Isolation and Characterization of a Novel Polycyclic Aromatic Hydrocarbon–Degrading Bacterium,<i>Sphingopyxis</i>sp. strain M2R2, Capable of Passive Spreading Motility Through Soil

LaRoe, Sarah L.; Wang, Bin; Han, Jong‐In

doi:10.1089/ees.2010.0054

Cited by 27 publications

(9 citation statements)

References 37 publications

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“…As explained in Section 7, in place of the usual Gramnegative LPS found in Alphaproteobacteria subclass of bacteria as well as in eukaryotes, the outer membrane of sphingomonads cells are comprised of glycosphingolipids (Yabuuchi et al, 1999). The characteristic feature of hydrophobicity of glycosphingolipids (GSLs), which interacts with and aids in the uptake of the substrate (PAH) into the cell envelope, possibly plays a significant role in improving the biodegradability of PAHs (Kawahara et al, 1999;LaRoe et al, 2010). The structure of GSLs can vary among species (Kawahara et al, 1999(Kawahara et al, , 2001LaRoe et al, 2010).…”

Section: The Presence Of Glycosphingolipids In Sphingomonad Cell Wallsmentioning

confidence: 99%

“…The characteristic feature of hydrophobicity of glycosphingolipids (GSLs), which interacts with and aids in the uptake of the substrate (PAH) into the cell envelope, possibly plays a significant role in improving the biodegradability of PAHs (Kawahara et al, 1999;LaRoe et al, 2010). The structure of GSLs can vary among species (Kawahara et al, 1999(Kawahara et al, , 2001LaRoe et al, 2010). Since the carbohydrate section of a GSL is markedly shorter than that of LPS, the cell surface of sphingomonads is more hydrophobic and negatively charged than that of other Gram-negative bacteria (Kawahara et al, 2001).…”

Section: The Presence Of Glycosphingolipids In Sphingomonad Cell Wallsmentioning

confidence: 99%

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Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Waigi

Kang

Goikavi

et al. 2015

International Biodeterioration & Biodegradation

155

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Section: The Presence Of Glycosphingolipids In Sphingomonad Cell Wallsmentioning

confidence: 99%

Section: The Presence Of Glycosphingolipids In Sphingomonad Cell Wallsmentioning

confidence: 99%

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Waigi

Kang

Goikavi

et al. 2015

International Biodeterioration & Biodegradation

155

View full text Add to dashboard Cite

“…(); (2) Al‐Mailem et al. (); (3) LaRoe, Wang, & Han (); (4) Al‐Mailem, Eliyas, et al (); (5) Al‐Awadhi, Al‐Mailem, Dashti, Hakam, et al. (); (6) Radwan, Mahmoud, Khanafer, Al‐Habib, & Al‐Hasan (); (7) Gauthier et al.…”

Section: Resultsmentioning

confidence: 99%

Capabilities and limitations of DGGE for the analysis of hydrocarbonoclastic prokaryotic communities directly in environmental samples

2017

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Prokaryotic communities in pristine and oil‐contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture‐dependent and culture‐independent approaches. The former technique was the dilution‐plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank. The plating method offered the advantages of capturing the targeted hydrocarbonoclastic microorganisms, counting them and providing cultures for further study. However, this technique could not capture more than a total of 15 different prokaryotic taxa. Those taxa belonged predominantly to the genera Alcanivorax, Pseudoxanthomonas, Bosea, Halomonas, and Marinobacter. The individual isolates in culture consumed between 19 and 50% of the available crude oil in 10 days. Although the culture‐independent approach revealed much more microbial diversity, it was not problem‐free. The subdivision primers exhibited satisfactory specificity, but they failed to capture all the available taxa. The universal bacterial primer pair ignored Actinobacteria altogether, although the primer pair specific for Actinobacteria captured many of them, for example, the genera Geodermatophilus, Streptomyces, Mycobacterium, Pontimonas, Rhodococcus, Blastococcus, Kocuria, and many others. Because most researchers worldwide use universal primers for PCR, this finding should be considered critically to avoid misleading interpretations.

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“…However, no pyrene degrading microorganisms could be enriched from the unfertilized soil sample under the isolation and cultivation conditions applied. All genera have been reported to be able to degrade PAHs: members of the genus Bordetella were shown to degrade phenanthrene and pyrene (Yuan et al 2009b), Sphingopyxis to degrade naphthalene and phenanthrene (LaRoe et al 2010) and Stenotrophomonas to degrade phenanthrene (Andreoni et al 2004), pyrene and other high molecular weight PAHs (Boonchan et al 1998). Based on the facts that the enrichment cultures showed growth and efficiently degraded pyrene, were highly stable, and all members were reported to be related to PAH degradation, we conclude that we isolated interdependent PAH degrading consortia.…”

Section: Discussionmentioning

confidence: 99%

Microbial communities in pyrene amended soil–compost mixture and fertilized soil

et al. 2017

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Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of 13C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH. We performed statistical analyses of bacterial genera abundance data based on total DNA and RNA (for comparison) extracted from the soil samples. The results revealed complex pyrene degrading communities with low abundance of individual degraders instead of a limited number of abundant key players. The bacterial degrader communities of the soil-compost mixture and soil fertilized with farmyard manure differed considerably in composition albeit showing similar degradation kinetics. Additional analyses were carried out on enrichment cultures and enabled the reconstruction of several nearly complete genomes, thus allowing to link microcosm and enrichment experiments. However, pyrene mineralizing bacteria enriched from the compost or unfertilized soil-compost samples did not dominate pyrene degradation in the soils. Based on the present findings, evaluations of PAH degrading microorganisms in complex soil mixtures with high organic matter content should not target abundant key degrading species, since the specific degraders may be highly diverse, of low abundance, and masked by high bacterial background.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-016-0306-9) contains supplementary material, which is available to authorized users.

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Isolation and Characterization of a Novel Polycyclic Aromatic Hydrocarbon–Degrading Bacterium,Sphingopyxissp. strain M2R2, Capable of Passive Spreading Motility Through Soil

Cited by 27 publications

References 37 publications

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

Capabilities and limitations of DGGE for the analysis of hydrocarbonoclastic prokaryotic communities directly in environmental samples

Microbial communities in pyrene amended soil–compost mixture and fertilized soil

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