Quantitative estimation of Dehalococcoides mccartyi at laboratory and field scale: Comparative study between CARD-FISH and Real Time PCR

Matturro, Bruna; Heavner, Gretchen L.; Richardson, Ruth; Rossetti, Simona

doi:10.1016/j.mimet.2013.02.011

Cited by 43 publications

(26 citation statements)

References 54 publications

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“…Despite qPCR is currently the method of choice for the quantification of alkB2 gene (Hassanshahian et al, 2014;Genovese et al, 2014) we showed that geneCARD-FISH may produce quantitative data significantly higher than those obtained by qPCR. This finding is in line with a previous comparative study performed between in situ hybridization techniques and PCR-based methods (Matturro et al, 2013).…”

Section: Discussionsupporting

confidence: 93%

“…Alternative strategies were recently suggested allowing the visualization of the genes directly within the microbial cells by applying biomolecular assays based on fluorescence in situ hybridization (Matturro et al, 2013). Despite qPCR is currently the method of choice for the quantification of alkB2 gene (Hassanshahian et al, 2014;Genovese et al, 2014) we showed that geneCARD-FISH may produce quantitative data significantly higher than those obtained by qPCR.…”

Section: Discussionmentioning

confidence: 82%

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In situ detection of alkB2 gene involved in Alcanivorax borkumensis SK2T hydrocarbon biodegradation

Matturro

Frascadore

Cappello

et al. 2016

Marine Pollution Bulletin

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 82%

In situ detection of alkB2 gene involved in Alcanivorax borkumensis SK2T hydrocarbon biodegradation

Matturro

Frascadore

Cappello

et al. 2016

Marine Pollution Bulletin

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“…Despite the problems stated, PCR-based methods present detection limits considerably higher than those obtained by cell quantification methods (Fig. 3) (Matturro et al 2013).…”

Section: Molecular Fingerprintingmentioning

confidence: 95%

Unveiling PHA-storing populations using molecular methods

Queirós

Lemos

Rossetti

et al. 2015

Appl Microbiol Biotechnol

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Enrichment of mixed microbial cultures (MMCs) in polyhydroxyalkanoate (PHA)-storing microorganisms must take place to develop a successful PHA production process. Moreover, throughout the operational period of a MMC system, the population needs to be checked in order to understand the changes in the performance that eventually occurred. For these reasons, it is necessary to monitor the population evolution, in order to identify the different groups of microorganisms and relate them with the storage capacity and kinetics of the MMC. Regarding this particular process, several culture-independent molecular techniques were already applied, with the use of hybridization techniques such fluorescence in situ hybridization and also PCR-based methods like denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, pyrosequencing, and quantitative PCR standing out. This review intends, thus, to look at the molecular methods currently applied in monitoring the PHA-storing population evolution and how they can be combined with the evolutionary engineering step in order to optimize the overall process.

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“…Reactions and standard curves were performed as already described in Matturro et al (2013b). Probe details and conditions are reported in probeBase (http://www.…”

Section: Card-fishmentioning

confidence: 99%

Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities

Matturro

Ubaldi

Grenni

et al. 2015

Environ Sci Pollut Res

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Polychlorobiphenyl (PCB) biodegradation was followed for 1 year in microcosms containing marine sediments collected from Mar Piccolo (Taranto, Italy) chronically contaminated by this class of hazardous compounds. The microcosms were performed under strictly anaerobic conditions with or without the addition of Dehalococcoides mccartyi, the main microorganism known to degrade PCBs through the anaerobic reductive dechlorination process. Thirty PCB congeners were monitored during the experiments revealing that the biodegradation occurred in all microcosms with a decrease in hepta-, hexa-, and penta-chlorobiphenyls (CBs) and a parallel increase in low chlorinated PCBs (tri-CBs and tetra-CBs). The concentrations of the most representative congeners detected in the original sediment, such as 245-245-CB and 2345-245-CB, and of the mixture 2356-34-CB+234-245-CB, decreased by 32.5, 23.8, and 46.7 %, respectively, after only 70 days of anaerobic incubation without any bioaugmentation treatment. Additionally, the structure and population dynamics of the microbial key players involved in the biodegradative process and of the entire mixed microbial community were accurately defined by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in both the original sediment and during the operation of the microcosm. The reductive dehalogenase genes of D. mccartyi, specifically involved in PCB dechlorination, were also quantified using real-time PCR (qPCR). Our results demonstrated that the autochthonous microbial community living in the marine sediment, including D. mccartyi (6.32E+06 16S rRNA gene copy numbers g(-1) sediment), was able to efficiently sustain the biodegradation of PCBs when controlled anaerobic conditions were imposed.

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Quantitative estimation of Dehalococcoides mccartyi at laboratory and field scale: Comparative study between CARD-FISH and Real Time PCR

Cited by 43 publications

References 54 publications

In situ detection of alkB2 gene involved in Alcanivorax borkumensis SK2T hydrocarbon biodegradation

In situ detection of alkB2 gene involved in Alcanivorax borkumensis SK2T hydrocarbon biodegradation

Unveiling PHA-storing populations using molecular methods

Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities

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