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Lewis M, Lainé K, Dawnay L, Lamont D, Scott K, Mariani S, Hӓnfling B, Dawnay N. The forensic potential of environmental DNA (eDNA) in freshwater wildlife crime investigations: From research to application. Sci Justice 2024; 64:443-454. [PMID: 39025568 DOI: 10.1016/j.scijus.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/07/2024] [Accepted: 06/15/2024] [Indexed: 07/20/2024]
Abstract
Environmental DNA (eDNA) is widely used in biodiversity, conservation, and ecological studies but despite its successes, similar approaches have not yet been regularly applied to assist in wildlife crime investigations. The purpose of this paper is to review current eDNA methods and assess their potential forensic application in freshwater environments considering collection, transport and persistence, analysis, and interpretation, while identifying additional research required to present eDNA evidence in court. An extensive review of the literature suggests that commonly used collection methods can be easily adapted for forensic frameworks providing they address the appropriate investigative questions and take into consideration the uniqueness of the target species, its habitat, and the requirements of the end user. The use of eDNA methods to inform conservationists, monitor biodiversity and impacts of climate change, and detect invasive species and pathogens shows confidence within the scientific community, making the acceptance of these methods by the criminal justice system highly possible. To contextualise the potential application of eDNA on forensic investigations, two test cases are explored involving i) species detection and ii) species localisation. Recommendations for future work within the forensic eDNA discipline include development of suitable standardised collection methods, considered collection strategies, forensically validated assays and publication of procedures and empirical research studies to support implementation within the legal system.
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Affiliation(s)
- Matthew Lewis
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Katie Lainé
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Louise Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; International Study Centre, Liverpool John Moores University, Mount Pleasant, Liverpool, UK
| | - David Lamont
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Kirstie Scott
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Stefano Mariani
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Bernd Hӓnfling
- Institute for Biodiversity and Freshwater Conservation, University of the Highlands and Islands, Inverness, UK
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK.
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2
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Grbin D, Geček S, Miljanović A, Pavić D, Hudina S, Žučko J, Rieder J, Pisano SRR, Adrian-Kalchhauser I, Bielen A. Comparison of exoskeleton microbial communities of co-occurring native and invasive crayfish species. J Invertebr Pathol 2023; 201:107996. [PMID: 37783231 DOI: 10.1016/j.jip.2023.107996] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/04/2023]
Abstract
Host-associated microbial communities are an important determinant of individual fitness and have recently been highlighted as one of the factors influencing the success of invasive species. Invasive hosts introduce their microbes into the new environment, and then both the host and its associated microbes enter into a series of interactions with the native macroscopic and microscopic biota. As these processes are largely unexplored, we aimed to compare the exoskeletal microbial communities of co-occurring and phylogenetically related crayfish: the native narrow-clawed crayfish Pontastacus leptodactylus and the invasive signal crayfish Pacifastacus leniusculus from the recently invaded Korana River, Croatia. The results of high-throughput 16S rRNA sequencing showed that the exoskeletal microbiome of both species is very diverse, significantly influenced by the local environment and dominated by low abundance bacterial families from the phylum Proteobacteria. Furthermore, the exoskeletal microbiomes of the crayfish species differed significantly in the composition and abundance of Amplicon Sequence Variants (ASVs), suggesting that they are to some extent shaped by species-specific intrinsic factors, despite sharing a common habitat. However, over 95% of the bacterial genera associated with the exoskeleton were detected in the exoskeleton samples of both native and invasive crayfish. We paid particular attention to two known crayfish pathogens, Aphanomyces astaci and Saprolegnia parasitica, and find that both species carry low amounts of both pathogens. On the side, we find that a non-standard ddPCR protocol outperforms standard qPCR test for A. astaci under low concentration conditions. Taken together, our results indicate the possibility of bidirectional mixing and homogenisation of exoskeleton microbiome. As such, they can serve as a baseline in future detangling of the processes that act together to shape the microbiomes of co-occuring native and invasive congeners during biological invasions.
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Affiliation(s)
- Dorotea Grbin
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia; Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
| | - Sunčana Geček
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Anđela Miljanović
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
| | - Dora Pavić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
| | - Sandra Hudina
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia.
| | - Jurica Žučko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
| | - Jessica Rieder
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland.
| | - Simone R R Pisano
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland.
| | - Irene Adrian-Kalchhauser
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland.
| | - Ana Bielen
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
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Galogahi FM, Christie M, Yadav AS, An H, Stratton H, Nguyen NT. Microfluidic encapsulation of DNAs in liquid beads for digital PCR application. Analyst 2023; 148:4064-4071. [PMID: 37469285 DOI: 10.1039/d3an00868a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Droplet-based microfluidics and digital polymerase chain reaction (PCR) hold significant promise for accurately detecting and quantifying pathogens. However, existing droplet-based digital PCR (ddPCR) applications have been relying exclusively on single emulsion droplets. Single emulsion droplets may not be suitable for applications such as identifying the source and pathways of water contamination where the templates must be protected against harsh environmental conditions. In this study, we developed a core-shell particle to serve as a protective framework for DNAs, with potential applications in digital PCR. We employed a high-throughput and facile flow-focusing microfluidic device to generate liquid beads, core-shell particles with liquid cores, which provided precise control over process parameters and consequently particle characteristics. Notably, the interfacial interaction between the core and shell liquids could be adjusted without adding surfactants to either phase. As maintaining stability is essential for ensuring the accuracy of digital PCR (dPCR), we investigated parameters that affect the stability of core-shell droplets, including surfactants in the continuous phase and core density. As a proof of concept, we encapsulated a series of human faecal DNA samples in the core-shell droplets and the subsequent liquid beads. The core-shell particles ensure contamination-free encapsulation of DNA in the core. The volume of the core droplets containing the PCR mixture is only 0.12 nL. Our experimental results indicate that the liquid beads formulated using our technique can amplify the encapsulated DNA and be used for digital PCR without interfering with the fluorescence signal. We successfully demonstrated the ability to detect and quantify DNA under varying concentrations. These findings provide new insights and a step change in digital PCR that could benefit various applications, including the detection and tracking of environmental pollution.
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Affiliation(s)
- Fariba Malekpour Galogahi
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Melody Christie
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Ajeet Singh Yadav
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Hongjie An
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Helen Stratton
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
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4
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Nuraeni U, Malau J, Astuti RT, Dewantoro A, Apriori D, Lusiana ED, Prasetya B. Droplet digital PCR versus real-time PCR for in-house validation of porcine detection and quantification protocol: An artificial recombinant plasmid approach. PLoS One 2023; 18:e0287712. [PMID: 37450440 PMCID: PMC10348585 DOI: 10.1371/journal.pone.0287712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Authenticity and traceability are essential for modern food and medicine inspection, and reliable techniques are important for the trade of halal foods, which reach more than 20 percent of the world market. A sensitive and accurate porcine detection method is required to develop a conformity assessment system that includes laboratory testing for porcine-free certification. This study proposes a procedure that could be incorporated into the development of a standardized control and protocol for real-time PCR (qPCR) methods and their traceability using droplet digital PCR (ddPCR). The design used a recombinant pUC57 plasmid as an amplification target to carry the 97 bp fragment of the porcine ATCB gene. The absolute quantification and linearity assessment showed high precision with R2 values of 0.9971 and 0.9998 for qPCR and ddPCR, respectively. In general, both methods showed comparable results in terms of linearity and detection limit. However, both limit of detection assessments showed high sensitivity, although ddPCR showed a slightly higher sensitivity than that of qPCR, especially at low DNA concentrations. Multiple-sample and inter-participatory testing evaluations revealed a high sensitivity, broad applicability, and robustness of the qPCR method. Therefore, we conclude that based on a recombinant plasmid analysis with a low quantity (less than five copy number), the digital PCR method produced more reliable results. These results could provide scientific information for regulatory authorities, especially those in Indonesia, to consider the development and formulation of a well-established qPCR protocol for porcine detection using expected DNA concentrations.
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Affiliation(s)
- Umi Nuraeni
- Laboratory of National Measurement Standards of Biology, The National Standard Agency of Indonesia (BSN), South Tangerang, Banten, Indonesia
| | - Jekmal Malau
- Department of Pharmacy, Faculty of Health Science, Universitas Singaperbangsa Karawang, West Java, Indonesia
| | - Retno Tri Astuti
- Department of Fisheries Product Technology, Faculty of Fisheries and Marine Science, Universitas Brawijaya, East Java, Indonesia
| | - Auraga Dewantoro
- Research Center for Genetic Engineering, The National Research and Innovation Agency of Indonesia (BRIN), Bogor, Indonesia
| | - Dini Apriori
- Laboratory of National Measurement Standards of Biology, The National Standard Agency of Indonesia (BSN), South Tangerang, Banten, Indonesia
| | - Evellin Dewi Lusiana
- Department of Aquatic Resource Management, Faculty of Fisheries and Marine Science, Universitas Brawijaya, East Java, Indonesia
| | - Bambang Prasetya
- Research Center for Testing Technology and Standards, The National Research and Innovation Agency of Indonesia (BRIN), South Tangerang, Indonesia
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5
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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6
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Hodgson LM, Cox BA, Lopez-Ruiz FJ, Gibberd MR, Thomas GJ, Zerihun A. Optimized Sample Processing Pipeline for PCR-Based Fungicide Resistance Quantification of Stubble-Borne Fungal Pathogens. PHYTOPATHOLOGY 2023; 113:321-333. [PMID: 36075052 DOI: 10.1094/phyto-07-22-0239-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Globally, yield losses associated with failed crop protection due to fungicide-resistant pathogens present an increasing problem. For stubble-borne pathogens, assessment of crop residues during the off-season could provide early fungicide resistance quantification for informed management decisions to mitigate yield losses. However, stubble assessment is hampered by assay inhibitors that are derived from decaying organic matter. To overcome assay inhibition from weathered stubble samples, we used a systems approach to quantify the frequency of resistance to demethylase inhibitor fungicides of the barley pathogen Pyrenophora teres f. teres. The system canvassed (i) 10 ball-milling conditions; (ii) four DNA extraction methodologies; and (iii) three column purification techniques for the provision of sufficient yield, quality, and purity of fungal DNA for a PCR-based fungicide resistance assay. Results show that DNA quantity and purity differed within each of the above three categories, with the optimized pipeline being (i) ball-milling samples in a 50-ml stainless steel canister for 5 min using a 20-mm ball at 30 revolutions s-1; (ii) a modified Brandfass method (extracted 64% more DNA than other methods assessed); and (iii) use of silica resin columns for the highest DNA concentration with optimal DNA purity. The chip-digital PCR assay, which quantified fungicide resistance from field samples, was unaffected by the DNA extraction method or purification technique, provided that thresholds of template quantity and purity were satisfied. In summary, this study has developed molecular pipeline options for pathogen fungicide resistance quantification from cereal stubbles, which can guide management for improved crop protection outcomes.
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Affiliation(s)
- Leon M Hodgson
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Belinda A Cox
- School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mark R Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Geoff J Thomas
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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7
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Pavić D, Grbin D, Hudina S, Prosenc Zmrzljak U, Miljanović A, Košir R, Varga F, Ćurko J, Marčić Z, Bielen A. Tracing the oomycete pathogen Saprolegnia parasitica in aquaculture and the environment. Sci Rep 2022; 12:16646. [PMID: 36198674 PMCID: PMC9534867 DOI: 10.1038/s41598-022-16553-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022] Open
Abstract
Saprolegnia parasitica causes saprolegniosis, a disease responsible for significant economic losses in aquaculture and declines of fish populations in the wild, but the knowledge of its distribution and prevalence in the environment is limited. We developed a fast, sensitive and specific S. parasitica droplet digital PCR (ddPCR) assay and demonstrated its applicability for the detection and quantification of the pathogen in environmental samples: swab DNA collected from the host (trout skin, surface of eggs) and environmental DNA extracted from water. The developed assay was used to assess how abiotic (i.e. physico-chemical parameters of the water) and biotic (health status of the host) factors influence the S. parasitica load in the environment. The pathogen load in water samples was positively correlated with some site-specific abiotic parameters such as electrical conductivity (EC) and calcium, while fluorides were negatively correlated, suggesting that physico-chemical parameters are important for determining S. parasitica load in natural waters. Furthermore, skin swabs of injured trout had significantly higher pathogen load than swabs collected from healthy fish, confirming that S. parasitica is a widespread opportunistic pathogen. Our results provide new insights into various environmental factors that influence the distribution and abundance of S. parasitica.
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Affiliation(s)
- Dora Pavić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Dorotea Grbin
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia.,Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | | | - Anđela Miljanović
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Rok Košir
- Labena Ltd, BIA Separations CRO - Molecular Biology Laboratory, 1000, Ljubljana, Slovenia
| | - Filip Varga
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, 10000, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, CoE CroP-BioDiv), 10000, Zagreb, Croatia
| | - Josip Ćurko
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Zoran Marčić
- Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia.
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8
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Foliage of Tropical Trees and Shrubs and Their Secondary Metabolites Modify In Vitro Ruminal Fermentation, Methane and Gas Production without a Tight Correlation with the Microbiota. Animals (Basel) 2022; 12:ani12192628. [PMID: 36230369 PMCID: PMC9559637 DOI: 10.3390/ani12192628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Ruminants, mainly cattle, contribute to greenhouse gases (GHG) emissions as methane (CH4) is produced by ruminal fermentation. Hence, various anti-methanogenic feed strategies have been studied, including the use of plants with secondary metabolites. This study evaluated in vitro ruminal fermentation metrics, microbial composition by digital droplet PCR (ddPCR) and the CH4 production of the foliage of several tropical trees and shrubs: Leucaena leucocephala, Moringa oleifera, Albizia lebbeck, Enterolobium cyclocarpum, Piscidia piscipula, Brosimum alicastrum, Lysiloma latisiliquum, Guazuma ulmifolia, Cnidoscolus aconitifolius, Gliricidia sepium and Bursera simaruba, using Cynodon plectostachyus grass as control. The results showed a wide variation in the chemical composition of the foliage, as well as in the ruminal microbiota. The crude protein (CP) content ranged from 11 to 25%, whereas the content of condensed tannins (CT) and saponins (S) was from 0.02 to 7%, and 3.2 to 6.6%, respectively. The greatest dry matter degradability (DMD) after 72 h was 69% and the least 35%, the latter coinciding with the least gas production (GP). A negative correlation was found between the CT and CH4 production, also between protozoa and fungi with the SGMT group of archaea. We concluded that the foliage of some tropical trees and shrubs has a high nutritional value and the potential to decrease CH4 production due to its CT content.
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Highly sensitive environmental DNA detection of topmouth gudgeon, Pseudorasbora parva: a comparison of qPCR and microfluidic qdPCR. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractTopmouth gudgeon is a freshwater fish species native to East Asia. Nowadays, P. parva is spread throughout Europe which is of concern because besides being considered one of the worst aquatic Invasive Alien Species (IAS) in Europe it is also a known vector of Spherotecum destruens, the rosette-like parasite lethal to other fish species. The present study describes the development and validation of a new species-specific assay based on hydrolysis probe chemistry to detect P. parva environmental DNA (eDNA) in water samples collected in a northern region of Italy (Friuli Venezia Giulia). Water samples were collected from 55 sites in an area where partial information on the occurrence of the species is available. eDNA was isolated from all samples and the presence of P. parva eDNA was tested by means of qPCR (quantitative PCR) and microfluidic qdPCR (quantitative digital PCR) techniques. Field results for both qPCR and qdPCR were largely in agreement in terms of detection (presence/absence). Thus, we judged the presence/absence by combining the results from the two methods and found that nine sites showed “strong positive” signal of P. parva eDNA (at least 2 positive replicates), 3 showed “suspected” (only 1 positive replicate), and 42 showed “absent”. The current study shows the strong potential of the newly developed eDNA approach to be a valuable addition to the monitoring of the highly invasive topmouth gudgeon in freshwater ecosystems.
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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11
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Basanisi MG, La Bella G, Nobili G, Raele DA, Cafiero MA, Coppola R, Damato AM, Fraccalvieri R, Sottili R, La Salandra G. Detection of Coxiella burnetii DNA in sheep and goat milk and dairy products by droplet digital PCR in south Italy. Int J Food Microbiol 2022; 366:109583. [PMID: 35182931 DOI: 10.1016/j.ijfoodmicro.2022.109583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
Abstract
Coxiella burnetii is a Gram-negative obligate intracellular bacterium that is responsible for Q fever, a common zoonosis which is present virtually worldwide. This microorganism infects a wide range of wild and domestic mammals, but the main reservoirs are cattle, goats and sheep, which also represent sources of human infection. A potential route of transmission of this pathogen to humans is the consumption of C. burnetii-contaminated raw milk or dairy products derived from contaminated raw milk, although the role of these foods as possible infection sources is controversial. The aims of this study were (i) to apply two ddPCR based assays targeting the C. burnetii IS1111 and icd genes for the detection and quantification of C. burnetii DNA, and (ii) to evaluate the occurrence of C. burnetii DNA in raw milk and raw milk products from sheep and goats in Apulia and Basilicata regions of Southern Italy. Of 413 milk and cheese samples tested, 78 were positive for the presence of C. burnetii DNA (18.9%), specifically, 68 of 285 milk samples (23.9%) and 10 of 128 cheese samples (7.8%) The presence of both IS1111 and icd genes was detected in only 2 (2.6%) of the 78 positive samples, while the remaining 76 (97.4%) were positive only for IS1111. C. burnetii DNA was specifically detected by the ddPCR method, whereas no cross-amplification was observed with the DNA of other foodborne bacterial pathogens. The sensitivity of the ddPCR method was determined as 0.35 and 0.56 copies/μL for IS1111 and icd genes, respectively. The findings of this study demonstrate the presence of C. burnetii DNA in a significant proportion of raw milk and dairy products. Although there is no conclusive epidemiological evidence that C. burnetii infection occurs via food, the presence of this organism in raw milk and dairy products made of raw milk should be considered a potential hazard. ddPCR is a useful tool to investigate the quality and safety of food products due to its sensitivity and precision, and could be applied to routine testing.
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Affiliation(s)
- Maria Grazia Basanisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy.
| | - Gianfranco La Bella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Gaia Nobili
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Donato Antonio Raele
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Maria Assunta Cafiero
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Rosa Coppola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Annita Maria Damato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Rosa Fraccalvieri
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Roldano Sottili
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Giovanna La Salandra
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
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12
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Feist SM, Lance RF. Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions. NEOBIOTA 2021. [DOI: 10.3897/neobiota.66.60751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.
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13
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Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique. Sci Rep 2021; 11:4372. [PMID: 33623060 PMCID: PMC7902826 DOI: 10.1038/s41598-021-83318-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/02/2021] [Indexed: 11/08/2022] Open
Abstract
The combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.
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14
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Selection and Validation of Reference Genes for RT-qPCR Analysis in Spinacia oleracea under Abiotic Stress. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4853632. [PMID: 33623781 PMCID: PMC7875621 DOI: 10.1155/2021/4853632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/16/2021] [Indexed: 11/17/2022]
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and convenient method for mRNA quantification. Selection of optimal reference gene(s) is an important step in RT-qPCR experiments. However, the stability of housekeeping genes in spinach (Spinacia oleracea) under various abiotic stresses is unclear. Evaluating the stability of candidate genes and determining the optimal gene(s) for normalization of gene expression in spinach are necessary to investigate the gene expression patterns during development and stress response. In this study, ten housekeeping genes, 18S ribosomal RNA (18S rRNA), actin, ADP ribosylation factor (ARF), cytochrome c oxidase subunit 5C (COX), cyclophilin (CYP), elongation factor 1-alpha (EF1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (H3), 50S ribosomal protein L2 (RPL2), and tubulin alpha chain (TUBα) from spinach, were selected as candidates in roots, stems, leaves, flowers, and seedlings in response to high temperature, CdCl2, NaCl, NaHCO3, and Na2CO3 stresses. The expression of these genes was quantified by RT-qPCR and evaluated by NormFinder, BestKeeper, and geNorm. 18S rRNA, actin, ARF, COX, CYP, EF1α, GAPDH, H3, and RPL2 were detected as optimal reference genes for gene expression analysis of different organs and stress responses. The results were further confirmed by the expression pattern normalized with different reference genes of two heat-responsive genes. Here, we optimized the detection method of the gene expression pattern in spinach. Our results provide the optimal candidate reference genes which were crucial for RT-qPCR analysis.
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15
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Spilsberg B, Sekse C, Urdahl AM, Nesse LL, Johannessen GS. Persistence of a Stx-Encoding Bacteriophage in Minced Meat Investigated by Application of an Improved DNA Extraction Method and Digital Droplet PCR. Front Microbiol 2021; 11:581575. [PMID: 33552009 PMCID: PMC7855172 DOI: 10.3389/fmicb.2020.581575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/01/2020] [Indexed: 12/01/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens with Shiga toxins as the main virulence factor. Shiga toxins are encoded on Shiga toxin-encoding bacteriophages (Stx phages). Stx phages may exist as free bacteriophages in the environment or in foods or as prophages integrated into the host genome. From a food safety perspective, it is important to have knowledge on the survival and persistence of Stx phages in food products since these may integrate into the bacterial hosts through transduction if conditions are right. Here, we present the results from a study investigating the survival of a Stx phage in minced meat from beef stored at a suboptimal temperature (8°C) for food storage along with modifications and optimizations of the methods applied. Minced meat from beef was inoculated with known levels of a labeled Stx phage prior to storage. Phage filtrates were used for plaque assays and DNA extraction, followed by real-time PCR and digital droplet PCR (ddPCR). The results from the pilot study suggested that the initial DNA extraction protocol was not optimal, and several modifications were tested before a final protocol was defined. The final DNA extraction protocol comprised ultra-centrifugation of the entire phage filtrate for concentrating phages and two times phenol–chloroform extraction. The protocol was used for two spiking experiments. The DNA extraction protocol resulted in flexibility in the amount of DNA available for use in PCR analyses, ultimately increasing the sensitivity of the method used for quantification of phages in a sample. All three quantification methods employed (i.e., plaque assays, real-time PCR, and ddPCR) showed similar trends in the development of the phages during storage, where ddPCR has the benefit of giving absolute quantification of DNA copies in a simple experimental setup. The results indicate that the Stx phages persist and remain infective for at least 20 days under the storage conditions used in the present study. Stx phages in foods might represent a potential risk for humans. Although it can be speculated that transduction may take place at 8°C with subsequent forming of STEC, it can be expected to be a rare event. However, such an event may possibly take place under more optimal conditions, such as an increase in storage temperature of foods or in the gastrointestinal tract of humans.
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Affiliation(s)
- B Spilsberg
- Section for Molecular Biology, Norwegian Veterinary Institute, Oslo, Norway
| | - C Sekse
- Section for Molecular Biology, Norwegian Veterinary Institute, Oslo, Norway
| | - Anne M Urdahl
- Section for Food Safety and Animal Health Research, Norwegian Veterinary Institute, Oslo, Norway
| | - Live L Nesse
- Section for Food Safety and Animal Health Research, Norwegian Veterinary Institute, Oslo, Norway
| | - Gro S Johannessen
- Section for Food Safety and Animal Health Research, Norwegian Veterinary Institute, Oslo, Norway
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16
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Maldonado-González MM, Del Pilar Martínez-Diz M, Andrés-Sodupe M, Bujanda R, Díaz-Losada E, Gramaje D. Quantification of Cadophora luteo-olivacea From Grapevine Nursery Stock and Vineyard Soil Using Droplet Digital PCR. PLANT DISEASE 2020; 104:2269-2274. [PMID: 32568630 DOI: 10.1094/pdis-09-19-2035-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cadophora luteo-olivacea is the most prevalent Cadophora species associated with Petri disease and esca of grapevine. Accurate, early, and specific detection and quantification of C. luteo-olivacea are essential to alert growers and nurseries to the presence of the pathogens in soil and to prevent the spread of this pathogen through grapevine planting material. The aim of this study was to develop molecular tools to detect and quantify C. luteo-olivacea inoculum from environmental samples. Species specific primers based on the β-tubulin gene and a TaqMan probe for droplet digital PCR (ddPCR) and quantitative PCR (qPCR) were first developed to detect and quantify purified DNA of the target fungus. Specificity tests showed that the primers were able to amplify the C. luteo-olivacea DNA (20 isolates) while none of the 29 nontarget fungal species (58 isolates) tested were amplified. The ddPCR was shown to be more sensitive compared with qPCR in the detection and quantification of C. luteo-olivacea at very low concentrations and was further selected to accurately detect and quantify the fungus from environmental samples. Twenty-five of the 94 grafting plants (26.6%) analyzed by ddPCR tested positive to C. luteo-olivacea DNA (>3 copies/µl). C. luteo-olivacea was barely detected from vineyard soils. The procedure employed in this study revealed the presence of the pathogen in symptomless vines, which makes implementation of this technique suitable for certification schemes of C. luteo-olivacea-free grapevine planting material.
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Affiliation(s)
- María Mercedes Maldonado-González
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - María Del Pilar Martínez-Diz
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
- Universidade da Coruña, Facultade de Ciencias, Zapateira, 15071, A Coruña, Spain
| | - Marcos Andrés-Sodupe
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Rebeca Bujanda
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Emilia Díaz-Losada
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
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17
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Rapid and sensitive detection of Salmonella spp. in raw minced meat samples using droplet digital PCR. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03531-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Lindner L, Cayrou P, Jacquot S, Birling MC, Herault Y, Pavlovic G. Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies. Methods 2020; 191:95-106. [PMID: 32721466 DOI: 10.1016/j.ymeth.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/23/2020] [Accepted: 07/16/2020] [Indexed: 01/05/2023] Open
Abstract
Droplet digital PCR (ddPCR) is a recent method developed for the quantification of nucleic acids sequences. It is an evolution of PCR methodology incorporating two principal differences: a PCR reaction is performed in thousands of water-oil emulsion droplets and fluorescence is measured at the end of PCR amplification. It leads to the precise and reproducible quantification of DNA and RNA sequences. Here, we present quantitative methods for DNA and RNA analysis using Bio-Rad QX100 or QX200 systems, respectively. The aim of these methods is to provide useful molecular tools for validating genetically altered animal models such as those subject to CRISPR/Cas9 genome editing, as well for expression or CNV studies. A standard procedure for simultaneous DNA and RNA extraction adapted for mouse organs is also described. These methods were initially designed for mouse studies but also work for samples from other species like rat or human. In our lab, thousands of samples and hundreds of target genes from genetically altered lines were examined using these methods. This large dataset was analyzed to evaluate technical optimizations and limitations. Finally, we propose additional recommendations to be included in dMIQE (Minimum information for publication of quantitative digital PCR experiments) guidelines when using ddPCR instruments.
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Affiliation(s)
- Loic Lindner
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Pauline Cayrou
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Sylvie Jacquot
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Yann Herault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France.
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19
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Sidstedt M, Rådström P, Hedman J. PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions. Anal Bioanal Chem 2020; 412:2009-2023. [PMID: 32052066 PMCID: PMC7072044 DOI: 10.1007/s00216-020-02490-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/24/2022]
Abstract
DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.
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Affiliation(s)
- Maja Sidstedt
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Johannes Hedman
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden.
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
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20
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Del Pilar Martínez-Diz M, Andrés-Sodupe M, Berbegal M, Bujanda R, Díaz-Losada E, Gramaje D. Droplet Digital PCR Technology for Detection of Ilyonectria liriodendri from Grapevine Environmental Samples. PLANT DISEASE 2020; 104:1144-1150. [PMID: 32053059 DOI: 10.1094/pdis-03-19-0529-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Black-foot disease is one of the most important soilborne diseases affecting planting material in grapevine nurseries and young vineyards. Accurate, early, and specific detection and quantification of black-foot disease causing fungi are essential to alert growers and nurseries to the presence of the pathogens in soil, and to prevent the spread of these pathogens through grapevines using certified pathogen-free planting material and development of resistance. We comparatively assessed the accuracy, efficiency, and specificity of droplet digital PCR (ddPCR) and real-time PCR (qPCR) techniques for the detection and quantification of Ilyonectria liriodendri in bulk and rhizosphere soils, as well as grapevine endorhizosphere. Fungal abundance was not affected by soil-plant fractions. Both techniques showed a high degree of correlation across the samples assessed (R2 = 0.95) with ddPCR being more sensitive to lower target concentrations. Roots of asymptomatic vines were found to be a microbial niche that is inhabited by black-foot disease fungi.
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Affiliation(s)
- María Del Pilar Martínez-Diz
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
- Universidade da Coruña, Facultade de Ciencias, Zapateira, 15071 A Coruña, Spain
| | - Marcos Andrés-Sodupe
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Mónica Berbegal
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Rebeca Bujanda
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Emilia Díaz-Losada
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
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21
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Jikumaru A, Ishii S, Fukudome T, Kawahara Y, Iguchi A, Masago Y, Nukazawa K, Suzuki Y. Fast, sensitive, and reliable detection of waterborne pathogens by digital PCR after coagulation and foam concentration. J Biosci Bioeng 2020; 130:76-81. [PMID: 32147250 DOI: 10.1016/j.jbiosc.2020.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022]
Abstract
The quantification of pathogens is important for assessing water safety and preventing disease outbreaks. Culture-independent approaches, such as quantitative PCR (qPCR) and digital PCR (dPCR), are useful techniques for quantifying pathogens in water samples. However, since pathogens are usually present at low concentrations in water, it is necessary to concentrate microbial cells before extracting their DNA. Many existing microbial concentration methods are inefficient or take a long time to perform. In this study, we applied a coagulation and foam separation method to concentrate environmental water samples of between 1000 and 5000 mL to 100 μL of DNA (i.e., a 1-5 × 104-fold concentration). The concentration process took <1 h. The DNA samples were then used to quantify various target pathogens using dPCR. One gene, the Shiga toxin gene (stx2) of Shiga toxin-producing Escherichia coli, was detected at 32 copies/100 mL in a river water sample. The coagulation and foam concentration method followed by dPCR reported herein is a fast, sensitive, and reliable method to quantify pathogen genes in environmental water samples.
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Affiliation(s)
- Atsushi Jikumaru
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Satoshi Ishii
- Department of Soil, Water, and Climate, University of Minnesota, MN 55108-6028, USA; BioTechnology Institute, University of Minnesota, MN 55108-1095, USA
| | - Tomoko Fukudome
- Miyazaki Prefecture Institute for Public Health and Environment, 2-3-2 Gakuen Kibanadai-Nishi, Miyazaki 889-2155, Japan
| | - Yasuhiko Kawahara
- Miyazaki Prefecture Institute for Public Health and Environment, 2-3-2 Gakuen Kibanadai-Nishi, Miyazaki 889-2155, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Yoshifumi Masago
- Center for Social and Environmental Systems Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-City, Ibaraki 305-8506, Japan
| | - Kei Nukazawa
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan.
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22
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Cao Y, Yu M, Dong G, Chen B, Zhang B. Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules 2020; 25:molecules25030706. [PMID: 32041334 PMCID: PMC7037809 DOI: 10.3390/molecules25030706] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
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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Affiliation(s)
| | | | | | - Bing Chen
- Correspondence: (B.C.); (B.Z.); Tel.: +1-709-864-8958 (B.C.); +1-709-864-3301 (B.Z.)
| | - Baiyu Zhang
- Correspondence: (B.C.); (B.Z.); Tel.: +1-709-864-8958 (B.C.); +1-709-864-3301 (B.Z.)
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23
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Basanisi MG, La Bella G, Nobili G, Coppola R, Damato AM, Cafiero MA, La Salandra G. Application of the novel Droplet digital PCR technology for identification of meat species. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14486] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maria Grazia Basanisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB) Via Manfredonia, 20 71121 Foggia Italy
| | - Gianfranco La Bella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB) Via Manfredonia, 20 71121 Foggia Italy
| | - Gaia Nobili
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB) Via Manfredonia, 20 71121 Foggia Italy
| | - Rosa Coppola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB) Via Manfredonia, 20 71121 Foggia Italy
| | - Annita Maria Damato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB) Via Manfredonia, 20 71121 Foggia Italy
| | - Maria Assunta Cafiero
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB) Via Manfredonia, 20 71121 Foggia Italy
| | - Giovanna La Salandra
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB) Via Manfredonia, 20 71121 Foggia Italy
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24
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de Melo-Silva AJ, Lucena JP, Hueneburg T. The evolution of molecular diagnosis using digital polymerase chain reaction to detect cancer via cell-free DNA and circulating tumor cells. Cell Biol Int 2019; 44:735-743. [PMID: 31829466 DOI: 10.1002/cbin.11286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/10/2019] [Indexed: 01/05/2023]
Abstract
Cancer is one of the most important causes of death worldwide. The onset of cancer may be initiated due to a variety of factors such as environment, genetics or even due to personal lifestyle choices. To counteract this tremendous increase, the demand for a new technology has risen. By this means, the use of digital polymerase chain reaction (dPCR) has been shown to be a promising methodology in the early detection of many types of cancers. Furthermore, several researchers confirmed that the use of tumor cell-free DNA (cfDNA) and circulating tumor cells (CTC) in peripheral blood is essential in revealing an early prognosis of such diseases. Besides this, it was established that dPCR might be used in a much more efficient, accurate, and reliable manner to amplify a variety of genetic material up to the identification of mutations in hematological diseases. Therefore, this article demonstrates the differences between conventional PCR and dPCR as a molecular technique to detect the early onset of cancer. Furthermore, CTC and cfDNA were officially approved by the Food and Drug Administration as new biological biomarkers in cancer development and monitoring.
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Affiliation(s)
- Alex José de Melo-Silva
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Jessica Paula Lucena
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Thomas Hueneburg
- University of Technology Sydney, Sydney, 2007, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne-Vic, 3010 Parkeville VIC, Australia
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Scalable Production of Monodisperse Functional Microspheres by Multilayer Parallelization of High Aspect Ratio Microfluidic Channels. MICROMACHINES 2019; 10:mi10090592. [PMID: 31509956 PMCID: PMC6780626 DOI: 10.3390/mi10090592] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/07/2019] [Accepted: 09/08/2019] [Indexed: 01/31/2023]
Abstract
Droplet microfluidics enables the generation of highly uniform emulsions with excellent stability, precise control over droplet volume, and morphology, which offer superior platforms over conventional technologies for material synthesis and biological assays. However, it remains a challenge to scale up the production of the microfluidic devices due to their complicated geometry and long-term reliability. In this study, we present a high-throughput droplet generator by parallelization of high aspect ratio rectangular structures, which enables facile and scalable generation of uniform droplets without the need to precisely control external flow conditions. A multilayer device is formed by stacking layer-by-layer of the polydimethylsiloxane (PDMS) replica patterned with parallelized generators. By feeding the sample fluid into the device immersed in the carrying fluid, we used the multilayer device with 1200 parallelized generators to generate monodisperse droplets (~45 μm in diameter with a coefficient of variation <3%) at a frequency of 25 kHz. We demonstrate this approach is versatile for a wide range of materials by synthesis of polyacrylamide hydrogel and Poly (l-lactide-co-glycolide) (PLGA) through water-in-oil (W/O) and oil-in-water (O/W) emulsion templates, respectively. The combined scalability and robustness of such droplet emulsion technology is promising for production of monodisperse functional materials for large-scale applications.
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26
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Dupas E, Legendre B, Olivier V, Poliakoff F, Manceau C, Cunty A. Comparison of real-time PCR and droplet digital PCR for the detection of Xylella fastidiosa in plants. J Microbiol Methods 2019; 162:86-95. [DOI: 10.1016/j.mimet.2019.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 12/14/2022]
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Wörmer L, Hoshino T, Bowles MW, Viehweger B, Adhikari RR, Xiao N, Uramoto GI, Könneke M, Lazar CS, Morono Y, Inagaki F, Hinrichs KU. Microbial dormancy in the marine subsurface: Global endospore abundance and response to burial. SCIENCE ADVANCES 2019; 5:eaav1024. [PMID: 30801015 PMCID: PMC6382399 DOI: 10.1126/sciadv.aav1024] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/11/2019] [Indexed: 05/19/2023]
Abstract
Marine sediments host an unexpectedly large microbial biosphere, suggesting unique microbial mechanisms for surviving burial and slow metabolic turnover. Although dormancy is generally considered an important survival strategy, its specific role in subsurface sediments remains unclear. We quantified dormant bacterial endospores in 331 marine sediment samples from diverse depositional types and geographical origins. The abundance of endospores relative to vegetative cells increased with burial depth and endospores became dominant below 25 m, with an estimated population of 2.5 × 1028 to 1.9 × 1029 endospores in the uppermost kilometer of sediment and a corresponding biomass carbon of 4.6 to 35 Pg surpassing that of vegetative cells. Our data further identify distinct endospore subgroups with divergent resistance to burial and aging. Endospores may shape the deep biosphere by providing a core population for colonization of new habitats and/or through low-frequency germination to sustain slow growth in this environment.
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Affiliation(s)
- Lars Wörmer
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
- Corresponding author.
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | | | - Bernhard Viehweger
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Rishi R. Adhikari
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Nan Xiao
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | - Go-ichiro Uramoto
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Center for Advanced Marine Core Research, Kochi University, Kochi 783-8502, Japan
| | - Martin Könneke
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Cassandre S. Lazar
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
- Department of Biological Sciences, Université du Québec à Montréal (UQAM), Montreal, Quebec H3C 3P8, Canada
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - Kai-Uwe Hinrichs
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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29
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Malic L, Daoud J, Geissler M, Boutin A, Lukic L, Janta M, Elmanzalawy A, Veres T. Epigenetic subtyping of white blood cells using a thermoplastic elastomer-based microfluidic emulsification device for multiplexed, methylation-specific digital droplet PCR. Analyst 2019; 144:6541-6553. [DOI: 10.1039/c9an01316d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Digital droplet PCR for epigenetic leukocyte subtyping from clinically relevant samples is implemented using a thermoplastic elastomer microfluidic droplet generator as a first step towards an economical, customizable and easily deployable system.
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Affiliation(s)
- Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Alex Boutin
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Ljuboje Lukic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Mojra Janta
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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30
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Sreejith KR, Ooi CH, Jin J, Dao DV, Nguyen NT. Digital polymerase chain reaction technology - recent advances and future perspectives. LAB ON A CHIP 2018; 18:3717-3732. [PMID: 30402632 DOI: 10.1039/c8lc00990b] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has remained a "hot topic" in the last two decades due to its potential applications in cell biology, genetic engineering, and medical diagnostics. Various advanced techniques have been reported on sample dispersion, thermal cycling and output monitoring of digital PCR. However, a fully automated, low-cost and handheld digital PCR platform has not been reported in the literature. This paper attempts to critically evaluate the recent developments in techniques for sample dispersion, thermal cycling and output evaluation for dPCR. The techniques are discussed in terms of hardware simplicity, portability, cost-effectiveness and suitability for automation. The present paper also discusses the research gaps observed in each step of dPCR and concludes with possible improvements toward portable, low-cost and automatic digital PCR systems.
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Affiliation(s)
- Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
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31
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Hoshino T, Inagaki F. Abundance and distribution of Archaea in the subseafloor sedimentary biosphere. ISME JOURNAL 2018; 13:227-231. [PMID: 30116037 PMCID: PMC6298964 DOI: 10.1038/s41396-018-0253-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/28/2018] [Accepted: 07/11/2018] [Indexed: 12/12/2022]
Abstract
Subseafloor sedimentary environments harbor a remarkable number of microorganisms that constitute anaerobic and aerobic microbial ecosystems beneath the ocean margins and open-ocean gyres, respectively. Microbial biomass and diversity richness generally decrease with increasing sediment depth and burial time. However, there has been a long-standing debate over the contribution and distribution of Archaea in the subseafloor sedimentary biosphere. Here we show the global quantification of archaeal and bacterial 16S rRNA genes in 221 sediment core samples obtained from diverse oceanographic settings through scientific ocean drilling using microfluidic digital PCR. We estimated that archaeal cells constitute 37.3% of the total microbial cells (40.0% and 12.8% in the ocean margin and open-ocean sites, respectively), corresponding to 1.1 × 1029 cells on Earth. In addition, the relative abundance of archaeal 16S rRNA genes generally decreased with the depth of water in the overlying sedimentary habitat, suggesting that Archaea may be more sensitive to nutrient quality and quantity supplied from the overlying ocean.
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Affiliation(s)
- Tatsuhiko Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan. .,Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, 236-0001, Japan.
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32
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Rusch JC, Hansen H, Strand DA, Markussen T, Hytterød S, Vrålstad T. Catching the fish with the worm: a case study on eDNA detection of the monogenean parasite Gyrodactylus salaris and two of its hosts, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Parasit Vectors 2018; 11:333. [PMID: 29866158 PMCID: PMC5987472 DOI: 10.1186/s13071-018-2916-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/25/2018] [Indexed: 01/20/2023] Open
Abstract
Background Environmental DNA (eDNA) monitoring is growing increasingly popular in aquatic systems as a valuable complementary method to conventional monitoring. However, such tools have not yet been extensively applied for metazoan fish parasite monitoring. The fish ectoparasite Gyrodactylus salaris, introduced into Norway in 1975, has caused severe damage to Atlantic salmon populations and fisheries. Successful eradication of the parasite has been carried out in several river systems in Norway, and Atlantic salmon remain infected in only seven rivers, including three in the Drammen region. In this particular infection region, a prerequisite for treatment is to establish whether G. salaris is also present on rainbow trout upstream of the salmon migration barrier. Here, we developed and tested eDNA approaches to complement conventional surveillance methods. Methods Water samples (2 × 5 l) were filtered on-site through glass fibre filters from nine locations in the Drammen watercourse, and DNA was extracted with a CTAB protocol. We developed a qPCR assay for G. salaris targeting the nuclear ribosomal ITS1 region, and we implemented published assays targeting the mitochondrial cytochrome-b and NADH-regions for Atlantic salmon and rainbow trout, respectively. All assays were transferred successfully to droplet digital PCR (ddPCR). Results All qPCR/ddPCR assays performed well both on tissue samples and on field samples, demonstrating the applicability of eDNA detection for G. salaris, rainbow trout and Atlantic salmon in natural water systems. With ddPCR we eliminated a low cross-amplification of Gyrodactylus derjavinoides observed using qPCR, thus increasing specificity and sensitivity substantially. Duplex ddPCR for G. salaris and Atlantic salmon was successfully implemented and can be used as a method in future surveillance programs. The presence of G. salaris eDNA in the infected River Lierelva was documented, while not elsewhere. Rainbow trout eDNA was only detected at localities where the positives could be attributed to eDNA release from upstream land-based rainbow trout farms. Electrofishing supported the absence of rainbow trout in all of the localities. Conclusions We provide a reliable field and laboratory protocol for eDNA detection of G. salaris, Atlantic salmon and rainbow trout, that can complement conventional surveillance programs and substantially reduce the sacrifice of live fish. We also show that ddPCR outperforms qPCR with respect to the specific detection of G. salaris.
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Affiliation(s)
- Johannes C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway.,Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316, Oslo, Norway
| | - Haakon Hansen
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway.
| | - David A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway
| | - Turhan Markussen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 8146, Dep, NO-0033, Oslo, Norway
| | - Sigurd Hytterød
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway
| | - Trude Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106, Oslo, Norway
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Nunoura T, Nishizawa M, Hirai M, Shimamura S, Harnvoravongchai P, Koide O, Morono Y, Fukui T, Inagaki F, Miyazaki J, Takaki Y, Takai K. Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes Environ 2018; 33:186-194. [PMID: 29806625 PMCID: PMC6031389 DOI: 10.1264/jsme2.me17194] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, "Ca. Marinimicrobia" (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and "Ca. Woesearchaeota" (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.
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Affiliation(s)
- Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Manabu Nishizawa
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Osamu Koide
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology (JAMSTEC).,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science Technology (JAMSTEC)
| | - Junichi Miyazaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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Haramoto E, Kitajima M, Hata A, Torrey JR, Masago Y, Sano D, Katayama H. A review on recent progress in the detection methods and prevalence of human enteric viruses in water. WATER RESEARCH 2018; 135:168-186. [PMID: 29471200 DOI: 10.1016/j.watres.2018.02.004] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 05/17/2023]
Abstract
Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.
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Affiliation(s)
- Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Akihiko Hata
- Integrated Research System for Sustainability Science, Institutes for Advanced Study, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Jason R Torrey
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Yoshifumi Masago
- Institute for the Advanced Study of Sustainability, United Nations University, 5-53-70 Jingumae, Shibuya-ku, Tokyo 150-8925, Japan.
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Hiroyuki Katayama
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Vietnam Japan University, Luu Huu Phuoc Road, My Dinh 1 Ward, Nam Tu Liem District, Ha Noi, Vietnam.
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Sheik CS, Reese BK, Twing KI, Sylvan JB, Grim SL, Schrenk MO, Sogin ML, Colwell FS. Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life. Front Microbiol 2018; 9:840. [PMID: 29780369 PMCID: PMC5945997 DOI: 10.3389/fmicb.2018.00840] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/12/2018] [Indexed: 11/15/2022] Open
Abstract
Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.
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Affiliation(s)
- Cody S Sheik
- Department of Biology and Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, United States
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, United States
| | - Katrina I Twing
- Department of Biology, The University of Utah, Salt Lake City, UT, United States
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Sharon L Grim
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, United States
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Frederick S Colwell
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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36
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Quan PL, Sauzade M, Brouzes E. dPCR: A Technology Review. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1271. [PMID: 29677144 PMCID: PMC5948698 DOI: 10.3390/s18041271] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/13/2018] [Accepted: 04/15/2018] [Indexed: 12/17/2022]
Abstract
Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson distribution. Each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence. The proportion of PCR-positive partitions suffices to determine the concentration of the target sequence without a need for calibration. Advances in microfluidics enabled the current revolution of digital quantification by providing efficient partitioning methods. In this review, we compare the fundamental concepts behind the quantification of nucleic acids by dPCR and quantitative real-time PCR (qPCR). We detail the underlying statistics of dPCR and explain how it defines its precision and performance metrics. We review the different microfluidic digital PCR formats, present their underlying physical principles, and analyze the technological evolution of dPCR platforms. We present the novel multiplexing strategies enabled by dPCR and examine how isothermal amplification could be an alternative to PCR in digital assays. Finally, we determine whether the theoretical advantages of dPCR over qPCR hold true by perusing studies that directly compare assays implemented with both methods.
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Affiliation(s)
- Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Martin Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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Hunter ME, Meigs-Friend G, Ferrante JA, Takoukam Kamla A, Dorazio RM, Keith-Diagne L, Luna F, Lanyon JM, Reid JP. Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00880] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Molinari C, Abou Khouzam R, Salvi S, Rossi T, Ranzani GN, Calistri D. Detection of a CDH1 Rare Transcript Variant in Fresh-frozen Gastric Cancer Tissues by Chip-based Digital PCR. J Vis Exp 2018. [PMID: 29443099 DOI: 10.3791/57066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
CDH1a, a non-canonical transcript of the CDH1 gene, has been found to be expressed in some gastric cancer (GC) cell lines, whereas it is absent in normal gastric mucosa. Recently, we detected CDH1a transcript variant in fresh-frozen tumor tissues obtained from patients with GC. The expression of this variant in tissue samples was investigated by the chip-based digital PCR (dPCR) approach presented here. dPCR offers the potential for an accurate, robust, and highly sensitive measurement of nucleic acids and is increasingly utilized for many applications in different fields. dPCR is capable of detecting rare targets; in addition, dPCR offers the possibility for absolute and precise quantification of nucleic acids without the need for calibrators and standard curves. In fact, the reaction partitioning enriches the target from the background, which improves amplification efficiency and tolerance to inhibitors. Such characteristics make dPCR an optimal tool for the detection of the CDH1a rare transcript.
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Affiliation(s)
- Chiara Molinari
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS;
| | | | - Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Tania Rossi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | | | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
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39
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Species identification and animal authentication in meat products: a review. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2017. [DOI: 10.1007/s11694-017-9625-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Ricchi M, Bertasio C, Boniotti MB, Vicari N, Russo S, Tilola M, Bellotti MA, Bertasi B. Comparison among the Quantification of Bacterial Pathogens by qPCR, dPCR, and Cultural Methods. Front Microbiol 2017; 8:1174. [PMID: 28702010 PMCID: PMC5487435 DOI: 10.3389/fmicb.2017.01174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 06/08/2017] [Indexed: 11/13/2022] Open
Abstract
The demand for rapid methods for the quantification of pathogens is increasing. Among these methods, those based on nucleic acids amplification (quantitative PCRs) are the most widespread worldwide. Together with the qPCR, a new approach named digital PCR (dPCR), has rapidly gained importance. The aim of our study was to compare the results obtained using two different dPCR systems and one qPCR in the quantification of three different bacterial pathogens: Listeria monocytogenes, Francisella tularensis, and Mycobacterium avium subsp. paratuberculosis. For this purpose, three pre-existing qPCRs were used, while the same primers and probes, as well as PCR conditions, were transferred to two different dPCR systems: the QX200 (Bio-Rad) and the Quant Studio 3D (Applied Biosystems). The limits of detection and limits of quantification for all pathogens, and all PCR approaches applied, were determined using genomic pure DNAs. The quantification of unknown decimal suspensions of the three bacteria obtained by the three different PCR approaches was compared through the Linear Regression and Bland and Altman analyses. Our results suggest that, both dPCRs are able to quantify the same amount of bacteria, while the comparison among dPCRs and qPCRs, showed both over and under-estimation of the bacteria present in the unknown suspensions. Our results showed qPCR over-estimated the amount of M. avium subsp. paratuberculosis and F. tularensis cells. On the contrary, qPCR, compared to QX200 dPCR, under-estimated the amount of L. monocytogenes cells. However, the maximum difference among PCRs approaches was <0.5 Log10, while cultural methods underestimated the number of bacteria by one to two Log10 for Francisella tularensis and Mycobacterium avium subsp. paratuberculosis. On the other hand, cultural and PCRs methods quantified the same amount of bacteria for L. monocytogenes, suggesting for this last pathogen, PCRs approaches can be considered as a valid alternative to the cultural ones.
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Affiliation(s)
- Matteo Ricchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini," National Reference Centre for ParatuberculosisPodenzano, Italy
| | - Cristina Bertasio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini," National Reference Centre for Tuberculosis from M. bovisBrescia, Italy
| | - Maria B Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini," National Reference Centre for Tuberculosis from M. bovisBrescia, Italy
| | - Nadia Vicari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, National Reference Laboratory for Tularemia, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini"Pavia, Italy
| | - Simone Russo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini," National Reference Centre for ParatuberculosisPodenzano, Italy
| | - Michela Tilola
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini," Reparto Tecnologie Acidi Nucleici Applicate Agli AlimentiBrescia, Italy
| | - Marco A Bellotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, National Reference Laboratory for Tularemia, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini"Pavia, Italy
| | - Barbara Bertasi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini," Reparto Tecnologie Acidi Nucleici Applicate Agli AlimentiBrescia, Italy
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Hoshino T, Toki T, Ijiri A, Morono Y, Machiyama H, Ashi J, Okamura K, Inagaki F. Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes. Front Microbiol 2017; 8:1135. [PMID: 28676800 PMCID: PMC5476839 DOI: 10.3389/fmicb.2017.01135] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/06/2017] [Indexed: 11/23/2022] Open
Abstract
Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into the overlying seawater. Although SMVs act as a natural pipeline connecting the Earth’s surface and subsurface biospheres, the dispersal of deep-biosphere microorganisms and their ecological roles remain largely unknown. In this study, we investigated the microbial communities in sediment and overlying seawater at two SMVs located on the Ryukyu Trench off Tanegashima Island, southern Japan. The microbial communities in mud volcano sediments were generally distinct from those in the overlying seawaters and in the well-stratified Pacific margin sediments collected at the Peru Margin, the Juan de Fuca Ridge flank off Oregon, and offshore of Shimokita Peninsula, northeastern Japan. Nevertheless, in-depth analysis of different taxonomic groups at the sub-species level revealed that the taxon affiliated with Atribacteria, heterotrophic anaerobic bacteria that typically occur in organic-rich anoxic subseafloor sediments, were commonly found not only in SMV sediments but also in the overlying seawater. We designed a new oligonucleotide probe for detecting Atribacteria using the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). CARD-FISH, digital PCR and sequencing analysis of 16S rRNA genes consistently showed that Atribacteria are abundant in the methane plumes of the two SMVs (0.58 and 1.5 × 104 cells/mL, respectively) but not in surrounding waters, suggesting that microbial cells in subseafloor sediments are dispersed as “deep-biosphere seeds” into the ocean. These findings may have important implications for the microbial transmigration between the deep subseafloor biosphere and the hydrosphere.
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Affiliation(s)
- Tatsuhiko Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Tomohiro Toki
- Faculty of Science, University of the RyukyusNishihara, Japan
| | - Akira Ijiri
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Hideaki Machiyama
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Juichiro Ashi
- Atmosphere and Ocean Research Institute, The University of TokyoTokyo, Japan
| | - Kei Okamura
- Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi UniversityNankoku, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science TechnologyYokohama, Japan
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42
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Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment. Sci Rep 2017; 7:2400. [PMID: 28546547 PMCID: PMC5445093 DOI: 10.1038/s41598-017-02295-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 04/10/2017] [Indexed: 11/08/2022] Open
Abstract
The factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10-60-fold in uppermost sediments that are irrigated and mixed by macrofauna. This bioturbation is indicated by visual observations of sediment color and faunal tracks, by porewater profiles of dissolved inorganic carbon and sulfate, and by distributions of unsupported 210Pb and 137Cs. Below the depth of bioturbation, the relative abundances of archaeal genes increase, accounting for one third of 16S rRNA genes in the sulfate zone, and half of 16S rRNA genes in the sulfate-methane transition zone and methane zone. Phylogenetic analyses reveal a strong shift in bacterial and archaeal community structure from bioturbated sediments to underlying layers. Stable isotopic analyses on organic matter and porewater geochemical gradients suggest that macrofauna mediate bacterial dominance and affect microbial community structure in bioturbated sediment by introducing fresh organic matter and high-energy electron acceptors from overlying seawater. Below the zone of bioturbation, organic matter content and the presence of sulfate exert key influences on bacterial and archaeal abundances and overall microbial community structure.
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43
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Hoshino T, Hamada Y. Estimation of the influence of sequencing errors and distribution of random-sequence tags on quantitative sequencing. J Biosci Bioeng 2017; 124:359-364. [PMID: 28457659 DOI: 10.1016/j.jbiosc.2017.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/27/2017] [Accepted: 04/05/2017] [Indexed: 11/18/2022]
Abstract
To simultaneously sequence and quantify target DNA, quantitative sequencing (qSeq) employs stochastic labeling of target DNA molecules with random-sequence tags (RSTs). This recently developed approach allows parallel quantification of hundreds of microorganisms in natural habitats in a single sequencing run. Yet, no study has addressed to what extent sequencing errors affect quantification and how many sequence reads are needed for quantification. Here, we addressed those issues by using numerical simulations and experimental data from second-generation sequencing of various RSTs. We found that heterogeneous distribution of observed RSTs affected the number of sequence reads required to quantitate target genes, whereas the effect of sequencing errors is smaller than of the RSTs distribution. Because of the heterogeneous RSTs distribution, 15-fold more sequence reads than the number of observed RSTs should be obtained to retrieve almost all RSTs needed for quantification; in that case, quantification error is estimated to be within 5%.
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Affiliation(s)
- Tatsuhiko Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan; Geobiotechnology Group, Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan.
| | - Yohei Hamada
- Fault Mechanics Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
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44
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Rebollar EA, Woodhams DC, LaBumbard B, Kielgast J, Harris RN. Prevalence and pathogen load estimates for the fungus Batrachochytrium dendrobatidis are impacted by ITS DNA copy number variation. DISEASES OF AQUATIC ORGANISMS 2017; 123:213-226. [PMID: 28322208 DOI: 10.3354/dao03097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses of organisms from all 3 domains of life. In fungi, the copy number of the internal transcribed spacer (ITS) is used to detect abundance of pathogens causing diseases such as chytridiomycosis in amphibians and white nose syndrome in bats. Chytridiomycosis is caused by the fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), and is responsible for declines and extinctions of amphibians worldwide. Over a decade ago, a qPCR assay was developed to determine Bd prevalence and pathogen load. Here, we demonstrate the effect that ITS copy number variation in Bd strains can have on the estimation of prevalence and pathogen load. We used data sets from different amphibian species to simulate how ITS copy number affects prevalence and pathogen load. In addition, we tested 2 methods (gBlocks® synthetic standards and digital PCR) to determine ITS copy number in Bd strains. Our results show that assumptions about the ITS copy number can lead to under- or overestimation of Bd prevalence and pathogen load. The use of synthetic standards replicated previously published estimates of ITS copy number, whereas dPCR resulted in estimates that were consistently lower than previously published estimates. Standardizing methods will assist with comparison across studies and produce reliable estimates of prevalence and pathogen load in the wild, while using the same Bd strain for exposure experiments and zoospore standards in qPCR remains the best method for estimating parameters used in epidemiological studies.
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Affiliation(s)
- Eria A Rebollar
- Biology Department, James Madison University, 951 Carrier Dr., MSC 7801, Harrisonburg, Virginia 22807, USA
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45
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Acosta Soto L, Santísima-Trinidad AB, Bornay-Llinares FJ, Martín González M, Pascual Valero JA, Ros Muñoz M. Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7515409. [PMID: 28377928 PMCID: PMC5362715 DOI: 10.1155/2017/7515409] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/10/2017] [Accepted: 01/16/2017] [Indexed: 12/13/2022]
Abstract
The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks.
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Affiliation(s)
- Lucrecia Acosta Soto
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, Espinardo, 30100 Murcia, Spain
- Área de Parasitología, Departamento de Agroquímica y Medio Ambiente, Universidad Miguel Hernández de Elche, Ctra Valencia Km 8.7, San Juan, 03550 Alicante, Spain
| | - Ana Belén Santísima-Trinidad
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, Espinardo, 30100 Murcia, Spain
| | - Fernando Jorge Bornay-Llinares
- Área de Parasitología, Departamento de Agroquímica y Medio Ambiente, Universidad Miguel Hernández de Elche, Ctra Valencia Km 8.7, San Juan, 03550 Alicante, Spain
| | | | - José Antonio Pascual Valero
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, Espinardo, 30100 Murcia, Spain
| | - Margarita Ros Muñoz
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, Espinardo, 30100 Murcia, Spain
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Yanagawa K, Ijiri A, Breuker A, Sakai S, Miyoshi Y, Kawagucci S, Noguchi T, Hirai M, Schippers A, Ishibashi JI, Takaki Y, Sunamura M, Urabe T, Nunoura T, Takai K. Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor. THE ISME JOURNAL 2017; 11:529-542. [PMID: 27754478 PMCID: PMC5270560 DOI: 10.1038/ismej.2016.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/26/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023]
Abstract
Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ13C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106-198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field.
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Affiliation(s)
- Katsunori Yanagawa
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Department of Earth and Planetary Science, University of Tokyo, Tokyo, Japan
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Akira Ijiri
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kochi, Japan
| | - Anja Breuker
- Geomicrobiology, Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Sanae Sakai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Youko Miyoshi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuroh Noguchi
- Interdisciplinary Science Unit, Multidisciplinary Science Cluster, Research and Education Faculty, Kochi University, Kochi, Japan
| | - Miho Hirai
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Axel Schippers
- Geomicrobiology, Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Jun-ichiro Ishibashi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Michinari Sunamura
- Department of Earth and Planetary Science, University of Tokyo, Tokyo, Japan
| | - Tetsuro Urabe
- Department of Earth and Planetary Science, University of Tokyo, Tokyo, Japan
| | - Takuro Nunoura
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Farkas K, Hassard F, McDonald JE, Malham SK, Jones DL. Evaluation of Molecular Methods for the Detection and Quantification of Pathogen-Derived Nucleic Acids in Sediment. Front Microbiol 2017; 8:53. [PMID: 28174565 PMCID: PMC5258707 DOI: 10.3389/fmicb.2017.00053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/09/2017] [Indexed: 11/24/2022] Open
Abstract
The accurate detection of pathogens in environmental matrices, such as sediment, is critical in understanding pathogen fate and behavior in the environment. In this study, we assessed the usefulness of methods for the detection and quantification of Vibrio spp. and norovirus (NoV) nucleic acids in sediment. For bacteria, a commonly used direct method using hexadecyltrimethylammonium bromide (CTAB) and phenol-chloroform-isoamyl alcohol (PCI) extraction was optimized, whereas for NoV, direct and indirect (virus elution-concentration) methods were evaluated. For quantification, commercially available quantitative PCR (qPCR) and reverse transcription qPCR (RT-qPCR) kits were tested alongside a digital PCR (dPCR) approach. CTAB-based extraction combined with 16 h polyethylene glycol 6000 (PEG6000) precipitation was found to be suitable for the direct extraction of high abundance bacterial and viral nucleic acids. For the indirect extraction of viral RNA, beef extract-based elution followed by PEG6000 precipitation and extraction using the NucliSENS® MiniMag® Nucleic Acid Purification System and the PowerViral® Environmental RNA/DNA Isolation Kit and qRT-PCR resulted in 83-112 and 63-69% recoveries of NoV, respectively. dPCR resulted in lower viral recoveries (47 and 9%) and ~4 orders of magnitude lower Vibrio concentrations (3.6-4.6 log10 gc/100 g sediment) than was observed using qPCR. The use of internal controls during viral quantification revealed that the RT step was more affected by inhibitors than the amplification. The methods described here are suitable for the enumeration of viral and/or bacterial pathogens in sediment, however the use of internal controls to assess efficiency is recommended.
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Affiliation(s)
- Kata Farkas
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, Wales
| | | | | | | | - Davey L. Jones
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, Wales
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Sidstedt M, Romsos EL, Hedell R, Ansell R, Steffen CR, Vallone PM, Rådström P, Hedman J. Accurate Digital Polymerase Chain Reaction Quantification of Challenging Samples Applying Inhibitor-Tolerant DNA Polymerases. Anal Chem 2017; 89:1642-1649. [PMID: 28118703 DOI: 10.1021/acs.analchem.6b03746] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Digital PCR (dPCR) enables absolute quantification of nucleic acids by partitioning of the sample into hundreds or thousands of minute reactions. By assuming a Poisson distribution for the number of DNA fragments present in each chamber, the DNA concentration is determined without the need for a standard curve. However, when analyzing nucleic acids from complex matrixes such as soil and blood, the dPCR quantification can be biased due to the presence of inhibitory compounds. In this study, we evaluated the impact of varying the DNA polymerase in chamber-based dPCR for both pure and impure samples using the common PCR inhibitor humic acid (HA) as a model. We compared the TaqMan Universal PCR Master Mix with two alternative DNA polymerases: ExTaq HS and Immolase. By using Bayesian modeling, we show that there is no difference among the tested DNA polymerases in terms of accuracy of absolute quantification for pure template samples, i.e., without HA present. For samples containing HA, there were great differences in performance: the TaqMan Universal PCR Master Mix failed to correctly quantify DNA with more than 13 pg/nL HA, whereas Immolase (1 U) could handle up to 375 pg/nL HA. Furthermore, we found that BSA had a moderate positive effect for the TaqMan Universal PCR Master Mix, enabling accurate quantification for 25 pg/nL HA. Increasing the amount of DNA polymerase from 1 to 5 U had a strong effect for ExTaq HS, elevating HA-tolerance four times. We also show that the average Cq values of positive reactions may be used as a measure of inhibition effects, e.g., to determine whether or not a dPCR quantification result is reliable. The statistical models developed to objectively analyze the data may also be applied in quality control. We conclude that the choice of DNA polymerase in dPCR is crucial for the accuracy of quantification when analyzing challenging samples.
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Affiliation(s)
- Maja Sidstedt
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden.,Swedish National Forensic Centre , SE-581 94 Linköping, Sweden
| | - Erica L Romsos
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Ronny Hedell
- Swedish National Forensic Centre , SE-581 94 Linköping, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Ricky Ansell
- Swedish National Forensic Centre , SE-581 94 Linköping, Sweden.,Department of Physics, Chemistry and Biology, IFM, Linköping University , SE-581 83 Linköping, Sweden
| | - Carolyn R Steffen
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Peter M Vallone
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden
| | - Johannes Hedman
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden.,Swedish National Forensic Centre , SE-581 94 Linköping, Sweden
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Hoshino T, Inagaki F. Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes. PLoS One 2017; 12:e0169431. [PMID: 28052139 PMCID: PMC5215600 DOI: 10.1371/journal.pone.0169431] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 12/16/2016] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5’ end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103 to 5.0 × 104 copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.
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Affiliation(s)
- Tatsuhiko Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
- Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC, Nankoku, Kochi, Japan
- * E-mail:
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
- Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC, Nankoku, Kochi, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, Kanagawa, Japan
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50
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Ofner A, Moore DG, Rühs PA, Schwendimann P, Eggersdorfer M, Amstad E, Weitz DA, Studart AR. High‐Throughput Step Emulsification for the Production of Functional Materials Using a Glass Microfluidic Device. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201600472] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alessandro Ofner
- Complex Materials Department of Materials ETH Zurich 8093 Zurich Switzerland
| | - David G. Moore
- Complex Materials Department of Materials ETH Zurich 8093 Zurich Switzerland
| | - Patrick A. Rühs
- Complex Materials Department of Materials ETH Zurich 8093 Zurich Switzerland
| | - Pascal Schwendimann
- Complex Materials Department of Materials ETH Zurich 8093 Zurich Switzerland
| | - Maximilian Eggersdorfer
- Department of Physics and School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA
| | - Esther Amstad
- Institute of Materials EPF Lausanne 1015 Lausanne Switzerland
| | - David A. Weitz
- Department of Physics and School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA
| | - André R. Studart
- Complex Materials Department of Materials ETH Zurich 8093 Zurich Switzerland
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