Antibacterial metabolites synthesized by psychrotrophic bacteria isolated from cold-freshwater environments

The ability of three psychrotrophic Gram-negative bacilli isolated from Chilean Patagonian cold freshwater rivers to produce bioactive metabolites was evaluated. The strains were isolated from cold waters rivers and identified by their biochemical properties and 16S rRNA gene analysis. The metabolites fractions showing antibacterial activity were obtained by solvent extraction and partially characterized by gas–mass chromatography (GC-MS). Antibacterial activity of the fractions was evaluated by an agar-well diffusion test upon 14 bacterial strains, both Gram positive and Gram negative. Thermal and proteolytic resistances of the antibacterial metabolites fractions were also evaluated. Molecular analysis allows the identification of the three Patagonian strains as Pseudomonas sp. RG-6 (Pseudomonas brenneri 99.6 % identity), Pseudomonas sp. RG-8 (Pseudomonas trivialis 99.6 % identity) and Yersinia sp. RP-3 (Yersinia aldovae 99.5 % identity). These extracts were able to inhibit both Gram-positive and Gram-negative bacteria but not Listeria monocytogenes. The antibacterial activity of the filtrated supernatants was lost at temperatures ≥60 °C, and was not affected by proteinase K treatment. The chemical structure of the active molecule remains to be elucidated, although the GC-MS analysis of the filtrates suggests that compounds like sesquiterpenes derivatives from β-maaliene or δ-selinene could be responsible of this antibacterial activity. Pristine cold freshwater streams showed to be interesting sources of metabolites-producing microorganisms with antibacterial activity.     

Plant growth promoting bacteria from Crocus sativus rhizosphere

Present study deals with the isolation of rhizobacteria and selection of plant growth promoting bacteria from Crocus sativus (Saffron) rhizosphere during its flowering period (October–November). Bacterial load was compared between rhizosphere and bulk soil by counting CFU/gm of roots and soil respectively, and was found to be ~40 times more in rhizosphere. In total 100 bacterial isolates were selected randomly from rhizosphere and bulk soil (50 each) and screened for in-vitro and in vivo plant growth promoting properties. The randomly isolated bacteria were identified by microscopy, biochemical tests and sequence homology of V1–V3 region of 16S rRNA gene. Polyphasic identification categorized Saffron rhizobacteria and bulk soil bacteria into sixteen different bacterial species with Bacillus aryabhattai (WRF5-rhizosphere; WBF3, WBF4A and WBF4B-bulk soil) common to both rhizosphere as well as bulk soil. Pseudomonas sp. in rhizosphere and Bacillus and Brevibacterium sp. in the bulk soil were the predominant genera respectively. The isolated rhizobacteria were screened for plant growth promotion activity like phosphate solubilization, siderophore and indole acetic acid production. 50 % produced siderophore and 33 % were able to solubilize phosphate whereas all the rhizobacterial isolates produced indole acetic acid. The six potential PGPR showing in vitro activities were used in pot trial to check their efficacy in vivo. These bacteria consortia demonstrated in vivo PGP activity and can be used as PGPR in Saffron as biofertilizers.This is the first report on the isolation of rhizobacteria from the Saffron rhizosphere, screening for plant growth promoting bacteria and their effect on the growth of Saffron plant.     

Characterization of GP21 and GP12: Two Potential Probiotic Bacteria Isolated from the Gastrointestinal Tract of Atlantic Cod

This study evaluated the probiotic potential of GP21 (Pseudomonas sp.) and GP12 (Psychrobacter sp.), two bacteria isolated from the intestinal tract of a cold-water fish, Atlantic cod. The antagonistic activity of the two intestinal bacteria against two fish pathogens (Vibrio anguillarum and Aeromonas salmonicida subsp. salmonicida) was studied under different physical conditions. Further, their resistance to physiological barriers and their ability to form biofilms were examined. In addition, a test was conducted to confirm that the isolates were not pathogenic to the host fish. The two bacteria exhibited differences in their antagonism to the pathogens. Both were active against V. anguillarum at mildly acidic conditions over a 5-day period. The activity of GP21 against A. salmonicida was greater at pH 7–8. The maximum antagonistic activity was observed at a temperature of 15°C and at a salt concentration of 15 ppt for both the isolates. They did not produce acids, could release siderophores and tolerated both the acidic environment and the bile salts. Their ability to form biofilms was high around 15°C and when iron was supplemented in the medium at 5 μmol l^?1. There was no mortality of fish during the pathogenicity experiment, confirming the safety of both isolates for further applications. Considering the favorable characteristics identified here, it could be concluded that GP21 and GP12 isolated from the gastrointestinal tract of Atlantic cod are potential probiotic candidates.     

A cellulose-decomposing bacterial association

The structure of a cellulose-decomposing bacterial association was described using phenotypic and phylogenetic characteristics. Based on their morphological, physiological, and biochemical characteristics, the bacteria isolated from the association were identified as Sporocytophaga sp., Xanthomonas sp, and Pseudomonas sp. The phylogenetic analysis based on comparison of 16S rRNA gene fragments obtained from the association revealed six bacterial species belonging to the clusters of Alcaligenes sp., Ochrobactrum sp., Sphingomonas sp., Achromobacter sp., Pseudomonas sp., and Flexibacteriaceae (Sporocytophaga).     

Diverse Responses to UV-B Radiation and Repair Mechanisms of Bacteria Isolated from High-Altitude Aquatic Environments

Acinetobacter johnsonii A2 isolated from the natural community of Laguna Azul (Andean Mountains at 4,560 m above sea level), Serratia marcescens MF42, Pseudomonas sp. strain MF8 isolated from the planktonic community, and Cytophaga sp. strain MF7 isolated from the benthic community from Laguna Pozuelos (Andean Puna at 3,600 m above sea level) were subjected to UV-B (3,931 J m⁻²) irradiation. In addition, a marine Pseudomonas putida strain, 2IDINH, and a second Acinetobacter johnsonii strain, ATCC 17909, were used as external controls. Resistance to UV-B and kinetic rates of light-dependent (UV-A [315 to 400 nm] and cool white light [400 to 700 nm]) and -independent reactivation following exposure were determined by measuring the survival (expressed as CFU) and accumulation of cyclobutane pyrimidine dimers (CPD). Significant differences in survival after UV-B irradiation were observed: Acinetobacter johnsonii A2, 48%; Acinetobacter johnsonii ATCC 17909, 20%; Pseudomonas sp. strain MF8, 40%; marine Pseudomonas putida strain 2IDINH, 12%; Cytophaga sp. strain MF7, 20%; and Serratia marcescens, 21%. Most bacteria exhibited little DNA damage (between 40 and 80 CPD/Mb), except for the benthic isolate Cytophaga sp. strain MF7 (400 CPD/Mb) and Acinetobacter johnsonii ATCC 17909 (160 CPD/Mb). The recovery strategies through dark and light repair were different in all strains. The most efficient in recovering were both Acinetobacter johnsonii A2 and Cytophaga sp. strain MF7; Serratia marcescens MF42 showed intermediate recovery, and in both Pseudomonas strains, recovery was essentially zero. The UV-B responses and recovery abilities of the different bacteria were consistent with the irradiation levels in their native environment.     

Isolation and characterization of aerobic,culturable, arsenic-tolerant bacteria from lead–zinc mine tailing in southern China

Bioremediation of arsenic (As) pollution is an important environmental issue. The present investigation was carried out to isolate As-resistant novel bacteria and characterize their As transformation and tolerance ability. A total of 170 As-resistant bacteria were isolated from As-contaminated soils at the Kangjiawan lead–zinc tailing mine, located in Hunan Province, southern China. Thirteen As-resistant isolates were screened by exposure to 260 mM Na₂HAsO₄·7H₂O, most of which showed a very high level of resistance to As⁵⁺ (MIC?≥?600 mM) and As³⁺ (MIC?≥?10 mM). Sequence analysis of 16S rRNA genes indicated that the 13 isolates tested belong to the phyla Firmicutes, Proteobacteria and Actinobacteria, and these isolates were assigned to eight genera, Bacillus, Williamsia, Citricoccus, Rhodococcus, Arthrobacter, Ochrobactrum, Pseudomonas and Sphingomonas. Genes involved in As resistance were present in 11 of the isolates. All 13 strains transformed As (1 mM); the oxidation and reduction rates were 5–30% and 10–51.2% within 72 h, respectively. The rates of oxidation by Bacillus sp. Tw1 and Pseudomonas spp. Tw224 peaked at 42.48 and 34.94% at 120 h, respectively. For Pseudomonas spp. Tw224 and Bacillus sp. Tw133, the highest reduction rates were 52.01% at 48 h and 48.66% at 144 h, respectively. Our findings will facilitate further research into As metabolism and bioremediation of As pollution by genome sequencing and genes modification.     

Gene cloning and biochemical characterization of 4-N-trimethylaminobutyraldehyde dehydrogenase II from Pseudomonas sp. 13CM

The gene encoding 4-N-trimethylaminobutyraldehyde dehydrogenase (TMABaldehyde-DH) from Pseudomonas sp. 13CM, responsible for the conversion of 4-N-trimethylaminobutyraldehyde (TMABaldehyde) to γ-butyrobetaine in the carnitine biosynthesis pathway, isolated by shotgun cloning and expressed in Escherichia coli DH5α. The recombinant TMABaldehyde-DH was purified 19.5 fold to apparent homogeneity by hydrophobic and affinity chromatography and biochemically characterized. The enzyme was found to be a trimer with identical 52 kDa subunits. The isoelectric point was found to be 4.5. Optimum pH and temperature were found respectively as pH 9.5 and 40 °C. The K_m values for TMABaldehyde, 4-dimethylaminobutyraldehyde, and NAD+ were respectively, 0.31, 0.62, and 1.16 mM. The molecular and catalytic properties differed from those of TMABaldehyde-DH I, which was discovered initially in Pseudomonas sp. 13CM. The new enzyme, designated TMABaldehyde-DH II, structural gene was inserted into an expression vector pET24b (+) and over-expressed in E. coli BL21 (DE3) under the control of a T7 promoter. The recombinant TMABaldehyde-DH from Pseudomonas sp. 13CM can now be obtained in large quantity necessary for further biochemical characterization and applications.     

Enrichment and Isolation of Naphthalenesulfonic Acid-Utilizing Pseudomonads

Naphthalenesulfonate-degrading bacteria were obtained by continuous enrichment from a naphthalene-degrading population from sewage. In addition to naphthalene, Pseudomonas sp. A3 can utilize 2-naphthalenesulfonate (2NS) and Pseudomonas sp. C22 can utilize both 1-naphthalenesulfonate (1NS) and 2NS as sole carbon sources. In a mixture of 1NS and 2NS, the former substrate is utilized by strain C22 only after complete consumption of 2NS. During exponential growth, approximately 10% of the organic carbon of naphthalenesulfonates is temporarily excreted. These unidentified metabolites can readily be used by other bacteria, which, by supplying strain C22 with vitamins, allow optimal growth in stable mixed cultures. The degradative capability of Pseudomonas sp. A3 for 2NS was irreversibly lost under nonselective growth conditions and could be transferred from the wild type to a distinguishable cured strain of the wild type.     

Biochemical, molecular characterization and growth promoting effects of phosphate solubilizing Pseudomonas sp. isolated from weeds grown in salt range of Pakistan

Three species of phosphate solubilizing bacteria viz, Pseudomonas mendocina Khsr2, Pseudomonas stutzeri Khsr3 and Pseudomonas putida Khsr4 were isolated from roots of weeds Lactuca dissecta D. Don, Solanum surattense Burm. f and Sonchus arvensis L. respectively growing in Khewra salt range (EC: 2.3 dS m^?1; pH 8.6). Preliminary identification of bacterial isolate was made on the basis of morphological and biochemical characters and confirmed by partial 16S-rRNA gene sequencing. The genetic diversity among the isolates was evaluated by Randomly Amplified Polymorphic DNA finger printing and similarity matrix was measured. All the Pseudomonas sp. were capable of solubilizing phosphate, produced phytohormones: Indole-3-acetic acid, Gibberellic acid, Trans-zeatin riboside and Abscisic acid in culture media and were found to be efficient in stimulating root/shoot length and dry weight and proline contents of Zea mays L (advance germplasm line: Islamabad Gold) seedlings grown under normal and NaCl (20 dS m^?1) stress. The strain Pseudomonas stutzeri Khsr3 appears to be a potential candidate as bio-inoculant for saline fields.     

Pseudomonas aeruginosa and Achromobacter sp.: nitrifying aerobic denitrifiers have a plasmid encoding for denitrifying functional genes

In the present work, novel heterotrophic nitrifying and aerobic denitrifying bacteria have been isolated from greenwater system of coastal aquaculture. Based on the 16S rRNA gene, FAME analysis and biochemical test, the isolates have been identified as Pseudomonas aeruginosa and Achromobacter sp. These have been named as P. aeruginosa strain DBT1BNH3 and Achromobacter sp. strain DBTN3. Denitrifying functional genes such as nitrite reductase (nirS), nitric oxide reductase (qnorB) and nitrous oxide reductase (nosZ) genes have been identified. These strains found to have a 27 kb plasmid coding for nirS and nosZ. The possibility of horizontal transfer of plasmid among Pseudomonadaceae and Alcaligenaceae families in coastal aquaculture has been explored. Further, we have studied combined nitrification and oxygen tolerant denitrification potential in the same isolates.     

Assessment of atrazine decontamination by epiphytic root bacteria isolated from emergent hydrophytes

Aim of the study was to identify atrazine remediating bacteria that can potentially succeed in situ where they encounter varied environmental conditions. Three epiphytic root bacteria, genus Pseudomonas and Arthrobacter, were isolated from rhizoplanes of hydrophytes Acorus calamus, Typha latifolia, and Phragmites karka. Potential of these strains to decontaminate environmentally relevant concentrations of atrazine was determined in liquid atrazine medium (LAM) and Luria-Bertani (LB) medium at varying pH and temperature. There was an increase in decontamination by the strains with time upon exposure to 2.5 to 10 mg l^?1 atrazine over a period of 15 days, notably, in both minimal and nutrient-rich media. Growth in terms of O.D.₆₀₀ and biomass determined during the same period also showed a corresponding surge. Pseudomonas sp. strain AACB mitigated atrazine in a wide range of pH (5 to 8). Pseudomonas sp. strains AACB and TTLB decontaminated >?62% atrazine at 10 °C. All the strains exhibited plant growth–promoting traits in vitro, reported for the first time in the presence of atrazine. Strain AACB exhibits the novel trait of atrazine decontamination under harsh environmental conditions mimicked in lab. Strains isolated in the present study promise success in in situ remediation. Bioreactors and water treatment plants can be designed comprising the hydrophytes and the strains inoculated into their rhizospheres to improve efficacy of the treatment. They can be used to study plant-bacterium mutualistic symbiosis or other interactions occurring during atrazine mitigation.     

Response of Pseudomonas tolaasii,the causal agent of mushroom brown blotch disease to the volatile compounds produced by endofungal bacteria

Volatile organic compounds (VOCs) produced by bacteria have significant potential to control phytopathogens. In this study, the VOCs produced by endofungal bacteria Pseudomonas sp. Bi1, Bacillus sp. De3, Pantoea sp. Ma3 and Pseudomonas sp. De1 isolated from wild growing mushrooms were evaluated in vitro for their antagonistic activity against Pseudomonas tolaasii Pt18, the causal agent of mushroom brown blotch disease. The gas chromatography–mass spectrometry (GC–MS) analysis revealed that strains Pseudomonas sp. Bi1, Pseudomonas sp. De1, Bacillus sp. De3 and Pantoea sp. Ma3 produced eight, sixteen, nine, and twelve VOCs, respectively. All antagonistic endofungal bacteria produced VOCs which significantly reduced brown blotch symptoms on mushroom caps and inhibited the growth of P. tolaasii Pt18 at the varying levels. Scanning electron microscopy revealed severe morphological changes in cells of P. tolaasii Pt18 following exposure to the VOCs of Pseudomonas sp. Bi1 and De1. Furthermore, The VOCs produced by endofungal bacteria significantly reduced swarming, swimming, twitching, chemotaxis motility and biofilm formation by P. tolaasii Pt18 cells, which are essential contributors to pathogenicity. This is to first report about the inhibition effects of VOCs produced by antagonistic bacteria on virulence traits of P. tolaasii. Our findings provide new insights regarding the potential of antibacterial VOCs as a safe fumigant to control mushroom brown blotch disease.

     

Effects of organochlorines on microbial diversity and community structure in Phragmites australis rhizosphere

This study investigated the impacts of an organochlorine (OC, γ-hexachlorocyclohexane and chlorobenzenes) mixture on microbial communities associated to Phragmites australis rhizosphere. Seventy-eight distinct colony morphotypes were isolated, cultivated and analysed by 16S rDNA sequence analysis. Toxicity tests confirmed sensitivity (e.g. Hevizibacter, Acidovorax) or tolerance (e.g. Bacillus, Aeromonas, Pseudomonas, Sphingomonas) of isolates. Rhizosphere analysis by pyrosequencing showed the microbial adaptation induced by OC exposure. Among the most abundant molecular operational taxonomic units, 80 % appeared to be tolerant (55 % opportunist, 25 % unaffected) and 20 % sensitive. P. australis rhizosphere exposed to OCs was dominated by phylotypes related to α-, β- and γ-Proteobacteria. Specific genera were identified which were previously described as chlorinated organic pollutant degraders: Sphingomonas sp., Pseudomonas sp., Devosia sp. and Sphingobium sp. P. australis could be suitable plants to maintain their rhizosphere active microbial population which can tolerate OCs and potentially improve the OC remediation process in part by biodegradation.     

Adhesive properties of predominant bacteria in raw cow’s milk to bovine mammary gland epithelial cells

Various bacteria have been found in raw cow’s milk, and identifying milk microflora and its functions is critical for maintaining cow health and farm hygiene. Although studies on pathogens and spoilage bacteria in milk have been widely reported, the relationship between milk bacteria, including nonpathogenic bacteria, and the bovine udder is poorly understood. We investigated milk microflora over 1 year using a culture-dependent method and culture-independent analysis by denaturing gradient gel electrophoresis. Among 240 isolates, Lactococcus lactis (81/240) was predominant. The predominant genera were Lactococcus, Stenotrophomonas, Microbacterium, Chryseobacterium, Serratia and Pseudomonas. Among seven strains belonging to these predominant genera, two strains of L. lactis (ssp. lactis and ssp. cremoris) exhibited the highest adherence to bovine mammary gland epithelial cells (BMECs) derived from the bovine udder; 3.4 % of the inoculated bacteria adhered to BMECs. This was followed by Serratia sp. (1.6 %), Microbacterium sp. (0.8 %), Stenotrophomonas maltophilia (0.5 %), Pseudomonas sp. (0.3 %) and Chryseobacterium sp. (0.1 %). The two L. lactis isolates exhibited higher adherence to BMECs than type strains and isolates of various origins.     

Screening siderophore producing bacteria as potential biological control agent for fungal rice pathogens in Thailand

Rice (Oryza sativa) is a staple food in Thailand and, in addition, feeds around one half of the world’s population. Therefore, diseases of rice are of special concern. Rice is destroyed by 2 main pathogens, Fusarium oxysporum and Pyricularia oryzae the causative agents of root rot and blast in rice respectively. These pathogens result in low grain yield in Thailand and other Southeast Asian countries. Soil samples were taken from paddy fields in Northern Thailand and bacteria were isolated using the soil dilution plate method on Nutrient agar. Isolation yielded 216 bacterial isolates which were subsequently tested for their siderophore production and effectiveness in inhibiting mycelial growth in vitro of the rice pathogenic fungi; Alternaria sp., Fusarium oxysporum, Pyricularia oryzae and Sclerotium sp., the causal agent of leaf spot, root rot, blast and stem rot in rice. It was found that 23% of the bacteria isolated produced siderophore on solid plating medium and liquid medium, In dual culture technique, the siderophore producing rhizobacteria showed a strong antagonistic effect against the Alternaria (35.4%), Fusarium oxysporum (37.5%), Pyricularia oryzae (31.2%) and Sclerotium sp. (10.4%) strains tested. Streptomyces sp. strain A 130 and Pseudomonas sp. strain MW 2.6 in particular showed a significant higher antagonistic effect against Alternaria sp. while Ochrobactrum anthropi D 5.2 exhibited a good antagonistic effect against F. oxysporum. Bacillus firmus D 4.1 inhibited P. oryzae and Kocuria rhizophila 4(2.1.1) strongly inhibited Sclerotium sp. P. aureofaciens AR 1 was the best siderophore producer overall and secreted hydroxamate type siderophore. This strain exhibits an in vitro antagonistic effect against Alternaria sp., F. oxysporum and P. oryzae. Siderophore production in this isolate was maximal after 15 days and at an optimal temperature of 30°C, yielding 99.96 ± 0.46 μg ml^?1 of siderophore. The most effective isolates were identified by biochemical tests and molecular techniques as members of the Genus Bacillus, Pseudomonas and Kocuria including B. firmus D 4.1, P. aureofaciens AR1 and Kocuria rhizophila 4(2.1.1). The study demonstrated antagonistic activity towards the target pathogens discussed and are thus potential agents for biocontrol of soil borne diseases of rice in Thailand and other countries.     

Beneficial native bacteria improve survival and mycorrhization of desert truffle mycorrhizal plants in nursery conditions

Sixty-four native bacterial colonies were isolated from mycorrhizal roots of Helianthemum almeriense colonized by Terfezia claveryi, mycorrhizosphere soil, and peridium of T. claveryi to evaluate their effect on mycorrhizal plant production. Based on the phylogenetic analysis of the 16S rDNA partial sequence, 45 different strains from 17 genera were gathered. The largest genera were Pseudomonas (40.8 % of the isolated strains), Bacillus (12.2 % of isolated strains), and Varivorax (8.2 % of isolated strains). All the bacteria were characterized phenotypically and by their plant growth-promoting rhizobacteria (PGPR) traits (auxin and siderophore production, phosphate solubilization, and ACC deaminase activity). Only bacterial combinations with several PGPR traits or Pseudomonas sp. strain 5, which presents three different PGPR traits, had a positive effect on plant survival and growth. Particularly relevant were the bacterial treatments involving auxin release, which significantly increased the root-shoot ratio and mycorrhizal colonization. Moreover, Pseudomonas mandelii strain 29 was able to considerably increase mycorrhizal colonization but not plant growth, and could be considered as mycorrhiza-helper bacteria. Therefore, the mycorrhizal roots, mycorrhizosphere soil, and peridium of desert truffles are environments enriched in bacteria which may be used to increase the survival and mycorrhization in the desert truffle plant production system at a semi-industrial scale.     

Antimony-Oxidizing Bacteria Isolated from Antimony-Contaminated Sediment – A Phylogenetic Study

Twelve antimony-resistant bacteria were isolated from sediment collected in the vicinity of an antimony oxide-producing factory in Korea. Eight of these strains were heterotrophic Sb(III)-oxidizing bacteria. Phylogenetic study showed that the Sb(III)-oxidizing bacteria fell within two subdivisions of Proteobacteria. Cupriavidus sp. NL4 and Comamonas sp. NL11 belong to the subdivision β-Proteobacteria. Acinetobacter sp. NL1, Acinetobacter sp. NL12, Pseudomonas sp. NL2, Pseudomonas sp. NL5, Pseudomonas sp. NL6, and Pseudomonas sp. NL10 are the members of the γ-subdivision of the Proteobacteria. Among them, Cupriavidus sp. NL4 completely oxidized 100 μmoles of Sb(III) per liter of medium in 500 h, while the other strains were not able to oxidize all of the Sb(III) in the medium, even with longer incubation. The results imply that diverse bacterial lineages are able to detoxify sites polluted with Sb(III) by oxidizing it to Sb(V), and to contribute to antimony cycling in natural environments.     

Pseudomonas silesiensis sp. nov. strain A3T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence

Microorganisms classified in to the Pseudomonas genus are a ubiquitous bacteria inhabiting variety of environmental niches and have been isolated from soil, sediment, water and different parts of higher organisms (plants and animals). Members of this genus are known for their metabolic versatility and are able to utilize different chemical compounds as a source of carbon, nitrogen or phosphorus, which makes them an interesting microorganism for bioremediation or bio-transformation. Moreover, Pseudomonas sp. has been described as a microorganism that can easily adapt to new environmental conditions due to its resistance to the presence of high concentrations of heavy metals or chemical pollution. Here we present the isolation and analysis of Pseudomonas silesiensis sp. nov. strain A3^T isolated from peaty soil used in a biological wastewater treatment plant exploited by a pesticide packaging company. Phylogenetic MLSA analysis of 4 housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), complete genome sequence comparison (ANIb, Tetranucleotide identity, digital DDH), FAME analysis, and other biochemical tests indicate the A3^T strain (type strain PCM 2856^T = DSM 103370^T) differs significantly from the closest relative species and therefore represents a new species within the Pseudomonas genus. Moreover, bioinformatic analysis of the complete sequenced genome showed that it consists of 6,823,539 bp with a 59.58 mol% G + C content and does not contain any additional plasmids. Genome annotation predicted the presence of 6066 genes, of which 5875 are coding proteins and 96 are RNA genes.     

Nodulation in black locust by the Gammaproteobacteria Pseudomonas sp. and the Betaproteobacteria Burkholderia sp.

Nodulation abilities of bacteria in the subclasses Gammaproteobacteria and Betaproteobacteria on black locust (Robinia pseudoacacia) were tested. Pseudomonas sp., Burkholderia sp., Klebsiella sp., and Paenibacillus sp. were isolated from surface-sterilized black locust nodules, but their nodulation ability is unknown. The aims of this study were to determine if these bacteria are symbiotic. The species and genera of the strains were determined by RFLP analysis and DNA sequencing of 16S rRNA gene. Inoculation tests and histological studies revealed that Pseudomonas sp. and Burkholderia sp. formed nodules on black locust and also developed differentiated nodule tissue. Furthermore, a phylogenetic analysis of nodA and a BLASTN analysis of the nodC, nifH, and nifHD genes revealed that these symbiotic genes of Pseudomonas sp. and Burkholderia sp. have high similarities with those of rhizobial species, indicating that the strains acquired the symbiotic genes from rhizobial species in the soil. Therefore, in an actual rhizosphere, bacterial diversity of nodulating legumes may be broader than expected in the Alpha-, Beta-, and Gammaproteobacteria subclasses. The results indicate the importance of horizontal gene transfer for establishing symbiotic interactions in the rhizosphere.     

Staphylococcus sp. KW-07 contains nahH gene encoding catechol 2,3-dioxygenase for phenanthrene degradation and a test in soil microcosm

We isolated three species of phenanthrene-degrading bacteria from oil-contaminated soils and marine sediment, and assessed the potential use of these bacteria for bioremediation of soils contaminated by polycyclic aromatic hydrocarbons (PAHs). Based on 16S rDNA sequences, these bacteria were Staphylococcus sp. KW-07 and Pseudomonas sp. CH-11 from soil, and Ochrobactrum sp. CH-19 from the marine sediment. By PCR amplification, catechol 2,3-dioxygenase genes (nahH genes) mediating PAH degradation in the chromosome of Staphylococcus sp. KW-07 and Ochrobactrum sp. CH-19, and in plasmid DNA of Pseudomonas sp. CH-11 were detected. All isolates had a similar optimal growth temperature (25 °C) and optimal growth pH (7.0) in a minimal salt medium (MSM) with 0.1% (w/v) phenanthrene as the sole source of carbon and energy. Pseudomonas sp. CH-11 and Staphylococcus sp. KW-07 degraded 90% of added phenanthrene in 3 days and Ochrobactrum sp. CH-19 degraded 90% of the phenanthrene in 7 days under laboratory batch culture conditions. However, Staphylococcus sp. KW-07 was the most effective among the three strains in degradation of phenanthrene in soil. After inoculation of 1 × 10¹¹ cells of Staphylococcus sp. KW-07, over 90% degradation of 0.1% phenanthrene (0.1 g/100 g soil) was achieved after 1 month at 25 °C. The results collectively suggest that the Staphylococcus sp. KW-07 strain isolated may be useful in bioremediation of PAH-contaminated soils.