Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sediments
Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used s...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-07-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00695/full |
| _version_ | 1818586693698060288 |
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| author | Tony eGutierrez Jennifer F Biddle Andreas eTeske Michael eAitken |
| author_facet | Tony eGutierrez Jennifer F Biddle Andreas eTeske Michael eAitken |
| author_sort | Tony eGutierrez |
| collection | DOAJ |
| description | Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used stable-isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under aerobic conditions in sediments from Guaymas Basin with uniformly labeled [13C]phenanthrene. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from phenanthrene enrichments) were identified to belong to the genus Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Cycloclasticus to determine their abundance in sediment incubations amended with unlabeled phenanthrene and showed substantial increases in gene abundance during the experiments. We also isolated a strain, BG-2, representing the SIP-identified Cycloclasticus sequence (99.9% 16S rRNA gene sequence identity), and used this strain to provide direct evidence of phenanthrene degradation and mineralization. In addition, we isolated Halomonas, Thalassospira and Lutibacterium spp. with demonstrable phenanthrene-degrading capacity from Guaymas Basin sediment. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of PAH-degrading bacteria in the deep-sea. |
| first_indexed | 2024-12-16T08:57:01Z |
| format | Article |
| id | doaj.art-a9255be176434e0abadfdfb2c2b17327 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-16T08:57:01Z |
| publishDate | 2015-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-a9255be176434e0abadfdfb2c2b173272022-12-21T22:37:16ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-07-01610.3389/fmicb.2015.00695149000Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sedimentsTony eGutierrez0Jennifer F Biddle1Andreas eTeske2Michael eAitken3Heriot-Watt UniversityUniversity of DelawareUniversity of North Carolina at Chapel HillUniversity of North Carolina at Chapel HillMarine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used stable-isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under aerobic conditions in sediments from Guaymas Basin with uniformly labeled [13C]phenanthrene. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from phenanthrene enrichments) were identified to belong to the genus Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Cycloclasticus to determine their abundance in sediment incubations amended with unlabeled phenanthrene and showed substantial increases in gene abundance during the experiments. We also isolated a strain, BG-2, representing the SIP-identified Cycloclasticus sequence (99.9% 16S rRNA gene sequence identity), and used this strain to provide direct evidence of phenanthrene degradation and mineralization. In addition, we isolated Halomonas, Thalassospira and Lutibacterium spp. with demonstrable phenanthrene-degrading capacity from Guaymas Basin sediment. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of PAH-degrading bacteria in the deep-sea.http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00695/fullhydrocarbon degradationstable isotope probingdeep seaGuaymas basinmarine environmentpolycyclic aromatic hydrocarbons (PAHs) |
| spellingShingle | Tony eGutierrez Jennifer F Biddle Andreas eTeske Michael eAitken Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sediments Frontiers in Microbiology hydrocarbon degradation stable isotope probing deep sea Guaymas basin marine environment polycyclic aromatic hydrocarbons (PAHs) |
| title | Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sediments |
| title_full | Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sediments |
| title_fullStr | Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sediments |
| title_full_unstemmed | Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sediments |
| title_short | Cultivation-dependent and cultivation-independent characterisation of hydrocarbon-degrading bacteria in Guaymas Basin sediments |
| title_sort | cultivation dependent and cultivation independent characterisation of hydrocarbon degrading bacteria in guaymas basin sediments |
| topic | hydrocarbon degradation stable isotope probing deep sea Guaymas basin marine environment polycyclic aromatic hydrocarbons (PAHs) |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00695/full |
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