Determining the identity and roles of oil‐metabolizing marine bacteria from the Thames estuary, UK

Abstract

Crude oil is a complex mixture of different hydrocarbons. While diverse bacterial communities can degrade oil, the specific roles of individual members within such communities remain unclear. To identify the key bacterial taxa involved in aerobic degradation of specific hydrocarbons, microcosm experiments were established using seawater from Stanford le Hope, Thames estuary, UK, adjacent to a major oil refinery. In all microcosms, hydrocarbon degradation was significant within 10 weeks, ranging from > 99% of low-molecular-weight alkanes (C(10)-C(18)), 41-84% of high-molecular-weight alkanes (C(20)-C(32)) and pristane, and 32-88% of polycyclic aromatic hydrocarbons (PAHs). Analysis of 16S rRNA sequences from clone libraries and denaturing gradient gel electrophoresis (DGGE) indicated that, except when incubated with fluorene, PAH-degrading communities were dominated by Cycloclasticus. Moreover, PAH-degrading communities were distinct from those in microcosms containing alkanes. Degradation of the branched alkane, pristane, was carried out almost exclusively by Alcanivorax. Bacteria related to Thalassolituus oleivorans (99-100% identity) were the dominant known alkane degraders in n-alkane (C(12)-C(32)) microcosms, while Roseobacter-related bacteria were also consistently found in these microcosms. However, in contrast to previous studies, Thalassolituus, rather than Alcanivorax, was dominant in crude oil-enriched microcosms. The communities in n-decane microcosms differed from those in microcosms supplemented with less volatile alkanes, with a phylogenetically distinct species of Thalassolituus out-competing T. oleivorans. These data suggest that the diversity and importance of the genus Thalassolituus is greater than previously established. Overall, these experiments demonstrate how degradation of different petroleum hydrocarbons is partitioned between different bacterial taxa, which together as a community can remediate petroleum hydrocarbon-impacted estuarine environments.

Obligate oil-degrading marine bacteria

“…Microcosms of Thames salt marsh water from a site close to an oil refinery that were experimentally spiked with crude oil or oil constituents showed blooms of Thalassolituus spp. and Roseobacter spp., when spiked with crude oil, Alcanivorax spp., when spiked with the branched aliphatic hydrocarbon pristine, and Cycloclasticus spp., when spiked with PAHs [34]). A complementary study to analyze the effects of temperature and added nutrients revealed that Alcanivorax only appeared when nutrients were added, and that organisms affiliated to the genus Oleispira (first isolated as a cold-adapted OHCB from crude-oil enrichments of Antarctic seawater [15], bloomed in microcosms maintained at 4°C [59].…”

“…The GenBank and RDP databases currently contain 16S rRNA gene sequences of 59 Thalassolituus-like bacteria originating from microbial communities inhabiting both marine (Baltic, Barents, Mediterranean, North, Okhotsk and South China seas, and the Atlantic, Pacific and Polar oceans) and terrestrial environments (subsurface caves and ground waters) [34,35]. In contrast, all of the 38 sequences in the databases assigned to the genus Cycloclasticus were retrieved exclusively from marine microbial communities, or PAH-supplemented enrichments thereof [10,12,36,37].…”

Microbial biodegradation of aromatic alkanoic naphthenic acids is affected by the degree of alkyl side chain branching

“…Plasmids were extracted using the Qiagen plasmid extraction kit (Qiagen). Clone libraries were screened by PCR amplification using primers for positions 341-534 in Escherichia coli (Muyzer et al 1993) and Denaturing Gradient Gel Electrophoresis performed as described previously (McKew et al, 2007), except gels were silver-stained as described by Nicol et al (2005). Representative clones from each library were selected and sequenced using the primer pG 0 (Edwards et al, 1989) (Source Bioscience Ltd., Cambridge, UK).…”

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“…Previously, Roseobacter-related bacteria have been implicated in the degradation of nhexadecane 40 , crude oil 41 , and n-alkane 11 . McKew and colleagues 11 suggested the possible inhibition of Roseobacter by some compounds within crude oil, such as PAHs, since Roseobacter clones could be found in 16-23% of the total library from decane, hexadecane, and alkane microcosms, but only 3% of their clones were found in crude oil microcosms and none were found in PAH microcosms. However, the findings in our study indicate that a member of Rhodobacteraceae also plays a role in PAH degradation.…”

“…Among these bacteria, Cycloclasticus is expected to be of great use for PAH biodegradation of oil-polluted seawater 5,9 . Culture-independent studies have also revealed that bacteria in the genus Cycloclasticus are the dominant PAH-degrading bacteria after oil spills in marine environments 10,11 .…”