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Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments.

Gutierrez T, Biddle JF, Teske A, Aitken MD - Front Microbiol (2015)

Bottom Line: 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 PHE 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 PHE degradation and mineralization.In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-degrading capacity from Guaymas Basin sediment.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ; School of Life Sciences, Heriot-Watt University, Edinburgh UK.

ABSTRACT
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 [(13)C]-phenanthrene (PHE). The dominant sequences in clone libraries constructed from (13)C-enriched bacterial DNA (from PHE 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 PHE 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 PHE degradation and mineralization. In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-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.

No MeSH data available.


Related in: MedlinePlus

In situ still photographs of sampling sites during Alvin dives 4567 and 4571, obtained with the Alvin frame-grabber system (http://4dgeo.whoi.edu/alvin). The (Top) image shows the benthic sediment without microbial mats or hydrothermal features sampled during dive 4567; the (Bottom) image shows the microbial mats and sulfur precipitates on the sediment surface that reveal hydrothermal influence. Right, photo of core 4571-2 after shipboard retrieval; the reddish spots are oil droplets in the sediment core.
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Figure 1: In situ still photographs of sampling sites during Alvin dives 4567 and 4571, obtained with the Alvin frame-grabber system (http://4dgeo.whoi.edu/alvin). The (Top) image shows the benthic sediment without microbial mats or hydrothermal features sampled during dive 4567; the (Bottom) image shows the microbial mats and sulfur precipitates on the sediment surface that reveal hydrothermal influence. Right, photo of core 4571-2 after shipboard retrieval; the reddish spots are oil droplets in the sediment core.

Mentions: Samples were collected in 2009 on R/V Atlantis cruise AT15-56 by push coring with the submersible Alvin. Core 4567-24 was collected on November 28, 2009 from cold non-hydrothermal sediment with an in situ temperature of +4 to 5°C throughout the sediment core, no free sulfide, and no overlying bacterial mat, at a water depth of 2011 m at 27°0.542′N, 111°24.488′W. Core 4571-2 was collected on December 2, 2009 from a site with oil-rich sediments next to a well-developed Beggiatoa mat, at a water depth of 2007 m at 27°0.388′N, 111°24.560′W (Figure 1). This core was characterized by high porewater sulfide concentrations in the range of 2–4.5 mM, and an in situ temperature gradient of ca. 10°C at the surface to near 50°C at 40 cm depth, as measured with Alvin’s Heatflow probe (McKay et al., 2012). Cores were brought to the surface, immediately transferred and kept in a cold room +4°C, then sectioned by depth. At the time of collection, aliquots of the core samples 0–4 cm below seafloor were stored in sterile Falcon tubes and kept at +4°C for subsequent use within 2 weeks in enrichment, mineralization, degradation, and SIP experiments (described below).


Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments.

Gutierrez T, Biddle JF, Teske A, Aitken MD - Front Microbiol (2015)

In situ still photographs of sampling sites during Alvin dives 4567 and 4571, obtained with the Alvin frame-grabber system (http://4dgeo.whoi.edu/alvin). The (Top) image shows the benthic sediment without microbial mats or hydrothermal features sampled during dive 4567; the (Bottom) image shows the microbial mats and sulfur precipitates on the sediment surface that reveal hydrothermal influence. Right, photo of core 4571-2 after shipboard retrieval; the reddish spots are oil droplets in the sediment core.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493657&req=5

Figure 1: In situ still photographs of sampling sites during Alvin dives 4567 and 4571, obtained with the Alvin frame-grabber system (http://4dgeo.whoi.edu/alvin). The (Top) image shows the benthic sediment without microbial mats or hydrothermal features sampled during dive 4567; the (Bottom) image shows the microbial mats and sulfur precipitates on the sediment surface that reveal hydrothermal influence. Right, photo of core 4571-2 after shipboard retrieval; the reddish spots are oil droplets in the sediment core.
Mentions: Samples were collected in 2009 on R/V Atlantis cruise AT15-56 by push coring with the submersible Alvin. Core 4567-24 was collected on November 28, 2009 from cold non-hydrothermal sediment with an in situ temperature of +4 to 5°C throughout the sediment core, no free sulfide, and no overlying bacterial mat, at a water depth of 2011 m at 27°0.542′N, 111°24.488′W. Core 4571-2 was collected on December 2, 2009 from a site with oil-rich sediments next to a well-developed Beggiatoa mat, at a water depth of 2007 m at 27°0.388′N, 111°24.560′W (Figure 1). This core was characterized by high porewater sulfide concentrations in the range of 2–4.5 mM, and an in situ temperature gradient of ca. 10°C at the surface to near 50°C at 40 cm depth, as measured with Alvin’s Heatflow probe (McKay et al., 2012). Cores were brought to the surface, immediately transferred and kept in a cold room +4°C, then sectioned by depth. At the time of collection, aliquots of the core samples 0–4 cm below seafloor were stored in sterile Falcon tubes and kept at +4°C for subsequent use within 2 weeks in enrichment, mineralization, degradation, and SIP experiments (described below).

Bottom Line: 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 PHE 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 PHE degradation and mineralization.In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-degrading capacity from Guaymas Basin sediment.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC USA ; School of Life Sciences, Heriot-Watt University, Edinburgh UK.

ABSTRACT
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 [(13)C]-phenanthrene (PHE). The dominant sequences in clone libraries constructed from (13)C-enriched bacterial DNA (from PHE 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 PHE 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 PHE degradation and mineralization. In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-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.

No MeSH data available.


Related in: MedlinePlus