28 results on '"Shu Harn Te"'
Search Results
2. Correction for Zhang et al., 'Isolation and Characterization of the First Freshwater Cyanophage Infecting Pseudanabaena '
- Author
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Dong Zhang, Fang You, Yiliang He, Shu Harn Te, and Karina Yew-Hoong Gin
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Virology ,Insect Science ,Immunology ,Author Correction ,Microbiology - Published
- 2023
3. Corrected and Republished from: 'Isolation and Characterization of the First Freshwater Cyanophage Infecting Pseudanabaena '
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Dong Zhang, Fang You, Yiliang He, Shu Harn Te, and Karina Yew-Hoong Gin
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Virology ,Insect Science ,Immunology ,Microbiology - Abstract
This study presents the isolation of the very first freshwater cyanophage, PA-SR01, that infects Pseudanabaena , and fills an important knowledge gap on freshwater cyanophages as well as cyanophages infecting Pseudanabaena .
- Published
- 2023
4. Impacts of Microcystis on the Dissemination of the Antibiotic Resistome in Cyanobacterial Blooms
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Karina Yew-Hoong Gin, Wenxuan Li, Feijian Mao, Shu Harn Te, and Yiliang He
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biology ,medicine.drug_class ,Ecology ,Antibiotics ,Heterotrophic bacteria ,Cyanobacterial bloom ,biology.organism_classification ,Freshwater ecosystem ,Resistome ,Antibiotic resistance ,Chemistry (miscellaneous) ,Microcystis ,medicine ,Environmental Chemistry ,Chemical Engineering (miscellaneous) ,Water Science and Technology - Abstract
Antimicrobial resistance and harmful cyanobacterial bloom are two health concerns of freshwater ecosystems; a lot of studies have been conducted on these threats. However, few studies have been con...
- Published
- 2021
5. Effects of Light and Temperature on the Metabolic Profiling of Two Habitat-Dependent Bloom-Forming Cyanobacteria
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Bijayalaxmi Mohanty, Seyed Mohammad Majedi, Shruti Pavagadhi, Shu Harn Te, Chek Yin Boo, Karina Yew-Hoong Gin, and Sanjay Swarup
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Hapalosiphon ,Endocrinology, Diabetes and Metabolism ,fungi ,temperature ,light ,cyanobacteria ,metabolomics ,Molecular Biology ,Biochemistry ,Planktothricoides - Abstract
Rapid proliferation of cyanobacteria in both benthic and suspended (planktonic) habitats is a major threat to environmental safety, as they produce nuisance compounds such as cytotoxins and off-flavors, which degrade the safety and quality of water supplies. Temperature and light irradiance are two of the key factors in regulating the occurrence of algal blooms and production of major off-flavors. However, the role of these factors in regulating the growth and metabolism is poorly explored for both benthic and planktonic cyanobacteria. To fill this gap, we studied the effects of light and temperature on the growth and metabolic profiling of both benthic (Hapalosiphon sp. MRB220) and planktonic (Planktothricoides sp. SR001) environmental species collected from a freshwater reservoir in Singapore. Moreover, this study is the first report on the metabolic profiling of cyanobacteria belonging to two different habitats in response to altered environmental conditions. The highest growth rate of both species was observed at the highest light intensity (100 μmol photons/m²/s) and at a temperature of 33 °C. Systematic metabolite profiling analysis suggested that temperature had a more profound effect on metabolome of the Hapalosiphon, whereas light had a greater effect in the case of Planktothricoides. Interestingly, Planktothricoides sp. SR001 showed a specialized adaptation mechanism via biosynthesis of arginine, and metabolism of cysteine and methionine to survive and withstand higher temperatures of 38 °C and higher. Hence, the mode of strategies for coping with different light and temperature conditions was correlated with the growth and alteration in metabolic activities for physiological and ecological adaptations in both species. In addition, we putatively identified a number of unique metabolites with a broad range of antimicrobial activities in both species in response to both light and temperature. These metabolites could play a role in the dominant behavior of these species in suppressing competition during bloom formation. Overall, this study elucidated novel insights into the effects of environmental factors on the growth, metabolism, and adaptation strategies of cyanobacteria from two different habitats, and could be useful in controlling their harmful effects on human health and environmental concerns.
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- 2022
6. Application of a Mechanistic Model for the Prediction of Microcystin Production by
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Nur Hanisah, Bte Sukarji, Yiliang, He, Shu Harn, Te, and Karina Yew-Hoong, Gin
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Bacteriological Techniques ,Lakes ,Singapore ,Tropical Climate ,Microcystis ,Microcystins ,Models, Theoretical ,Laboratories - Abstract
Microcystin is an algal toxin that is commonly found in eutrophic freshwaters throughout the world. Many studies have been conducted to elucidate the factors affecting its production, but few studies have attempted mechanistic models of its production to aid water managers in predicting its occurrence. Here, a mechanistic model was developed based on microcystin production by
- Published
- 2021
7. Multi-class secondary metabolites in cyanobacterial blooms from a tropical water body: Distribution patterns and real-time prediction
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Luhua You, Xuneng Tong, Shu Harn Te, Ngoc Han Tran, Nur Hanisah bte Sukarji, Yiliang He, and Karina Yew-Hoong Gin
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Lakes ,Tropical Climate ,Environmental Engineering ,Cyanobacteria Toxins ,Microcystins ,Ecological Modeling ,Chlorophyll A ,Eutrophication ,Cyanobacteria ,Pollution ,Waste Management and Disposal ,Water Science and Technology ,Civil and Structural Engineering - Abstract
Cyanobacterial blooms that produce toxins occur in freshwaters worldwide and yet, the occurrence and distribution patterns of many cyanobacterial secondary metabolites particularly in tropical regions are still not fully understood. Moreover, predictive models for these metabolites by using easily accessible water quality indicators are rarely discussed. In this study, we investigated the co-occurrence and spatiotemporal trends of 18 well-known and less-studied cyanobacterial metabolites (including [D-Asp3] microcystin-LR (DM-LR), [D-Asp3] microcystin-RR (DM-RR), microcystin-HilR (MC-HilR), microcystin-HtyR (MC-HtyR), microcystin-LA (MC-LA), microcystin-LF (MC-LF), microcystin-LR (MC-LR), microcystin-LW (MC-LW), microcystin-LY (MC-LY), microcystin-RR (MC-RR) and microcystin-WR (MC-WR), Anatoxin-a (ATX-a), homoanatoxin-a (HATX-a), cylindrospermospin (CYN), nodularin (NOD), anabaenopeptin A (AptA) and anabaenopeptin B (AptB)) in a tropical freshwater lake often plagued with blooms. Random forest (RF) models were developed to predict MCs and CYN and assess the relative importance of 22 potential predictors that determined their concentrations. The results showed that 11 MCs, CYN, ATX-a, HATX-a, AptA and AptB were found at least once in the studied water body, with MC-RR and CYN being the most frequently occurring, intracellularly and extracellularly. AptA and AptB were detected for the first time in tropical freshwaters at low concentrations. The metabolite profiles were highly variable at both temporal and spatial scales, in line with spatially different phytoplankton assemblages. Notably, MCs decreased with the increase of CYN, possibly revealing interspecific competition of cyanobacteria. The rapid RF prediction models for MCs and CYN were successfully developed using 4 identified drivers (i.e., chlorophyll-a, total carbon, rainfall and ammonium for MCs prediction; and chloride, total carbon, rainfall and nitrate for CYN prediction). The established models can help to better understand the potential relationships between cyanotoxins and environmental variables as well as provide useful information for making policy decisions.
- Published
- 2021
8. Cyanophage dynamics in a tropical urban freshwater lake
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Dong Zhang, Shu Harn Te, Yiliang He, and Karina Yew-Hoong Gin
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Ecology ,General Decision Sciences ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
9. Environmental factors influence cylindrospermopsin production ofCylindrospermopsis raciborskii(CR12)
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Karina Yew-Hoong Gin, Nur Hazimah Mohamed Nor, Shu Harn Te, and Maxine A. D. Mowe
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chemistry.chemical_compound ,Ecology ,chemistry ,biology ,Botany ,Cylindrospermopsin ,Aquatic Science ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematics ,Cylindrospermopsis raciborskii - Published
- 2019
10. Occurrence and distribution of viruses and picoplankton in tropical freshwater bodies determined by flow cytometry
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Karina Yew-Hoong Gin, Kalaivani Mani, Shin Giek Goh, Xiaoqiong Gu, Yi Yang, Yiliang He, and Shu Harn Te
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Environmental Engineering ,0208 environmental biotechnology ,Fresh Water ,02 engineering and technology ,010501 environmental sciences ,Biology ,01 natural sciences ,Freshwater ecosystem ,Nutrient ,Phytoplankton ,Picoplankton ,Waste Management and Disposal ,Ecosystem ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,Bacteria ,Ecology ,Ecological Modeling ,Flow Cytometry ,Pollution ,020801 environmental engineering ,Microbial population biology ,Viruses ,Biological dispersal ,Water quality ,Surface water - Abstract
This study aimed to examine the drivers in shaping the occurrence and distribution of total viruses and picoplankton in tropical freshwater ecosystems. Flow cytometry was used to quantify the concentrations of total viruses, picoheterotrophs, picophytoplankton, and picocyanobacteria. Three land use patterns (urban-, agriculture- and parkland-dominated) were evaluated using ArcGIS. Significant correlations were observed between water-borne microbial targets and water quality parameters (0.175 ≤ |r| ≤ 0.441), nutrients (0.250 ≤ r ≤ 0.570) and land use factors (0.200 ≤ |r| ≤ 0.460). In particular, the concentrations of total viruses and picoheterotrophic cells were higher in catchments whereas the abundances of picophytoplankton and picocyanobacteria were higher in reservoirs. Total viruses and picoplankton had higher concentrations in urban- and agriculture-dominated areas, probably due to anthropogenic inputs and agricultural inputs, respectively. Although surface water is a complex matrix influenced by niche-based (i.e., physicochemical properties, nutrients, land use impact etc.) and neutral-based factors (i.e., ecological drift, dispersal and species), land use patterns could help to elucidate the occurrence and distribution of the total microbial community at the macroscopic level. Meanwhile, inter-correlations among viruses, picoplankton and picoheterotrophs (0.715 ≤ r ≤ 0.990) also substantiates their mutual interactions in influencing the microbial community. Furthermore, the relationships between total microbial cells and bacterial and viral indicators were also investigated. Concentrations of total viruses, picoplankton and picoheterotrophs were positively correlated with bacterial indicators (0.427 ≤ r ≤ 0.590) and viral indicators (0.201 ≤ r ≤ 0.563). These results indicated that faecal and viral contamination could contribute to the numbers of total viruses and bacteria.
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- 2019
11. Biodiversity, phylogeny and toxin production profile of cyanobacterial strains isolated from lake Latyan in Iran
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Yasaman Tavakoli, Karina Yew-Hoong Gin, Shu Harn Te, Luhua You, and Fatemeh Mohammadipanah
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0106 biological sciences ,Cyanobacteria ,Plant Science ,Microcystin ,010501 environmental sciences ,Aquatic Science ,Iran ,01 natural sciences ,chemistry.chemical_compound ,Dry weight ,Tandem Mass Spectrometry ,Botany ,Phylogeny ,0105 earth and related environmental sciences ,Nostocales ,chemistry.chemical_classification ,Synechococcales ,biology ,010604 marine biology & hydrobiology ,Biodiversity ,biology.organism_classification ,Lakes ,chemistry ,Cylindrospermopsin ,Oscillatoriales ,Artemia salina ,Chromatography, Liquid - Abstract
Monitoring toxigenic cyanobacteria in freshwaters is of great importance due to the adverse health impacts on humans and aquatic organisms. Here we studied cyanobacterial occurrence and biodiversity in a drinking water reservoir in Tehran province, Iran. In total, nine different species representing three orders of Synechococcales, Oscillatoriales and Nostocales were isolated and classified into six families and seven genera ranging from 92.3% to 99.0% similarities in their partial 16S rDNA with GenBank sequences. The cultures were analyzed for cyanotoxins production by the Artemia salina bioassay, ultrahigh performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and also screened for the presence of marker genes involved in toxins production. Ethyl acetate extracts of three strains showed more than 50% mortality on A. salina larvae after 24 h at a concentration of 500 µg/ml. Production of at least one of the cyanotoxins, microcystin (MC), cylindrospermopsin (CYN) and anatoxin-a (ATX-a), was detected in 6 of the strains. Seven MC variants with a total concentration of 130.6 ng/mg of biomass dry weight were detected for the strain Phormidium sp. UTMC6001 and molecular screening of the mcyE gene also confirmed the presence of this biomarker in its genome. Our study also revealed the production of CYN in a novel picocyanobacterial strain Cyanobium sp. UTMC6007 at 1.0 ng/mg of biomass dry weight. Considering the limited information on freshwater toxic cyanobacteria taxonomy in the Middle East, these findings will expand our knowledge and consequently aid in development of new water management policies in future.
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- 2020
12. Isolation and Characterization of the First Freshwater Cyanophage Infecting Pseudanabaena
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Fang You, Karina Yew-Hoong Gin, Yiliang He, Shu Harn Te, and Dong Zhang
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Genetics ,Phylogenetic tree ,Lineage (evolution) ,Immunology ,Cyanophage ,Biology ,Microbiology ,Genome ,Lytic cycle ,Metagenomics ,Virology ,Insect Science ,ORFS ,Gene - Abstract
Cyanobacteria are the major primary producers in both freshwater and marine environments. However, the majority of freshwater cyanophages remain unknown due to the limited number of cyanophage isolates. In this study, we present a novel lytic freshwater cyanophage, PA-SR01, which was isolated from the Singapore Serangoon Reservoir. To our knowledge, this is the first isolate of a cyanophage that has been found to infect the cyanobacterium Pseudanabaena PA-SR01 has a narrow host range, a short latent period, and is chloroform sensitive. Distinct from the majority of cyanophage isolates, PA-SR01 has a tailless morphology. It is a double-stranded DNA virus with a 137,012-bp genome. Functional annotation for the predicted open reading frames (ORFs) of the PA-SR01 genome identified genes with putative functions related to DNA metabolism, structural proteins, lysis, host-derived metabolic genes, and DNA packaging. Out of 166 predicted ORFs, only 17 ORFs have homology with genes with known function. Phylogenetic analysis of the major capsid protein and terminase large subunit further suggests that phage PA-SR01 is evolutionary distinct from known cyanophages. Metagenomics sequence recruitment onto the PA-SR01 genome indicates that PA-SR01 represents a new evolutionary lineage of phage which shares considerable genetic similarities with phage sequences in aquatic environments and could play key ecological roles.IMPORTANCE This study presents the isolation of the very first freshwater cyanophage, PA-SR01, that infects Pseudanabaena, and fills an important knowledge gap on freshwater cyanophages as well as cyanophages infecting Pseudanabaena.
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- 2020
13. Isolation and Characterization of the First Freshwater Cyanophage Infecting
- Author
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Dong, Zhang, Fang, You, Yiliang, He, Shu Harn, Te, and Karina Yew-Hoong, Gin
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Fresh Water ,cyanophages ,DNA ,Genome, Viral ,Sequence Analysis, DNA ,Cyanobacteria ,Biological Evolution ,Host Specificity ,full genome ,Open Reading Frames ,Pseudanabaena ,Genetic Diversity and Evolution ,Bacteriophages ,Capsid Proteins ,Metagenomics ,freshwater ,isolation ,Phylogeny - Abstract
This study presents the isolation of the very first freshwater cyanophage, PA-SR01, that infects Pseudanabaena, and fills an important knowledge gap on freshwater cyanophages as well as cyanophages infecting Pseudanabaena., Cyanobacteria are the major primary producers in both freshwater and marine environments. However, the majority of freshwater cyanophages remain unknown due to the limited number of cyanophage isolates. In this study, we present a novel lytic freshwater cyanophage, PA-SR01, which was isolated from the Singapore Serangoon Reservoir. To our knowledge, this is the first isolate of a cyanophage that has been found to infect the cyanobacterium Pseudanabaena. PA-SR01 has a narrow host range, a short latent period, and is chloroform sensitive. Distinct from the majority of cyanophage isolates, PA-SR01 has a tailless morphology. It is a double-stranded DNA virus with a 137,012-bp genome. Functional annotation for the predicted open reading frames (ORFs) of the PA-SR01 genome identified genes with putative functions related to DNA metabolism, structural proteins, lysis, host-derived metabolic genes, and DNA packaging. Out of 166 predicted ORFs, only 17 ORFs have homology with genes with known function. Phylogenetic analysis of the major capsid protein and terminase large subunit further suggests that phage PA-SR01 is evolutionary distinct from known cyanophages. Metagenomics sequence recruitment onto the PA-SR01 genome indicates that PA-SR01 represents a new evolutionary lineage of phage which shares considerable genetic similarities with phage sequences in aquatic environments and could play key ecological roles. IMPORTANCE This study presents the isolation of the very first freshwater cyanophage, PA-SR01, that infects Pseudanabaena, and fills an important knowledge gap on freshwater cyanophages as well as cyanophages infecting Pseudanabaena.
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- 2020
14. Application of a Mechanistic Model for the Prediction of Microcystin Production by Microcystis in Lab Cultures and Tropical Lake
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Nur Hanisah bte Sukarji, Yiliang He, Shu Harn Te, and Karina Yew-Hoong Gin
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Health, Toxicology and Mutagenesis ,microcystin ,Microcystis ,mechanistic model ,nitrogen ,temperature ,phosphorus ,decay ,Toxicology - Abstract
Microcystin is an algal toxin that is commonly found in eutrophic freshwaters throughout the world. Many studies have been conducted to elucidate the factors affecting its production, but few studies have attempted mechanistic models of its production to aid water managers in predicting its occurrence. Here, a mechanistic model was developed based on microcystin production by Microcystis spp. under laboratory culture and ambient field conditions. The model was built on STELLA, a dynamic modelling software, and is based on constitutive cell quota that varies with nitrogen, phosphorus, and temperature. In addition to these factors, varying the decay rate of microcystin according to its proportion in the intracellular and extracellular phase was important for the model’s performance. With all these effects, the model predicted most of the observations with a model efficiency that was >0.72 and >0.45 for the lab and field conditions respectively. However, some large discrepancies were observed. These may have arisen from the non-constitutive microcystin production that appear to have a precondition of nitrogen abundance. Another reason for the large root mean square error is that cell quota is affected by factors differently between strains.
- Published
- 2022
15. Seasonal variation in the bacterial community composition of a large estuarine reservoir and response to cyanobacterial proliferation
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Karina Yew-Hoong Gin, Yiliang He, Cong Xu, Jason N. Woodhouse, Lei Chen, Zheng Xu, and Shu Harn Te
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DNA, Bacterial ,0301 basic medicine ,Cyanobacteria ,Environmental Engineering ,Health, Toxicology and Mutagenesis ,010501 environmental sciences ,01 natural sciences ,Actinobacteria ,03 medical and health sciences ,Rivers ,Environmental Chemistry ,Ecosystem ,Relative species abundance ,0105 earth and related environmental sciences ,Bacteria ,biology ,Ecology ,Public Health, Environmental and Occupational Health ,High-Throughput Nucleotide Sequencing ,Bacteroidetes ,General Medicine ,General Chemistry ,Synechococcus ,biology.organism_classification ,Pollution ,030104 developmental biology ,Microbial population biology ,bacteria ,Seasons ,Proteobacteria ,Estuaries - Abstract
This study employed high-throughput sequencing (HTS) to understand the variations in microbial community in the largest estuary reservoir located at the Yangtze River for a year. Correlations between the heterotrophic bacterial and cyanobacterial communities in the estuarine ecosystem were also investigated. Significant spatial and temporal changes were observed in the microbial community composition at all sites. These differences were mainly reflected on the variations of bacterial relative abundance. The modularity analysis on the network indicate that bacterial community response to the variations of environmental factors in the form of co-occurrence/exclusion patterns. In warm season, Synechococcus spp. being the dominant Cyanobacteria taxa exhibited high relative abundance in the reservoir. Water temperature was the critical driver for the proliferation of Synechococcus . Moreover, heterotrophic bacteria belonging to Actinobacteria, Proteobacteria (α-, β-, and γ-Proteobacteria), Bacteroidetes and Chlorobi, exhibited positive correlations with Synechococcus . The co-occurrence of these bacterial OTUs suggests that specific taxa may benefit from the proliferation of Synechococcus . In cold season, bacterial OTUs belonging to Actinobacteria and Bacteroidetes shown co-occurrence pattern with salt ions (including K + , Na + , Mg 2+ , Ca 2+ , Cl − and SO 4 2− ) inside the reservoir. In conclusion, further research is required to investigate the ecological functions of these taxa in estuarine ecosystems.
- Published
- 2018
16. Geospatial distribution of viromes in tropical freshwater ecosystems
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Karina Yew-Hoong Gin, Nazanin Saeidi, Qi Xiang Martin Tay, Shu Harn Te, Janelle R. Thompson, Xiaoqiong Gu, Ariel Kushmaro, and Shin Giek Goh
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0301 basic medicine ,Geospatial distribution ,Environmental Engineering ,food.ingredient ,Fresh Water ,Freshwater ecosystem ,Article ,03 medical and health sciences ,food ,Caudovirales ,Abundance (ecology) ,Mimiviridae ,Human virome ,Waste Management and Disposal ,Relative species abundance ,Water Science and Technology ,Civil and Structural Engineering ,Dicistroviridae ,Singapore ,Spatial Analysis ,Diversity ,biology ,Virome ,Ecology ,Ecological Modeling ,Freshwater ecosystems ,Human-related viruses ,biology.organism_classification ,Pollution ,030104 developmental biology ,Cyclovirus ,Viruses ,Land use ,Environmental Monitoring - Abstract
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588, Graphical abstract Image 1, Highlights • Land use is the main driver of the viral community structure in surface waters. • 66 viral families were detected and 66% of the annotated virome was bacteriophages. • Reservoirs showed a higher Shannon diversity (10.4) than upstream tributaries (8.4). • Sequences closely related to human picobirnavirus and cyclovirus were detected. • The relative abundance of PMMoV sequences was correlated with RT-qPCR measurements.
- Published
- 2018
17. Cyanobacterial risk prevention under global warming using an extended Bayesian network
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Christine A. Shoemaker, Xiao Liu, Yee Van Fan, Shu Harn Te, Peng Jiang, Jingjie Zhang, Jiří Jaromír Klemeš, and Karina Yew-Hoong Gin
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Renewable Energy, Sustainability and the Environment ,business.industry ,020209 energy ,Strategy and Management ,Preventive control ,05 social sciences ,Water source ,Global warming ,Environmental resource management ,Inference ,Bayesian network ,02 engineering and technology ,Building and Construction ,Industrial and Manufacturing Engineering ,050501 criminology ,0202 electrical engineering, electronic engineering, information engineering ,Environmental science ,Risk prevention ,Risk assessment ,business ,Recreation ,0505 law ,General Environmental Science - Abstract
Cyanobacterial blooms under global warming are increasing worldwide, producing emerging contaminants, which threaten the health of human beings and aquatic ecosystems. The health burdens warrant the development of a useful risk-assessment tool and a holistic preventive-control scheme to prevent cyanobacterial blooms. This paper aims to integrate cyanobacterial risk assessment and risk preventive control by investigating the relationships amongst cyanobacterial blooms and multi-dimensional influencing variables. Two challenges hinder such a task. First, the time-series variations in cyanobacteria and influencing variables are uncertain and nonlinear. Second, there rarely exists an explicit modelling framework for integrating cyanobacterial risk assessment and risk preventive control. This study builds an extended Bayesian network model and proposes an integrated framework with functions of assessment, inference, preventive control, and visualisation of the risk of cyanobacterial blooms. Field data from a tropical lake are used to evaluate the model and framework. The proposed model achieves better performance than the seven models in comparison. The cyanobacterial risk is anticipated to increase by 38.5% under global warming. On the contrary, guided by the model and framework, the risk could be reduced by about 60% by taking the identified risk preventive control scheme. The cyanobacterial risk prevention would reduce aquatic emerging contaminants in drinking and recreational water sources.
- Published
- 2021
18. Latent Variable Structured Bayesian Network for Cyanobacterial Risk Pre-control
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Karina Yew-Hoong Gin, Peng Jiang, Xiao Liu, Shu Harn Te, and Ji Zhang
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010504 meteorology & atmospheric sciences ,Computer science ,business.industry ,Bayesian network ,Inference ,Latent variable ,010501 environmental sciences ,Machine learning ,computer.software_genre ,01 natural sciences ,Data modeling ,Nonlinear system ,Systematic risk ,Probability distribution ,Sensitivity (control systems) ,Artificial intelligence ,business ,computer ,0105 earth and related environmental sciences - Abstract
Cyanobacterial blooms increasingly pose threats to ecosystems and human health. This paper is aimed to propose systematic risk pre-control schemes by understanding the complex causalities between cyanobacteria and multiple influencing variables. This research remains a challenge for three reasons. Firstly, the time-series evolution of cyanobacteria is characterized by deep uncertainties and nonlinear dynamics. Secondly, latent variables with hidden information usually exist in this kind of complex aquatic system. Thirdly, it is difficult to identify an efficient pre-control scheme that specifies variables for preferential regulation. To address these problems, we propose a latent variable structured Bayesian network model and a corresponding parameter learning algorithm. The model is tested by real-time spatio-temporal data. The computational results reveal that the proposed model demonstrates better performance in terms of inference accuracy and degree of system understanding. Based on sensitivity analysis and combination-effect analysis, a systematic risk pre-control scheme is proposed for decision-makers to prevent cyanobacterial blooms under the scenario of global warming.
- Published
- 2018
19. The Characteristics and Dynamics of Cyanobacteria–Heterotrophic Bacteria Between Two Estuarine Reservoirs – Tropical Versus Sub-Tropical Regions
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Zheng Xu, Shu Harn Te, Yiliang He, and Karina Yew-Hoong Gin
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0301 basic medicine ,Microbiology (medical) ,Cyanobacteria ,biology ,Ecology ,030106 microbiology ,cyanobacteria–heterotrophic bacteria ,lcsh:QR1-502 ,Illumina MiSeq sequencing ,Subtropics ,Bacterial growth ,biology.organism_classification ,Synechococcus ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,molecular ecological network ,Microbial population biology ,Microcystis ,Temperate climate ,Water environment ,microbial community ,estuarine reservoir ,Original Research - Abstract
In this study, Illumina MiSeq sequencing technique was employed to explore the characteristics and dynamics of cyanobacteria–heterotrophic bacteria between two estuarine reservoirs in sub-tropical (reservoir A in Shanghai) and tropical (reservoir B in Singapore) regions. The results indicated that significant differences in bacterial community composition were found between two estuarine reservoirs, which influenced by varied environmental variables. The environmental heterogeneity in reservoir A was much higher, which indicated that the composition of bacterial community in reservoir A was more complex. In contrast, reservoir B provided a suitable and temperate water environment conditions for bacterial growth, which resulted in higher community diversity and less co-exclusion correlations. The molecular ecological network indicated that the presence of dominant bacterial community in each of the reservoir were significant different. These differences mainly reflected the responses of bacterial community to the variations of environmental variables. Although Synechococcus was the dominant cyanobacterial species in both reservoirs, it exhibited co-occurrence patterns with different heterotrophic bacteria between reservoirs. In addition, the cyanobacteria–heterotrophic bacteria interaction exhibited highly dynamic variations, which was affected by nutrition and survive space. Also, the co-occurrence of Microcystis and Pseudanabaena found in reservoir B implied that the non-N-fixing Microcystis accompanied with N-fixing Pseudanabeana occurrence in freshwater lakes, so as to better meet the demand for nitrogen source.
- Published
- 2018
20. Novel cyanotoxin-producing Synechococcus in tropical lakes
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Jerome Wai Kit Kok, Ngoc Han Tran, Karina Yew-Hoong Gin, Zhi Yang Sim, Wenxuan Li, Kwan Chien Goh, Shu Harn Te, and Yiliang He
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Cyanobacteria ,Environmental Engineering ,Harmful Algal Bloom ,Bacterial Toxins ,0208 environmental biotechnology ,02 engineering and technology ,010501 environmental sciences ,01 natural sciences ,Algal bloom ,Anatoxin-a ,chemistry.chemical_compound ,Humans ,Uracil ,Waste Management and Disposal ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,Synechococcus ,biology ,Ecology ,Anabaena ,Ecological Modeling ,fungi ,Cyanotoxin ,biology.organism_classification ,Pollution ,020801 environmental engineering ,Lakes ,chemistry ,Productivity (ecology) ,Cylindrospermopsin - Abstract
Picocyanobacteria are small cyanobacteria, being about 0.8–1.5 µm in size. They are present in freshwater environments all over the world and are known to cause harmful algal blooms, although their effects are not well understood. Algal blooms are important to manage because they threaten freshwater resources, with potentially severe effects on ecological and human health. There is also increased urgency due to urbanization and climate change trends which are expected to exacerbate these bloom dynamics. These changes are expected to especially favour picocyanobacteria groups, emphasizing the need for better characterization of their effects in the environment. In this study, we report the discovery that Synechococcus sp. could produce cylindrospermopsin (CYN) and anatoxin-a (ATX). This ability had never been previously reported for this species. Their toxin genes were also partial compared to other major producers such as Raphidiopsis sp. and Anabaena sp., demonstrating potentially unique synthesis pathways that provides insight into the various mechanisms of genetic variation that drives toxin synthesis. The Synechococcus sp. strains were found to produce about 9.0 × 10−5–6.8 × 10−4 fg CYN cell−1 and 4.7 × 10−4–1.5 × 10−2 fg ATX cell−1. The potential for Synechococcus sp. to be toxic highlights a global concern due to its widespread distribution, and through environmental trends that increasingly favour its productivity within freshwater systems around the world.
- Published
- 2021
21. Biotransformation of Sulfluramid (N-ethyl perfluorooctane sulfonamide) and dynamics of associated rhizospheric microbial community in microcosms of wetland plants
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Yi Yang, Tingru Yin, Martin Reinhard, Yiliang He, Shu Harn Te, Karina Yew-Hoong Gin, and Huiting Chen
- Subjects
Environmental Engineering ,Health, Toxicology and Mutagenesis ,0208 environmental biotechnology ,02 engineering and technology ,010501 environmental sciences ,01 natural sciences ,Biotransformation ,Environmental Chemistry ,0105 earth and related environmental sciences ,Rhizosphere ,Fluorocarbons ,Sulfonamides ,biology ,Chemistry ,Public Health, Environmental and Occupational Health ,General Medicine ,General Chemistry ,Biodegradation ,biology.organism_classification ,Pollution ,Anoxic waters ,Methanomethylovorans ,020801 environmental engineering ,Biodegradation, Environmental ,Microbial population biology ,Environmental chemistry ,Wetlands ,Microcosm ,Anaerobic exercise - Abstract
Although the use of Sulfluramid (N-ethyl perfluorooctane sulfonamide (N-EtFOSA)) has been restricted by the Stockholm Convention, it is still frequently detected in the environmental matrices and in use in some countries. Employing constructed wetlands as treatment systems requires understanding of the biodegradation process in the rhizosphere and the effect of contaminants on the microbes of wetlands. This study aimed to investigate the interactions between the microbial community and N-EtFOSA under aerobic and anaerobic conditions. Aerobic biotransformation of N-EtFOSA occurred with a half-life of 0.51 day and yielded 85.1 mol% PFOS of after 91 days. Kinetic modelling revealed that cleavage of the S N was the rate-limiting degradation step. Biotransformation was not observed under anaerobic and anoxic conditions, suggesting that N-EtFOSA is recalcitrant to biodegradation without dissolved oxygen. Under aerobic condition, the presence of N-EtFOSA and its biotransformation products decreased the microbial richness and diversity and exerted selective pressure on the microbial community. Enrichment of Methylocaldum was significant (49%) in the presence of N-EtFOSA compared to unexposed conditions (11%), suggesting that Methylocaldum is relatively tolerant to N-EtFOSA and potentially degrading N-EtFOSA. Under anaerobic conditions, the microbial richness and diversity were not significantly altered by the presence of N-EtFOSA. Only Methanomethylovorans increased significantly in the spiked microcosm (30% vs. 20%). These findings provide knowledge for comprehending the contribution of N-EtFOSA to other PFASs in various environmental conditions, information about microbial community changes in response to PFASs and robust microbial species which can degrade N-EtFOSA in the environment.
- Published
- 2018
22. Removal of cyanobacteria from synthetic and real water by dielectric barrier discharge process
- Author
-
Stephanie Ting Yu Chew, Shu Harn Te, Tuti Mariana Lim, and Yi Zhang
- Subjects
Chlorophyll ,Cyanobacteria ,Salinity ,Chlorophyll a ,Health, Toxicology and Mutagenesis ,Fresh Water ,Dielectric barrier discharge ,Biology ,Cell morphology ,Water Purification ,chemistry.chemical_compound ,Environmental Chemistry ,Ecotoxicology ,Total organic carbon ,Chlorophyll A ,Environmental engineering ,Parts-per notation ,Water ,General Medicine ,biology.organism_classification ,Pollution ,chemistry ,Environmental chemistry ,Feasibility Studies ,Water Microbiology - Abstract
The feasibility of cyanobacteria removal from freshwater by a dielectric barrier discharge (DBD) process is investigated. Seven commercial and environmental cyanobacteria strains, as well as real algae-laden water, were tested. The removal of the cyanobacteria was evaluated by analyzing the changes in chlorophyll a content, total organic carbon (TOC) concentration, and cell morphology. Nearly total removal of chlorophyll a was achieved within 20 min, while the TOC analysis exhibited an increase-decrease-increase trend in 60 min of treatment, likely due to the oxidation of intracellular and intercellular materials. Observation under light microscopy revealed the disruption of intracellular and intercellular structures within 5 min of DBD treatment and thus supported the TOC analysis. Increasing the salinity of the medium from 0 to 5 parts per thousand (ppt) improved treatment efficiency, where similar level of chlorophyll a removal (around 93%) was achieved in only half the treatment time. Application of DBD on real algae-laden water from a fish farm yielded higher treatment efficiency than in synthetic medium, indicating the promising application of DBD as a means to control cyanobacteria bloom in fresh and estuary water bodies.
- Published
- 2015
23. Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001
- Author
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Janelle R. Thompson, Karina Yew-Hoong Gin, Shu Harn Te, BoonFei Tan, and Chek Yin Boo
- Subjects
0301 basic medicine ,Whole genome sequencing ,Genetics ,2-methylisoborneol ,lcsh:QH426-470 ,Planktothricoides ,Operon ,Strain (biology) ,Metabolite ,Genomics ,Biology ,Genome ,lcsh:Genetics ,03 medical and health sciences ,chemistry.chemical_compound ,Viridisamide A ,030104 developmental biology ,Cyanobactin ,chemistry ,Biosynthesis ,Phormidiaceae ,Extended Genome Report ,Gene - Abstract
Planktothricoides is a free-living filamentous cyanobacterium belonging to the order Oscillatoriales and the family Phormidiaceae, capable of forming bloom in fresh and brackish waters. A unicyanobacterial non-axenic culture dominated by Planktothricoides sp. SR001 was obtained from a freshwater reservoir in Singapore. The draft genome presented here is the first tropical freshwater Planktothricoides sp. ever sequenced. The genome of 7.0Mbp contains 5,776 genes predicted using the JGI IMG pipeline. The whole genome sequence allows identification of genes encoding for nitrogen-fixation, accessory photosynthetic pigments and biosynthesis of an off-flavor compound, 2-methylisoborneol, which has been experimentally verified here based on metabolite detection. In addition, strain SR001 genome contains an operon putatively involved in the production of a linear tripeptide cyanobactin related to viridisamide A and aeruginosamide, with the later known to possess anti-microbial or cytotoxic effect.
- Published
- 2017
24. Relationship of Microbiota and Cyanobacterial Secondary Metabolites in Planktothricoides-Dominated Bloom
- Author
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Karina Yew-Hoong Gin, Janelle R. Thompson, BoonFei Tan, and Shu Harn Te
- Subjects
0301 basic medicine ,biology ,Ecology ,Microbiota ,fungi ,030106 microbiology ,Community structure ,Fresh Water ,General Chemistry ,Eutrophication ,Synechococcus ,biology.organism_classification ,Cyanobacteria ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Phytoplankton ,Environmental Chemistry ,Water quality ,Proteobacteria ,Bloom ,Diel vertical migration - Abstract
The identification of phytoplankton species and microbial biodiversity is necessary to assess water ecosystem health and the quality of water resources. We investigated the short-term (2 days) vertical and diel variations in bacterial community structure and microbially derived secondary metabolites during a cyanobacterial bloom that emerged in a highly urbanized tropical reservoir. The waterbody was largely dominated by the cyanobacteria Planktothricoides spp., together with the Synechococcus, Pseudanabaena, Prochlorothrix, and Limnothrix. Spatial differences (i.e., water depth) rather than temporal differences (i.e., day versus night) better-explained the short-term variability in water quality parameters and bacterial community composition. Difference in bacterial structure suggested a resource-driven distribution pattern for the community. We found that the freshwater bacterial community associated with cyanobacterial blooms is largely conserved at the phylum level, with Proteobacteria (β-proteobateria), Bacteroidetes, and Actinobacteria as the main taxa despite the cyanobacterial species present and geographical (Asia, Europe, Australia, and North America) or climatic distinctions. Through multivariate statistical analyses of the bacterial community, environmental parameters, and secondary metabolite concentrations, we observed positive relationships between the occurrences of cyanobacterial groups and off-flavor compounds (2-methyisoborneol and β-ionone), suggesting a cyanobacterial origin. This study demonstrates the potential of 16S rRNA gene amplicon sequencing as a supporting tool in algal bloom monitoring or water-resource management.
- Published
- 2017
25. The dynamics of cyanobacteria and microcystin production in a tropical reservoir of Singapore
- Author
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Karina Yew-Hoong Gin and Shu Harn Te
- Subjects
chemistry.chemical_classification ,Cyanobacteria ,education.field_of_study ,biology ,Anabaena ,Population ,Plant Science ,Microcystin ,Aquatic Science ,biology.organism_classification ,Nutrient ,Algae ,chemistry ,Microcystis ,Botany ,Food science ,Eutrophication ,education - Abstract
The temporal variations in cyanobacteria and microcystin production in a tropical reservoir, Kranji Reservoir in Singapore, were studied from February 2008 to August 2009 by using molecular techniques and enzyme-linked immunosorbent assay (ELISA) respectively. Results from PCR and qPCR showed that Microcystis and Anabaena were present (mean concentrations 4.16 × 10 6 gene copies/mL and 4.47 × 10 4 gene copies/mL respectively) and were well correlated to each other ( P Microcystis was the primary microcystin producer. The average percentage of toxigenic Microcystis spp. was 55.92%, whereas no Anabaena -specific microcystin producing gene was detected. Microcystis -specific microcystin-producing genes mcyB and mcyD were detected in all the samples, together with dominant detection of mcyA and mcyE genes. However, a low positive detection rate was observed for mcyC . Due to the combined effects of high temperature, light and nutrient conditions in this tropical reservoir, the Microcystis cell concentrations were higher and more uniform compared to other Microcystis blooms reported in subtropical and temperate regions. Furthermore, the proportion of toxigenic Microcystis in the total Microcystis population was considerably higher. Principle component analysis and multiple linear regression analysis showed that total nitrogen and total phosphorus were positively correlated with the abundances of total Microcystis and toxigenic Microcystis . In addition, total nitrogen, pH and dissolved oxygen were positively correlated with the microcystin concentration.
- Published
- 2011
26. Variations of Bacterial Community Composition and Functions in an Estuary Reservoir during Spring and Summer Alternation
- Author
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Yiliang He, Karina Yew-Hoong Gin, Cong Xu, Shu Harn Te, and Zheng Xu
- Subjects
DNA, Bacterial ,0301 basic medicine ,China ,reservoir ,Carbohydrate transport ,Health, Toxicology and Mutagenesis ,Microorganism ,Heterotroph ,lcsh:Medicine ,Toxicology ,bacterial community ,Article ,03 medical and health sciences ,Yangtze estuary ,Abundance (ecology) ,RNA, Ribosomal, 16S ,16S rRNA gene sequencing ,geography ,geography.geographical_feature_category ,Bacteria ,biology ,Ecology ,Chlorophyll A ,Microbiota ,lcsh:R ,Estuary ,Synechococcus ,biology.organism_classification ,030104 developmental biology ,Microbial population biology ,Metagenomics ,microbial metabolisms ,Seasons ,shotgun metagenomic sequencing ,Estuaries ,Water Microbiology ,Environmental Monitoring - Abstract
In this study, we focused on the dynamics of bacterial community composition in a large reservoir in the Yangtze estuary during spring and summer seasons, especially the variations of functional mechanisms of microbial community during the seasonal alternation between spring and summer. Both 16S rRNA gene sequencing and shotgun metagenomic sequencing technology were used for these purposes. The results indicated that obvious variations of bacterial community structures were found at different sites. Particle-associated bacterial taxa exhibited higher abundance at the inlet site, which was closer to the Yangtze River with a high level of turbidity. In other sites, Synechococcus, as the most dominant cyanobacterial species, revealed high abundance driven by increased temperature. Moreover, some heterotrophic bacterial taxa revealed high abundance following the increased Synechococcus in summer, which indicated potential correlations about carbon source utilization between these microorganisms. In addition, the shotgun metagenomic data indicated during the period of seasonal alternation between spring and summer, the carbohydrate transport and metabolism, energy production and conversion, translation/ribosomal biogenesis, and cell wall/membrane/envelope biogenesis were significantly enhanced at the exit site. However, the course of cell cycle control/division was more active at the internal site.
- Published
- 2018
27. Comparison of Quantitative PCR and Droplet Digital PCR Multiplex Assays for Two Genera of Bloom-Forming Cyanobacteria, Cylindrospermopsis and Microcystis
- Author
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Shu Harn Te, Enid Yingru Chen, and Karina Yew-Hoong Gin
- Subjects
Microbiological Techniques ,Microcystis ,Cost-Benefit Analysis ,Microcystin ,Computational biology ,Real-Time Polymerase Chain Reaction ,Applied Microbiology and Biotechnology ,Sensitivity and Specificity ,Microbiology ,chemistry.chemical_compound ,Multiplex polymerase chain reaction ,Methods ,Digital polymerase chain reaction ,Multiplex ,DNA Primers ,chemistry.chemical_classification ,Ecology ,biology ,Cylindrospermopsis ,biology.organism_classification ,Real-time polymerase chain reaction ,chemistry ,Cylindrospermopsin ,Oligonucleotide Probes ,Multiplex Polymerase Chain Reaction ,Food Science ,Biotechnology - Abstract
The increasing occurrence of harmful cyanobacterial blooms, often linked to deteriorated water quality and adverse public health effects, has become a worldwide concern in recent decades. The use of molecular techniques such as real-time quantitative PCR (qPCR) has become increasingly popular in the detection and monitoring of harmful cyanobacterial species. Multiplex qPCR assays that quantify several toxigenic cyanobacterial species have been established previously; however, there is no molecular assay that detects several bloom-forming species simultaneously. Microcystis and Cylindrospermopsis are the two most commonly found genera and are known to be able to produce microcystin and cylindrospermopsin hepatotoxins. In this study, we designed primers and probes which enable quantification of these genera based on the RNA polymerase C1 gene for Cylindrospermopsis species and the c-phycocyanin beta subunit-like gene for Microcystis species. Duplex assays were developed for two molecular techniques—qPCR and droplet digital PCR (ddPCR). After optimization, both qPCR and ddPCR assays have high linearity and quantitative correlations for standards. Comparisons of the two techniques showed that qPCR has higher sensitivity, a wider linear dynamic range, and shorter analysis time and that it was more cost-effective, making it a suitable method for initial screening. However, the ddPCR approach has lower variability and was able to handle the PCR inhibition and competitive effects found in duplex assays, thus providing more precise and accurate analysis for bloom samples.
- Published
- 2015
28. Sample Preparation of Microbial Contaminants in Water
- Author
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Karina Yew-Hoong Gin, Tiong Gim Aw, Shu Harn Te, and Shin Giek Goh
- Subjects
Alternative methods ,Propidium monoazide ,Environmental chemistry ,Microbial contaminants ,medicine ,Pathogenic bacteria ,Sample preparation ,Toxic algae ,Biology ,medicine.disease_cause ,Immunomagnetic separation ,Pulp and paper industry ,Ethidium monoazide - Abstract
A proper assessment of microbial water quality is necessary to give early warning of disease outbreak and protect public health. Conventional methods of analysis typically require the culturing of indicator microbes, but inherent problems exist, such as lengthy time of analysis and the inability to detect nonculturable species. Alternative methods exist (e.g., molecular and optical methods), which are faster but require adequate sampling preparation techniques. This chapter discusses some of the more common techniques used including filtration, centrifugation, and immunomagnetic separation as preconcentration techniques, the use of propidium monoazide and ethidium monoazide for preparing samples for analysis with molecular tools (e.g., polymerase chain reaction), and sample preservation/treatment for long-term storage. These methods are applied to the analysis of pathogenic bacteria, viruses, protozoans, and toxic algae (including their toxins).
- Published
- 2012
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