scholarly journals Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2606-2612 ◽  
Author(s):  
Virginia Cuadrado ◽  
Margarita Gomila ◽  
Luciano Merini ◽  
Ana M. Giulietti ◽  
Edward R. B. Moore
Keyword(s):  
Agricultural Soil ◽  
Bacterial Consortium ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Systematic Analysis ◽  
Hybridization Data ◽  
Degrading Bacterium ◽  
History Of ◽  
Pampa Region ◽  
Herbicide Use

A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6T, the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6T did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5–4.5 % NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5 %; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA–DNA hybridization data revealed low levels of genomic DNA similarity (less than 30 %) between strain CPDB6T and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16 : 1ω7c) and hexadecanoic (16 : 0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6T was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6T (=CCUG 55948T=CCM-A-29:1289T) as the type strain.

scholarly journals Camelimonas fluminis sp. nov., a cyhalothrin-degrading bacterium isolated from river water

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3109-3114 ◽  
Author(s):  
Long Zhang ◽  
Man Song ◽  
Qin Cao ◽  
Shang Wu ◽  
Yan Zhao ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Hybridization Data ◽  
Degrading Bacterium ◽  
Total Dna ◽  
Hanjiang River ◽  
The 16S Rrna Gene

An aerobic, Gram-stain-negative, short rod-shaped, non-spore-forming, cyhalothrin-degrading bacterial strain, XZ2T, was isolated from the surface water of Hanjiang River in Wuhan, China. Strain XZ2T grew optimally at pH 6.0, 30 °C and in the absence of NaCl. The G+C content of the total DNA was 64.1 mol%. The 16S rRNA gene sequence of strain XZ2T showed the highest similarity to that of Camelimonas lactis M 2040T (99.1 %), followed by Camelimonas abortus UK34/07-5T (95.9 %) and Chelatococcus daeguensis K106T (95.3 %). The major cellular fatty acids of strain XZ2T were C19 : 0 cyclo ω8c (63.1 %), C16 : 0 (15.0 %) and C18 : 1ω7c/C18 : 1ω6c (summed feature 8; 8.9 %). C18 : 0 3-OH was also detected as the major hydroxylated fatty acid. The respiratory quinone was ubiquinone Q-10. The polar lipid profile included the major compounds phosphatidylcholine and diphosphatidylglycerol, and moderate amounts of phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The predominant compound in the polyamine pattern was spermidine. These chemotaxonomic data supported the affiliation of strain XZ2T to the genus Camelimonas. The DNA–DNA hybridization value between strain XZ2T and Camelimonas lactis M 2040T was 43.5 ± 0.6 %. DNA–DNA hybridization data as well as biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiations between strain XZ2T and Camelimonas lactis M 2040T. Therefore, strain XZ2T represents a novel species of the genus Camelimonas, for which the name Camelimonas fluminis sp. nov. is proposed. The type strain is XZ2T ( = KCTC 42282T = ACCC 19738T).

scholarly journals Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment

2005 ◽  
Vol 55 (3) ◽  
pp. 1181-1186 ◽  
Author(s):  
Chenli Liu ◽  
Zongze Shao
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Alkane Hydroxylase ◽  
Biochemical Tests ◽  
Deep Sea Sediment ◽  
Degrading Bacterium ◽  
Internal Transcribed Spacer Sequences

Two bacterial strains, B-5T and NO1A, were isolated from the surface water of the Bohai Sea and deep-sea sediment of the east Pacific Ocean, respectively. Both strains were halophilic, aerobic, Gram-negative, non-spore-forming, catalase- and oxidase-positive motile rods. They grew on a restricted spectrum of organic compounds, including some organic acids and alkanes. On the basis of 16S rRNA gene sequence similarity, strains B-5T and NO1A were shown to belong to the γ-Proteobacteria. Highest similarity values were found with Alcanivorax venustensis (95·2 %), Alcanivorax jadensis (94·6 %) and Alcanivorax borkumensis (94·1 %). Principal fatty acids of both strains were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. The chemotaxonomically characteristic fatty acid C19 : 0 cyclo ω8c was also detected. On the basis of the above, together with results of physiological and biochemical tests, DNA–DNA hybridization, comparisons of 16S–23S internal transcribed spacer sequences and comparisons of the partial deduced amino acid sequence of alkane hydroxylase, both strains were affiliated to the genus Alcanivorax but were differentiated from recognized Alcanivorax species. Therefore, a novel species, Alcanivorax dieselolei sp. nov., represented by strains B-5T and NO1A is proposed, with the type strain B-5T (=DSM 16502T=CGMCC 1.3690T).

scholarly journals Degradation of 2,3,7,8-TCDD by a consortium of bacterial strains isolated from heavil herbicide/dioxin contaminated soil in Bienhoa airbase

2020 ◽  
Vol 16 (4) ◽  
pp. 777-784
Author(s):  
Pham Quang Huy ◽  
Nguyen Kim Thoa ◽  
Dang Thi Cam Ha
Keyword(s):  
Contaminated Soil ◽  
Large Scale ◽  
Morphological Characteristics ◽  
Bacterial Consortium ◽  
Soil Extract ◽  
High Ratio ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Agrobacterium Strain ◽  
Microbial Strains

From two different soil sources in Bienhoa airbase (heavy herbicide/dioxin contaminated West-South region and bioremediated cell), five microbial strains were isolated and their 2,3,7,8-TCDD biodegrability in consortium was investigated. Based on the colony and cell morphological characteristics as well as 16S rRNA gene sequences, these strains were classified into 5 genera, including Methylobacterium (strain BHBi1), Hydrocarboniphaga (strain BHBi4), Agrobacterium (strain BHBi5), Bosea (strain BHBi7) and Microbacterium (strain BH09). Two strains BHBi7 and BHBi4 were the first representatives of the genera Bosea and Hydrocarboniphaga that were isolated from heavyly herbicide/dioxin contaminated soil. All five strains were able to grow well in mineral salt medium (MSM) supplemented with soil extract (SE) containing 2,3,7,8-TCDD (this congener is the main soil total compound toxicity) and other congeners, including PCDDs, PCDFs, 2,4,5-T, 2,4-D, PAHs and their intermediates. This microbial consortium degraded 2,537.34 ngTEQ/kg of 2,3,7,8-TCDD congener in soil, equivalent to 59.1% lost of total toxicity in comparison to the control without bacterial seeding (4,294.12 ng TEQ/kg). Such a high ratio of dioxin degradation by a bacterial consortium was reported here for the first time, contributing more evidences for convincing the successful dioxin bioremediation of “Active Landfill” technology at large scale in Z1 area at Bienhoa airbase, Dongnai, Vietnam.

scholarly journals Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium

2007 ◽  
Vol 57 (12) ◽  
pp. 2754-2757 ◽  
Author(s):  
Jing-Liang Xu ◽  
Jian He ◽  
Zhi-Chun Wang ◽  
Kun Wang ◽  
Wen-Jun Li ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Rhodococcus Erythropolis ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Mycolic Acids ◽  
Hybridization Data ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Good Agreement

A Gram-positive, aerobic, non-motile, mesophilic strain, djl-6T, able to degrade carbendazim, was isolated from a carbendazim-contaminated soil sample from Jiangsu province, China. The taxonomic position of this isolate was analysed by using a polyphasic approach. Chemotaxonomic analysis including peptidoglycan type, diagnostic sugar composition, fatty acid profile, menaquinones, polar lipids and mycolic acids showed that the characteristics of strain djl-6T were in good agreement with those of the genus Rhodococcus. DNA–DNA hybridization showed that it had low genomic relatedness with Rhodococcus baikonurensis DSM 44587T (31.8 %), Rhodococcus erythropolis DSM 43066T (23.8 %) and Rhodococcus globerulus DSM 43954T (17.7 %), the three type strains to which strain djl-6T was most closely related based on 16S rRNA gene sequence analysis (99.78, 99.25 and 98.91 % similarity, respectively). Based on the phenotypic properties and DNA–DNA hybridization data, strain djl-6T (=CGMCC 1.6580T =KCTC 19205T) is proposed as the type strain of a novel Rhodococcus species, Rhodococcus qingshengii sp. nov.

scholarly journals Rhodanobacter sp. Strain BPC1 in a Benzo[a]pyrene-Mineralizing Bacterial Consortium

2002 ◽  
Vol 68 (12) ◽  
pp. 5826-5833 ◽  
Author(s):  
Robert A. Kanaly ◽  
Shigeaki Harayama ◽  
Kazuya Watanabe
Keyword(s):  
Bacterial Consortium ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Competitive Pcr ◽  
Pcr Assay ◽  
Biochemical Tests ◽  
Supernatant Liquid ◽  
Gene Sequence Analysis ◽  
High Boiling Point ◽  
Fuel Distillate

ABSTRACT A bacterial consortium which rapidly mineralizes benzo[a]pyrene when it is grown on a high-boiling-point diesel fuel distillate (HBD) was recovered from soil and maintained for approximately 3 years. Previous studies have shown that mobilization of benzo[a]pyrene into the supernatant liquid precedes mineralization of this compound (R. Kanaly, R. Bartha, K. Watanabe, and S. Harayama, Appl. Environ. Microbiol. 66:4205-4211, 2000). In the present study, we found that sterilized supernatant liquid filtrate (SSLF) obtained from the growing consortium stimulated mineralization of benzo[a]pyrene when it was readministered to a consortium inoculum without HBD. Following this observation, eight bacterial strains were isolated from the consortium, and SSLF of each of them was assayed for the ability to stimulate benzo[a]pyrene mineralization by the original consortium. The SSLF obtained from one strain, designated BPC1, most vigorously stimulated benzo[a]pyrene mineralization by the original consortium; its effect was more than twofold greater than the effect of the SSLF obtained from the original consortium. A 16S rRNA gene sequence analysis and biochemical tests identified strain BPC1 as a member of the genus Rhodanobacter, whose type strain, Rhodanobacter lindaniclasticus RP5557, which was isolated for its ability to grow on the pesticide lindane, is not extant. Strain BPC1 could not grow on lindane, benzo[a]pyrene, simple hydrocarbons, and HBD in pure culture. In contrast, a competitive PCR assay indicated that strain BPC1 grew in the consortium fed only HBD and benzo[a]pyrene. This growth of BPC1 was concomitant with growth of the total bacterial consortium and preceded the initiation of benzo[a]pyrene mineralization. These results suggest that strain BPC1 has a specialized niche in the benzo[a]pyrene-mineralizing consortium; namely, it grows on metabolites produced by fellow members and contributes to benzo[a]pyrene mineralization by increasing the bioavailability of this compound.

Isolation, development and identification of salt-tolerant bacterial consortium from crude-oil-contaminated soil for degradation of di-azo dye Reactive Blue 220

2015 ◽  
Vol 72 (2) ◽  
pp. 311-321 ◽  
Author(s):  
Vipul R. Patel ◽  
Nikhil Bhatt
Keyword(s):  
Oxygen Demand ◽  
Bacterial Consortium ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Cod Reduction ◽  
Spectrometry Analysis ◽  
Wide Range

The objective of this study was development and characterization of a halophilic bacterial consortium for rapid decolorization and degradation of a wide range of dyes and their mixtures. The 16S rRNA gene analysis of developed halophilic consortium VN.1 showed that the bacterial consortium contained six bacterial strains, which were identified as Pseudomonas fluorescens HM480360, Enterobacter aerogenes HM480361, Shewanella sp. HM589853, Arthrobacter nicotianae HM480363, Bacillus beijingensis HM480362 and Pseudomonas aeruginosa JQ659549. Halophilic consortium VN.1 was able to decolorize up to 2,500 mg/L RB220 with >85% chemical oxygen demand (COD) reduction under static condition at 30 °C and pH 8.0 in the presence of 7% NaCl. VN.1 also exhibited more than 85% COD reduction with >25 mg/(L h) rate of decolorization in the case of different reactive dye mixtures. We propose the symmetric cleavage of RB220 using Fourier transform infrared, high-performance liquid chromatography (HPLC), nuclear magnetic resonance and gas chromatography-mass spectrometry analysis, and confirmed the formation of sodium-4-aminobenzenesulfonate, sodium-6-aminonepthalenesulfonate, and sodiumbenzene/nepthalenesulfonate. Toxicity studies confirm that the biodegraded products of RB220 effluent stimulate the growth of plants as well as the bacterial community responsible for soil fertility.

scholarly journals Characterization of Sporohalobacter salinus sp. nov., an anaerobic, halophilic, fermentative bacterium isolated from a hypersaline lake

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 543-548 ◽  
Author(s):  
Manel Ben Abdallah ◽  
Fatma Karray ◽  
Najla Mhiri ◽  
Jean-Luc Cayol ◽  
Jean-Luc Tholozan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Major Product ◽  
Hypersaline Lake ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Hybridization Data

Halophilic, obligately anaerobic, Gram-stain-negative bacterial strains were isolated from a sediment sample taken from under the salt crust of El-Jerid hypersaline lake in southern Tunisia by using tryptone or glucose as the substrate. One strain, CEJFT1BT, was characterized phenotypically and phylogenetically. Cells were non-motile, non-spore-forming, short rods. Strain CEJFT1BT was able to grow in the presence of 5–30 % (w/v) NaCl (optimum 20 %) and at 30–60 °C (optimum 45 °C). It grew at pH 5.5–7.8 and the optimum pH for growth was 6.8. The isolate required yeast extract for growth. Substrates utilized by strain CEJFT1BT as the sole carbon source included glucose, fructose, sucrose, pyruvate, Casamino acids and starch. Individual amino acids such as glutamate, lysine, methionine, serine, tyrosine, and amino acid mixtures formed by the Stickland reaction such as alanine-glycine, valine-proline, leucine-proline, isoleucine-proline were also utilized. Products of glucose fermentation were acetate (major product), butyrate, H2 and CO2. The genomic DNA G+C content of strain CEJFT1BT was 32.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CEJFT1BT should be assigned to the genus Sporohalobacter . The sequence similarity between strain CEJFT1BT and Sporohalobacter lortetii was 98.5 %, but DNA–DNA hybridization between the two strains revealed a relatedness value of 56.4 %, indicating that they are not related at the species level. The combination of phylogenetic analysis, DNA–DNA hybridization data, and differences in substrate utilization support the view that strain CEJFT1BT represents a novel species of the genus Sporohalobacter , for which the name Sporohalobacter salinus sp. nov. is proposed. The type strain is CEJFT1BT ( = DSM 26781T = JCM 19279T).

scholarly journals Combined Effect of Laboratory-Simulated Fire and Chromium Pollution on Microbial Communities in an Agricultural Soil

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 587
Author(s):  
Ida Rascio ◽  
Maddalena Curci ◽  
Concetta Eliana Gattullo ◽  
Anna Lavecchia ◽  
Mohammad Yaghoubi Khanghahi ◽  
...  
Keyword(s):  
Soil Properties ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Agricultural Soil ◽  
Crop Residues ◽  
Soil Microbial Communities ◽  
Soil Conditions ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Soil Microbial

Fire events in agricultural soils can modify not only soil properties but also the structure of soil microbial communities, especially in soils containing high concentrations of potentially toxic elements (PTEs). The recolonization of burned soils can in fact favor the proliferation of certain microorganisms, more adaptable to post-fire soil conditions and higher PTE availability, over others. In this study, we simulated with laboratory experiments the microbial recolonization of an agricultural soil containing high Cr concentrations after heating at 500 °C for 30 min, to mimic the burning of crop residues. Changes in soil properties and Cr speciation were assessed, as well as soil microbial structure by means of 16S rRNA gene sequencing. Both altered soil conditions and increased Cr availability, especially Cr(VI), appeared to be responsible for the reduction in species diversity in heated soils and the proliferation of Firmicutes. Indeed, already after 3 days from the heat treatment, Firmicutes increased from 14% to 60% relative abundance. In particular, Paenibacillus was the most abundant genus identified after the simulation, with an average relative abundance of 40%. These bacteria are known to be good fire-responders and Cr-tolerant. These results could be useful to identify bacterial strains to be used as bioindicators of altered environments and for the recovery of fire-impacted polluted sites.

scholarly journals Campylobacter insulaenigrae bacteremia with meningitis: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Moe Kyotani ◽  
Tsuneaki Kenzaka ◽  
Hozuka Akita ◽  
Soichi Arakawa
Keyword(s):  
Blood Culture ◽  
Marine Mammals ◽  
Chronic Subdural Hematoma ◽  
16S Rrna Gene Sequencing ◽  
Enhancement Effect ◽  
Rrna Gene ◽  
Clinical Report ◽  
Bacterial Strains ◽  
Fisher Syndrome ◽  
First Case

Abstract Background The bacterium Campylobacter insulaenigrae was first isolated from marine mammals of Scotland in 2004. Only one case of C. insulaenigrae infection in humans has been previously reported. Case presentation An 89-year-old Japanese man without dementia was admitted to our hospital, because he presented with a fever of 38 °C and weakness in right leg since 5 days. He had organized chronic subdural hematoma (CSH), and no history of pre-infection. At the time of admission, he had paralysis of the extraocular muscle, ataxia, and low manual muscle test score of the right side. He was suspected to have Miller Fisher syndrome; however, these symptoms improved without any treatment. On day 22 in the hospital, the patient presented a fever of 38.8 °C, left cranial nerve disorder, and hemiplegia. On day 25, the patient presented with signs of meningeal irritation; cerebrospinal fluid examination indicated an increase in the number of apocytes and a low glucose level. A contrast magnetic resonance imaging (MRI) scan of the patient’s head indicated a contrast enhancement effect in his right meninges. The blood culture showed presence of spirillums; 16S rRNA gene sequencing confirmed that the spirillums in the blood culture were Campylobacter insulaenigrae (C. insulaenigrae). We started treatment with meropenem for bacteremia and meningitis. When the symptoms improved, meropenem was replaced with ampicillin, based on the result of the drug sensitivity test. The treatment continued for 4 weeks. Conclusions We report the first case of meningitis caused by C. insulaenigrae bacteremia in humans, and the second clinical report of C. insulaenigrae infection in humans. The bacterial strains isolated from humans and marine mammals had different genotypes. This suggests that different genotypes could be responsible for differences in the hosts. Further case studies are needed to establish the reasons behind the difference in the manifestations of C. insulaenigrae infections reported so far.

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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