Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel)

Gontikaki, Evangelia; Potts, Lloyd D.; Anderson, James A.; Witte, Ursula

doi:10.1111/jam.14030

Cited by 46 publications

(29 citation statements)

References 68 publications

(149 reference statements)

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“…This result was not unexpected, as it has been previously reported [33]. The taxa identified in the microbiome of the diesel-degrading consortium are in agreement with previous works, where it has been shown what Pseudomonas is one of the most abundant genera on hydrocarbon-polluted soils [34,57,58] and Aquabacterium and Chryseobacterium are also common members in hydrocarbon-degrading bacterial communities [58,59]. Although Pseudomonas also rules the degradation of PAHs in sediments [60], other genera present in the diesel-degrading consortium belonging to the Sphingomonadaceae family have also been previously reported to be responsible for the degradation of different PAHs [61,62].…”

Section: Resultssupporting

confidence: 92%

Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Garrido‐Sanz

Redondo‐Nieto

Guirado

et al. 2019

Genes

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Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

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Section: Resultssupporting

confidence: 92%

Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Garrido‐Sanz

Redondo‐Nieto

Guirado

et al. 2019

Genes

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“…Alcanivorax was not represented in the 20 most abundant taxa in the Hatton–Rockall Basin deep‐sea sediments in this study. Alcanivorax dominated an enriched HDB community from continental shelf sediments of the FSC but was absent from deepwater sediments (500–1,000 m) in the same area (Gontikaki et al, ; Potts et al, ). This study confirms the piezosensitivity of Alcanivorax that may explain its absence from deepwater hydrocarbon‐degrading microbial communities following the DwH oil spill (Kimes et al, ; Scoma et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have reported a synchronous negative effect of deep‐sea conditions of high P and low T on the growth of Halomonas isolates (Kaye & Baross, ). Halomonas also represented 5%–9% of taxa in enrichment cultures from continental shelf sediments in the FSC but was absent from deepwater libraries (Gontikaki, Potts, Anderson, & Witte, ; Potts et al, ). Despite being previously encountered in cold, oil‐contaminated marine environments (Deppe, Richnow, Michaelis, & Antranikian, ; Gerdes, Brinkmeyer, Dieckmann, & Helmke, ), Marinobacter was encountered in higher relative abundance at 0.1 MPa and 20°C in this study.…”

Section: Discussionmentioning

confidence: 99%

Pressure and temperature effects on deep‐sea hydrocarbon‐degrading microbial communities in subarctic sediments

et al. 2018

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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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“…Interestingly, most of the phylotypes detected as differentially abundant in the shallow group are related to hydrocarbon degradation, such as Microcoleus ( Sánchez et al, 2005 ), Ahrensia ( Gontikaki et al, 2018 ), and Thermococcus ( Mardanov et al, 2009 ), and more specific genera such as Tropicimonas ( Harwati et al, 2009 ), Dethiosulfatibacter ( Muangchinda et al, 2013 ), Cellulosimicrobium ( Qin et al, 2018 ), Roseobacter ( Liu et al, 2016 ), Prolixibacter ( Li et al, 2012 ), Desulfuromusa ( Ramos et al, 2013 ), Oceanicola ( Hassanshahian and Boroujeni, 2016 ), and Salinivibrio ( Selvarajan et al, 2017 ) are involved in aromatic hydrocarbons degradation, supporting our hypothesis that this abiotic factor modulates the bacterial communities in the shallow region. We also found other genera such as Psychrilyobacter , which participates in the anaerobic degradation of organic matter ( Graue et al, 2012 ), and Dehalococcoides ( Nuzzo et al, 2017 ) and Dehalobacterium ( Yimiti et al, 2011 ), which detoxify anoxic contamination in marine sediments, such as polychlorinated biphenyls.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico

et al. 2018

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Marine sediments are an example of one of the most complex microbial habitats. These bacterial communities play an important role in several biogeochemical cycles in the marine ecosystem. In particular, the Gulf of Mexico has a ubiquitous concentration of hydrocarbons in its sediments, representing a very interesting niche to explore. Additionally, the Mexican government has opened its oil industry, offering several exploration and production blocks in shallow and deep water in the southwestern Gulf of Mexico (swGoM), from which there are no public results of conducted studies. Given the higher risk of large-scale oil spills, the design of contingency plans and mitigation activities before oil exploitation is of growing concern. Therefore, a bacterial taxonomic baseline profile is crucial to understanding the impact of any eventual oil spill. Here, we show a genus level taxonomic profile to elucidate the bacterial baseline, pointing out richness and relative abundance, as well as relationships with 79 abiotic parameters, in an area encompassing ∼150,000 km2, including a region where the exploitation of new oil wells has already been authorized. Our results describe for the first time the bacterial landscape of the swGoM, establishing a bacterial baseline “core” of 450 genera for marine sediments in this region. We can also differentiate bacterial populations from shallow and deep zones of the swGoM based on their community structure. Shallow sediments have been chronically exposed to aromatic hydrocarbons, unlike deep zones. Our results reveal that the bacterial community structure is particularly enriched with hydrocarbon-degrading bacteria in the shallow zone, where a greater aromatic hydrocarbon concentration was determined. Differences in the bacterial communities in the swGoM were also observed through a comprehensive comparative analysis relative to various marine sediment sequencing projects, including sampled sites from the Deep Water Horizon oil spill. This study in the swGoM provides clues to the bacterial population adaptation to the ubiquitous presence of hydrocarbons and reveals organisms such as Thioprofundum bacteria with potential applications in ecological surveillance. This resource will allow us to differentiate between natural conditions and alterations generated by oil extraction activities, which, in turn, enables us to assess the environmental impact of such activities.

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Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel)

Cited by 46 publications

References 68 publications

Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Pressure and temperature effects on deep‐sea hydrocarbon‐degrading microbial communities in subarctic sediments

Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico

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