Identification of microbial key-indicators of oil contamination at sea through tracking of oil biotransformation: An Arctic field and laboratory study

Królicka, Adriana; Boccadoro, Catherine; Nilsen, Mari Mæland; Demir‐Hilton, Elif; Birch, James M.; Preston, Christina M.; Scholin, Chris; Baussant, Thierry

doi:10.1016/j.scitotenv.2019.133715

Cited by 26 publications

(19 citation statements)

References 69 publications

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“…The first is the detection limit of key microbial indicators during biodegradation. Krolicka et al [77] quantified 16S rRNA and the GyrB markers to assess temporal microbial variability of oil contaminants in seawater. However, GryB gene is a single-copy gene, which is hardly used for quantification by qPCR at low abundance, and they mentioned to employ ddPCR to overcome the challenge.…”

Section: Microbial Enumerationmentioning

confidence: 99%

Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation

Cao

Dong

et al. 2020

Molecules

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Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.

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Section: Microbial Enumerationmentioning

confidence: 99%

Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation

Cao

Dong

et al. 2020

Molecules

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“…Microorganisms from melted sea ice have been shown to degrade oil compounds in the Arctic region, whereas different microbial consortia from seawater have also been reported to take part in this process [5,27,28]. Bacterial genera such as Pelagibacter, Octadecabacter, Sulfitobacter, Colwellia [29], Cycloclasticus [29,30], Alcanivorax, Marinobacter, Thallassolituus [30], and Oleispira [29][30][31], to name a few, are often associated with oil compound degradation in Arctic areas. However, the information about the genetic potential of hydrocarbon degradation in the sea ice of Arctic areas is still not sufficient.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice

et al. 2022

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The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good- and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.

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“…DNA extraction DNA extraction of the filtered seawater samples was performed using a method that mimics the ESP DNA extraction workflow (42) with slight modifications as described in (45). After extraction, the concentration of DNA in each sample was measured using the Qubit dsDNA HS (High Sensitivity) Kit (Thermo Fisher Scientific, Carlsbad, California, USA) before the samples were stored at -20 °C.…”

Section: Sample Preparation and Analytical Workmentioning

confidence: 99%

Sea lice(Lepeophtherius salmonis)detection and quantification around aquaculture installations using environmental DNA

Królicka

Nilsen

Provan

et al. 2021

Preprint

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The naturally occurring ectoparasite salmon lice (Lepeophtherirus salmonis) poses a great challenge for the salmon farming industry, as well as for wild salmonids in the Northern hemisphere. To better control the infestation pressure and protect the production, there is a need to provide fish farmers with sensitive and efficient tools for rapid early detection and monitoring of the parasitic load. This can be achieved by targeting L. salmonis DNA in environmental samples. Here, we developed and tested a new L. salmonis specific DNA-based assay (qPCR assay) for detection and quantification from seawater samples using an analytical pipeline compatible with the Environmental Sample Processor (ESP) for autonomous water sample analysis of gene targets. Specificity of the L. salmonis qPCR assay was demonstrated through in-silico DNA analyses covering sequences of different L. salmonis isolates. Seawater was spiked with known numbers of nauplii and copepodite free-swimming (planktonic) stages of L. salmonis to investigate the relationship with the number of marker gene copies (MGC). Finally, field samples collected at different times of the year in the vicinity of a salmon production farm in Western Norway were analyzed for L. salmonis detection and quantification. The assay specificity was high and a high correlation between MGC and planktonic stages of L. salmonis was established in the laboratory conditions. In the field, L. salmonis DNA was consequently detected, but with MGC number below that expected for one copepodite or nauplii. We concluded that only L. salmonis tissue or eDNA residues were detected. This novel study opens for a fully automatized L. salmonis DNA quantification using ESP robotic to monitor the parasitic load, but the challenge remains the adequate sampling of a volume of seawater sufficiently large to be representative of outbreaks and load around fish farms.

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Identification of microbial key-indicators of oil contamination at sea through tracking of oil biotransformation: An Arctic field and laboratory study

Cited by 26 publications

References 69 publications

Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation

Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation

Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice

Sea lice(Lepeophtherius salmonis)detection and quantification around aquaculture installations using environmental DNA

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