Efficient biodegradation of naphthalene by a newly characterized indigenous Achromobacter sp. FBHYA2 isolated from Tehran Oil Refinery Complex

2012 ◽  
Vol 66 (3) ◽  
pp. 594-602 ◽  
Author(s):  
Sima Farjadfard ◽  
Seyyed Mehdi Borghei ◽  
Amir Hessam Hassani ◽  
Bagher Yakhchali ◽  
Mehdi Ardjmand ◽  
...  
Keyword(s):  
Aromatic Hydrocarbons ◽  
Optimal Growth ◽  
Sole Source ◽  
Growth Conditions ◽  
American Petroleum Institute ◽  
Oil Refinery ◽  
Rrna Gene ◽  
Significant Difference ◽  
Aliphatic And Aromatic Hydrocarbons ◽  
Achromobacter Sp

A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30 °C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals (aliphatic and aromatic hydrocarbons) was also investigated. No biosurfactant was detected during bacterial growth on any aliphatic/aromatic hydrocarbons. The results of hydrophobicity measurements showed no significant difference between naphthalene- and LB-grown cells. The capability of the strain FBHYA2 to degrade naphthalene completely and rapidly without the need to secrete biosurfactant may make it an ideal candidate to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sites.

scholarly journals Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment

2010 ◽  
Vol 60 (12) ◽  
pp. 2996-3001 ◽  
Author(s):  
Shi-Ping Tian ◽  
Yong-Xia Wang ◽  
Bin Hu ◽  
Xiao-Xia Zhang ◽  
Wei Xiao ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Soda Lake ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
Respective Type

A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1 ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 10.7 %) and C17 : 1 ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).

scholarly journals Characterization a Novel Butyric Acid-Producing Bacterium Collinsella aerofaciens Subsp. Shenzhenensis Subsp. Nov.

2019 ◽  
Vol 7 (3) ◽  
pp. 78 ◽  
Author(s):  
Panpan Qin ◽  
Yuanqiang Zou ◽  
Ying Dai ◽  
Guangwen Luo ◽  
Xiaowei Zhang ◽  
...  
Keyword(s):  
Butyric Acid ◽  
Dna Hybridization ◽  
Type Strain ◽  
Inflammatory Diseases ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Human Gut ◽  
Positive Growth ◽  
The 16S Rrna Gene

Butyrate-producing bacteria can biosynthesize butyrate and alleviate inflammatory diseases. However, few studies have reported that the genus Collinsella has the ability to produce butyric acid. Here, our study depicts a Collinsella strain, which is a rod-shaped obligate anaerobe that is able to produce butyric acid. This microorganism was isolated from a human gut, and the optimal growth conditions were found to be 37 °C on PYG medium with pH 6.5. The 16S rRNA gene sequence demonstrated that this microorganism shared 99.93% similarity with C. aerofaciens ATCC 25986T, which was higher than the threshold (98.65%) for differentiating two species. Digital DNA–DNA hybridization and average nucleotide identity values also supported that this microorganism belonged to the species C. aerofaciens. Distinct phenotypic characteristics between TF06-26 and the type strain of C. aerofaciens, such as the fermentation of D-lactose, D-fructose and D-maltose, positive growth under pH 5 and 0.2% (w/v) cholate, suggested this strain was a novel subspecies. Comparative genome analysis revealed that butyric acid kinase and phosphate butyryltransferase enzymes were coded exclusively by this strain, indicating a specific butyric acid-producing function of this C. aerofaciens subspecies within the genus Collinsella. Thus, Collinsella aerofaciens subsp. shenzhenensis subsp. nov. was proposed, with set strain TF06-26T (=CGMCC 1.5216T = DSM 105138T) as the type strain.

scholarly journals Chryseobacterium shandongense sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1860-1865 ◽  
Author(s):  
Fan Yang ◽  
Hong-ming Liu ◽  
Rong Zhang ◽  
Ding-bin Chen ◽  
Xiang Wang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Rrna Gene Sequence ◽  
Yellow Orange ◽  
The 16S Rrna Gene

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow–orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3T was closely related to the strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain YF-3T was 37 mol%. The DNA–DNA relatedness levels between strain YF-3T and the most closely related strains, C. hispalense AG13T and C. taiwanense Soil-3-27T, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. is proposed. The type strain is YF-3T ( = CCTCC AB 2014060T = JCM 30154T).

scholarly journals Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4769-4775 ◽  
Author(s):  
Jeremy A. Dodsworth ◽  
John C. Ong ◽  
Amanda J. Williams ◽  
Alice C. Dohnalkova ◽  
Brian P. Hedlund
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Casamino Acids

An obligately thermophilic, chemolithotrophic, microaerophilic bacterium, designated strain GBS1T, was isolated from the water column of Great Boiling Spring, Nevada, USA. Thiosulfate was required for growth. Although capable of autotrophy, growth of GBS1T was enhanced in the presence of acetate, peptone or Casamino acids. Growth occurred at 70–85 °C with an optimum at 80 °C, at pH 6.50–7.75 with an optimum at pH 7.25, with 0.5–8 % oxygen with an optimum at 1–2 % and with ≤ 200 mM NaCl. The doubling time under optimal growth conditions was 1.3 h, with a final mean cell density of 6.2 ± 0.5 × 107 cells ml− 1. Non-motile, rod-shaped cells 1.4–2.4 × 0.4–0.6 μm in size occurred singly or in pairs. The major cellular fatty acids (>5 % of the total) were C20 : 1ω9c, C18 : 0, C16 : 0 and C20 : 0. Phylogenetic analysis of the GBS1T 16S rRNA gene sequence indicated an affiliation with Thermocrinis ruber and other species of the genus Thermocrinis, but determination of 16S rRNA gene sequence similarity ( ≤ 97.10 %) and in silico estimated DNA–DNA hybridization values ( ≤ 18.4 %) with the type strains of recognized Thermocrinis species indicate that the novel strain is distinct from described species. Based on phenotypic, genotypic and phylogenetic characteristics, a novel species, Thermocrinis jamiesonii sp. nov., is proposed, with GBS1T ( = JCM 19133T = DSM 27162T) as the type strain.

scholarly journals Carboxydocella manganica sp. nov., a thermophilic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium from a Kamchatka hot spring

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 890-894 ◽  
Author(s):  
G. B. Slobodkina ◽  
A. N. Panteleeva ◽  
T. G. Sokolova ◽  
E. A. Bonch-Osmolovskaya ◽  
A. I. Slobodkin
Keyword(s):  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Kamchatka Peninsula ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Bacterium Strain

A thermophilic, anaerobic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium (strain SLM 61T) was isolated from a terrestrial hot spring on the Kamchatka peninsula. The cells were straight rods, 0.5–0.6 µm in diameter and 1.0–6.0 µm long, and exhibited tumbling motility by means of peritrichous flagellation. The strain grew at 26–70 °C, with an optimum at 58–60 °C, and at pH 5.5–8.0, with an optimum at pH 6.5. Growth of SLM 61T was observed at 0–2.0 % (w/v) NaCl, with an optimum at 0.5 % (w/v). The generation time under optimal growth conditions was 40 min. Strain SLM 61T grew and reduced Mn(IV), Fe(III) or nitrate with a number of organic acids and complex proteinaceous compounds as electron donors. It was capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor, Fe(III) but not Mn(IV) or nitrate as an electron acceptor and CO2 as a carbon source. It also was able to ferment pyruvate, yeast extract, glucose, fructose, sucrose and maltose. The G+C content of DNA of strain SLM 61T was 50.9 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Carboxydocella thermautotrophica 41T (96.9 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Carboxydocella manganica sp. nov. is proposed. The type strain is SLM 61T ( = DSM 23132T  = VKM B-2609T). C. manganica is the first described representative of the genus Carboxydocella that possesses the ability to reduce metals and does not utilize CO.

scholarly journals Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s

2020 ◽  
Author(s):  
Estelle Mühle ◽  
Chloé Abry ◽  
Priscilla Leclerc ◽  
Gogoa-Marthe Goly ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Sole Source ◽  
Major Fatty Acid ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Description

Genome sequence analysis of two strains collected in Canada at the end of the 1970s and deposited in 1998 at the Collection de l’Institut Pasteur has led to the taxonomic description of a novel fish-associated species in the genus Flavobacterium . Both strains, CIP 105534T and CIP 105535, were yellow-pigmented, Gram-stain-negative, non-spore-forming rod-shaped bacteria that exhibited gliding motility. They grew aerobically in a temperature range from 5 to 30 °C with optimal growth at 25 °C on trypticase soy or Reasoner's 2A agar but they did not grow on marine agar. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH (shown as summed feature 3), C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 0. The major polyamine was sym-homospermidine. Phosphatidylethanolamine and, most notably, ornithine-containing lipid OL2 and unidentified aminophospholipid APL1 were major polar lipids. A yellow pigment spot was visible after chromatographic analysis. The predominant respiratory quinone was MK-6. The G+C content of the two genomes was 34 mol% and their size was around 5.8 Mb. Comparison of the 16S rRNA gene sequences with those of the closely related type strains showed high levels of relatedness with Flavobacterium collinsii and Flavobacterium pectinovorum . All average nucleotide identity (ANI) and digital DNA–DNA hybridization values estimated against publicly available Flavobacterium genome assemblies were lower than 90 and 30 %, respectively. Phylogenetic, phenotypic and chemotaxonomic data indicated that the two strains represent a novel species of the genus Flavobacterium , for which the name Flavobacterium bizetiae sp. nov. is proposed. The type strain is CIP 105534T (=LMG 1342T). The unique ability of F. bizetiae to use melibiose as a sole source of carbon could provide a simple phenotypic test to discriminate F. bizetiae from its closest relatives.

scholarly journals Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 456 ◽  
Author(s):  
Daniel Garrido-Sanz ◽  
Miguel Redondo-Nieto ◽  
María Guirado ◽  
Oscar Pindado Jiménez ◽  
Rocío Millán ◽  
...  
Keyword(s):  
Aromatic Hydrocarbons ◽  
Bacterial Consortium ◽  
Polluted Soil ◽  
Total Petroleum Hydrocarbons ◽  
Ring Cleavage ◽  
Rrna Gene ◽  
Initial Oxidation ◽  
Microbiome Composition ◽  
Genes Encoding ◽  
Aliphatic And Aromatic Hydrocarbons

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

scholarly journals Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland

2006 ◽  
Vol 56 (12) ◽  
pp. 2887-2892 ◽  
Author(s):  
Mariane Schmidt ◽  
Anders Priemé ◽  
Peter Stougaard
Keyword(s):  
Gene Sequence ◽  
Unsaturated Fatty Acids ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Psychrophilic Bacterium ◽  
The Novel ◽  
Alkaliphilic Bacterium

A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71T belonged to the family ‘Flexibacteraceae’ in the phylum Bacteroidetes. Strain GCM71T, together with five related isolates from ikaite columns, formed a separate cluster with 86–93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71T was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA–DNA hybridization between strain GCM71T and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71T were pH 9.2–10.0, 5 °C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90–97 %), with a high abundance of iso-C17 : 1 ω9c (17.5 %), iso-C17 : 0 3-OH (17.5 %) and summed feature 3, comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71T (=DSM 17998T=LMG 23454T) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.

scholarly journals Benzoic acid-degrading halophilic strain Halomonas sp. D2

2021 ◽  
pp. 171-177
Author(s):  
Darya I. Usanina ◽  
◽  
Anna A. Pyankova ◽  
Elena G. Plotnikova ◽  
◽  
...  
Keyword(s):  
Benzoic Acid ◽  
Aromatic Hydrocarbons ◽  
Environmental Pollutants ◽  
Sole Source ◽  
Saline Soils ◽  
Rrna Gene ◽  
Clay Deposits ◽  
Perm Krai ◽  
The Rich ◽  
The 16S Rrna Gene

Benzoic acid is widely used in various fields of industry, and it is a intermediate in the bacterial catabolism of many aromatic compounds, environmental pollutants. Halomonas sp. D2 strain, isolated from clay deposits of the salt mine of the Verkhnekamsky salt deposit (Solikamsk, Perm krai) is capable of using benzoic acid (BA) as a sole source of carbon and energy. Halomonas sp. D2 grows in the rich Raymond’s medium in the presence of 10-300 g/L NaCl and in the mineral medium with BA (1 g/L) in the presence of 30-70 g/L NaCl. The gene (benA) encoding the benzoate 1,2-dioxygenase alpha subunit was detected in the strain D2. Analysis of benA gene of the strain D2 showed the highest similarity (94.86%) with benA gene of Halomonas taeanensis BH539T with which the strain D2 is the most phylogenetically close in the 16S rRNA gene (99.43% similarity). The revealed properties of Halomonas sp. D2 strain makes it promising for use in biotechnologies for the restoration of saline soils and water contaminated with aromatic hydrocarbons.

Thermosipho ferrireducens sp.nov., an anaerobic thermophilic iron(III)-reducing bacterium isolated from a deep-sea hydrothermal sulfide deposits

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Yao Chen ◽  
Yang He ◽  
Zongze Shao ◽  
Xiqiu Han ◽  
Danling Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Carlsberg Ridge

A thermophilic, anaerobic, iron-reducing bacterium strain JL129W03T (=KCTC 15905T=MCCC 1A14213T) was isolated from a sulfide sample collected from the Daxi hydrothermal field (60.5° E, 6.4° N, 2919 m depth) on the Carlsberg Ridge, northwest Indian Ocean. Cells grew at 55–75 °C(optimum, 70 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and at NaCl concentrations of 1.5–4.5 % (w/v; optimum 3.0 %). Under optimal growth conditions, the generation time was around 85 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, carbohydrates, organic acids and one amino acid. It was anaerobic and facultatively dependent on elemental sulphur and various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulphate, thiosulfate or nitrate. The G+C content of its genomic DNA was 34.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that its closest relative was Thermosipho atlanticus DV1140T with 95.81 % 16S rRNA sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Thermosipho , for which the name Thermosipho ferrireducens sp. nov. is proposed. The type strain is strain JL129W03T (=KCTC 15905T;=MCCC 1A14213T).

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