistant bacterial strain SDCr-5, identified as Ochrobactrum intermedium on the basis of 16S rRNA gene sequencing, was tolerant to high concentrations of Cr(VI) up to 15 mg ml(-1) in acetate minimal medium. O. intermedium SDCr-5 reduced Cr(VI) under a wide range of concentrations from 100 to 1500 microg ml(-1) and reduction was optimum at 37 degrees C and pH 7. It reduced 200 and 721 microg ml(-1) Cr(VI) within 72 and 96 h, respectively. The rate of Cr(VI) reduction increased with concentration from 100 to 1500 microg ml(-1). The presence of heavy metal cations such as Cu(2+), Co(2+), Mn(2+) and Ni(2+) stimulated Cr(VI) reduction. Strain SDCr-5 might be useful for Cr(VI) detoxification under a wide range of environmental conditions.

Growth stimulatory effect of Ochrobactrum intermedium and Bacillus cereus on Vigna radiata plants

AIMS

This study assessed the plant growth-promoting ability of the bacterial strains Ochrobactrum intermedium (isolate CrT-1) and Bacillus cereus (isolate S-6).

METHODS AND RESULTS

Two chromium resistant bacterial strains isolated from chromium-contaminated wastewater and soils were identified as O. intermedium CrT-1 and B. cereus S-6. These strains were inoculated on seeds of mungbean Vigna radiata var NM-92, which were germinated and grown under chromate salts (300 microg ml(-1) of CrCl(3)or K(2)CrO(4)). The data show that Cr(VI) was more toxic because of its better availability to plants roots when compared with Cr(III). The major part of Cr(VI) supplied to the seedlings was reduced to Cr(III) in the rhizosphere by the bacterial strains, thus lowering the toxicity of chromium to seedlings.

CONCLUSIONS

Strains have significant Cr(VI) resistance and reduction potential and have ability to enhance mungbean plant growth under chromium stress.

SIGNIFICANCE AND IMPACT OF THE STUDY

These strains could be utilized for the growth of economically important cash crops as well as for the bioremediation of chromium-polluted soils.

[Isolation and characterization of a sodium dodecyl benzene sulfonate degrading bacterial strain]

A bacterial strain, designated as WZR-A, which could utilize sodium dodecyl benzene sulfonate (SDBS) as sole carbon and energy source for growth, was isolated from contaminated river. The strain was identified as Ochrobactrum anthropi based on its morphological and physiological properties, and 16S rDNA sequence analysis. The optimum pH and temperature for cell growth and SDBS degradation were 7.0 and 30 degrees U, respectively. The degradation rate of SDBS by strain WZR-A was higher than 80% when its concentration was lower than 400mg/L. The results of whole cell protein SDS-PAGE electrophoresis showed that there were very obvious differences in the total cell protein composition of the strain between before and after SDBS induction. The enzyme distribution experiment showed that the enzymes relative SDBS degradation in the bacterium was intracellular one. Results from the characterization of degradation substrates together with the detection of activities of relative catabolic enzymes in crude extracts indicated that the aromatic ring cracking of SDBS by the strain probably via the modified ortho cleavage pathway and the strain could use broader spectrum substrates. A large plasmid was detected by utilizing plasmid isolating and curing technique and it was found that the genes involved in SDBS degradation were likely located on the plasmid.

Isolation and characterization of a bacterial strain of the genus Ochrobactrum with methyl parathion mineralizing activity

AIMS

To isolate and characterize a methyl parathion (MP)-mineralizing bacterium, and to elucidate the degradative pathway of MP and localize the responsible degrading genes.

METHODS AND RESULTS

A bacterial strain, designated B2, capable of mineralizing MP was isolated from the MP-polluted soil. Analysis of the 16S rRNA gene sequence and phenotypic analysis suggested that strain B2 had a close relationship with Ochrobactrum anthropi. B2 could totally degrade MP and four metabolites [p-nitrophenol (PNP), 4-nitrocatechol (4-NC), 1,2,4-benzenetriol (BT) and hydroquinone (HQ)] were identified by HPLC and gas chromatography-mass spectrometry analyses. Plasmid curing of strain B2 resulted in the loss of ability of B2 to degrade PNP, but not the ability to hydrolyse MP.

CONCLUSIONS

Ochrobactrum sp. B2 can mineralize MP rapidly via PNP, 4-NC, BT and HQ pathway. B2 harbours a plasmid encoding the ability to degrade PNP, while MP-hydrolysing activity is encoded on the bacterial chromosome.

SIGNIFICANCE AND IMPACT OF THE STUDY

This new bacterial strain (B2) capable of mineralizing MP will be useful in a pure-culture remediation process of organophosphate pesticides and their metabolites such as nitroaromatics.

Evaluation of significance of bacteria in larval development of Cochliomyia macellaria (Diptera: Calliphoridae)

Bacteria were isolated and identified from the digestive tract of the secondary screwworm, Cochliomyia macellaria (F.) (Diptera: Calliphoridae), and their role in the larval development of this insect was assessed in laboratory bioassays. The analysis of 16S rDNA sequences revealed that the bacterial isolates represented four species: Providencia sp., Escherichia coli O157:H7 (Escherich), Enterococcus faecalis (Orla-Jensen), and Ochrobactrum sp. (Holmes). Developmental assays demonstrated that C. macellaria larvae are able to develop on a sterile blood agar, and no bacteria are required to complete larval development. Indeed, developmental times were shorter and survival rates of C. macellaria on a sterile blood agar and the modified Harris rearing diet were greater compared with that on the blood agar inoculated with individual and mixed bacterial isolates. The cultures of Ochrobactrum sp. and E. faecalis supported larval development to a significantly greater extent than those of Providencia sp. and E. coli O157:H7. The presence of bacteria in newly emerged C. macellaria adults also was assessed and revealed that the bacteria in the gut of larvae can survive pupation and colonize the gut of adult flies. This study shows that development of larvae of C. macellaria does not depend on bacteria and that some bacterial isolates negatively impact larval development.

Involvement of coenzyme M during aerobic biodegradation of vinyl chloride and ethene by Pseudomonas putida strain AJ and Ochrobactrum sp. strain TD

The involvement of coenzyme M in aerobic biodegradation of vinyl chloride and ethene in Pseudomonas putida strain AJ and Ochrobactrum sp. strain TD was demonstrated using PCR, hybridization, and enzyme assays. The results of this study extend the range of eubacteria known to use epoxyalkane:coenzyme M transferase.