Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities

McQuillan, Jonathan S.; Robidart, Julie

doi:10.1016/j.copbio.2016.11.022

Cited by 55 publications

(51 citation statements)

References 45 publications

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“…Real time measurement of E. coli culture kinetics in which bacterial replication is measured by proxy using, for example, electrical impedance or gas pressure measurements can reduce the time to positivity, but may still require long cultivation periods when starting with low cell numbers. To address this problem, a number of new approaches have been devised to reduce the delay between sampling and intervention, including (i) the development of portable or deployable in situ analytical technologies which obviate the need to return samples to a centralised lab (McQuillan and Robidart, 2017), and (ii) rapid molecular bio-analytical methods which can provide meaningful data in the order of minutes to hours (Heijnen and Medema, 2009;Maheux et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

A highly specific Escherichia coli qPCR and its comparison with existing methods for environmental waters

et al. 2017

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a b s t r a c tThe presence of Escherichia coli in environmental waters is considered as evidence of faecal contamination and is therefore commonly used as an indicator in both water quality and food safety analysis. The long period of time between sample collection and obtaining results from existing culture based methods means that contamination events may already impact public health by the time they are detected. The adoption of molecular based methods for E. coli could significantly reduce the time to detection. A new quantitative real-time PCR (qPCR) assay was developed to detect the ybbW gene sequence, which was found to be 100% exclusive and inclusive (specific and sensitive) for E. coli and directly compared for its ability to quantify E. coli in environmental waters against colony counts, quantitative real-time NASBA (qNASBA) targeting clpB and qPCR targeting uidA. Of the 87 E. coli strains tested, 100% were found to be ybbW positive, 94.2% were culture positive, 100% were clpB positive and 98.9% were uidA positive. The qPCR assays had a linear range of quantification over several orders of magnitude, and had high amplification efficiencies when using single isolates as a template. This compared favourably with qNASBA which showed poor linearity and amplification efficiency. When the assays were applied to environmental water samples, qNASBA was unable to reliably quantify E. coli while both qPCR assays were capable of predicting E. coli concentrations in environmental waters. This study highlights the inability of qNASBA targeting mRNA to quantify E. coli in environmental waters, and presents the first E. coli qPCR assay with 100% target exclusivity. The application of a highly exclusive and inclusive qPCR assay has the potential to allow water quality managers to reliably and rapidly detect and quantify E. coli and therefore take appropriate measures to reduce the risk to public health posed by faecal contamination.Crown

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Section: Introductionmentioning

confidence: 99%

A highly specific Escherichia coli qPCR and its comparison with existing methods for environmental waters

et al. 2017

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“…Niskin bottles) can take as long as 30 min, allowing for substantial, possibly stress-induced changes in the metatranscriptome (Edgcomb et al, 2016). A variety of recently developed in situ samplers, implemented with optional RNA fixation mechanisms, permit a more reliable sampling of environmental RNA (Feike et al, 2012;McQuillan and Robidart, 2017). Nevertheless, activity profiling of microorganisms based on mRNA remains questionable due to the poor correlations of mRNA with protein levels (Greenbaum et al, 2003;Wang et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Highly variable mRNA half‐life time within marine bacterial taxa and functional genes

Steiner

Corte

Geijo

et al. 2019

Environmental Microbiology

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Summary Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half‐life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half‐life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half‐live times shorter than 10 min. Significant differences were found in the half‐life time between mRNA and rRNA. The half‐life time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half‐life times of the metatranscriptome corresponded to transcripts from the same clusters of orthologous groups (COGs) in all bacterial classes. The prevalence of short mRNA half‐life time in genes related to defence mechanisms and motility indicate a tight connection of RNA decay rate to environmental stressors. The short half‐life time of RNA and its high variability needs to be considered when assessing metatranscriptomes especially in environmental samples.

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“…3). Studies on auxotrophy indicate that metabolic dependencies such as the passive exchange of certain amino acids, particularly those that are synthetically costly, can have a stabilizing effect on microbial communities (Mee et al 2014) and that stronger metabolic dependencies yield more cooperative microbial communities that increase cell growth (Estrela and Brown 2013). These findings suggest that metabolite exchange, as required by auxotrophic microbes, could result in an overall more productive community.…”

Section: Auxotrophymentioning

confidence: 99%

Hidden in plain sight: The importance of cryptic interactions in marine plankton

Millette

Große

Johnson

et al. 2018

Limnol Oceanogr Letters

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Here, we present a range of interactions, which we term "cryptic interactions." These are interactions that occur throughout the marine planktonic foodweb but are currently largely overlooked by established methods, which mean large-scale data collection for these interactions is limited. Despite this, current evidence suggests some of these interactions may have perceptible impacts on foodweb dynamics and model results. Incorporation of cryptic interactions into models is especially important for those interactions involving the transport of nutrients or energy. Our aim is to highlight a range of cryptic interactions across the plankton foodweb, where they exist, and models that have taken steps to incorporate these interactions. Additionally, it is discussed where additional research and effort is required to continue advancing our understanding of these cryptic interactions. We call for more collaboration between ecologists and modelers in order to incorporate cryptic interactions into biogeochemical and foodweb models. Scientific Significance StatementGeneralizations in foodweb modeling have helped scientists explain and study interactions within the aquatic environment. Established methods focus on quantifying and qualifying these generalizations, but rapid technological advancements in recent years have revealed that our generalizations of interactions may obscure significant processes within the plankton community. We explore a range of interactions within the planktonic foodweb that are "cryptic" because existing methods are biased against them with the intention of highlighting a range of cryptic interactions and the potential impact of overlooking them in future research. We discuss how including these interactions in biogeochemical and foodweb models alters our understanding of the transfer of carbon and other materials from one species/functional group to another and highlight examples of recent models that have incorporated cryptic interactions.1

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Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities

Cited by 55 publications

References 45 publications

A highly specific Escherichia coli qPCR and its comparison with existing methods for environmental waters

A highly specific Escherichia coli qPCR and its comparison with existing methods for environmental waters

Highly variable mRNA half‐life time within marine bacterial taxa and functional genes

Hidden in plain sight: The importance of cryptic interactions in marine plankton

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