Isolation and characterization of bacteria from the rhizosphere of wheat

In this study, we isolated bacteria from rhizosphere and endorhizophere of wheat crops of the central region of Argentina. The isolates were phenotypically characterized and the restriction patterns of 16S rDNA (ARDRA) using endonuclease AluI were analysed. Representative isolates were used to evaluate the effect of the inoculation on the growth of wheat under greenhouse conditions. The effects of plant growth-promoting bacteria on wheat plants were studied by evaluating shoot fresh and dry weights and root fresh and dry weights. One native strain increased the shoot and root dry biomass by 23% and 45% respectively. Other strains increased the shoot dry biomass. A 1.5 kb fragment of the 16S rRNA gene of one isolate was sequenced. This isolate showed high identity with different species of Pseudomonas.     

Quorum-sensing molecules: Sampling,identification and characterization of N-acyl-homoserine lactone in Vibrio sp

Quorum sensing (QS) is a mechanism by which gram-negative bacteria regulate their gene expression by making use of cell density. QS is triggered by a small molecule known as an autoinducer. Typically, gram-negative bacteria such as Vibrio produce signaling molecules called acyl homoserine lactones (AHLs). However, their levels are very low, making them difficult to detect. We used thin layer chromatography (TLC) to examine AHLs in different Vibrio species, such as Vibrio alginolyticus, Vibrio parahemolyticus, and Vibrio cholerae, against a standard- Chromobacterium violaceum. Further, AHLs were characterised by high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC–MS). C4-HSL (N- butanoyl- L- homoserine lactone), C6-HSL (N- hexanoyl- L- homoserine lactone), 3-oxo-C8-HSL (N-(3-Oxooctanoyl)-DL-homoserine lactone), C8-HSL (N- octanoyl- L- homoserine lactone), C₁10-HSL (N- decanoyl- L- homoserine lactone), C12-HSL (N- dodecanoyl- L- homoserine lactone) and C14-HSL (N- tetradecanoyl- L- homoserine lactone) were identified from Vibrio. These results may provide a basis for blocking the AHL molecules of Vibrio, thereby reducing their pathogenicity and eliminating the need for antimicrobials.     

Isolation and characterization of fenamiphos degrading bacteria

The biological factors responsible for the microbial breakdown of the organophosphorus nematicide fenamiphos were investigated. Microorganisms responsible for the enhanced degradation of fenamiphos were isolated from soil that had a long application history of this nematicide. Bacteria proved to be the most important group of microbes responsible for the fenamiphos biodegradation process. Seventeen bacterial isolates utilized the pure active ingredient fenamiphos as a carbon source. Sixteen isolates rapidly degraded the active ingredient in Nemacur 5GR. Most of the fenamiphos degrading bacteria were Microbacterium species, although Sinorhizobium, Brevundimonas, Ralstonia and Cupriavidus were also identified. This array of gram positive and gram negative fenamiphos degrading bacteria appeared to be pesticide-specific, since cross-degradation toward fosthiazate, another organophosphorus pesticide used for nematode control, did not occur. It was established that the phylogenetical relationship among nematicide degrading bacteria is closer than that to non-degrading isolates.     

Isolation and characterization of bacteria degrading polychlorinated biphenyls from transformer oil

Polychlorinated biphenyls from transformer oil were degraded in liquid culture under aerobic conditions using a mixed bacterial culture isolated from a transformer oil sample with a high content of polychlorinated biphenyls and other hydrocarbons. Four strains were identified, three of them corresponded to genusBacillus, the other one toErwinia. Bacteria in the transformer oil could remove as much as 65% of polychlorinated biphenyls (88%W/V in the transformer oil). Additional data showed that the two isolated strains ofB. lentus were able to grow on transformer oil and degrade polychlorinated biphenyls by 80 and 83%. Our results provide evidence that microorganisms occurring in transformer oil have the potential to degrade polychlorinated biphenyls.     

Isolation and characterization of lignin‐degrading bacteria from rainforest soils

The deconstruction of lignin to enhance the release of fermentable sugars from plant cell walls presents a challenge for biofuels production from lignocellulosic biomass. The discovery of novel lignin‐degrading enzymes from bacteria could provide advantages over fungal enzymes in terms of their production and relative ease of protein engineering. In this study, 140 bacterial strains isolated from soils of a biodiversity‐rich rainforest in Peru were screened based on their oxidative activity on ABTS, a laccase substrate. Strain C6 (Bacillus pumilus) and strain B7 (Bacillus atrophaeus) were selected for their high laccase activity and identified by 16S rDNA analysis. Strains B7 and C6 degraded fragments of Kraft lignin and the lignin model dimer guaiacylglycerol‐β‐guaiacyl ether, the most abundant linkage in lignin. Finally, LC–MS analysis of incubations of strains B7 and C6 with poplar biomass in rich and minimal media revealed that a higher number of compounds were released in the minimal medium than in the rich one. These findings provide important evidence that bacterial enzymes can degrade and/or modify lignin and contribute to the release of fermentable sugars from lignocellulose. Biotechnol. Bioeng. 2013; 110: 1616–1626. © 2013 Wiley Periodicals, Inc.     

Growth and yield of potato plants inoculated with rhizosphere bacteria

Pot and field experiments on small plots were carried out to study the effect of isolates ofPseudomonas fluorescens-putida bacteria, applied to potato tubers, on the growth response of potato plants. Inoculation of tuber pieces with the isolates in pot experiments caused a better growth of young potato plant (111 % increase). The effect depended on the viable count in the bacterial suspension and on growth conditions of the plants. Inoculation of potato seed pieces before planting in field experiments caused a 4 –30 % improvement in plant growth and tuber yield. The complex action of inoculation with rhizobacteria apparently caused changes in the microflora colonizing the roots and stolons, which in turn brought about a better growth and yield.     

Performance evaluation of potent phosphate solubilizing bacteria in potato rhizosphere

Three phosphate solubilizing bacterial isolates identified as Pantoea agglomerans strain P5, Microbacterium laevaniformans strain P7 and Pseudomonas putida strain P13 were assessed for mutual relationships among them, competitiveness with soil microorganisms and associations with plant root using luxAB reporter genes for follow-up studies. Synergism between either P. agglomerans or M. laevaniformans, as acid-producing bacteria, and P. putida, as a strong phosphatase producer, was consistently observed both in liquid culture medium and in root rhizosphere. All laboratory, greenhouse and field experiments proved that these three isolates compete well with naturally occurring soil microorganisms. Consistently, the combinations of either P. agglomerans or M. laevaniformans strains with Pseudomonas putida led to higher biomass and potato tuber in greenhouse and in field trials. It is conceivable that combinations of an acid- and a phosphatase-producing bacterium would allow simultaneous utilization of both inorganic and organic phosphorus compounds preserving the soil structure.     

苯酚降解菌的分离及培养特性研究

对南充市郊炼油厂活性污泥进行富集,驯化筛选得到2株能以苯酚作为唯一碳源和能源生长的菌株,编号为S1,S2,两菌株可耐10,000mg/L左右的苯酚浓度,实验得出其最佳生长条件为pH7-8,温度25℃-30℃,在适宜条件下,对苯酚有较好的降解能力,而且苯对两菌株的生长表现为抑制作用。     

Isolation and characterization of novel bacteria degrading polycyclic aromatic hydrocarbons from polluted Greek soils

Three bacterial strains, designated as Wphe1, Sphe1, and Ophe1, were isolated from Greek soils contaminated with polycyclic aromatic hydrocarbon (PAH)-containing waste from the wood processing, steel, and oil refinery industries. Wphe1, Sphe1, and Ophe1 were characterized and identified as species of Pseudomonas, Microbacterium, and Paracoccus, respectively, based on Gram staining, biochemical tests, phospholipid analysis, FAME analysis, G+C content and 16S rRNA gene sequence analysis. The results of gas chromatography showed that strain Wphe1 degraded naphthalene, phenanthrene, and m-cresol over a wide temperature range; strain Sphe1 was a degrader of phenanthrene and n-alkanes; most interestingly, strain Ophe1 degraded anthracene, phenanthrene, fluorene, fluoranthene, chrysene, and pyrene, as well as cresol compounds and n-alkanes as sole carbon source. This is the first report of a representative of the genus Paracoccus capable of degrading PAHs with such versatility. These three strains may be useful for bioremediation applications.     

Exploration of hitherto-uncultured bacteria from the rhizosphere

The rhizosphere environment selects a particular microbial community that arises from the one present in bulk soil due to the release of particular compounds in exudates and different opportunities for microbial colonization. During plant–microorganism coevolution, microbial functions supporting plant health and productivity have developed, of which most are described in cultured plant-associated bacteria. This review discusses the state of the art concerning the ecology of the hitherto-uncultured bacteria of the rhizosphere environment, focusing on Acidobacteria, Verrucomicrobia and Planctomycetes . Furthermore, a strategy is proposed to recover bacterial isolates from these taxa from the rhizosphere environment.     

Two dissimilar N-acyl-homoserine lactone acylases of Pseudomonas syringae influence colony and biofilm morphology

Plant aerial surfaces comprise a complex habitat for microorganisms, and many plant-associated bacteria, such as the pathogen Pseudomonas syringae, exhibit density-dependent survival on leaves by utilizing quorum sensing (QS). QS is often mediated by diffusible signals called N-acyl-homoserine lactones (AHLs), and P. syringae utilizes N-3-oxo-hexanoyl-dl-homoserine lactone (3OC6HSL) to control traits influencing epiphytic fitness and virulence. The P. syringae pathovar syringae B728a genome sequence revealed two putative AHL acylases, termed HacA (Psyr_1971) and HacB (Psyr_4858), which are N-terminal nucleophile hydrolases that inactivate AHLs by cleaving their amide bonds. HacA is a secreted AHL acylase that degrades only long-chain (C > or = 8) AHLs, while HacB is not secreted and degrades all tested AHLs. Targeted disruptions of hacA, hacB, and hacA and hacB together do not alter endogenous 3OC6HSL levels under the tested conditions. Surprisingly, targeted disruptions of hacA alone and hacA and hacB together confer complementable phenotypes that are very similar to autoaggregative phenotypes seen in other species. While AHL acylases might enable P. syringae B728a to degrade signals of competing species and block expression of their QS-dependent traits, these enzymes also play fundamental roles in biofilm formation.     

Relationships between rhizoplane and rhizosphere bacteria and verticillium wilt resistance in potato

Six cultivars and breeding lines of potato (Solanum tuberosum) differing in susceptibility to verticillium wilt caused by Verticillium dahliae were studied with respect to quantitative and qualitative differences in the bacterial flora of their soil and rhizosphere-rhizoplane. Although, no association was observed between the types of bacteria that inhabited the soil or roots of wilt resistant and susceptible cultivars, quantitative differences were evident. These differences provide the first direct evidence that potato genotypes can influence bacterial populations. Bacterial populations were 9–25-fold higher on roots than in the adjacent soil. As the plants aged, the total number of rootcolonizing bacteria increased between 15 and 245%. Pseudomonas spp. were the most abundant microbes in the soil and rhizosphere-rhizoplane. The bacteria antagonistic to V. dahliae in vitro were identified as members of the genera Bacillus, Pseudomonas, Flavobacterium, and Gluconobacter. A statistically significant trend was evident toward the association of antagonistic bacteria with the more resistant potato cultivars.     

Isolation and characterization of surfactant degrading bacteria in a marine environment

Abstract Sea water and sediment samples taken near the coasts of Hyeres bay (France) were used for anionic surfactant titrations with surface and bottom waters and the finest part of sediments. The capacity for surfactant degradation by the 'in situ' microflora was evaluated. By using a selective plating technique 26 strains able to utilize anionic surfactant were isolated from the selected bacterial communities. Their ability to degrade anionic surfactant was verified according to the biodegradation standard method. Isolated strains were characterized by morphological and physiological properties using API 20 NE micro-method. All tested strains were Gram negative, strictly aerobic, rod or helical shaped. Their weak utilization of phenolic substrates suggests that they degrade preferentially the alkyl chain of the surfactant molecule. Biodegradation was more efficient with bacterial communities rather than with any isolated strains. Such observations indicate that complete mineralization involves several other so far non-isolated strains which complete the degradation initiated by the isolated strains.     

Isolation and characterization of diazotrophic growth promoting bacteria from rhizosphere of agricultural crops of Korea

Free-living nitrogen fixing bacteria were isolated from rhizosphere of seven different plant namely sesame, maize, wheat, soybean, lettuce, pepper and rice grown in Chungbuk Province, Korea. Five isolates with nitrogenase activity above 150nmol(-1) mg(-1) protein were identified based on, phenotypic and 16S rDNA sequences analysis. The strains were identified as Stenotrophomonas maltophilia (PM-1, PM-26), Bacillus fusiformis (PM-5, PM-24) and Pseudomonas fluorescens (PM-13), respectively. All the isolates produced indole-3-acetic acid (IAA), in the presence of tryptophan, ranging from 100.4 microg ml(-1) (PM-13) to 255 microg ml(-1) (PM-24). The isolate PM-24 (Bacillus fusiformis) exhibiting highest nitrogenase activity (3677.81 nmol h(-1) mg(-1) protein) and IAA production (255microg ml(-1)) has a promising potential for developing as a plant growth promoting rhizobacteria.     

Isolation and characterization of four novel Gram-positive bacteria associated with the rhizosphere of two endemorelict plants capable of degrading a broad range of aromatic substrates

Four new Gram-positive, phenol-degrading strains were isolated from the rhizospheres of endemorelict plants Ramonda serbica and Ramonda nathaliae known to exude high amounts of phenolics in the soil. Isolates were designated Bacillus sp. PS1, Bacillus sp. PS11, Streptomyces sp. PS12, and Streptomyces sp. PN1 based on 16S rDNA sequence and biochemical analysis. In addition to their ability to tolerate and utilize high amounts of phenol of either up to 800 or up to 1,400 mg l⁻¹ without apparent inhibition in growth, all four strains were also able to degrade a broad range of aromatic substrates including benzene, toluene, ethylbenzene, xylenes, styrene, halogenated benzenes, and naphthalene. Isolates were able to grow in pure culture and in defined mixed culture on phenol and on the mixture of BTEX (benzene, toluene, ethylbenzene, and xylenes) compounds as a sole source of carbon and energy. Pure culture of Bacillus sp. PS11 yielded 1.5-fold higher biomass amounts in comparison to mixed culture, under all conditions. Strains successfully degraded phenol in the soil model system (2 g kg⁻¹) within 6 days. Activities of phenol hydroxylase, catechol 1,2-dioxygenase, and catechol 2,3-dioxygenase were detected and analyzed from the crude cell extract of the isolates. While all four strains use ortho degradation pathway, enzyme indicative of meta degradation pathway (catechol 2,3-dioxygenase) was also detected in Bacillus sp. PS11 and Streptomyces sp. PN1. Phenol degradation activities were induced 2 h after supplementation by phenol, but not by catechol. Catechol slightly inhibited activity of catechol 2,3-dioxygenase in strains PS11 and PN1.     

Bacterial structure and characterization of plant growth promoting and oil degrading bacteria from the rhizospheres of mangrove plants

Most oil from oceanic spills converges on coastal ecosystems, such as mangrove forests, which are threatened with worldwide disappearance. Particular bacteria that inhabit the rhizosphere of local plant species can stimulate plant development through various mechanisms; it would be advantageous if these would also be capable of degrading oil. Such bacteria may be important in the preservation or recuperation of mangrove forests impacted by oil spills. This study aimed to compare the bacterial structure, isolate and evaluate bacteria able to degrade oil and stimulate plant growth, from the rhizospheres of three mangrove plant species. These features are particularly important taking into account recent policies for mangrove bioreme-diation, implying that oil degradation as well as plant maintenance and health are key targets. Fifty-seven morphotypes were isolated from the mangrove rhizospheres on Bushneil-Haas (BH) medium supplemented with oil as the sole carbon source and tested for plant growth promotion. Of this strains, 60% potentially fixed nitrogen, 16% showed antimicrobial activity, 84% produced siderophores, 51% had the capacity to solubilize phosphate, and 33% produced the indole acetic acid hormone. Using gas chromatography, we evaluated the oil-degrading potential of ten selected strains that had different morphologies and showed Plant Growth Promoting Rhizobacteria (PGPR) features. The ten tested strains showed a promising degradation profile for at least one compound present in the oil. Among degrader strains, 46% had promising PGPR potential, having at least three of the above capacities. These strains might be used as a consortium, allowing the concomitant degradation of oil and stimulation of mangrove plant survival and maintenance.     

A probable aculeacin A acylase from the Ralstonia solanacearum GMI1000 is N-acyl-homoserine lactone acylase with quorum-quenching activity

Background

Extraintestinal pathogenic Escherichia coli (ExPEC) strains of serotype O1:K1:H7/NM are frequently implicated in neonatal meningitis, urinary tract infections and septicemia in humans. They are also commonly isolated from colibacillosis in poultry. Studies to determine the similarities of ExPEC from different origins have indicated that avian strains potentially have zoonotic properties.

Results

A total of 59 ExPEC O1:K1:H7/NM isolates (21 from avian colibacillosis, 15 from human meningitis, and 23 from human urinary tract infection and septicemia) originated from four countries were characterized by phylogenetic PCR grouping, Multilocus Sequence Typing (MLST), Pulsed Field Gel Electrophoresis (PFGE) and genotyping based on several genes known for their association with ExPEC or avian pathogenic Escherichia coli (APEC) virulence. APEC and human ExPEC isolates differed significantly in their assignments to phylogenetic groups, being phylogroup B2 more prevalent among APEC than among human ExPEC (95% vs. 53%, P = 0.001), whereas phylogroup D was almost exclusively associated with human ExPEC (47% vs. 5%, P = 0.0000). Seven virulence genes showed significant differences, being fimAv _MT78 and sat genes linked to human isolates, while papGII, tsh, iron, cvaC and iss were significantly associated to APEC. By MLST, 39 of 40 ExPEC belonging to phylogroup B2, and 17 of 19 belonging to phylogroup D exhibited the Sequence Types (STs) ST95 and ST59, respectively. Additionally, two novel STs (ST1013 and ST1006) were established. Considering strains sharing the same ST, phylogenetic group, virulence genotype and PFGE cluster to belong to the same subclone, five subclones were detected; one of those grouped six strains of human and animal origin from two countries.

Conclusion

Present results reveal that the clonal group B2 O1:K1:H7/NM ST95, detected in strains of animal and human origin, recovered from different dates and geographic sources, provides evidence that some APEC isolates may act as potential pathogens for humans and, consequently, poultry as a foodborne source, suggesting no host specificity for this type of isolates. A novel and important finding has been the detection of the clonal group D O1:K1:H7/NM ST59 almost exclusively in humans, carrying pathogenic genes linked to the phylogenetic group D. This finding would suggest D O1:K1:H7/NM ST59 as a host specific pathotype for humans.