Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons

A Gram-stain-negative, motile, rod-shaped, orange-pigmented bacterium able to degrade polycyclic aromatic hydrocarbons was isolated from deep-sea sediment of the Atlantic Ocean and subjected to a polyphasic taxonomic study. The strain, designated s21-N3T, could grow at 4–37 °C (optimum 28 °C), at pH 5–10 (optimum pH 7–8) and with 1–7 % (w/v) NaCl (optimum 2–3 %). Strain s21-N3T was positive for nitrate reduction, denitrification, aesculin hydrolysis, oxidase and catalase, but negative for indole production and urease. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain s21-N3T formed a distinct branch within the genus Erythrobacter, sharing high similarities with three closely related strains, Erythrobacter marinus HWDM-33T (98.67 %), ‘Erythrobacter luteus’ KA37 (97.80 %) and Erythrobacter gangjinensis K7-2T (97.59 %). The similarities between strain s21-N3T and other type strains of recognized species within the genus Erythrobacter ranged from 95.00 to 96.47 %. The digital DNA–DNA hybridization values and average nucleotide identity (ANI) values between strain s21-N3T and the three closely related strains Erythrobacter marinus HWDM-33T, ‘Erythrobacter luteus’ KA37 and Erythrobacter gangjinensis K7-2T were 18.60, 18.00 and 18.50 % and 74.24, 72.49 and 72.54 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and summed feature 3 (C16 : 1ω7c/ω6c). The respiratory lipoquinone was identified as Q-10. The major polar lipids comprised sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The G+C content of the chromosomal DNA was determined to be 58.18 mol%. The combined genotypic and phenotypic distinctiveness demonstrated that strain s21-N3T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter atlanticus sp. nov. is proposed, with the type strain s21-N3T ( = MCCC 1A00519T = KCTC 42697T).

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Genetic diversity of bacterial strains isolated from soils, contaminated with polycyclic aromatic hydrocarbons, by 16S rRNA gene sequencing and amplified fragment length polymorphism fingerprinting

Microbiological Research ◽

10.1016/j.micres.2005.07.006 ◽

2006 ◽

Vol 161 (2) ◽

pp. 150-157 ◽

Cited By ~ 7

Author(s):

G. La Rosa ◽

E. De Carolis ◽

M. Sali ◽

M. Papacchini ◽

C. Riccardi ◽

...

Keyword(s):

Genetic Diversity ◽

Polycyclic Aromatic Hydrocarbons ◽

Aromatic Hydrocarbons ◽

Fragment Length Polymorphism ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Bacterial Strains ◽

Polycyclic Aromatic ◽

Rrna Gene Sequencing

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Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

10.1101/777730 ◽

2019 ◽

Cited By ~ 2

Author(s):

Ella T. Sieradzki ◽

Michael Morando ◽

Jed A. Fuhrman

Keyword(s):

Polycyclic Aromatic Hydrocarbons ◽

Los Angeles ◽

Stable Isotope ◽

Aromatic Hydrocarbons ◽

Degradation Pathway ◽

Stable Isotope Probing ◽

Rrna Gene ◽

Port Of Los Angeles ◽

Polycyclic Aromatic ◽

Bacterial Biodegradation

AbstractBacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by low chronic inputs can respond to an acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We show a switch in the composition of the PAH degrading community from diverse early-responding generalists to late-blooming specialized degraders. This switch demonstrates the ability of the local seed community of degraders at the Port of LA to incorporate carbon from PAHs independently of a labile-hydrocarbon degrading succession. We were able to directly show that assembled genomes belonged to naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in any of those genomes and even when combining genes from the entire microbial community. We use metabolic pathways identified in those genomes to generate metagenomic-based recommendations for future optimization of PAHs bioremediation.

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Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons

Applied and Environmental Microbiology ◽

10.1128/aem.70.4.1944-1955.2004 ◽

2004 ◽

Vol 70 (4) ◽

pp. 1944-1955 ◽

Cited By ~ 182

Author(s):

Natalie M. E. J. Leys ◽

Annemie Ryngaert ◽

Leen Bastiaens ◽

Willy Verstraete ◽

Eva M. Top ◽

...

Keyword(s):

Polycyclic Aromatic Hydrocarbons ◽

16S Rrna ◽

16S Rrna Gene ◽

Aromatic Hydrocarbons ◽

Contaminated Soils ◽

Denaturing Gradient Gel Electrophoresis ◽

Rrna Gene ◽

Soil Dna ◽

Detection Techniques ◽

Polycyclic Aromatic

ABSTRACT Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 104 CFU g of soil−1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.

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Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.013532-0 ◽

2010 ◽

Vol 60 (3) ◽

pp. 504-509 ◽

Cited By ~ 17

Author(s):

Arturo Rodríguez-Blanco ◽

Gilles Vetion ◽

Marie-Line Escande ◽

Daniel Delille ◽

Jean-François Ghiglione

Keyword(s):

Polycyclic Aromatic Hydrocarbons ◽

16S Rrna ◽

16S Rrna Gene ◽

Molecular Mass ◽

Aromatic Hydrocarbons ◽

Direct Sequencing ◽

High Molecular Mass ◽

Intertidal Sediment ◽

Rrna Gene ◽

Polycyclic Aromatic

A Gram-negative, rod-shaped, halotolerant bacterium, designated strain CEE_131T, which degraded high-molecular-mass polycyclic aromatic hydrocarbons of four and five rings, was isolated from intertidal sediment of Corcubion Ria in Cee, A Coruña, Spain. Direct sequencing showed ambiguities and suggested heterogeneity. Cloned 16S rRNA gene sequence PCR products yielded five different sequences varying at five positions. Strain CEE_131T showed rather distant relationships to its phylogenetically closest neighbours, including the genera Rheinheimera and Serratia, exhibiting 91 % sequence similarity with Rheinheimera perlucida BA131T and Serratia proteamaculans subsp. quinovora DSM 4597T. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. The DNA G+C content was 41.7 mol%. On the basis of these distinct phenotypic and genotypic characteristics, strain CEE_131T is considered to represent a novel species in a new genus in the class Gammaproteobacteria, for which the name Gallaecimonas pentaromativorans gen. nov., sp. nov. is proposed. The type strain is CEE_131T (=DSM 21945T=CECT 7479T).

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Degradation of Polycyclic Aromatic Hydrocarbons by a Newly Discovered Enteric Bacterium, Leclercia adecarboxylata

Applied and Environmental Microbiology ◽

10.1128/aem.70.5.3163-3166.2004 ◽

2004 ◽

Vol 70 (5) ◽

pp. 3163-3166 ◽

Cited By ~ 62

Author(s):

Priyangshu Manab Sarma ◽

Dhruva Bhattacharya ◽

S. Krishnan ◽

Banwari Lal

Keyword(s):

Polycyclic Aromatic Hydrocarbons ◽

Aromatic Hydrocarbons ◽

Molecular Typing ◽

Sole Carbon Source ◽

Clinical Strain ◽

Oily Sludge ◽

Rrna Gene ◽

Enteric Bacterium ◽

Polycyclic Aromatic ◽

The 16S Rrna Gene

ABSTRACT A bacterial strain, PS4040, capable of degrading polycyclic aromatic hydrocarbons for use as the sole carbon source was isolated from oily-sludge-contaminated soil. The 16S rRNA gene showed 98.8% homology to that of Leclercia adecarboxylata. Comparative molecular typing with the clinical strain of L. adecarboxylata revealed that there were few comigrating and few distinct amplimers among them.

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Effective Removal of Alkanes and Polycyclic Aromatic Hydrocarbons by Bacteria from Soil Chronically Exposed to Crude Petroleum Oil

10.21203/rs.3.rs-207407/v1 ◽

2021 ◽

Author(s):

Eman Afkar ◽

Aly M. Hafez ◽

Rashid I.H. Ibrahim ◽

Munirah Aldayel

Keyword(s):

Polycyclic Aromatic Hydrocarbons ◽

Crude Oil ◽

Aromatic Hydrocarbons ◽

Oil Spills ◽

Practical Significance ◽

Gas Chromatography Mass Spectrometry ◽

Rrna Gene ◽

Bacterial Strains ◽

Polycyclic Aromatic ◽

Long Chain

Abstract In this study, two bacterial strains isolated from an oil-contaminated soil, designated as AramcoS2 and AramcoS4 were able to degrade crude oil, long-chain n-alkanes of C10 to C20; (n-decane, n-undecane, n-dodecane, n-tridecane, n-tetradecane, n-pentadecane, n-hexadecane, n-heptadecane, n-octadecane n-nonadecane, and n-eicosane) and polycyclic aromatic hydrocarbons (PAHs) including biphenyl, naphthalene, and anthracene. Gas chromatography-mass spectrometry (GC-MS) technique was conducted to analyze and identify the crude oil residues after biodegradation. AramcoS2 and AramcoS4 were able to reduce the concentration of long-chain n-alkanes of C10-C20 efficiently on average by 77% of the original concentration. Both isolates could also degrade PAHs on average by 67% of the original concentration within 7 and 14 days of incubation at 30ºC, pH=6.8±0.2. The 16S rRNA gene sequences of AramcoS2 and S4 classified these isolates as Actinobacteria; well-known alkanes and PAHs degraders. The nucleotide sequences of AramcoS2 and AramcoS4 were submitted to the GenBank database under the accession numbers MN142506 and MN142551, respectively. Both isolates can be used to restore the environments contaminated with crude oil components. They should be of great practical significance both in bioremediation of soil contaminated with crude oil and bio-treatment of oil spills on surface water.

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Molecular Characterization of Fusarium Solani Degrades a Mixture of Low and High Molecular Weight Polycyclic Aromatic Hydrocarbons

The Open Biotechnology Journal ◽

10.2174/1874070701711010027 ◽

2017 ◽

Vol 11 (1) ◽

pp. 27-35 ◽

Cited By ~ 5

Author(s):

Abd El-Latif Hesham ◽

Elsayed A. Mohamed ◽

Asmaa M.M. Mawad ◽

Ameer Elfarash ◽

Bahaa S. Abd El-Fattah ◽

...

Keyword(s):

Molecular Weight ◽

Polycyclic Aromatic Hydrocarbons ◽

High Molecular Weight ◽

Aromatic Hydrocarbons ◽

Fusarium Solani ◽

Polluted Soil ◽

White Rot ◽

White Rot Fungus ◽

Rrna Gene ◽

Polycyclic Aromatic

Objectives:This study evaluates the ability of a non-white rot fungus strain, HESHAM-1, to degrade a mixture of low (naphthalene and phenanthrene) and high (chrysene and benzo(a)pyrene) molecular weight polycyclic aromatic hydrocarbons (LMW and HMW PAHs).Methods:Strain HESHAM-1 was isolated from oil polluted soil by enrichment method using phenanthrene as the sole source of carbon and energy. The strain showed the ability to tolerate and degrade a mixture of both low and high molecular weight PAHs. In the presences of LMW-PAHs (naphthalene and phenanthrene) as co-substrate, chrysene and benzo(a)pyrene (HMW-PAHs) were, respectively degraded by the fungus strain HESHAM-1 which was confirmed by GC-MS analyses.Results:The degradation rate was found as 84.82% for naphthalene, 40.09% for phenanthrene, 57.84% for chrysene and 71.06% for benzo(a)pyrene at the end of 10 days. This is the first report describing the biodegradation of a mixture of four PAH compounds by non-white rot fungus strain HESHAM-1 isolated from Egyptian oil-polluted soil. The fungus strain HESHAM-1 was identified by morphological characteristics and molecular genetics technique based on PCR amplification and sequencing of the internal transcribed spacers (ITSs) of the rDNA region and intervening 5.8S rRNA gene. Blast result and phylogenetic analysis of gene sequencing suggested that strain HESHAM-1 was closely related toFusarium solaniwith 100% sequence identity.Conclusion:The present study clearly demonstrates that, strain HESHAM-1 could be used to remove the crude oil from the environment.

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