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An enhanced bioindicator for calorimetric monitoring of prophage-activating chemicals in the trace concentration range.

ABSTRACT: Viruses that infect bacteria (bacteriophages) can either lyse bacteria directly or integrate their genome into the bacterial genome. In the latter case, the viral genome (called prophage) remains dormant, and both phages and bacteria are able to survive in this state. But the silent prophages can be reactivated by, e.g., chemicals, accompanied by the release of substantial quantities of phage particles that further infect other phage-sensitive bacteria, thus harming ecosystems or technical systems by way of a viral bloom. Recently, a calorimetric method was developed to monitor the prophage-activating properties of chemicals. The method evaluates the difference in the metabolic heat of the Escherichia coli bioindicator with (?+) and without (?-) lambda prophages under the influence of the test substances. Simulations and experiments clearly demonstrate that the sensitivity of the test can be significantly improved, when a customized mixture of ?+ and ?- E. coli strains is used for enhanced bioindication. Hence, the new method mirrors a common situation in nature, where bacteria with and without prophages coexist. In summary, a monitoring method is suggested that provides quick results (after few hours) and offers both the option for automation with low workload (requires only a few minutes) and usage of commercially available instruments.

SUBMITTER: Xu J

PROVIDER: S-EPMC6999466 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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An enhanced bioindicator for calorimetric monitoring of prophage-activating chemicals in the trace concentration range.

Xu Juan J Jiang Feng-Lei FL Liu Yi Y Kiesel Bärbel B Maskow Thomas T

Engineering in life sciences 20180601 7

Viruses that infect bacteria (bacteriophages) can either lyse bacteria directly or integrate their genome into the bacterial genome. In the latter case, the viral genome (called prophage) remains dormant, and both phages and bacteria are able to survive in this state. But the silent prophages can be reactivated by, e.g., chemicals, accompanied by the release of substantial quantities of phage particles that further infect other phage-sensitive bacteria, thus harming ecosystems or technical syste ...[more]

PMID: 32624928

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Project description:INTRODUCTION:Invertebrate communities are central to many environmental monitoring programs. In freshwater ecosystems, aquatic macroinvertebrates are collected, identified and then used to infer ecosystem condition. Yet the key step of species identification is often not taken, as it requires a high level of taxonomic expertise, which is lacking in most organizations, or species cannot be identified as they are morphologically cryptic or represent little known groups. Identifying species using DNA sequences can overcome many of these issues; with the power of next generation sequencing (NGS), using DNA sequences for routine monitoring becomes feasible. RESULTS:In this study, we test if NGS can be used to identify species from field-collected samples in an important bioindicator group, the Chironomidae. We show that Cytochrome oxidase I (COI) and Cytochrome B (CytB) sequences provide accurate DNA barcodes for chironomid species. We then develop a NGS analysis pipeline to identifying species using megablast searches of high quality sequences generated using 454 pyrosequencing against comprehensive reference libraries of Sanger-sequenced voucher specimens. We find that 454 generated COI sequences successfully identified up to 96% of species in samples, but this increased up to 99% when combined with CytB sequences. Accurate identification depends on having at least five sequences for a species; below this level species not expected in samples were detected. Incorrect incorporation of some multiplex identifiers (MID's) used to tag samples was a likely cause, and most errors could be detected when using MID tags on forward and reverse primers. We also found a strong quantitative relationship between the number of 454 sequences and individuals showing that it may be possible to estimate the abundance of species from 454 pyrosequencing data. CONCLUSIONS:Next generation sequencing using two genes was successful for identifying chironomid species. However, when detecting species from 454 pyrosequencing data sets it was critical to include known individuals for quality control and to establish thresholds for detecting species. The NGS approach developed here can lead to routine species-level diagnostic monitoring of aquatic ecosystems.

Dataset Information

An enhanced bioindicator for calorimetric monitoring of prophage-activating chemicals in the trace concentration range.

Publications

An enhanced bioindicator for calorimetric monitoring of prophage-activating chemicals in the trace concentration range.

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