Development of specific oligonucleotide probes for the identification and <i>in situ</i> detection of hydrocarbon‐degrading <i>Alcanivorax</i> strains

Syutsubo, Kazuaki; Kishira, Hideo; Harayama, Shigeaki

doi:10.1046/j.1462-2920.2001.00204.x

Cited by 89 publications

(65 citation statements)

References 23 publications

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“…5 1C) were distinctive features of the plume (Camilli et al, 2010), these factors may have arrested the potential for Alcanivorax to bloom. Alternatively, their suppressed growth may be attributed to a limit in the availability of nitrogen and phosphorous (Harayama et al, 1999;Kasai et al, 2001Kasai et al, , 2002aSyutsubo et al, 2001). Alcanivorax, however, was the dominant hydrocarbon-degrading bacterial group enriched by oil contamination of Gulf beach sands from the DWH spill (Kostka et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

et al. 2013

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The massive influx of crude oil into the Gulf of Mexico during the Deepwater Horizon (DWH) disaster triggered dramatic microbial community shifts in surface oil slick and deep plume waters. Previous work had shown several taxa, notably DWH Oceanospirillales, Cycloclasticus and Colwellia, were found to be enriched in these waters based on their dominance in conventional clone and pyrosequencing libraries and were thought to have had a significant role in the degradation of the oil. However, this type of community analysis data failed to provide direct evidence on the functional properties, such as hydrocarbon degradation of organisms. Using DNA-based stable-isotope probing with uniformly 13 C-labelled hydrocarbons, we identified several aliphatic (Alcanivorax, Marinobacter)-and polycyclic aromatic hydrocarbon (Alteromonas, Cycloclasticus, Colwellia)-degrading bacteria. We also isolated several strains (Alcanivorax, Alteromonas, Cycloclasticus, Halomonas, Marinobacter and Pseudoalteromonas) with demonstrable hydrocarbon-degrading qualities from surface slick and plume water samples collected during the active phase of the spill. Some of these organisms accounted for the majority of sequence reads representing their respective taxa in a pyrosequencing data set constructed from the same and additional water column samples. Hitherto, Alcanivorax was not identified in any of the previous water column studies analysing the microbial response to the spill and we discuss its failure to respond to the oil. Collectively, our data provide unequivocal evidence on the hydrocarbondegrading qualities for some of the dominant taxa enriched in surface and plume waters during the DWH oil spill, and a more complete understanding of their role in the fate of the oil.

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Section: Discussionmentioning

confidence: 99%

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

et al. 2013

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“…Obligate hydrocarbon-degrading bacteria, including Cycloclasticus, Thalassolituus, Oleiphilus, Oleispira, and Alcanivorax species, have been isolated from geographically diverse coastal and open-ocean regions in all seas, in sediments and both surface and deep waters, including areas with minimal oil pollution (9)(10)(11)35). Alcanivorax species are typically among the dominant bacteria found metabolizing crude oil during large spill events (34)(35)(36)(37)(38). Other bacteria, including Marinobacter, Pseudomonas, and Acinetobacter species, which can use hydrocarbons in addition to a broader range of carbon sources, have also been detected in oilpolluted ocean samples (10,34).…”

Section: Both Obligate and Facultative Hydrocarbon-degrading Bacteriamentioning

confidence: 99%

“…Information on population sizes of specific hydrocarbon degraders in the environment is limited, with estimates of Alcanivorax varying between 10 1 and 5 × 10 3 cells/mL (35,41). However, in most studies Alcanivorax cell numbers are below the detection limit (34), as assayed via quantitative PCR (5, 6) or in situ hybridization (36), and their population dynamics in the oligotrophic ocean are unknown. To determine the yield of A. borkumensis SK2 on cyanobacterial alkanes, cells were grown in artificial sea water (ASW) medium either without any organic carbon or containing only the minimum amount of heptadecane that could be added to the culture.…”

Section: Cyanobacterial Hydrocarbon Production Can Support Populationmentioning

confidence: 99%

Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle

Lea‐Smith

Biller

Davey

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

174

122

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Hydrocarbons are ubiquitous in the ocean, where alkanes such as pentadecane and heptadecane can be found even in waters minimally polluted with crude oil. Populations of hydrocarbon-degrading bacteria, which are responsible for the turnover of these compounds, are also found throughout marine systems, including in unpolluted waters. These observations suggest the existence of an unknown and widespread source of hydrocarbons in the oceans. Here, we report that strains of the two most abundant marine cyanobacteria, Prochlorococcus and Synechococcus, produce and accumulate hydrocarbons, predominantly C15 and C17 alkanes, between 0.022 and 0.368% of dry cell weight. Based on global population sizes and turnover rates, we estimate that these species have the capacity to produce 2-540 pg alkanes per mL per day, which translates into a global ocean yield of ∼308-771 million tons of hydrocarbons annually. We also demonstrate that both obligate and facultative marine hydrocarbon-degrading bacteria can consume cyanobacterial alkanes, which likely prevents these hydrocarbons from accumulating in the environment. Our findings implicate cyanobacteria and hydrocarbon degraders as key players in a notable internal hydrocarbon cycle within the upper ocean, where alkanes are continually produced and subsequently consumed within days. Furthermore we show that cyanobacterial alkane production is likely sufficient to sustain populations of hydrocarbon-degrading bacteria, whose abundances can rapidly expand upon localized release of crude oil from natural seepage and human activities.cyanobacteria | hydrocarbons | hydrocarbon cycle | hydrocarbon-degrading bacteria | oil remediation

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“…Since the first description of A. borkumensis in 1998, it has been detected in many marine and coastal habitats worldwide including the Mediterranean Sea, the Pacific Ocean, the Japanese and Chinese Seas and the Arctic Sea 3,4,[6][7][8][9] .…”

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confidence: 99%

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

et al. 2006

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Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation–related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills. Supplementary information The online version of this article (doi:10.1038/nbt1232) contains supplementary material, which is available to authorized users.

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Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon‐degrading Alcanivorax strains

Cited by 89 publications

References 23 publications

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

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