Description of bacteria able to degrade isoquinoline in pure culture

1994 ◽  
Vol 40 (7) ◽  
pp. 555-560 ◽  
Author(s):  
J. Aislabie ◽  
N. K. Richards ◽  
T. C. Lyttle
Keyword(s):  
Heterocyclic Compound ◽  
Pure Culture ◽  
Sole Source ◽  
Broth Culture ◽  
Gram Negative ◽  
Carbon And Nitrogen ◽  
The Family ◽  
Nitrogen Heterocyclic

Isoquinoline is a nitrogen heterocyclic compound that is associated with coal- and oil-derived wastes. Four strains of bacteria able to degrade isoquinoline in pure culture were isolated from sites known to be contaminated with oil. Isoquinoline was used as the sole source of carbon and nitrogen by these isolates. Isoquinoline was initially transformed to 1-hydroxyisoquinoline, which accumulated in the broth culture, and then disappeared. The four strains isolated were Gram negative, aerobic, rod-shaped bacteria with polar flagella. The strains have been presumptively identified as members of the family Comamonadaceae.Key words: isoquinoline degradation, Comamonadaceae.not available

scholarly journals Genome Analysis ofFimbriiglobus ruberSP5T, a Planctomycete with Confirmed Chitinolytic Capability

2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Nikolai V. Ravin ◽  
Andrey L. Rakitin ◽  
Anastasia A. Ivanova ◽  
Alexey V. Beletsky ◽  
Irina S. Kulichevskaya ◽  
...  
Keyword(s):  
Sole Source ◽  
Major Constituent ◽  
Special Importance ◽  
Gene Encoding ◽  
Fungal Cell ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Type Iv ◽  
The Family ◽  
Weak Growth

ABSTRACTMembers of the bacterial orderPlanctomycetaleshave often been observed in associations with Crustacea. The ability to degrade chitin, however, has never been reported for any of the cultured planctomycetes although utilization ofN-acetylglucosamine (GlcNAc) as a sole carbon and nitrogen source is well recognized for these bacteria. Here, we demonstrate the chitinolytic capability of a member of the familyGemmataceae,Fimbriiglobus ruberSP5T, which was isolated from a peat bog. As revealed by metatranscriptomic analysis of chitin-amended peat, the pool of 16S rRNA reads fromF. ruberincreased in response to chitin availability. Strain SP5Tdisplayed only weak growth on amorphous chitin as a sole source of carbon but grew well with chitin as a source of nitrogen. The genome ofF. ruberSP5Tis 12.364 Mb in size and is the largest among all currently determined planctomycete genomes. It encodes several enzymes putatively involved in chitin degradation, including two chitinases affiliated with the glycoside hydrolase (GH) family GH18, GH20 family β-N-acetylglucosaminidase, and the complete set of enzymes required for utilization of GlcNAc. The gene encoding one of the predicted chitinases was expressed inEscherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The genome also contains genes required for the assembly of type IV pili, which may be used to adhere to chitin and possibly other biopolymers. The ability to use chitin as a source of nitrogen is of special importance for planctomycetes that inhabit N-depleted ombrotrophic wetlands.IMPORTANCEPlanctomycetes represent an important part of the microbial community inSphagnum-dominated peatlands, but their potential functions in these ecosystems remain poorly understood. This study reports the presence of chitinolytic potential in one of the recently described peat-inhabiting members of the familyGemmataceae,Fimbriiglobus ruberSP5T. This planctomycete uses chitin, a major constituent of fungal cell walls and exoskeletons of peat-inhabiting arthropods, as a source of nitrogen in N-depleted ombrotrophicSphagnum-dominated peatlands. This study reports the chitin-degrading capability of representatives of the orderPlanctomycetales.

OBSERVATIONS ON THE CULTURE AND MAINTENANCE OF A FREE-LIVING AMOEBA

1956 ◽  
Vol 2 (5) ◽  
pp. 511-513
Author(s):  
A. Bakerspigel
Keyword(s):  
Pure Culture ◽  
Agar Medium ◽  
Sole Source ◽  
Malt Agar ◽  
Free Living ◽  
Gram Negative ◽  
Negative Bacillus ◽  
The Past ◽  
Gram Negative Bacillus ◽  
Free Living Amoeba

A free-living amoeba isolated from creek water could be grown at 24 °C. on a solid malt agar medium together with a pure culture of a motile Gram-negative bacillus, isolated from the same sample of water. The bacilli apparently served as the sole source of food for the trophozoites, the malt in the medium being-utilized by the bacilli for their own growth. In addition, the encysted form has been maintained on this medium at 24 °C. for the past 12 months and at 4 °C. for 10 months. Transfers to fresh medium of cysts from such cultures yielded numerous trophozoites after 12 hr. incubation at 24 °C, provided that metabolically active bacilli were present.

scholarly journals Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Diseased Ayu (Plecoglossus altivelis altivelis) Caught at Three Sites in the Kagami River in Kochi, Japan

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Hazuki Yamashita ◽  
Takayuki Wada ◽  
Yusuke Kato ◽  
Takuji Ikeda ◽  
Masayuki Imajoh
Keyword(s):  
Draft Genome ◽  
Psychrophilic Bacterium ◽  
Genome Sequences ◽  
Plecoglossus Altivelis ◽  
Gram Negative ◽  
Content Type ◽  
Flavobacterium Psychrophilum ◽  
Skin Ulcers ◽  
The Family

Flavobacterium psychrophilum is a Gram-negative, psychrophilic bacterium within the family Flavobacteriaceae. Here, we report the draft genome sequences of three F. psychrophilum strains isolated from skin ulcers of diseased ayu caught by tomozuri angling at three sites in the Kagami River in Japan.

scholarly journals Formation in vitro of colistin resistance in carbapenem-resistant Gram-negative bacteria and its biological cost

2021 ◽  
Author(s):  
D. V. Tapalski ◽  
T. A. Petrovskaya ◽  
A. E. Kozlov
Keyword(s):  
Broth Culture ◽  
Exponential Growth Phase ◽  
Lag Phase ◽  
Gram Negative Bacteria ◽  
Colistin Resistance ◽  
Gram Negative ◽  
Broth Microdilution Method ◽  
Resistant Mutants ◽  
Biological Cost

Introduction. The spread of resistance to carbapenems among gram-negative bacteria have led to an increase in the consumption of polymyxins and the emergence of certain strains resistant to them. Polymyxin resistance is mainly associated with mutations in chromosomal genes. The development of mutational resistance to antibiotics can lead to a decrease in the viability of bacteria, which is manifested by an increase in the duration of the cell cycle, a decrease in virulence and competitive fitness. The purpose of the study was to assess in vitro the intensity of the formation of colistin resistance in carbapenemresistant clinical isolates of gram-negative bacteria, the stability of the formed emerged resistance and its biological cost.Materials and methods. For 46 strains of Klebsiella pneumoniae, 77 strains of Pseudomonas aeruginosa and 42 strains of Acinetobacter baumannii, real time polymerase chain reaction (PCR) was used to detect the genes of carbapenemases, the minimum inhibitory concentrations (MIC) of meropenem and colistin were determined by broth microdilution method. The selection of resistant subpopulations on Muller–Hinton agar with the addition of 16 mg/l colistin was carried out. For colistin-resistant mutants and their isogenic sensitive strains, the kinetic parameters of growth in broth culture were determined. Incubation and result recording were performed on an Infinite M200 microplate reader for 18.5 hours at 35°C with measurement of light scatter in the wells every 15 minutes.Results. The production of carbapenemases MBL VIM in P. aeruginosa, MBL NDM, KPC and OXA-48 in K. pneumoniae, OXA-23 and OXA-40 in A. baumannii was observed. All strains were sensitive to colistin (MIC varied from 0.062 to 2 mg/l). The colony growth on a selective medium with16 mg/l colistin was observed for 97.8% of K. pneumoniae strains, 16.9% of P. aeruginosa strains, and 61.9% of A. baumannii strains. The mutational nature of colistin resistance was confirmed for 21.7% of K. pneumoniae strains. For colistin-resistant mutants of K. pneumoniae, a significant increase in the duration of the lag phase (Tlag) was observed: 225.6 ± 7.037 min in the wild-type susceptible strains and 245.5 ± 8.726 in resistant mutants, p = 0.037. The indicators of the doubling time of the number of microbial cells in the exponential growth phase (Tdoubling) and the area under the bacterial growth curve did not differ significantly.Conclusion. A high frequency of formation of colistin resistance in vitro in carbapenemase-producing strains of K. pneumoniae was observed. The absence of significant changes in the kinetics of microbial growth in resistant strains makes it possible to predict the further spread of mutational resistance to colistin, as well as its preservation in microbial populations of K. pneumoniae even in the case of limiting the use of this antibiotic. 

scholarly journals Amino Acid-Mediated Induction of the Basic Amino Acid-Specific Outer Membrane Porin OprD from Pseudomonas aeruginosa

1999 ◽  
Vol 181 (17) ◽  
pp. 5426-5432 ◽  
Author(s):  
Martina M. Ochs ◽  
Chung-Dar Lu ◽  
Robert E. W. Hancock ◽  
Ahmed T. Abdelal
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Regulatory Protein ◽  
Basic Amino Acid ◽  
Sole Source ◽  
Activation Mechanism ◽  
Beta Lactam ◽  
Mobility Shift ◽  
Carbon And Nitrogen

ABSTRACT Pseudomonas aeruginosa can utilize arginine and other amino acids as both carbon and nitrogen sources. Earlier studies have shown that the specific porin OprD facilitates the diffusion of basic amino acids as well as the structurally analogous beta-lactam antibiotic imipenem. The studies reported here showed that the expression of OprD was strongly induced when arginine, histidine, glutamate, or alanine served as the sole source of carbon. The addition of succinate exerted a negative effect on induction ofoprD, likely due to catabolite repression. The arginine-mediated induction was dependent on the regulatory protein ArgR, and binding of purified ArgR to its operator upstream of theoprD gene was demonstrated by gel mobility shift and DNase assays. The expression of OprD induced by glutamate as the carbon source, however, was independent of ArgR, indicating the presence of more than a single activation mechanism. In addition, it was observed that the levels of OprD responded strongly to glutamate and alanine as the sole sources of nitrogen. Thus, that the expression ofoprD is linked to both carbon and nitrogen metabolism ofPseudomonas aeruginosa.

scholarly journals Lipopolysaccharide-Trap-Fc, a Multifunctional Agent To Battle Gram-Negative Bacteria

2009 ◽  
Vol 77 (7) ◽  
pp. 2925-2931 ◽  
Author(s):  
Philipp Groß ◽  
Katharina Brandl ◽  
Christine Dierkes ◽  
Jürgen Schölmerich ◽  
Bernd Salzberger ◽  
...  
Keyword(s):  
Myeloid Differentiation ◽  
Gram Negative Bacteria ◽  
Bacterial Sepsis ◽  
Tlr Signaling ◽  
Monocytic Cells ◽  
Gram Negative ◽  
The Family ◽  
Myeloid Differentiation Factor ◽  
Lps Treatment

ABSTRACT The family of Toll-like receptors (TLRs) plays a pivotal role in host defense against pathogens. However, overstimulation of these receptors may lead to uncontrolled general inflammation and eventually to systemic organ dysfunction or failure. With the intent to control overwhelming inflammation during gram-negative bacterial sepsis, we constructed soluble fusion proteins of the lipopolysaccharide (LPS)-receptor complex to modulate TLR signaling in multiple ways. The extracellular domain of mouse TLR4 and mouse myeloid differentiation factor 2 (MD-2) fusions (LPS-Trap) were linked to human immunoglobulin G Fc domains (LPS-Trap-Fc). In addition to the ability to bind LPS or gram-negative bacteria and to inhibit interleukin-6 secretion of monocytic cells after LPS treatment, LPS-Trap-Fc was able to opsonize fluorescent Escherichia coli particles. This led to enhancement of phagocytosis by monocytic cells which was strictly dependent on the presence of the Fc region. Moreover, only LPS-Trap-Fc- and not LPS-Trap-coated bacteria were sensitized to complement killing. Therefore, LPS-Trap-Fc not only neutralizes LPS but also, after binding to bacteria, enhances phagocytosis and complement-mediated killing and could thus act as a multifunctional agent to fight gram-negative bacteria in vivo.

scholarly journals Degradation of Polycyclic Aromatic Hydrocarbons by Moderately Halophilic Bacteria from Luzon Salt Beds

2018 ◽  
Vol 8 (19) ◽  
Author(s):  
Carolyn L. Nanca ◽  
Kimberly D. Neri ◽  
Anna Christina R. Ngo ◽  
Reuel M. Bennett ◽  
Gina R. Dedeles
Keyword(s):  
Molecular Weight ◽  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Halophilic Bacteria ◽  
Sole Source ◽  
The Philippines ◽  
Liquid Fuels ◽  
Gram Positive ◽  
Gram Negative ◽  
Polycyclic Aromatic

Background. Polycyclic aromatic hydrocarbons (PAHs) are common environmental contaminants which are highly toxic due to their carcinogenic and mutagenic effects. They are released into the environment by incomplete combustion of solid and liquid fuels, accidental spillage of oils and seepage from industrial activities. One of the promising processes mitigating PAHs is through biodegradation. However, conventional microbiological treatment processes do not function well at high salt concentrations. Hence, utilization of halophilic bacteria should be considered. Objectives. This study aimed to assess the ability of halophilic bacteria isolated from local salt beds in Pangasinan and Cavite, the Philippines, to degrade PAHs pyrene, fluorene and fluoranthene. Methods. Polycyclic aromatic hydrocarbon-tolerant halophilic bacteria collected from two sampling sites were phenotypically characterized, molecularly identified and tested to determine their potential to degrade the PAHs pyrene, fluorene and fluoranthene at a hypersaline condition. Best PAH degraders were then assayed to identify the optimal degradation using such parameters as pH, temperature and PAH concentration. Testing for enzyme degradation was also done to determine their baseline information. Extraction and analysis of degraded PAHs were performed using centrifugation and UV-vis spectrophotometry. Results. Twelve isolates from both collection sites tolerated and grew in culture with selected PAHs. These were identified into four genera (Halobacillus, Halomonas, Chromohalobacter, and Pontibacillus). Selected best isolates in a series of biodegradation assays with the above-mentioned parameters were Halobacillus B (Collection of Microbial Strains (CMS) 1802) (=trueperi) (Gram-positive) for pyrene and fluoranthene, and Halomonas A (CMS 1901) (Gram-negative) for fluorene. Degrader biomass and PAH degradation were invariably negatively correlated. Qualitative tests with and without peptone as a nitrogen source implied enzymatic degradation. Discussion. Polycyclic aromatic hydrocarbons utilized by these halophilic bacteria served as a sole source of carbon and energy. Implications of biodegradation of the two best isolates show that high molecular weight (HMW) (4-ring) pyrene tends to be degraded better by Gram-positive bacteria and low molecular weight (3-ring) fluorene by Gram-negative degraders. Conclusions. Halophilic bacteria constitute an untapped natural resource for biotechnology in the Philippines. The present study demonstrated their potential use in bioremediation of recalcitrant hydrocarbons in the environment. Competing Interests. The authors declare no competing financial interests.

scholarly journals Molecular Mechanism ofN,N-Dimethylformamide Degradation inMethylobacteriumsp. Strain DM1

2019 ◽  
Vol 85 (12) ◽  
Author(s):  
Xinyu Lu ◽  
Weiwei Wang ◽  
Lige Zhang ◽  
Haiyang Hu ◽  
Ping Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Gene Clusters ◽  
Sole Source ◽  
Human Beings ◽  
Sequencing Data ◽  
Carbon And Nitrogen ◽  
Redundant Genes ◽  
Evolutionary Advantage ◽  
Redundant Gene ◽  
Phenotype Identification

ABSTRACTN,N-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings. Herein, an efficient DMF-degrading strain, DM1, was isolated and identified asMethylobacteriumsp. This strain can use DMF as the sole source of carbon and nitrogen. Whole-genome sequencing of strain DM1 revealed that it has a 5.66-Mbp chromosome and a 200-kbp megaplasmid. The plasmid pLVM1 specifically harbors the genes essential for the initial steps of DMF degradation, and the chromosome carries the genes facilitating subsequent methylotrophic metabolism. Through analysis of the transcriptome sequencing data, the complete mineralization pathway and redundant gene clusters of DMF degradation were elucidated. The dimethylformamidase (DMFase) gene was heterologously expressed, and DMFase was purified and characterized. Plasmid pLVM1 is catabolically crucial for DMF utilization, as evidenced by the phenotype identification of the plasmid-free strain. This study systematically elucidates the molecular mechanisms of DMF degradation byMethylobacterium.IMPORTANCEDMF is a hazardous pollutant that has been used in the chemical industry, pharmaceutical manufacturing, and agriculture. Biodegradation as a method for removing DMF has received increasing attention. Here, we identified an efficient DMF degrader,Methylobacteriumsp. strain DM1, and characterized the complete DMF mineralization pathway and enzymatic properties of DMFase in this strain. This study provides insights into the molecular mechanisms and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting the emergence of new ecotypes ofMethylobacterium.

scholarly journals Crystal Structures of Klebsiella pneumoniae Dihydrofolate Reductase Bound to Propargyl-Linked Antifolates Reveal Features for Potency and Selectivity

2014 ◽  
Vol 58 (12) ◽  
pp. 7484-7491 ◽  
Author(s):  
Kristen M. Lamb ◽  
Michael N. Lombardo ◽  
Jeremy Alverson ◽  
Nigel D. Priestley ◽  
Dennis L. Wright ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Crystal Structures ◽  
Dihydrofolate Reductase ◽  
Next Generation ◽  
Gram Negative ◽  
Content Type ◽  
Resistant Species ◽  
Loop Conformations ◽  
The Family ◽  
Dihydrofolate Reductases

ABSTRACTResistance to the antibacterial antifolate trimethoprim (TMP) is increasing in members of the familyEnterobacteriaceae, driving the design of next-generation antifolates effective against these Gram-negative pathogens. The propargyl-linked antifolates are potent inhibitors of dihydrofolate reductases (DHFR) from several TMP-sensitive and -resistant species, includingKlebsiella pneumoniae. Recently, we have determined that these antifolates inhibit the growth of strains ofK. pneumoniae, some with MIC values of 1 μg/ml. In order to further the design of potent and selective antifolates against members of theEnterobacteriaceae, we determined the first crystal structures ofK. pneumoniaeDHFR bound to two of the propargyl-linked antifolates. These structures highlight that interactions with Leu 28, Ile 50, Ile 94, and Leu 54 are necessary for potency; comparison with structures of human DHFR bound to the same inhibitors reveal differences in residues (N64E, P61G, F31L, and V115I) and loop conformations (residues 49 to 53) that may be exploited for selectivity.

Biodegradation of cyanide by Rhodococcus UKMP-5M

Biologia ◽  
2013 ◽  
Vol 68 (2) ◽  
Author(s):  
Maegala Nallapan Maniyam ◽  
Fridelina Sjahrir ◽  
Abdul Ibrahim ◽  
Anthony Cass
Keyword(s):  
Contaminated Soils ◽  
Nitrile Hydratase ◽  
Sole Source ◽  
Optimum Conditions ◽  
Carbon And Nitrogen ◽  
Bacterial Enzyme ◽  
End Products ◽  
Treatment Facilities ◽  
Organic Nutrients ◽  
Structural Levels

AbstractA new bacterial strain, Rhodococcus UKMP-5M isolated from petroleum-contaminated soils demonstrated promising potential to biodegrade cyanide to non-toxic end-products. Ammonia and formate were found as final products during growth of the isolate with KCN as the sole nitrogen source. Formamide was not detected as one of the end-products suggesting that the biodegradation of cyanide by Rhodococcus UKMP-5M may have proceeded via a hydrolytic pathway involving the bacterial enzyme cyanidase. No growth of the bacterium was observed when KCN was supplied as the sole source of carbon and nitrogen even though marginal reduction in the concentration of cyanide was recorded, indicating the toxic effect of cyanide even in cyanide-degrading microorganisms. The cyanide biodegradation ability of Rhodococcus UKMP-5M was greatly affected by the presence of organic nutrients in the medium. Medium containing glucose and yeast extract promoted the highest growth rate of the bacterium which simultaneously assisted complete biodegradation of 0.1 mM KCN within 24 hours of incubation. It was found that growth and cyanide biodegradation occurred optimally at 30°C and pH 6.3 with glucose as the preferred carbon source. Acetonitrile was used as an inducer to enhance cyanide biodegradation since the enzymes nitrile hydratase and/or nitrilase have similarity at both the amino acid and structural levels to that of cyanidase. The findings from this study should be of great interest from an environmental and health point of views since the optimum conditions discovered in the present study bear a close resemblance to the actual scenario of cyanide wastewater treatment facilities.

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