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Nguyen VD, Nguyen HQ, Bui KH, Ko YS, Park BJ, Seo TS. A handheld-type total integrated capillary electrophoresis system for SARS-CoV-2 diagnostics: Power, fluorescence detection, and data analysis by smartphone. Biosens Bioelectron 2022; 195:113632. [PMID: 34571485 DOI: 10.1016/j.bios.2021.113632] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/23/2022]
Abstract
A micro-capillary electrophoresis (μCE) system is one of the widely adopted techniques in the molecular diagnostics and DNA sequencing due to the benefits of high resolution, rapid analysis, and low reagent consumption, but due to the requirements of bulky high-power suppliers and an expensive laser-induced fluorescence detector module, the conventional set-up of μCE system is not adequate for point-of-care (POC) molecular diagnostics. In this study, we constructed a miniaturized and integrated μCE system which can be manipulated by a smartphone. The smartphone not only powers two boost converters and an excited laser, but also controls the relay for the power switch. Moreover, the complementary metal-oxide-semiconductor (CMOS) camera of the smartphone was used for detecting the fluorescence signal of amplicons amplified with reverse transcription-polymerase chain reaction (RT-PCR). We also developed a web-based application so that the raw data of the recorded fluorescence intensity versus the running time can display typical capillary electropherograms on the smartphone. The total size of the hand-held μCE system was 9.6 cm [Width] × 22 cm [Length] × 15.5 cm [Height], and the weight was ∼1 kg, which is suitable for POC DNA testing. In the integrated smartphone-associated μCE system, we could accurately analyze two genes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), namely N gene and S gene along with two bracket ladders in 6 min to identify SARS-CoV-2. Such an advanced μCE platform can be applied for a variety of on-site molecular diagnostics fields with user-friendliness.
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Affiliation(s)
- Van Dan Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Huynh Quoc Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Khang Hoang Bui
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Young Soo Ko
- Department of Chemical Engineering and Department of Future Convergence Engineering, Kongju National University, Cheonan City, Chungcheongnam-do, Republic of Korea
| | - Bum Jun Park
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea
| | - Tae Seok Seo
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 17140, Republic of Korea.
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Yu K, Li P, He Y, Zhang B, Chen Y, Yang J. Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants. WATER RESEARCH 2020; 187:116450. [PMID: 32998097 DOI: 10.1016/j.watres.2020.116450] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/31/2020] [Accepted: 09/22/2020] [Indexed: 05/25/2023]
Abstract
Serious concerns have been raised regarding antibiotic resistance genes (ARGs) with respect to their potential threat to human health. Wastewater treatment plants (WWTPs) have been considered to be hotspots for ARGs. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) was used to profile size-dependent ARGs and mobile genetic elements (MGEs) divided by particle-associated (PA) assemblages (>3.0-μm), free-living (FL) bacteria (0.2 - 3.0-μm) and cell-free (CF) DNA (< 0.2-μm) in two full-scale WWTPs (plants A and B) and a receiving stream. The results revealed that FL-ARGs were predominant in WWTPs and the receiving stream, especially in the final effluent of both plants. More than 40 types of CF-ARGs and CF-MGEs were detected with absolute abundances ranging from 6.0 ± 0.7 × 105 to 1.0 ± 0.2 × 108 copies/mL in wastewater, and relatively high abundances were also detected in the final effluent of the two plants, suggesting that CF-ARGs were important sources spreading from the WWTPs to the receiving environment. Plant A exhibited higher log-removal of size-fractionated ARGs and MGEs than was observed for plant B, which was attributed to the enhanced settleability of PA assemblages and FL bacteria by additional macrophytes and chemical coagulants. Ultraviolet disinfection had limited effects on ARGs and MGEs of the PA and FL fractions, which was probably ascribed to the protective matrices of the particles and cell walls. The bacterial communities of the two plants were significantly different among the size fractions (p < 0.01). The variation partitioning analysis (VPA) indicated that the microbial community structures and MGEs contributed a variation of 68.2% in total to the relative abundance changes of size-fractionated ARGs. Procrustes analyses and Mantel tests showed that the relative abundances of ARGs were significantly correlated with bacterial community structures. These results suggested that the bacterial community structures and MGEs might have been the main drivers of the size-fractionated ARG disseminations. This study provides novel insights into size-fractionated ARGs and MGEs in full-scale WWTPs and may lead to the identification of key targets to control the spread of ARGs.
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Affiliation(s)
- Kaifeng Yu
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Peng Li
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.; Shanghai Institute of Pollution Control and Ecological Security, 800 Dongchuan Road, Shanghai 200240, China.
| | - Bo Zhang
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yihan Chen
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 246011, China
| | - Jinghan Yang
- School of Environmental and Municipal Engineering, Lanzhou Jiao Tong University, Lanzhou 730070, China
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Cunha EN, de Souza MFB, Lanza DCF, Lima JPMS. A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum. PLoS One 2020; 15:e0240536. [PMID: 33057447 PMCID: PMC7561130 DOI: 10.1371/journal.pone.0240536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid detection by electrophoresis is still a quick and accessible technique for many diagnosis methods, primarily at research laboratories or at the point of care units. Standard protocols detect DNA/RNA molecules through specific bound chemical dyes using a UV-transilluminator or UV-photo documentation system. However, the acquisition costs and availability of these devices, mainly the ones with photography and internet connection capabilities, can be prohibitive, especially in developing countries public health units. Also, ultraviolet radiation is a common additional risk factor to professionals that use electrophoresis-based nucleic acid detection. With that in mind, this work describes the development of a low-cost DNA/RNA detection smart system capable of obtaining qualitative and semi-quantitative data from gel analysis. The proposed device explores the visible light absorption range of commonly used DNA/RNA dyes using readily available parts, and simple manufacturing processes, such as light-emitting diodes (LEDs) and 3D impression. By applying IoT techniques, our system covers a wide range of color spectrum in order to detect bands from various commercially used dyes, using Bluetooth communication and a smartphone for hardware control, image capturing, and sharing. The project also enables process scalability and has low manufacturing and maintenance costs. The use of LEDs at the visible spectrum can achieve very reproducible images, providing a high potential for rapid and point-of-care diagnostics as well as applications in several fields such as healthcare, agriculture, and aquaculture.
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Affiliation(s)
- Eduardo Nogueira Cunha
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
| | - Maria Fernanda Bezerra de Souza
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - Daniel Carlos Ferreira Lanza
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - João Paulo Matos Santos Lima
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Natal, Brazil
- * E-mail:
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Agramont J, Gutiérrez-Cortez S, Joffré E, Sjöling Å, Calderon Toledo C. Fecal Pollution Drives Antibiotic Resistance and Class 1 Integron Abundance in Aquatic Environments of the Bolivian Andes Impacted by Mining and Wastewater. Microorganisms 2020; 8:microorganisms8081122. [PMID: 32722600 PMCID: PMC7464395 DOI: 10.3390/microorganisms8081122] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/18/2020] [Accepted: 07/23/2020] [Indexed: 11/29/2022] Open
Abstract
An increased abundance of antibiotic resistance genes (ARGs) in aquatic environments has been linked to environmental pollution. Mining polluted sites with high concentration of metals could favor the in situ coselection of ARGs, whereas wastewater discharges release fecal antibiotic resistant bacteria in the environment. To study the effect of human fecal contamination and mining pollution, water and sediment samples affected by mining activities and sewage discharges were collected from three lakes in Bolivia, the pristine Andean lake Pata Khota, the Milluni Chico lake directly impacted by acid mine drainage, and the Uru-Uru lake located close to Oruro city and highly polluted by mining activities and human wastewater discharges. Physicochemical parameters, including metal composition, were analyzed in water and sediment samples. ARGs were screened for and verified by quantitative polymerase chain reaction (PCR) together with the mobile element class 1 integron (intl1), as well as crAssphage, a marker of human fecal pollution. The gene intl1 was positively correlated with sul1, sul2, tetA, and blaOXA-2. CrAssphage was only detected in the Uru-Uru lake, and its tributaries and significantly higher abundance of ARGs were found in these sites. Multivariate analysis showed that crAssphage abundance, electrical conductivity, and pH were positively correlated with higher levels of intl1 and ARGs. Taken together, our results suggest that fecal pollution is the major driver of higher levels of ARGs and intl1 in environments contaminated by wastewater and mining activities.
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Affiliation(s)
- Jorge Agramont
- Environmental Microbiology Unit, Institute of Molecular Biology and Biotechnology, Universidad Mayor de San Andrés, La Paz, Bolivia;
- Correspondence: (J.A.); (S.G.-C.)
| | - Sergio Gutiérrez-Cortez
- Environmental Microbiology Unit, Institute of Molecular Biology and Biotechnology, Universidad Mayor de San Andrés, La Paz, Bolivia;
- Correspondence: (J.A.); (S.G.-C.)
| | - Enrique Joffré
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 23109 Stockholm, Sweden; (E.J.); (Å.S.)
- Centre for Translational Microbiome Research, Karolinska Institutet, 23109 Stockholm, Sweden
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 23109 Stockholm, Sweden; (E.J.); (Å.S.)
- Centre for Translational Microbiome Research, Karolinska Institutet, 23109 Stockholm, Sweden
| | - Carla Calderon Toledo
- Environmental Microbiology Unit, Institute of Molecular Biology and Biotechnology, Universidad Mayor de San Andrés, La Paz, Bolivia;
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Kongprajug A, Chyerochana N, Mongkolsuk S, Sirikanchana K. Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8232-8244. [PMID: 32484662 DOI: 10.1021/acs.est.0c01559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log10 copies/g and 0.41 log10 copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log10 copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.
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Affiliation(s)
- Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
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Truu M, Ostonen I, Preem JK, Lõhmus K, Nõlvak H, Ligi T, Rosenvald K, Parts K, Kupper P, Truu J. Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand. Front Microbiol 2017; 8:557. [PMID: 28421053 PMCID: PMC5376589 DOI: 10.3389/fmicb.2017.00557] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/16/2017] [Indexed: 01/05/2023] Open
Abstract
Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch (Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N2O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity.
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Affiliation(s)
- Marika Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Jens-Konrad Preem
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Krista Lõhmus
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Hiie Nõlvak
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Teele Ligi
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Katrin Rosenvald
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Kaarin Parts
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Priit Kupper
- Department of Botany, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
| | - Jaak Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of TartuTartu, Estonia
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LapF and Its Regulation by Fis Affect the Cell Surface Hydrophobicity of Pseudomonas putida. PLoS One 2016; 11:e0166078. [PMID: 27812186 PMCID: PMC5094663 DOI: 10.1371/journal.pone.0166078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/21/2016] [Indexed: 11/19/2022] Open
Abstract
The ability of bacteria to regulate cell surface hydrophobicity is important for the adaptation to different environmental conditions. The hydrophobicity of cell surface can be determined by several factors, including outer membrane and surface proteins. In this study, we report that an adhesin LapF influences cell surface hydrophobicity of Pseudomonas putida. Cells lacking LapF are less hydrophobic than wild-type cells in stationary growth phase. Moreover, the overexpression of the global regulator Fis decreases surface hydrophobicity by repressing the expression of lapF. Flow cytometry analysis revealed that bacteria producing LapF are more viable when confronted with methanol (a hydrophilic compound) but are more susceptible to 1-octanol (a hydrophobic compound). Thus, these results revealed that LapF is the hydrophobicity factor for the cell surface of P. putida.
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Dynamics of Bacterial Community Abundance and Structure in Horizontal Subsurface Flow Wetland Mesocosms Treating Municipal Wastewater. WATER 2016. [DOI: 10.3390/w8100457] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Nõlvak H, Truu M, Kanger K, Tampere M, Espenberg M, Loit E, Raave H, Truu J. Inorganic and organic fertilizers impact the abundance and proportion of antibiotic resistance and integron-integrase genes in agricultural grassland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:678-689. [PMID: 27115621 DOI: 10.1016/j.scitotenv.2016.04.035] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
Soil fertilization with animal manure or its digestate may facilitate an important antibiotic resistance dissemination route from anthropogenic sources to the environment. This study examines the effect of mineral fertilizer (NH4NO3), cattle slurry and cattle slurry digestate amendment on the abundance and proportion dynamics of five antibiotic resistance genes (ARGs) and two classes of integron-integrase genes (intI1 and intI2) in agricultural grassland soil. Fertilization was performed thrice throughout one vegetation period. The targeted ARGs (sul1, tetA, blaCTX-M, blaOXA2 and qnrS) encode resistance to several major antibiotic classes used in veterinary medicine such as sulfonamides, tetracycline, cephalosporins, penicillin and fluoroquinolones, respectively. The non-fertilized grassland soil contained a stable background of tetA, blaCTX-M and sul1 genes. The type of applied fertilizer significantly affected ARGs and integron-integrase genes abundances and proportions in the bacterial community (p<0.001 in both cases), explaining 67.04% of the abundance and 42.95% of the proportion variations in the grassland soil. Both cattle slurry and cattle slurry digestate proved to be considerable sources of ARGs, especially sul1, as well as integron-integrases. Sul1, intI1 and intI2 levels in grassland soil were elevated in response to each organic fertilizer's application event, but this increase was followed by a stage of decrease, suggesting that microbes possessing these genes were predominantly entrained into soil via cattle slurry or its digestate application and had somewhat limited survival potential in a soil environment. However, the abundance of these three target genes did not decrease to a background level by the end of the study period. TetA was most abundant in mineral fertilizer treated soil and blaCTX-M in cattle slurry digestate amended soil. Despite significantly different abundances, the abundance dynamics of bacteria possessing these genes were similar (p<0.05 in all cases) in different treatments and resembled the dynamics of the whole bacterial community abundance in each soil treatment.
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Affiliation(s)
- Hiie Nõlvak
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Marika Truu
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Kärt Kanger
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Mailiis Tampere
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi St., 51014 Tartu, Estonia.
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Evelin Loit
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi St., 51014 Tartu, Estonia.
| | - Henn Raave
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 5 Kreutzwaldi St., 51014 Tartu, Estonia.
| | - Jaak Truu
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
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Qian L, Song H, Cai W. Determination of Bifidobacterium and Lactobacillus in breast milk of healthy women by digital PCR. Benef Microbes 2016; 7:559-69. [PMID: 27241905 DOI: 10.3920/bm2015.0195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Breast milk is one of the most important sources of postnatal microbes. Quantitative real-time polymerase chain reaction (qRT-PCR) is currently used for the quantitative analysis of bacterial 16S rRNA genes in breast milk. However, this method relies on the use of standard curves and is imprecise when quantitating target DNA of low abundance. In contrast, droplet digital PCR (DD-PCR) provides an absolute quantitation without the need for calibration curves. A comparison between DD-PCR and qRT-PCR was conducted for the quantitation of Bifidobacterium and Lactobacillus 16S RNA genes in human breast milk, and the impacts of selected maternal factors were studied on the composition of these two bacteria in breast milk. From this study, DD-PCR reported between 0-34,460 16S rRNA gene copies of Bifidobacterium genera and between 1,108-634,000 16S rRNA gene copies of Lactobacillus genera in 1 ml breast milk. The 16S rRNA gene copy number of Lactobacillus genera was much greater than that of Bifidobacterium genera in breast milk. DD-PCR showed a 10-fold lower limit of quantitation as compared to qRT-PCR. A higher correlation and agreement was observed between qRT-PCR and DD-PCR in Lactobacillus quantitation as compared to Bifidobacterium quantitation. Based on our DD-PCR quantitation, a low abundance of Bifidobacterium bacteria in breast milk was correlated to higher pre-pregnancy body mass index (BMI). However, no significant difference was observed for these two bacteria in breast milk between mothers who had vaginal deliveries and caesarean deliveries. This study suggests that DD-PCR is a better tool to quantitate the bacterial load of breast milk compared to the conventional qRT-PCR method. The number of breast milk Bifidobacterium bacteria is influenced by maternal pre-pregnancy BMI.
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Affiliation(s)
- L Qian
- 1 Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University, School of Medicine, Kongjiang Road 1665, Shanghai 200092, China P.R.,2 Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Kongjiang Road 1665, Shanghai 200092, China P.R
| | - H Song
- 1 Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University, School of Medicine, Kongjiang Road 1665, Shanghai 200092, China P.R.,2 Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Kongjiang Road 1665, Shanghai 200092, China P.R
| | - W Cai
- 1 Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University, School of Medicine, Kongjiang Road 1665, Shanghai 200092, China P.R.,2 Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Kongjiang Road 1665, Shanghai 200092, China P.R
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11
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Romanazzi V, Traversi D, Lorenzi E, Gilli G. Effects of freezing storage on the DNA extraction and microbial evaluation from anaerobic digested sludges. BMC Res Notes 2015; 8:420. [PMID: 26347085 PMCID: PMC4562115 DOI: 10.1186/s13104-015-1407-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 08/31/2015] [Indexed: 11/17/2022] Open
Abstract
Background The anaerobic digestion is one of the most spread renewable energy technology. The input biomasses included various environmental problematic wastes such as sludge coming from wastewater treatment plant (WWTP) and organic fraction of municipal solid waste (OFMSW). As biomolecular procedures have become important tools for the microbial characterisation of anaerobic samples coming from the reactors, it is crucial sampling and extracting properly DNA in order to employ such types of techniques. The current study is aimed to evaluate how freezing temperature and length of storage at −20 °C influence both the extracted DNA yield and microbial community quantifications from digested sludge samples collected at full-scale plants. Results From WWTP sludge samples, we observed a reduction of DNA concentration comparing fresh and stored samples for 10 days at −20 °C (ANOVA test p < 0.0001), with an estimated DNA loss of approximately 65 % for such types of samples, however the methanogen communities can be assessed respecting the fresh conditions. From OFMSW sludge samples, we observed a reduction in extracted DNA (−90 %), after 120 frozen days, while microbial communities are determined respecting the fresh conditions within 2 months of frozen storage. Conclusions The remarkable effect of frozen storage on sludge samples suggests as the better procedure to perform the DNA extraction from fresh sample. On the other hand it is not generally possible, so approximately 2 months of storage at −20 °C appears to be suitable time at which DNA concentrations remain sufficient to perform coherent microbial characterization through quantitative qRT-PCR.
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Affiliation(s)
- Valeria Romanazzi
- Hygiene Division, Department of Public Health and Pediatrics, University of Torino, Via Santena 5 bis, 10126, Turin, Italy.
| | - Deborah Traversi
- Hygiene Division, Department of Public Health and Pediatrics, University of Torino, Via Santena 5 bis, 10126, Turin, Italy.
| | - Eugenio Lorenzi
- SMAT, Società Metropolitana Acque Torino S.p.A., Corso XI Febbraio 14, 10152, Turin, Italy.
| | - Giorgio Gilli
- Hygiene Division, Department of Public Health and Pediatrics, University of Torino, Via Santena 5 bis, 10126, Turin, Italy.
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Krustok I, Odlare M, Shabiimam M, Truu J, Truu M, Ligi T, Nehrenheim E. Characterization of algal and microbial community growth in a wastewater treating batch photo-bioreactor inoculated with lake water. ALGAL RES 2015. [DOI: 10.1016/j.algal.2015.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Tiirik K, Nõlvak H, Oopkaup K, Truu M, Preem JK, Heinaru A, Truu J. Characterization of the bacterioplankton community and its antibiotic resistance genes in the Baltic Sea. Biotechnol Appl Biochem 2014; 61:23-32. [DOI: 10.1002/bab.1144] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/18/2013] [Indexed: 12/27/2022]
Affiliation(s)
- Kertu Tiirik
- Institute of Ecology and Earth Sciences; Faculty of Science and Technology; University of Tartu; Tartu Estonia
| | - Hiie Nõlvak
- Institute of Ecology and Earth Sciences; Faculty of Science and Technology; University of Tartu; Tartu Estonia
| | - Kristjan Oopkaup
- Institute of Ecology and Earth Sciences; Faculty of Science and Technology; University of Tartu; Tartu Estonia
| | - Marika Truu
- Institute of Ecology and Earth Sciences; Faculty of Science and Technology; University of Tartu; Tartu Estonia
| | - Jens-Konrad Preem
- Institute of Ecology and Earth Sciences; Faculty of Science and Technology; University of Tartu; Tartu Estonia
| | - Ain Heinaru
- Institute of Molecular and Cell Biology; Faculty of Science and Technology; University of Tartu; Tartu Estonia
| | - Jaak Truu
- Institute of Ecology and Earth Sciences; Faculty of Science and Technology; University of Tartu; Tartu Estonia
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14
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Nõlvak H, Truu M, Tiirik K, Oopkaup K, Sildvee T, Kaasik A, Mander Ü, Truu J. Dynamics of antibiotic resistance genes and their relationships with system treatment efficiency in a horizontal subsurface flow constructed wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 461-462:636-44. [PMID: 23770545 DOI: 10.1016/j.scitotenv.2013.05.052] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/17/2013] [Accepted: 05/19/2013] [Indexed: 05/21/2023]
Abstract
Municipal wastewater treatment is one of the pathways by which antibiotic resistance genes from anthropogenic sources are introduced into natural ecosystems. This study examined the abundance and proportion dynamics of seven antibiotic resistance genes in the wetland media biofilm and in the influent and effluent of parallel horizontal subsurface flow mesocosm cells of a newly established hybrid constructed wetland treating municipal wastewater. The targeted genes (tetA, tetB, tetM, ermB, sul1, ampC, and qnrS) encode resistance to major antibiotic classes such as tetracyclines, macrolides, sulfonamides, penicillins, and fluoroquinolones, respectively. All targeted antibiotic resistance genes were detectable in the tested mesocosm environments, with the tetA, sul1, and qnrS genes being the most abundant in the mesocosm effluents. After initial fluctuation in the microbial community, target gene abundances and proportions stabilized in the wetland media biofilm. The abundance of 16S rRNA and antibiotic resistance genes, and the proportion of antibiotic resistance genes in the microbial community, were reduced during the wastewater treatment by the constructed wetland. The concentration of antibiotic resistance genes in the system effluent was similar to conventional wastewater treatment facilities; however, the mesocosms reduced sulfonamide resistance encoding sul1 concentrations more effectively than some traditional wastewater treatment options. The concentrations of antibiotic resistance genes in the wetland media biofilm and in effluent were affected by system operation parameters, especially time and temperature. The results also revealed a relationship between antibiotic resistance genes abundance and the removal efficiencies of NO2-N, NH4-N, and organic matter. Correlation analysis between the abundance of individual antibiotic resistance genes in the mesocosms influent, effluent and wetland media biofilm indicated that depending on antibiotic resistance gene type the microbes carrying these genes interact differently with microbial communities already present on the wetland media.
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Affiliation(s)
- Hiie Nõlvak
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
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Jung J, Choi S, Jung H, Scow KM, Park W. Primers for amplification of nitrous oxide reductase genes associated with Firmicutes and Bacteroidetes in organic-compound-rich soils. MICROBIOLOGY-SGM 2012. [PMID: 23197174 DOI: 10.1099/mic.0.060194-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nosZ gene encodes nitrous oxide reductase, a key enzyme in the nitrous oxide reduction that occurs during complete denitrification. Many conventional approaches have used Proteobacteria-based primers to detect nosZ in environmental samples. However, these primers often fail to detect nosZ in non-Proteobacteria strains, including Firmicutes (Gram-positive) and Bacteroidetes. In this study, newly designed nosZ primers successfully amplified this gene from five Geobacillus species (Firmicutes). The primers were used to construct nosZ clone libraries from DNA extracted from sludge and domestic animal feedlot soils, all with high organic carbon contents. After DNA sequencing, phylogenetic analysis identified many new nosZ sequences with high levels of homology to nosZ from Bacteroidetes, probably because of the high sequence similarity of nosZ from Firmicutes and Bacteroidetes, and a predominance of Bacteroidetes in feedlot environments. Three sets of new quantitative real-time PCR (qPCR) primers based on our clone library sequences were designed and tested for their specificities. Our data showed that only Bacteroidetes-related nosZ sequences were amplified, whereas conventional Proteobacteria-based primers amplified only Proteobacteria-related nosZ. Quantitative analysis of nosZ with the new qPCR primers recovered ~10(4) copies per 100 ng DNA. Thus, it appears that amplification with conventional primers is insufficient for developing an understanding of the diversity and abundance of nosZ genes in the environment.
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Affiliation(s)
- Jaejoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Sungjong Choi
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Hoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Kate M Scow
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Woojun Park
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
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