Effects of pressure and temperature on deep sea hydrocarbon-degrading microbial communities in subarctic sediments
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ABSTRACT:
PROVIDER: PRJEB25365 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2365230_1.fastq.gz | Fastqsanger.gz | |||
| ERR2365230_2.fastq.gz | Fastqsanger.gz | |||
| ERR2365240_1.fastq.gz | Fastqsanger.gz | |||
| ERR2365240_2.fastq.gz | Fastqsanger.gz | |||
| ERR2365221_1.fastq.gz | Fastqsanger.gz |
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Project description:The Hatton-Rockall Basin (North-East Atlantic) is an area with potential for deep-sea (2,900 m) hydrocarbon exploration. Following the Deepwater Horizon oil spill, many investigations into the responses of sediment microbial communities to oil pollution have been undertaken. However, hydrostatic pressure is a parameter that is often omitted due to the technical difficulties associated with conducting experiments at high pressure (>10 MPa). In this study, sediments from 2,900 m in the Hatton-Rockall Basin, following a one-week decompression period in a temperature-controlled room at 5°C, were incubated in factorial combinations of 0.1 and 30 MPa, 5 and 20°C, and contamination with a hydrocarbon mixture or uncontaminated controls to evaluate the effect of these environmental variables on the bacterial community composition. Our results revealed varying effects of pressure, temperature, and oil contamination on the composition of the bacterial community within the sediment. Temperature was the strongest determinant of differences in the bacterial community structure between samples followed by pressure. Oil contamination did not exert a strong change in the sediment bacterial community structure when pressure and temperature conditions were held at in situ levels (30 MPa and 5°C). The γ-proteobacteria Pseudomonas and Colwellia, and several Bacteroidetes dominated communities at 30 MPa. In contrast, hydrocarbon degraders such as Halomonas, Alcanivorax, and Marinobacter decreased in relative abundance at the same pressure. This study highlights the importance of considering hydrostatic pressure in ex situ investigations into hydrocarbon-degrading deepwater microbial communities.
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Project description:AimsThe aim of this study was the baseline description of oil-degrading sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination in FSC sediments.Methods and resultsOil-degrading sediment bacteria from 135, 500 and 1000 m were enriched in cultures with crude oil as the sole carbon source (at 12, 5 and 0°C respectively). The enriched communities were studied using culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. Bacterial isolates included well-known oil-degrading taxa and several that are reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at genus level particularly between the shallow and the deep, cold-water stations. Alcanivorax constituted 64% of clones at FSC135 but was absent at deeper stations. Pseudoalteromonas and Oleispira dominated the bacterial community at 500 and 1000 m.ConclusionsThe genus Oleispira emerged as a major player in the early stages of crude oil degradation in deep-sea sediments of the FSC particularly at subzero temperatures. This finding is offering a direction for future research into biomonitoring tools for the detection of low levels of crude oil contamination in the deep FSC, and possibly high latitude cold waters in general.Significance and impact of the studyOil and gas exploration in the FSC occurs at depths >1000 m but baseline environmental data necessary for the assessment of ecosystem recovery to prespill conditions in the event of an oil spill are lacking. This study will contribute to our ability to assess the impact of oil release in the FSC and guide the direction of bioremediation strategies tailored to the area.
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Project description:The bacteria involved in the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in deep sea subsurface environments are largely unknown. In order to reveal their biodiversity, sediments from 2.2 m under the bottom surface at a water depth of 3542 m were sampled on the Middle Atlantic Ridge with a gravity column sampler. The sediments were promptly enriched with either crude oil or a mixture of PAHs (naphthalene, phenanthrene and pyrene) as the sole carbon source, and further enriched with the PAH mixture mentioned above in the lab. The resulting consortia were named C2CO and C2PPN respectively. Their bacterial composition was analysed with plate cultivation, PCR-DGGE and 16S rDNA library analysis. On plates, isolates belonging to Pseudoalteromonas, Halomonas, Marinobacter, Thalassospira and Tistrella dominated the culturable populations. With PCR-DGGE, five major bands closely related to Cycloclasticus, Alteromonas, Thalassospira, Alcanivorax and Rhodospirillaceae were detected in consortium C2CO, while only one major band of Cycloclasticus was detected in consortium C2PPN. In addition, the dynamics of community structure in response to aromatic substrate alterations were examined. As a result, three ribotypes of Cycloclasticus were detected by 16S rDNA library analysis, one which played a key role in phenanthrene degradation; two Alteromonas bacteria dominated the naphthalene reselected consortium. Although bacteria of the two genera grew as the main members of the communities, none of them were isolated, probably owing to their poor cultivability. These results confirm that bacteria of Cycloclasticus are important obligate PAH degraders in marine environments, and coexist with other degrading bacteria that inhabit the deep subsurface sediment of the Atlantic. This supports the view that PAH accumulation and bioattenuation occur in remote areas consistently and continuously.
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Project description:Naphthalene- and phenanthrene-degrading bacteria in Puget Sound sediments were enumerated by most-probable-number enumeration procedures. Sediments from a creosote-contaminated Environmental Protection Agency Superfund Site (Eagle Harbor) contained from 10(4) to 10(7) polycyclic aromatic hydrocarbon (PAH)-degrading bacteria g (dry weight) of sediment-1, whereas the concentration at an uncontaminated site ranged from 10(3) to 10(4) g of sediment(-1). Isolates of PAH-degrading bacteria were obtained from these most-probable-number tubes as well as from sediment samples from noncontaminated sites and from bioreactors enriched with PAHs. The 18 resulting strains were grouped by whole-cell fatty acid analysis into two subgroups. The larger group of strains belonged to the newly described genus Cycloclasticus, whereas the other group contained members of the genus Vibrio. The Cycloclasticus group seems to be widespread in noncontaminated sediments. PAH degradation was confirmed in selected strains on the basis of removal of phenanthrene from growing cultures.
| S-EPMC168130 | biostudies-other
Project 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 [(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.
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Project description:The diversity of indigenous bacteria in sediments from several sites in the Elizabeth River (Virginia) able to degrade multiple polycyclic aromatic hydrocarbons (PAHs) was investigated by the use of classical selective enrichment and molecular analyses. Enrichment cultures containing naphthalene, phenanthrene, fluoranthene, or pyrene as a sole carbon and energy source were monitored by denaturing gradient gel electrophoresis (DGGE) to detect changes in the bacterial-community profile during enrichment and to determine whether the representative strains present were successfully cultured. The DGGE profiles of the final enrichments grown solely on naphthalene and pyrene showed no clear relationship with the site from which the inoculum was obtained. The enrichments grown solely on pyrene for two sample sites had >80% similarity, which suggests that common pyrene-degrading strains may be present in these sediments. The final enrichments grown on fluoranthene and phenanthrene remained diverse by site, suggesting that these strains may be influenced by environmental conditions. One hundred and one isolates were obtained, comprising representatives of the actinomycetes and alpha-, beta-, and gammaproteobacteria, including seven novel isolates with 16S rRNA gene sequences less than 98% similar to known strains. The ability to degrade multiple PAHs was demonstrated by mineralization of 14C-labeled substrate and growth in pure culture. This supports our hypothesis that a high diversity of bacterial strains with the ability to degrade multiple PAHs can be confirmed by the combined use of classical selective enrichment and molecular analyses. This large collection of diverse PAH-degrading strains provides a valuable resource for studies on mechanisms of PAH degradation and bioremediation.
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