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Jin H, Lim HJ, Liles MR, Chua B, Son A. Switchable inhibitory behavior of divalent magnesium ion in DNA hybridization-based gene quantification. Analyst 2022; 147:4845-4856. [DOI: 10.1039/d2an01164f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mg2+ ion is a switchable inhibitor that can cause either under or over-estimation at different concentrations in DNA hybridization based gene quantification.
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Affiliation(s)
- Hyowon Jin
- Department of Environmental Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Hyun Jeong Lim
- Department of Environmental Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA
| | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Beelee Chua
- School of Electrical Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Ahjeong Son
- Department of Environmental Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
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2
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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3
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Basim Y, Mohebali G, Jorfi S, Nabizadeh R, Ghadiri A, Moghadam MA, Soleymani F, Fard NJH. Comparison of performance and efficiency of four methods to extract genomic DNA from oil contaminated soils in southwestern of Iran. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2020; 18:463-468. [PMID: 33312575 PMCID: PMC7721925 DOI: 10.1007/s40201-020-00474-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/08/2020] [Indexed: 06/12/2023]
Abstract
The wide spectrum of oil industry activities caused soil contaminants, as environmental concern in many areas of the world. Bioremediation of oily soils, as biological approach done by bacteria and fungi, is very important to eliminate this pollution. In this study four different metagenomic protocols for DNA extraction has been tested in order to sequence and identify the native bacterial species involved in remediation of oily soils. In this regard, 3 manual methods and a soil DNA extraction kit are used. In manual protocol, physical processes including the addition of silica beads and freezing samples by liquid nitrogen, chemical methods such as treating the lysozyme, and lysis buffer and proteinase K as biochemical methods were utilized for optimal extraction. Quality and quantity of the extracted DNA analyzed using Agarose gel electrophoresis and Picodrop respectively. Then, the 16S rdna gene of bacteria amplified through universal primer for preparing a genomic library by PCR. Results showed that the highest concentration and quality of extracted DNA was obtained by protocol D which was about 135 μg/ul and 260/230 = 2.2 respectively. Moreover, 500 bp fragment amplified perfectly by using DNA extracted through protocol D in the PCR test. Therefore, protocol D can be used as an appropriate and effective way in order to study the microbial population of oily soils using direct extraction of DNA.
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Affiliation(s)
- Yalda Basim
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ghasemali Mohebali
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Sahand Jorfi
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ramin Nabizadeh
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ata Ghadiri
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehdi Ahmadi Moghadam
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Nowak KM, Miltner A, Poll C, Kandeler E, Streck T, Pagel H. Plant litter enhances degradation of the herbicide MCPA and increases formation of biogenic non-extractable residues in soil. ENVIRONMENT INTERNATIONAL 2020; 142:105867. [PMID: 32585504 DOI: 10.1016/j.envint.2020.105867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/22/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Amendment of soils with plant residues is common practice for improving soil quality. In addition to stimulated microbial activity, the supply of fresh soluble organic (C) from litter may accelerate the microbial degradation of chemicals in soils. Therefore, the aim of this study was to test whether the maize litter enhances degradation of 4-chloro-2-methylphenoxyacetic acid (MCPA) and increases formation of non-toxic biogenic non-extractable residues (bioNERs). Soil was amended with 13C6-MCPA and incubated with or without litter addition on the top. Three soil layers were sampled with increasing distance from the top: 0-2 mm, 2-5 mm and 5-20 mm; and the mass balance of 13C6-MCPA transformation determined. Maize litter promoted microbial activity, mineralization of 13C6-MCPA and bioNER formation in the upper two layers (0-2 and 2-5 mm). The mineralization of 13C6-MCPA in soil with litter increased to 27% compared to only 6% in the control. Accordingly, maize addition reduced the amount of extractable residual MCPA in soil from 77% (control) to 35% of initially applied 13C6-MCPA. While non-extractable residues (NERs) were <6% in control soil, litter addition raised NERs to 21%. Thereby, bioNERs comprised 14% of 13C6-MCPA equivalents. We found characteristic differences of bioNER formation with distance to litter. While total NERs in soil at a distance of 2-5 mm were mostly identified as 13C-bioNERs (97%), only 45-46% of total NERs were assigned to bioNERs in the 0-2 and 5-20 mm layers. Phospholipid fatty acid analysis indicated that fungi and Gram-negative bacteria were mainly involved in MCPA degradation. Maize-C particularly stimulated fungal activity in the adjacent soil, which presumably facilitated non-biogenic NER formation. The plant litter accelerated formation of both non-toxic bioNERs and non-biogenic NERs. More studies on the structural composition of non-biogenic NERs with toxicity potential are needed for future recommendations on litter addition in agriculture.
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Affiliation(s)
- Karolina M Nowak
- Technische Universität Berlin, Institute of Biotechnology, Chair of Geobiotechnology, Ackerstraße 76, 13355 Berlin, Germany; Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstr. 15, 04318 Leipzig, Germany.
| | - Anja Miltner
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstr. 15, 04318 Leipzig, Germany
| | - Christian Poll
- University of Hohenheim, Institute of Soil Science and Land Evaluation, Department of Soil Biology, Emil-Wolff-Str. 27, 70599 Stuttgart, Germany
| | - Ellen Kandeler
- University of Hohenheim, Institute of Soil Science and Land Evaluation, Department of Soil Biology, Emil-Wolff-Str. 27, 70599 Stuttgart, Germany
| | - Thilo Streck
- University of Hohenheim, Institute of Soil Science and Land Evaluation, Department of Biogeophysics, Emil-Wolff-Str. 27, 70599 Stuttgart, Germany
| | - Holger Pagel
- University of Hohenheim, Institute of Soil Science and Land Evaluation, Department of Biogeophysics, Emil-Wolff-Str. 27, 70599 Stuttgart, Germany
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Mbareche H, Veillette M, Teertstra W, Kegel W, Bilodeau GJ, Wösten HAB, Duchaine C. Recovery of Fungal Cells from Air Samples: a Tale of Loss and Gain. Appl Environ Microbiol 2019; 85:e02941-18. [PMID: 30824432 PMCID: PMC6495771 DOI: 10.1128/aem.02941-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/15/2019] [Indexed: 12/25/2022] Open
Abstract
There are limitations in establishing a direct link between fungal exposure and health effects due to the methodology used, among other reasons. Culture methods ignore the nonviable/uncultivable fraction of airborne fungi. Molecular methods allow for a better understanding of the environmental health impacts of microbial communities. However, there are challenges when applying these techniques to bioaerosols, particularly to fungal cells. This study reveals that there is a loss of fungal cells when samples are recovered from air using wet samplers and aimed to create and test an improved protocol for concentrating mold spores via filtration prior to DNA extraction. Results obtained using the new technique showed that up to 3 orders of magnitude more fungal DNA was retrieved from the samples using quantitative PCR. A sequencing approach with MiSeq revealed a different diversity profile depending on the methodology used. Specifically, 8 fungal families out of 19 families tested were highlighted to be differentially abundant in centrifuged and filtered samples. An experiment using laboratory settings showed the same spore loss during centrifugation for Aspergillus niger and Penicillium roquefortii strains. We believe that this work helped identify and address fungal cell loss during processing of air samples, including centrifugation steps, and propose an alternative method for a more accurate evaluation of fungal exposure and diversity.IMPORTANCE This work shed light on a significant issue regarding the loss of fungal spores when recovered from air samples using liquid medium and centrifugation to concentrate air particles before DNA extraction. We provide proof that the loss affects the overall fungal diversity of aerosols and that some taxa are differentially more affected than others. Furthermore, a laboratory experiment confirmed the environmental results obtained during field sampling. The filtration protocol described in this work offers a better description of the fungal diversity of aerosols and should be used in fungal aerosol studies.
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Affiliation(s)
- Hamza Mbareche
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, Quebec, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Marc Veillette
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, Quebec, Canada
| | - Wieke Teertstra
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Willem Kegel
- Department of Physical and Colloid Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Guillaume J Bilodeau
- Pathogen Identification Research Laboratory, Canadian Food Inspection Agency (CFIA), Ottawa, Canada
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Caroline Duchaine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, Quebec, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
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6
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Methods in Metagenomics and Environmental Biotechnology. NANOSCIENCE AND BIOTECHNOLOGY FOR ENVIRONMENTAL APPLICATIONS 2019. [DOI: 10.1007/978-3-319-97922-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Nowak KM, Telscher M, Seidel E, Miltner A. Unraveling microbial turnover and non-extractable residues of bromoxynil in soil microcosms with 13C-isotope probing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:769-777. [PMID: 30031310 DOI: 10.1016/j.envpol.2018.07.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/01/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
Bromoxynil is a widely used nitrile herbicide applied to maize and other cereals in many countries. To date, still little is known about bromoxynil turnover and the structural identity of bromoxynil non-extractable residues (NER) which are reported to occur in high amounts. Therefore, we investigated the microbial turnover of 13C-labeled bromoxynil for 32 days. A focus was laid on the estimation of biogenic NER based on the turnover of 13C into amino acids (AA). At the end, 25% of 13C6-bromoxynil equivalents were mineralized, 2% assigned to extractable residues and 72.5% to NER. Based on 12% in the 13C-total AA and an assumed share of AA of 50% in microbial biomass we arrived at 24% of total 13C-biogenic NER. About 33% of the total 13C-NER could thus be explained by 13C-biogenic NER; 67% was unknown and by definition xenobiotic NER with potential for toxicity. The 13C label from 13C6-bromoxynil was mainly detected in the humic acids (28.5%), but significant amounts were also found in non-humics (17.6%), fulvic acids (13.2%) and humins (12.7%). The 13C-total amino acids hydrolyzed from humic acids, humins and fulvic acids amounted to 5.2%, 6.1% and 1.2% of 13C6-bromoxynil equivalents, respectively, corresponding to total 13C-biogenic NER amounts of 10.4%, 12.2% and 2.4%. The humins contained mostly 13C-biogenic NER, whereas the humic and fulvic acids may be dominated by the xenobiotic NER. Due to the high proportion of unknown 13C-NER and particularly in the humic and fulvic acids, future studies should focus on the detailed characterization of these fractions.
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Affiliation(s)
- Karolina M Nowak
- Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstr. 15, 04318 Leipzig, Germany.
| | - Markus Telscher
- Bayer CropScience AG, Alfred-Nobel-Str. 50, 40789 Monheim am Rhein, Germany
| | - Erika Seidel
- Bayer CropScience AG, Alfred-Nobel-Str. 50, 40789 Monheim am Rhein, Germany
| | - Anja Miltner
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Biotechnology, Permoserstr. 15, 04318 Leipzig, Germany
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Mbareche H, Brisebois E, Veillette M, Duchaine C. Bioaerosol sampling and detection methods based on molecular approaches: No pain no gain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:2095-2104. [PMID: 28558432 DOI: 10.1016/j.scitotenv.2017.05.076] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 05/23/2023]
Abstract
Bioaerosols are among the less studied particles in the environment. The lack of standardization in sampling procedures, difficulties related to the effect of sampling processes on the integrity of microorganisms, and challenges associated with the application of environmental microbiology analyses and molecular and culture methods frighten many young scientists. Every microorganism has its own particularities and acts differently when aerosolized in various conditions. Because the air is an extremely biologically diluted environment, it is necessary to concentrate its content before any analysis is performed. Challenges faced when applying molecular methods to air samples reveal the need for a better standardization of approaches for cell and nucleic acid recovery, the choice of genetic markers, and interpretation of data. This paper presents a few of the limits and difficulties tackled when molecular methods are applied to bioaerosols, suggests some improvements by specifying the critical stages that should be considered when studying the microbial ecology of bioaerosols, and provides thoughtful insights on how to overcome the challenges encountered.
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Affiliation(s)
- Hamza Mbareche
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Université Laval, Canada.
| | - Evelyne Brisebois
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Université Laval, Canada
| | - Marc Veillette
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Université Laval, Canada
| | - Caroline Duchaine
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie, Université Laval, Canada.
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Arseneau JR, Steeves R, Laflamme M. Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues. Mol Ecol Resour 2016; 17:686-693. [PMID: 27768249 DOI: 10.1111/1755-0998.12616] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/25/2016] [Accepted: 09/09/2016] [Indexed: 11/30/2022]
Abstract
The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that coprecipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often coprecipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant-rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle. Comparisons of purity and molecular integrity showed that our in-house protocol yielded genomic DNA generally free of contaminants and shearing, whereas the traditional CTAB method and some of the commercial kits yielded DNA unsuitable for some applications of massively parallel sequencing. Our open-source MoLSC protocol provides a cost-effective, scalable, alternative DNA extraction method that can be easily optimized and adapted for sequencing applications in other contaminant-rich samples.
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Affiliation(s)
- Jean-René Arseneau
- Department of Fisheries and Oceans Canada, Gulf Fisheries Center, 343 Universite Avenue, Moncton, NB, E1C 9B6, Canada
| | - Royce Steeves
- Department of Fisheries and Oceans Canada, Gulf Fisheries Center, 343 Universite Avenue, Moncton, NB, E1C 9B6, Canada
| | - Mark Laflamme
- Department of Fisheries and Oceans Canada, Gulf Fisheries Center, 343 Universite Avenue, Moncton, NB, E1C 9B6, Canada
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Kobayashi Y, Hayashida E, Yokoyama K, Fujii K. A method for isolation of soil microbial DNA that is suitable for analysis of microbial cellulase genes. SEP SCI TECHNOL 2015. [DOI: 10.1080/01496395.2015.1119847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Hevia A, Delgado S, Margolles A, Sánchez B. Application of density gradient for the isolation of the fecal microbial stool component and the potential use thereof. Sci Rep 2015; 5:16807. [PMID: 26581409 PMCID: PMC4652190 DOI: 10.1038/srep16807] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/20/2015] [Indexed: 12/15/2022] Open
Abstract
The idea of considering the gut microbiota as a virtual human organ has led to the concept of fecal microbiota transplantation (FMT), which has recently been extremely successful in the treatment of cases of recurrent Clostridium difficile infection. Administration of safe, viable, and representative fecal microbiota is crucial for FMT. To our knowledge, suitable techniques and systematic conditions for separating the fecal microbiota from stool samples have not been thoroughly investigated. In this work we show the potential to separate stool microorganisms from the rest of fecal material using a procedure with a Nycodenz® density gradient, yielding 1010 viable bacteria per two grams of feces. This procedure did not affect the original microbiota composition in terms of viability, distribution and proportions, as assessed by a phylogenetic metagenomic approach. Obtaining the fecal microbiota by concentration and separation of the microorganisms from the rest of the stool components would allow the standardization of its recovery and its long-term preservation. FMT or similar microbiota restoration therapies could be used for the treatment of several disorders, or even for aesthetic purposes, so the method described in our work may contribute to the setting of the basis for the development of safe and standardized products.
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Affiliation(s)
- Arancha Hevia
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
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12
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13
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A Rapid and Economical Method for Efficient DNA Extraction from Diverse Soils Suitable for Metagenomic Applications. PLoS One 2015; 10:e0132441. [PMID: 26167854 PMCID: PMC4500551 DOI: 10.1371/journal.pone.0132441] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 06/15/2015] [Indexed: 11/19/2022] Open
Abstract
A rapid, cost effective method of metagenomic DNA extraction from soil is a useful tool for environmental microbiology. The present work describes an improved method of DNA extraction namely "powdered glass method" from diverse soils. The method involves the use of sterile glass powder for cell lysis followed by addition of 1% powdered activated charcoal (PAC) as purifying agent to remove humic substances. The method yielded substantial DNA (5.87 ± 0.04 μg/g of soil) with high purity (A260/280: 1.76 ± 0.05) and reduced humic substances (A340: 0.047 ± 0.03). The quality of the extracted DNA was compared against five different methods based on 16S rDNA PCR amplification, BamHI digestion and validated using quantitative PCR. The digested DNA was used for a metagenomic library construction with the transformation efficiency of 4 X 106 CFU mL-1. Besides providing rapid, efficient and economical extraction of metgenomic DNA from diverse soils, this method's applicability is also demonstrated for cultivated organisms (Gram positive B. subtilis NRRL-B-201, Gram negative E. coli MTCC40, and a microalgae C. sorokiniana UTEX#1666).
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14
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Mondino EA, Covacevich F, Studdert GA, Pimentel JP, Berbara RLL. Extracting DNA of nematodes communities from Argentine Pampas agricultural soils. AN ACAD BRAS CIENC 2015; 87:691-7. [PMID: 26131632 DOI: 10.1590/0001-3765201520130110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/02/2014] [Indexed: 11/21/2022] Open
Abstract
We examined four strategies (Tris/EDTA, sodium dodecyl sulfate, Chelex 100 resin and cetyltrimethylammonium bromide -CTAB-) for extracting nucleic acid (DNA) from communities of nematodes. Nematodes were isolated from an agricultural area under different management of long-term crop rotation experiment from Argentina during three seasons. After DNA extraction, Polymerase Chain Reaction-amplifications were performed and considered as indicators of successful DNA extraction. The CTAB combined with proteinase K and phenol-chloroform-isoamyl alcohol was the unique successful method because positive amplifications were obtained by using both eukaryotic and nematode specific primers. This work could contribute to biodiversity studies of nematodes on agroecosystems.
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Affiliation(s)
- Eduardo A Mondino
- Instituto de Agronomia, Departamento de Solos, Laboratório de Matéria Orgânica e Biologia do Solo, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil
| | | | | | - João P Pimentel
- Instituto de Biologia, Departamento de Entomologia e Fitopatologia, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil
| | - Ricardo L L Berbara
- Instituto de Agronomia, Departamento de Solos, Laboratório de Matéria Orgânica e Biologia do Solo, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil
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15
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Nnadozie CF, Lin J, Govinden R. Selective isolation of bacteria for metagenomic analysis: Impact of membrane characteristics on bacterial filterability. Biotechnol Prog 2015; 31:853-66. [DOI: 10.1002/btpr.2109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/20/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Chika F. Nnadozie
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences; University of KwaZulu-Natal (Westville Campus), Private Bag X54001; Durban 4000, South Africa
| | - Johnson Lin
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences; University of KwaZulu-Natal (Westville Campus), Private Bag X54001; Durban 4000, South Africa
| | - Roshini Govinden
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences; University of KwaZulu-Natal (Westville Campus), Private Bag X54001; Durban 4000, South Africa
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16
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Paul T, Basu S, Sarkar K. SPION-mediated soil DNA extraction and comparative analysis with conventional and commercial kit-based protocol. 3 Biotech 2014; 4:669-677. [PMID: 28324313 PMCID: PMC4235891 DOI: 10.1007/s13205-014-0232-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/03/2014] [Indexed: 12/04/2022] Open
Abstract
Direct isolation of soil DNA comes as an emerging technology to understand the microbial diversity of a particular environment circumventing the dependency on culturable methods. Soil DNA isolation is tough due to the presence of various organic components present in soil which interfere in extraction procedure. Here, we report a novel direct soil DNA extraction protocol utilizing bare superparamagnetic iron oxide nanoparticles and its comparison with conventional and commercial kit-based soil DNA extraction methods. The quality, quantity and feasibility of the recovered DNA from all the three methods towards various molecular techniques were checked. Our magnetic nanoparticle-based soil DNA extraction successfully yields pure DNA without any RNA or protein contamination as revealed by the nanodrop spectrophotometer and agarose gel electrophoretic study. Different methods of soil DNA extraction were evaluated on the basis of PCR, denaturing gradient gel electrophoresis and real-time PCR. Soil DNA extracted using conventional method fails to carry out critical molecular biology techniques where as magnetic nanoparticle-based soil DNA extraction gave good results which is comparable to commercial kit. This comparative study suggests that protocol described in this report is novel, less time consuming, cost effective with fewer handling steps and yields high quantity, good quality DNA from soil.
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Affiliation(s)
- Tanima Paul
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Semanti Basu
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India
| | - Keka Sarkar
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, India.
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Sharma S, Vakhlu J. Metagenomics as advanced screening methods for novel microbial metabolites. Microb Biotechnol 2014. [DOI: 10.1201/b17587-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Recent literature review of soil processing methods for recovery of Bacillus anthracis spores. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0932-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Sagar K, Singh SP, Goutam KK, Konwar BK. Assessment of five soil DNA extraction methods and a rapid laboratory-developed method for quality soil DNA extraction for 16S rDNA-based amplification and library construction. J Microbiol Methods 2014; 97:68-73. [DOI: 10.1016/j.mimet.2013.11.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 11/04/2013] [Accepted: 11/13/2013] [Indexed: 11/29/2022]
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Rittich B, Španová A. SPE and purification of DNA using magnetic particles. J Sep Sci 2013; 36:2472-85. [DOI: 10.1002/jssc.201300331] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Bohuslav Rittich
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
| | - Alena Španová
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
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Selection of DNA aptamers for capture and detection of Salmonella Typhimurium using a whole-cell SELEX approach in conjunction with cell sorting. Appl Microbiol Biotechnol 2013; 97:3677-86. [PMID: 23494620 DOI: 10.1007/s00253-013-4766-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 02/04/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Alternative ligands such as nucleic acid aptamers can be used for pathogen capture and detection and offer advantages over antibodies, including reduced cost, ease of production and modification, and improved stability. DNA aptamers demonstrating binding specificity to Salmonella enterica serovar Typhimurium were identified by whole-cell-systematic evolution of ligands by exponential enrichment (SELEX) beginning with a combinatorial library of biotin-labeled single stranded DNA molecules. Aptamer specificity was achieved using whole-cell counter-SELEX against select non-Salmonella genera. Aptamers binding to Salmonella were sorted, cloned, sequenced, and characterized for binding efficiency. Out of 18 candidate aptamers screened, aptamer S8-7 showed relatively high binding affinity with an apparent dissociation constant (K d value) of 1.73 ± 0.54 μM and was selected for further characterization. Binding exclusivity analysis of S8-7 showed low apparent cross-reactivity with other foodborne bacteria including Escherichia coli O157: H7 and Citrobacter braakii and moderate cross-reactivity with Bacillus cereus. Aptamer S8-7 was successfully used as a ligand for magnetic capture of serially diluted Salmonella Typhimurium cells, followed by downstream detection using qPCR. The lower limit of detection of the aptamer magnetic capture-qPCR assay was 10(2)-10(3) CFU equivalents of Salmonella Typhimurium in a 290-μl sample volume. Mean capture efficiency ranged from 3.6 to 12.6 %. Unique aspects of the study included (a) the use of SELEX targeting whole cells; (b) the application of flow cytometry for aptamer pool selection, thereby favoring purification of ligands with both high binding affinity and targeting abundant cell surface moieties; and (c) the use of pre-labeled primers that circumvented the need for post-selection ligand labeling. Taken together, this study provides proof-of-concept that biotinylated aptamers selected by whole-cell SELEX can be used in a qPCR-based capture-detection platform for Salmonella Typhimurium.
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Nowak KM, Girardi C, Miltner A, Gehre M, Schäffer A, Kästner M. Contribution of microorganisms to non-extractable residue formation during biodegradation of ibuprofen in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 445-446:377-384. [PMID: 23361042 DOI: 10.1016/j.scitotenv.2012.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 12/05/2012] [Accepted: 12/05/2012] [Indexed: 06/01/2023]
Abstract
Non-extractable residues (NER) formed during biodegradation of organic contaminants in soil are considered to be mainly composed of parent compounds or their primary metabolites with hazardous potential. However, in the case of biodegradable organic compounds, the soil NER may also contain microbial biomass components, for example fatty acids (FA) and amino acids (AA). After cell death, these biomolecules are subsequently incorporated into non-living soil organic matter (SOM) and are stabilised ultimately forming hardly extractable residues of biogenic origin. We investigated biodegradation of (13)C(6)-ibuprofen, in particular the metabolic incorporation of the (13)C-label into FA and AA and their fate in soil over 90 days. (13)C-FA and (13)C-AA amounts in the living microbial biomass fraction initially increased, then decreased over time and were continuously incorporated into the non-living SOM pool. The (13)C-FA in the non-living SOM remained stable from day 59 whereas the contents of (13)C-AA slightly increased until the end. After 90 days, nearly all NER were biogenic as they were made up almost completely by natural biomass compounds. The presented data demonstrated that the potential environmental risks related to the ibuprofen-derived NER are overestimated.
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Affiliation(s)
- Karolina M Nowak
- UFZ, Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstrasse 15, 04318 Leipzig, Germany.
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Leis B, Angelov A, Liebl W. Screening and expression of genes from metagenomes. ADVANCES IN APPLIED MICROBIOLOGY 2013; 83:1-68. [PMID: 23651593 DOI: 10.1016/b978-0-12-407678-5.00001-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microorganisms are the most abundant and widely spread organisms on earth. They colonize a huge variety of natural and anthropogenic environments, including very specialized ecological niches and even extreme habitats, which are made possible by the immense metabolic diversity and genetic adaptability of microbes. As most of the organisms from environmental samples defy cultivation, cultivation-independent metagenomics approaches have been applied since more than one decade to access and characterize the phylogenetic diversity in microbial communities as well as their metabolic potential and ecological functions. Thereby, metagenomics has fully emerged as an own scientific field for mining new biocatalysts for many industrially relevant processes in biotechnology and pharmaceutics. This review summarizes common metagenomic approaches ranging from sampling, isolation of nucleic acids, construction of metagenomic libraries and their evaluation. Sequence-based screenings implement next-generation sequencing platforms, microarrays or PCR-based methods, while function-based analysis covers heterologous expression of metagenomic libraries in diverse screening setups. Major constraints and advantages of each strategy are described. The importance of alternative host-vector systems is discussed, and in order to underline the role of phylogenetic and physiological distance from the gene donor and the expression host employed, a case study is presented that describes the screening of a genomic library from an extreme thermophilic bacterium in both Escherichia coli and Thermus thermophilus. Metatranscriptomics, metaproteomics and single-cell-based methods are expected to complement metagenomic screening efforts to identify novel biocatalysts from environmental samples.
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Affiliation(s)
- Benedikt Leis
- Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Bavaria, Germany
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Aida M, Kanemori M, Kubota N, Matada M, Sasayama Y, Fukumori Y. Distribution and Population of Free-Living Cells Related to Endosymbiont A Harbored in Oligobrachia mashikoi (a Siboglinid Polychaete) Inhabiting Tsukumo Bay. Microbes Environ 2012; 23:81-8. [PMID: 21558692 DOI: 10.1264/jsme2.23.81] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Beard worms (Siboglinidae, Polychaeta), which lack a mouth and a digestive tract, harbor thioautotrophic or methanotrophic bacteria in special cells called bacteriocytes. These endosymbionts have been considered to be trapped at a specific larval stage from the environment. Although many species of beard worms have been discovered in various abyssal seas, Oligobrachia mashikoi inhabits Tsukumo Bay which is only 25 m deep. At least seven types of endosymbionts (endosymbiont A-G) have been distinguished in O. mashikoi. In this study, we investigated the distribution pattern of free-living cells related to the major endosymbiont (endosymbiont A) in Tsukumo Bay by quantitative PCR targeting the 16S rRNA gene. The endosymbiont A-related phylotype was detected in almost all sediment samples collected from 23 points in Tsukumo Bay, ranging in copy number of the 16S rRNA gene from 2.22×10(4) to 1.42×10(6) copies per gram of dry-sediment. Furthermore, the free-living cells made up less than 9% of the total eubacterial population, suggesting that the O. mashikoi larvae precisely select candidates for their endosymbiont from bacterial flora in the environment. This is the first report on the ecological characterization of a free-living bacterium related to the endosymbiont of the siboglinid polychaete, O. mashikoi.
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Affiliation(s)
- Masato Aida
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University
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25
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Schrader C, Schielke A, Ellerbroek L, Johne R. PCR inhibitors - occurrence, properties and removal. J Appl Microbiol 2012; 113:1014-26. [PMID: 22747964 DOI: 10.1111/j.1365-2672.2012.05384.x] [Citation(s) in RCA: 1063] [Impact Index Per Article: 88.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/14/2012] [Accepted: 06/27/2012] [Indexed: 12/21/2022]
Abstract
The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false-negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix-specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.
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Affiliation(s)
- C Schrader
- Food Hygiene and Safety Concepts, Federal Institute for Risk Assessment, Berlin, Germany
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26
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Alaeddini R. Forensic implications of PCR inhibition—A review. Forensic Sci Int Genet 2012; 6:297-305. [DOI: 10.1016/j.fsigen.2011.08.006] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
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Kim GY, Wang X, Ahn H, Son A. Gene quantification by the NanoGene assay is resistant to inhibition by humic acids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:8873-8880. [PMID: 21899291 DOI: 10.1021/es2013402] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
NanoGene assay is a magnetic bead and quantum dot nanoparticles based gene quantification assay. It relies on a set of probe and signaling probe DNAs to capture the target DNA via hybridization. We have demonstrated the inhibition resistance of the NanoGene assay using humic acids laden genomic DNA (gDNA). At 1 μg of humic acid per mL, quantitiative PCR (qPCR) was inhibited to 0% of its quantification capability whereas NanoGene assay was able to maintain more than 60% of its quantification capability. To further increase the inhibition resistance of NanoGene assay at high concentration of humic acids, we have identified the specific mechanisms that are responsible for the inhibition. We examined five potential mechanisms with which the humic acids can partially inhibit our NanoGene assay. The mechanisms examined were (1) adsorption of humic acids on the particle surface; (2) particle aggregation induced by humic acids; (3) fluorescence quenching of quantum dots by humic acids during hybridization; (4) humic acids mimicking of target DNA; and (5) nonspecific binding between humic acids and target gDNA. The investigation showed that no adsorption of humic acids onto the particles' surface was observed for the humic acids' concentration. Particle aggregation and fluorescence quenching were also negligible. Humic acids also did not mimic the target gDNA except 1000 μg of humic acids per mL and hence should not contribute to the partial inhibition. Four of the above mechanisms were not related to the inhibition effect of humic acids particularly at the environmentally relevant concentrations (<100 μg/mL). However, a substantial amount of nonspecific binding was observed between the humic acids and target gDNA. This possibly results in lesser amount of target gDNA being captured by the probe and signaling DNA.
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Affiliation(s)
- Gha-Young Kim
- Department of Nuclear Fuel Cycle Technology Development, Korea Atomic Energy Research Institute, Yuseonggu, Daejeon, Republic of Korea
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Kim J, Miller CM, Shepherd MW, Liu X, Jiang X. Impact of indigenous microorganisms on Escherichia coli O157:H7 growth in cured compost. BIORESOURCE TECHNOLOGY 2011; 102:9619-9625. [PMID: 21875793 DOI: 10.1016/j.biortech.2011.07.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/13/2011] [Accepted: 07/16/2011] [Indexed: 05/31/2023]
Abstract
Both autoclaving and dry-heat treatments were applied to dairy manure-based compost to achieve target populations of indigenous microorganisms. A 3 strain-mixture of Escherichia coli O157:H7 of ca. 2 log CFU/g was inoculated into acclimated autoclaved compost (AAC) and dry heat-treated compost (DHTC) with different moistures, and stored at 8, 22, or 30 °C. Only selected groups of microorganisms grew in AAC during acclimation, whereas the relative ratio of each group of microorganisms was maintained in DHTC after heat treatment. E. coli O157:H7 grew more in AAC than DHTC in the presence of same level of indigenous mesophiles. However, control compost (no heat treatment) did not support E. coli O157:H7 growth. Our results revealed that both the type and population of indigenous microorganisms is critical for suppressing E. coli O157:H7 growth in compost, and dry-heat treatment can result in a compost product which resembles cured compost with different levels of indigenous microorganisms.
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Affiliation(s)
- Jinkyung Kim
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, SC 29634-0316, USA
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Detection of viable Cryptosporidium parvum in soil by reverse transcription-real-time PCR targeting hsp70 mRNA. Appl Environ Microbiol 2011; 77:6476-85. [PMID: 21803904 DOI: 10.1128/aem.00677-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extraction of high-quality mRNA from Cryptosporidium parvum is a key step in PCR detection of viable oocysts in environmental samples. Current methods for monitoring oocysts are limited to water samples; therefore, the goal of this study was to develop a rapid and sensitive procedure for Cryptosporidium detection in soil samples. The efficiencies of five RNA extraction methods were compared (mRNA extraction with the Dynabeads mRNA Direct kit after chemical and physical sample treatments, and total RNA extraction methods using the FastRNA Pro Soil-Direct, PowerSoil Total RNA, E.Z.N.A. soil RNA, and Norgen soil RNA purification kits) for the direct detection of Cryptosporidium with oocyst-spiked sandy, loamy, and clay soils by using TaqMan reverse transcription-PCR. The study also evaluated the presence of inhibitors by synthesis and incorporation of an internal positive control (IPC) RNA into reverse transcription amplifications, used different facilitators (bovine serum albumin, yeast RNA, salmon DNA, skim milk powder, casein, polyvinylpyrrolidone, sodium hexametaphosphate, and Salmonella enterica serovar Typhi) to mitigate RNA binding on soil components, and applied various treatments (β-mercaptoethanol and bead beating) to inactivate RNase and ensure the complete lysis of oocysts. The results of spiking studies showed that Salmonella cells most efficiently relieved binding of RNA. With the inclusion of Salmonella during extraction, the most efficient mRNA method was Dynabeads, with a detection limit of 6 × 10(2) oocysts g(-1) of sandy soil. The most efficient total RNA method was PowerSoil, with detection limits of 1.5 × 10(2), 1.5 × 10(3), and 1.5 × 10(4) C. parvum oocysts g(-1) soil for sandy, loamy, and clay samples, respectively.
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Delmont TO, Robe P, Clark I, Simonet P, Vogel TM. Metagenomic comparison of direct and indirect soil DNA extraction approaches. J Microbiol Methods 2011; 86:397-400. [PMID: 21723887 DOI: 10.1016/j.mimet.2011.06.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/15/2011] [Accepted: 06/18/2011] [Indexed: 11/26/2022]
Abstract
Full pyrosequencing runs of both direct-extracted (high yield, low DNA size) and indirect-extracted DNA (low yield, high DNA size) from the same prairie soil show that the sequence distribution of the majority of the metabolic functions and species detected were statistically similar. Although some microbial functions differed at the 95% confidence interval in bootstrap analyses, the overall functional diversity was the same.
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Affiliation(s)
- Tom O Delmont
- Environmental Microbial Genomics, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
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Li J, Li B, Zhou Y, Xu J, Zhao J. A rapid DNA extraction method for PCR amplification from wetland soils. Lett Appl Microbiol 2011; 52:626-33. [DOI: 10.1111/j.1472-765x.2011.03047.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Nowak KM, Miltner A, Gehre M, Schäffer A, Kästner M. Formation and fate of bound residues from microbial biomass during 2,4-D degradation in soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:999-1006. [PMID: 21186826 DOI: 10.1021/es103097f] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
During organic contaminant degradation in soil, bound or nonextractable residues (NER) are formed. Part of these residues may be biogenic, because degrading microorganisms assimilate carbon derived from the pollutant and mineralized CO(2) to form cellular components for example, [fatty acids (FA) and amino acids (AA)], which are subsequently stabilized within soil organic matter (SOM). We investigated the formation and fate of FA and AA from biodegradation of (13)C(6)-2,4-D in soil and the incorporation of the (13)C-label into living biomass via (13)CO(2) fixation. After 64 days of incubation, (13)C-AA in SOM indicated that 44% of the initially applied (13)C(6)-2,4-D equivalents had been converted to microbial biomass and finally to biogenic residues. The intermediate maximum of (13)C-FA in SOM indicated a 20% conversion of (13)C(6)-2,4-D to biomass, but (13)C-FA decreased to 50% of that value whereas (13)C-AA in the SOM remained stable. We provide the first evidence that nearly all bound residues from 2,4-D are biogenic, containing natural microbial residues stabilized in SOM. Because of biogenic residue formation, the potential risk of bound residues from readily metabolized xenobiotics in soils is highly overestimated. Hence, the formation of biogenic residues must be considered in general when performing mass balances of pollutant biodegradation in soils.
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Affiliation(s)
- Karolina M Nowak
- UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstraβe 15, 04318 Leipzig, Germany.
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Abstract
Due to the presence of inhibitors such as extracellular polymeric substances (EPSs) and salts, most microbial mat studies have relied on harsh methods of direct DNA extraction that result in DNA fragments too small for large-insert vector cloning. High molecular weight (HMW) DNA is crucial in functional metagenomic studies, because large fragments present greater access to genes of interest. Here we report improved methodologies for extracting HMW DNA from EPS-rich hypersaline microbial mats. The protocol uses a combination of microbial cell separation with mechanical and chemical methods for DNA extraction and purification followed by precipitation with polyethylene glycol (PEG). The protocol yields >2 µg HMW DNA (>48 kb) per gram of mat sample, with A260:280 ratios >1.7. In addition, 16S rRNA gene analysis using denaturing gradient gel electrophoresis and pyrosequencing showed that this protocol extracts representative DNA from microbial mat communities and results in higher overall calculated diversity indices compared with three other standard methods of DNA extraction. Our results show the importance of validating the DNA extraction methods used in metagenomic studies to ensure optimal recovery of microbial richness.
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Kakirde KS, Parsley LC, Liles MR. Size Does Matter: Application-driven Approaches for Soil Metagenomics. SOIL BIOLOGY & BIOCHEMISTRY 2010; 42:1911-1923. [PMID: 21076656 PMCID: PMC2976544 DOI: 10.1016/j.soilbio.2010.07.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Metagenomic analyses can provide extensive information on the structure, composition, and predicted gene functions of diverse environmental microbial assemblages. Each environment presents its own unique challenges to metagenomic investigation and requires a specifically designed approach to accommodate physicochemical and biotic factors unique to each environment that can pose technical hurdles and/or bias the metagenomic analyses. In particular, soils harbor an exceptional diversity of prokaryotes that are largely undescribed beyond the level of ribotype and are a potentially vast resource for natural product discovery. The successful application of a soil metagenomic approach depends on selecting the appropriate DNA extraction, purification, and if necessary, cloning methods for the intended downstream analyses. The most important technical considerations in a metagenomic study include obtaining a sufficient yield of high-purity DNA representing the targeted microorganisms within an environmental sample or enrichment and (if required) constructing a metagenomic library in a suitable vector and host. Size does matter in the context of the average insert size within a clone library or the sequence read length for a high-throughput sequencing approach. It is also imperative to select the appropriate metagenomic screening strategy to address the specific question(s) of interest, which should drive the selection of methods used in the earlier stages of a metagenomic project (e.g., DNA size, to clone or not to clone). Here, we present both the promising and problematic nature of soil metagenomics and discuss the factors that should be considered when selecting soil sampling, DNA extraction, purification, and cloning methods to implement based on the ultimate study objectives.
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Affiliation(s)
- Kavita S Kakirde
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
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Dwivedi HP, Jaykus LA. Detection of pathogens in foods: the current state-of-the-art and future directions. Crit Rev Microbiol 2010; 37:40-63. [PMID: 20925593 DOI: 10.3109/1040841x.2010.506430] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Over the last fifty years, microbiologists have developed reliable culture-based techniques to detect food borne pathogens. Although these are considered to be the "gold-standard," they remain cumbersome and time consuming. Despite the advent of rapid detection methods such as ELISA and PCR, it is clear that reduction and/or elimination of cultural enrichment will be essential in the quest for truly real-time detection methods. As such, there is an important role for bacterial concentration and purification from the sample matrix as a step preceding detection, so-called pre-analytical sample processing. This article reviews recent advancements in food borne pathogen detection and discusses future methods with a focus on pre-analytical sample processing, culture independent methods, and biosensors.
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Affiliation(s)
- Hari P Dwivedi
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC-27695-7624, USA.
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Chen PS, Tsai FT, Lin CK, Yang CY, Chan CC, Young CY, Lee CH. Ambient influenza and avian influenza virus during dust storm days and background days. ENVIRONMENTAL HEALTH PERSPECTIVES 2010; 118:1211-6. [PMID: 20435545 PMCID: PMC2944079 DOI: 10.1289/ehp.0901782] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 04/30/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND The spread of influenza and highly pathogenic avian influenza (H5N1) presents a significant threat to human health. Avian influenza outbreaks in downwind areas of Asian dust storms (ADS) suggest that viruses might be transported by dust storms. OBJECTIVES We developed a technique to measure ambient influenza and avian influenza viruses. We then used this technique to measure concentrations of these viruses on ADS days and background days, and to assess the relationships between ambient influenza and avian influenza viruses, and air pollutants. METHODS A high-volume air sampler was used in parallel with a filter cassette to evaluate spiked samples and unspiked samples. Then, air samples were monitored during ADS seasons using a filter cassette coupled with a real-time quantitative polymerase chain reaction (qPCR) assay. Air samples were monitored during ADS season (1 January to 31 May 2006). RESULTS We successfully quantified ambient influenza virus using the filtration/real-time qPCR method during ADS days and background days. To our knowledge, this is the first report describing the concentration of influenza virus in ambient air. In both the spiked and unspiked samples, the concentration of influenza virus sampled using the filter cassette was higher than that using the high-volume sampler. The concentration of ambient influenza A virus was significantly higher during the ADS days than during the background days. CONCLUSIONS Our data imply the possibility of long-range transport of influenza virus.
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Affiliation(s)
- Pei-Shih Chen
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City, Taiwan.
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37
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Critical evaluation of solid waste sample processing for DNA-based microbial community analysis. Biodegradation 2010; 22:189-204. [DOI: 10.1007/s10532-010-9387-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 07/01/2010] [Indexed: 10/19/2022]
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38
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Gotz A, Smalla K. Manure Enhances Plasmid Mobilization and Survival of Pseudomonas putida Introduced into Field Soil. Appl Environ Microbiol 2010; 63:1980-6. [PMID: 16535608 PMCID: PMC1389163 DOI: 10.1128/aem.63.5.1980-1986.1997] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report a field study on plasmid mobilization in an agricultural soil. The influence of pig manure on the mobilization of the IncQ plasmid pIE723 by indigenous plasmids or by the IncP(alpha) plasmid pGP527 into the recipient Pseudomonas putida UWC1 (Rif(supr) Nal(supr)) was studied in field soil. Six plots were prepared in duplicate, three of which were treated with manure prior to inoculation of the donor and recipient strains. As a donor strain, either Escherichia coli J53(pIE723) or E. coli 600(pIE723, pGP527) was used. Putative transconjugants obtained on a selective medium were confirmed by DNA hybridization and PCR. Plasmid mobilization by indigenous mobilizing plasmids was observed on two occasions in manured soil. Manuring of soil significantly enhanced the frequency of pIE723 mobilization by pGP527, since mobilization frequencies into P. putida UWC1 were at least 10-fold higher in manured soil than in nonmanured soil. Enhanced numbers of P. putida UWC1 transconjugant and recipient colonies could be observed in manured soil throughout the 79-day field test. Transfer of pIE723 or pG527 into indigenous soil or rhizosphere bacteria could not be detected when indigenous bacteria isolated by selective cultivation were screened for the presence of these plasmids by DNA hybridization. Furthermore, the presence of IncN-, IncP-, or IncQ-specific sequences was confirmed in total community DNA extracted directly from the manured or nonmanured soil by PCR. IncW plasmids were detectable only in manured soil, indicating entry of these plasmids into soil via manure.
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39
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Gulledge JS, Luna VA, Luna AJ, Zartman R, Cannons AC. Detection of low numbers of Bacillus anthracis spores in three soils using five commercial DNA extraction methods with and without an enrichment step. J Appl Microbiol 2010; 109:1509-20. [PMID: 20553343 DOI: 10.1111/j.1365-2672.2010.04774.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To (i) compare the limits of detection of Bacillus anthracis spores in three soils (one Florida, one Texas, and one a commercial Garden product) by PCR using DNA extracted with five commercial extraction kits and (ii) examine if removing organic acids or adding an enrichment step utilizing a growth medium will improve the detection limits. METHODS AND RESULTS Bacillus anthracis spores were added to soil aliquots and used immediately with a DNA extraction kit or pretreated to remove organics or incubated overnight in a selective growth medium before the DNA extraction was performed. Using hybridization and PCR assays for capC, pag and lef genes, 10(5) -10(6) B. anthracis spores were detected in untreated Florida soil, 10(4) -10(7) spores in untreated Texas soil and 10(6) -10(7) in Garden soil. Pretreatment did not reliably improve detection. DNA from untreated and pretreated soils was suitable for hybridization but not always for PCR. When 10(1) -10(2) spores were added to the soils and allowed to amplify in a growth medium selective for B. anthracis, DNA extracted using four methods reliably produced PCR acceptable DNA positive for the B. anthracis genes. CONCLUSIONS The quality of DNA extracted with commercial kits appears to be influenced by the soil type and pretreatment. Yet, with an enrichment step added, four of five extraction methods produced PCR suitable DNA and detected ≤10(2) spores. SIGNIFICANCE AND IMPACT OF THE STUDY The enrichment step could enhance the detection of B. anthracis spores in soils and small samples contaminated with soil.
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Affiliation(s)
- J S Gulledge
- Center for Biological Defense, College of Public Health, University of South Florida, Tampa, FL 33612, USA
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40
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Response to Questions Posed by the Food Safety and Inspection Service Regarding Determination of the Most Appropriate Technologies for the Food Safety and Inspection Service To Adopt in Performing Routine and Baseline Microbiological Analyses†,‡. J Food Prot 2010; 73:1160-200. [DOI: 10.4315/0362-028x-73.6.1160] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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41
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Assessing the bias linked to DNA recovery from biofiltration woodchips for microbial community investigation by fingerprinting. Appl Microbiol Biotechnol 2010; 85:779-790. [PMID: 19826809 DOI: 10.1007/s00253-009-2253-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 09/04/2009] [Accepted: 09/07/2009] [Indexed: 10/20/2022]
Abstract
In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.
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42
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Rodríguez-Mejía JL, Martínez-Anaya C, Folch-Mallol JL, Dantán-González E. A two-step electrodialysis method for DNA purification from polluted metallic environmental samples. Electrophoresis 2008; 29:3239-44. [PMID: 18601228 DOI: 10.1002/elps.200700829] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Extracting DNA from samples of polluted environments using standard methods often results in low yields of poor-quality material unsuited to subsequent manipulation and analysis by molecular biological techniques. Here, we report a novel two-step electrodialysis-based method for the extraction of DNA from environmental samples. This technique permits the rapid and efficient isolation of high-quality DNA based on its acidic nature, and without the requirement for phenol-chloroform-isoamyl alcohol cleanup and ethanol precipitation steps. Subsequent PCR, endonuclease restriction, and cloning reactions were successfully performed utilizing DNA obtained by electrodialysis, whereas some or all of these techniques failed using DNA extracted with two alternative methods. We also show that his technique is applicable to purify DNA from a range of polluted and nonpolluted samples.
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Affiliation(s)
- José Luis Rodríguez-Mejía
- Laboratorio de Biología Molecular de Hongos, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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43
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Stevens KA, Jaykus LA. Bacterial Separation and Concentration from Complex Sample Matrices: A Review. Crit Rev Microbiol 2008; 30:7-24. [PMID: 15116760 DOI: 10.1080/10408410490266410] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The use of many rapid detection technologies could be expanded if the bacteria were separated, concentrated, and purified from the sample matrix before detection. Specific advantages of bacterial concentration might include facilitating the detection of multiple bacterial strains; removal of matrix-associated assay inhibitors; and provision of adequate sample size reduction to allow for the use of representative food sample sizes and/or small media volumes. Furthermore, bacterial concentration could aid in improving sampling techniques needed to detect low levels of pathogens or sporadic contamination, which may perhaps reduce or even eliminate the need for cultural enrichment prior to detection. Although bacterial concentration methods such as centrifugation, filtration, and immunomagnetic separation have been reported for food systems, none of these is ideal and in many cases a technique optimized for one food system or microorganism is not readily adaptable to others. Indeed, the separation and subsequent concentration of bacterial cells from a food sample during sample preparation continues to be a stumbling block in the advancement of molecular methods for the detection of foodborne pathogens. The purpose of this review is to provide a detailed understanding of the science, possibilities, and limitations of separating and concentrating bacterial cells from the food matrix in an effort to further improve our ability to harness molecular methods for the rapid detection of foodborne pathogens.
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Affiliation(s)
- Kelly A Stevens
- Department of Food Science, College of Life Science and Agriculture, North Carolina State University, Raleigh, North Carolina 27695-7624, USA
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44
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Rajendhran J, Gunasekaran P. Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 2008; 26:576-90. [PMID: 18786627 DOI: 10.1016/j.biotechadv.2008.08.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 08/03/2008] [Accepted: 08/05/2008] [Indexed: 11/27/2022]
Abstract
Most of the microorganisms in nature are inaccessible as they are uncultivable in the laboratory. Metagenomic approaches promise the accessibility of the genetic resources and their potential applications. Genetic resources from terrestrial environments can be accessed by exploring the soil metagenome. Soil metagenomic analyses are usually initiated by the isolation of environmental DNAs. Several methods have been described for the direct isolation of environmental DNAs from soil and sediments. Application of metagenomics largely depends on the construction of genomic DNA libraries and subsequent high-throughput sequencing or library screening. Thus, obtaining large quantities of pure cloneable DNA from the environment is a prerequisite. This review discusses the recent developments related to efficient extraction and purification of soil metagenome highlighting the considerations for various metagenomic applications.
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Affiliation(s)
- J Rajendhran
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai-625 021, India
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Sharma P, Kumari H, Kumar M, Verma M, Kumari K, Malhotra S, Khurana J, Lal R. From bacterial genomics to metagenomics: concept, tools and recent advances. Indian J Microbiol 2008; 48:173-94. [PMID: 23100712 DOI: 10.1007/s12088-008-0031-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Accepted: 02/23/2008] [Indexed: 01/11/2023] Open
Abstract
In the last 20 years, the applications of genomics tools have completely transformed the field of microbial research. This has primarily happened due to revolution in sequencing technologies that have become available today. This review therefore, first describes the discoveries, upgradation and automation of sequencing techniques in a chronological order, followed by a brief discussion on microbial genomics. Some of the recently sequenced bacterial genomes are described to explain how complete genome data is now being used to derive interesting findings. Apart from the genomics of individual microbes, the study of unculturable microbiota from different environments is increasingly gaining importance. The second section is thus dedicated to the concept of metagenomics describing environmental DNA isolation, metagenomic library construction and screening methods to look for novel and potentially important genes, enzymes and biomolecules. It also deals with the pioneering studies in the area of metagenomics that are offering new insights into the previously unappreciated microbial world.
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Affiliation(s)
- Pooja Sharma
- Department of Zoology, University of Delhi, Delhi, 110 007 India
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Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, Handelsman J. Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms. Appl Environ Microbiol 2008; 74:3302-5. [PMID: 18359830 PMCID: PMC2394920 DOI: 10.1128/aem.02630-07] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 03/12/2008] [Indexed: 11/20/2022] Open
Abstract
We describe here an improved method for isolating, purifying, and cloning DNA from diverse soil microbiota. Soil microorganisms were extracted from soils and embedded and lysed within an agarose plug. Nucleases that copurified with the metagenomic DNA were removed by incubating plugs with a high-salt and -formamide solution. This method was used to construct large-insert soil metagenomic libraries.
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Affiliation(s)
- Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
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Rojas-Herrera R, Narváez-Zapata J, Zamudio-Maya M, Mena-Martínez ME. A simple silica-based method for metagenomic DNA extraction from soil and sediments. Mol Biotechnol 2008; 40:13-7. [PMID: 18373226 DOI: 10.1007/s12033-008-9061-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 03/04/2008] [Indexed: 11/30/2022]
Abstract
A new method is described for extraction of metagenomic DNA from soil and sediments which is based on DNA adsorption to silica without the use of phenol, ethanol precipitation or a cesium chloride gradient. High-quality DNA was obtained, and PCR inhibition was overcome by adding bovine serum albumin and adjusting magnesium concentration. By using PCR-DGGE with Firmicutes and lactic acid bacteria-specific primers the extracted metagenomic DNA was shown to contain a mixture of bacterial genomes. This method can be used for screening bacterial diversity in soil and sediment samples.
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Affiliation(s)
- R Rojas-Herrera
- Universidad Autónoma de Yucatán, Ciudad Industrial, Mérida, Yucatán, Mexico.
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48
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Zhao X, Yang L, Chen C, Xiao L, Jiang L, Ma Z, Zhu H, Yu Z, Yin D. Microbial diversity in lake sediments detected by PCR-DGGE. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11515-008-0044-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Abstract
Real-time PCR analysis is a sensitive template DNA quantitation strategy that has recently gained considerable attention in the forensic community. However, the utility of real-time PCR methods extends beyond quantitation and allows for simultaneous evaluation of template DNA extraction quality. This study presents a computational method that allows analysts to identify problematic samples with statistical reliability by comparing the amplification efficiencies of unknown template DNA samples with clean standards. In this study, assays with varying concentrations of tannic acid are used to evaluate and adjust sample-specific amplification efficiency calculation methods in order to optimize their inhibitor detection capabilities. Kinetic outlier detection and prediction boundaries are calculated to identify amplification efficiency outliers. Sample-specific amplification efficiencies calculated over a four-cycle interval starting at the threshold cycle can be used to detect reliably the presence of 0.4 ng of tannic acid in a 25 microL PCR reaction. This approach provides analysts with a precise measure of inhibition severity when template samples are compromised. Early detection of problematic samples allows analysts the opportunity to consider inhibitor mitigation strategies prior to genotype or DNA sequence analysis, thereby facilitating sample processing in high-throughput forensic operations.
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Affiliation(s)
- Elias J Kontanis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca NY 14853, USA.
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50
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Whitehouse CA, Hottel HE. Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Mol Cell Probes 2006; 21:92-6. [PMID: 17011748 DOI: 10.1016/j.mcp.2006.08.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 07/27/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
Francisella tularensis is the etiologic agent of the zoonotic disease tularemia and is thought to be maintained in the environment principally by various terrestrial and aquatic vertebrate animals. The organism is known to persist in water or mud for long periods of time and Francisella-specific DNA has been identified from water and soil. To gain a better understanding of the ecology and epidemiology of F. tularensis, it will be important to further explore its distribution in the environment. Therefore, methods must be established to efficiently extract Francisella-specific DNA from the soil and be able to eliminate potential PCR inhibitors. Thus, we evaluated five commercial DNA extraction kits for their ability to recover F. tularensis-specific DNA from soil samples and eliminate potential PCR inhibitors. The kits evaluated included the Puregene DNA purification kit, QIAamp Stool Mini kit, Epicentre Biotech SoilMaster DNA extraction kit, and the UltraClean and PowerMax soil DNA isolation kits from MoBio. Soil samples were spiked with gamma-irradiated F. tularensis SHU-4 strain (corresponding to a range from 10 to 10(5)CFU). Spiked samples were extracted with each kit and evaluated using a F. tularensis-specific real-time PCR assay and an internal positive control assay that measures the presence of potential PCR inhibitors. DNA extraction using the UltraClean and PowerMax kits resulted in the most consistently positive results at the lowest limit of detection (20 and 100CFU/g soil, respectively) for all soil types tested, suggesting that these kits can provide the most sensitive methods for extracting F. tularensis from environmental soil samples. Processing time and cost were also evaluated.
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Affiliation(s)
- Chris A Whitehouse
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA.
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