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Rainer Kurmayer
Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria

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Journal article
Published: 24 July 2021 in Microorganisms
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The cyanoHAB forming cyanobacteria Microcystis and Planktothrix frequently produce high intracellular amounts of microcystins (MCs) or anabaenopeptins (APs). In this study, chemically modified MCs and APs have been localized on a subcellular level in Microcystis and Planktothrix applying copper-catalyzed alkyne-azide cycloaddition (CuACC). For this purpose, three different non-natural amino acids carrying alkyne or azide moieties were fed to individual P. agardhii strains No371/1 and CYA126/8 as well as to M. aeruginosa strain Hofbauer showing promiscuous incorporation of various amino acid substrates during non-ribosomal peptide synthesis (NRPS). Moreover, CYA126/8 peptide knock-out mutants and non-toxic strain Synechocystis PCC6803 were processed under identical conditions. Simultaneous labeling of modified peptides with ALEXA405 and ALEXA488 and lipid staining with BODIPY 505/515 were performed to investigate the intracellular location of the modified peptides. Pearson correlation coefficients (PCC) obtained from confocal images were calculated between the different fluorophores and the natural autofluorescence (AF), and between labeled modified peptides and dyed lipids to investigate the spatial overlap between peptides and the photosynthetic complex, and between peptides and lipids. Overall, labeling of modified MCs (M. aeruginosa) and APs (P. agardhii) using both fluorophores revealed increased intensity in MC/AP producing strains. For Synechocystis lacking NRPS, no labeling using either ALEXA405 or ALEXA488 was observed. Lipid staining in M. aeruginosa and Synechocystis was intense while in Planktothrix it was more variable. When compared with AF, both modified peptides and lipids showed a heterologous distribution. In comparison, the correlation between stained lipids and labeled peptides was not increased suggesting a reduced spatial overlap.

ACS Style

Rubén Morón-Asensio; David Schuler; Anneliese Wiedlroither; Martin Offterdinger; Rainer Kurmayer. Differential Labeling of Chemically Modified Peptides and Lipids among Cyanobacteria Planktothrix and Microcystis. Microorganisms 2021, 9, 1578 .

AMA Style

Rubén Morón-Asensio, David Schuler, Anneliese Wiedlroither, Martin Offterdinger, Rainer Kurmayer. Differential Labeling of Chemically Modified Peptides and Lipids among Cyanobacteria Planktothrix and Microcystis. Microorganisms. 2021; 9 (8):1578.

Chicago/Turabian Style

Rubén Morón-Asensio; David Schuler; Anneliese Wiedlroither; Martin Offterdinger; Rainer Kurmayer. 2021. "Differential Labeling of Chemically Modified Peptides and Lipids among Cyanobacteria Planktothrix and Microcystis." Microorganisms 9, no. 8: 1578.

Journal article
Published: 27 May 2021 in Sustainability
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Mountain lakes are highly sensitive to global change, requiring sustainable management strategies that support crucial ecosystem services (ES). However, small mountain lakes are rarely in the focus of ES assessments, and indicators are potentially lacking. Therefore, this study aimed at comprehensively assessing key ES of 15 study lakes located in two regions in the European Alps. We involved local stakeholders and experts to identify important ES. We quantified eight ES in non-monetary terms, using 29 indicators based on limnological, spatial and socio-economic data. Finally, we evaluated ES in relation to the socio-ecological context of the study lakes. The most important ES included surface water for non-drinking purposes, maintaining populations and habitats, outdoor recreation, aesthetic value, entertainment and representation, scientific research, education as well as existence, option, or bequest value. Quantitative results indicate varying levels of ES across the study lakes. Based on 12 different socio-ecological variables, we identified four groups of lakes differing also in five ES. Maintaining populations and habitats, aesthetic value as well as existence, option or bequest value were rather independent from the socio-ecological context. Our findings contribute to a deeper understanding of ES of mountain lakes, also supporting the development of sustainable management strategies in mountain regions.

ACS Style

Uta Schirpke; Manuel Ebner; Hanna Pritsch; Veronika Fontana; Rainer Kurmayer. Quantifying Ecosystem Services of High Mountain Lakes across Different Socio-Ecological Contexts. Sustainability 2021, 13, 6051 .

AMA Style

Uta Schirpke, Manuel Ebner, Hanna Pritsch, Veronika Fontana, Rainer Kurmayer. Quantifying Ecosystem Services of High Mountain Lakes across Different Socio-Ecological Contexts. Sustainability. 2021; 13 (11):6051.

Chicago/Turabian Style

Uta Schirpke; Manuel Ebner; Hanna Pritsch; Veronika Fontana; Rainer Kurmayer. 2021. "Quantifying Ecosystem Services of High Mountain Lakes across Different Socio-Ecological Contexts." Sustainability 13, no. 11: 6051.

Conference paper
Published: 04 March 2021 in ARPHA Conference Abstracts
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Environmental DNA (eDNA) based methods (Fig. 1) are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Freshwater fish are actively involved in aquatic ecosystems functioning and diversity, contributing to the health, well-being and economy in every geographic realm. Unfortunately, many freshwater fish are experiencing critical population decline with risk of local or global extinction because of intense anthropogenic pressure. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. To evaluate the performance of the metabarcoding approach specifically designed to measure freshwater fish biodiversity in Alpine lakes and rivers, an intercalibration test was performed. This exercise forecasted the use of mock samples containing either tissue-extracted DNA of different target species or water collected from aquaculture tanks to mimic real environmental water sampling and processing. Moreover, three water samples collected in Lake Bourget (France) were used to compare the efficiency of taxonomic assignments in natural and mock community samples. Our results highlighted a good efficiency of the molecular laboratory protocols for HTS and a good amplification success of the selected primers, providing essential information concerning the taxonomic resolution of the 12S mitochondrial marker. As further confirmation, different concentration of species DNA in the mock samples were well represented by the relative read abundance. This preliminary test confirmed the applicability of eDNA metabarcoding analyses for the biomonitoring of freshwater fish inhabiting Alpine and perialpine lakes and rivers.

ACS Style

Giulia Riccioni; Isabelle Domaizon; Andrea Gandolfi; Massimo Pindo; Marine Vautier; Rainer Kurmayer; Peter Hufnagl; Stefanie Dobrovolny; Valentin Vasselon; Hans Rund; Jonas Bylemans; Cuong Tang; Josef Wanzenböck. Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up. ARPHA Conference Abstracts 2021, 4, e64927 .

AMA Style

Giulia Riccioni, Isabelle Domaizon, Andrea Gandolfi, Massimo Pindo, Marine Vautier, Rainer Kurmayer, Peter Hufnagl, Stefanie Dobrovolny, Valentin Vasselon, Hans Rund, Jonas Bylemans, Cuong Tang, Josef Wanzenböck. Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up. ARPHA Conference Abstracts. 2021; 4 ():e64927.

Chicago/Turabian Style

Giulia Riccioni; Isabelle Domaizon; Andrea Gandolfi; Massimo Pindo; Marine Vautier; Rainer Kurmayer; Peter Hufnagl; Stefanie Dobrovolny; Valentin Vasselon; Hans Rund; Jonas Bylemans; Cuong Tang; Josef Wanzenböck. 2021. "Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up." ARPHA Conference Abstracts 4, no. : e64927.

Journal article
Published: 29 October 2020 in Scientific Reports
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Determining exact viral titers in a given sample is essential for many environmental and clinical applications, e.g., for studying viral ecology or application of bacteriophages for food safety. However, virus quantification is not a simple task, especially for complex environmental samples. While clonal viral isolates can be quantified with relative high accuracy using virus-specific methods, i.e., plaque assay or quantitative real-time PCR, these methods are not valid for complex and diverse environmental samples. Moreover, it is not yet known how precisely laser-based methods, i.e., epifluorescence microscopy, flow cytometry, and nanoparticle tracking analysis, quantify environmental viruses. In the present study, we compared five state-of-the-art viral quantification methods by enumerating four model viral isolates of different genome and size characteristics as well as four different environmental water samples. Although Nanoparticle tracking analysis combined with gentle staining at 30 °C could be confirmed by this study to be a reliable quantification technique for tested environmental samples, environmental samples still lack an universally applicable and accurate quantification method. Special attention has to be put on optimal sample concentrations as well as optimized sample preparations, which are specific for each method. As our results show the inefficiency when enumerating small, or single-stranded DNA or RNA viruses, the global population of viruses is presumably higher than expected.

ACS Style

Judith Kaletta; Carolin Pickl; Christian Griebler; Andreas Klingl; Rainer Kurmayer; Li Deng. A rigorous assessment and comparison of enumeration methods for environmental viruses. Scientific Reports 2020, 10, 1 -12.

AMA Style

Judith Kaletta, Carolin Pickl, Christian Griebler, Andreas Klingl, Rainer Kurmayer, Li Deng. A rigorous assessment and comparison of enumeration methods for environmental viruses. Scientific Reports. 2020; 10 (1):1-12.

Chicago/Turabian Style

Judith Kaletta; Carolin Pickl; Christian Griebler; Andreas Klingl; Rainer Kurmayer; Li Deng. 2020. "A rigorous assessment and comparison of enumeration methods for environmental viruses." Scientific Reports 10, no. 1: 1-12.

Journal article
Published: 17 February 2020 in Scientific Reports
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Harmful algal blooms formed by colony-forming cyanobacteria deteriorate water resources by producing cyanotoxins, which frequently occur at high intracellular concentrations. We aimed to localize toxic microcystins (MCs) and bioactive anabaenopeptins (APs) at the subcellular level under noninvasive conditions. Since both metabolites are synthesized nonribosomally, the relaxed specificity of key enzymes catalyzing substrate activation allowed chemical labeling through a standard copper-catalyzed click chemistry reaction. The genera Planktothrix and Microcystis specifically incorporated unnatural amino acids such as N-propargyloxy-carbonyl-L-lysine or O-propargyl-L-tyrosine, resulting in modified AP or MC peptides carrying the incorporated alkyne moiety. The labeled cells were quantitatively differentiated from the unlabeled control cells. MCs and APs occurred intracellularly as distinct entities showing a cell-wide distribution but a lowered spatial overlap with natural autofluorescence. Using the immunofluorescence technique, colocalization with markers of individual organelles was utilized to relate the distribution of labeled MCs to cellular compartments, e.g., using RbcL and FtsZ (cytosol) and PsbA (thylakoids). The colocalization correlation coefficients calculated pairwise between organelles and autofluorescence were highly positive as opposed to the relatively low positive indices derived from labeled MCs. The lower correlation coefficients imply that only a portion of the labeled MC molecules were related spatially to the organelles in the cell.

ACS Style

Rainer Kurmayer; Elisabeth Entfellner; Thomas Weisse; Martin Offterdinger; Andrea Rentmeister; Li Deng. Chemically labeled toxins or bioactive peptides show a heterogeneous intracellular distribution and low spatial overlap with autofluorescence in bloom-forming cyanobacteria. Scientific Reports 2020, 10, 1 -15.

AMA Style

Rainer Kurmayer, Elisabeth Entfellner, Thomas Weisse, Martin Offterdinger, Andrea Rentmeister, Li Deng. Chemically labeled toxins or bioactive peptides show a heterogeneous intracellular distribution and low spatial overlap with autofluorescence in bloom-forming cyanobacteria. Scientific Reports. 2020; 10 (1):1-15.

Chicago/Turabian Style

Rainer Kurmayer; Elisabeth Entfellner; Thomas Weisse; Martin Offterdinger; Andrea Rentmeister; Li Deng. 2020. "Chemically labeled toxins or bioactive peptides show a heterogeneous intracellular distribution and low spatial overlap with autofluorescence in bloom-forming cyanobacteria." Scientific Reports 10, no. 1: 1-15.

Primary research paper
Published: 15 November 2019 in Hydrobiologia
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The disturbing effect of a short-term cooling period during summer on planktonic bacterial community structure of an alpine lake was investigated using 16S rDNA pyrosequencing. Proteobacteria, Actinobacteria, and Bacteroidetes constituted the most abundant phyla. During the sampling period (from July to August 2010), a sudden cooling period with high precipitation occurred, as indicated by a decrease in conductivity, calcium, and dissolved organic carbon concentration resulting from increased runoff. The relative abundance of Actinobacteria, Betaproteobacteria, and Cyanobacteria decreased during this short-term cooling period. Instead, a rapid shift from Betaproteobacteria to Gammaproteobacteria occurred, which was mainly caused by an increase of Acinetobacter rhizosphaerae. Soon after the short-term cooling period, warmer weather conditions got re-established and Betaproteobacteria recovered and became again dominant. Non-metric multi-dimensional scaling analysis and Venn diagrams revealed a planktonic bacterial community composition with high similarity at the beginning and the end of the growing season. Air temperature and precipitation were significantly correlated with the observed variation in operational taxonomic unit (OTU) relative abundance. It is concluded that, in response to the short-term cooling period, a distinct planktonic bacterial OTU community developed. It rapidly diminished, however, as summer conditions became re-established, implying the recovery of the original bacterial community structure.

ACS Style

Tianli Ma; Yiming Jiang; Ali H. A. Elbehery; Stephan Blank; Rainer Kurmayer; Li Deng. Resilience of planktonic bacterial community structure in response to short-term weather deterioration during the growing season in an alpine lake. Hydrobiologia 2019, 847, 535 -548.

AMA Style

Tianli Ma, Yiming Jiang, Ali H. A. Elbehery, Stephan Blank, Rainer Kurmayer, Li Deng. Resilience of planktonic bacterial community structure in response to short-term weather deterioration during the growing season in an alpine lake. Hydrobiologia. 2019; 847 (2):535-548.

Chicago/Turabian Style

Tianli Ma; Yiming Jiang; Ali H. A. Elbehery; Stephan Blank; Rainer Kurmayer; Li Deng. 2019. "Resilience of planktonic bacterial community structure in response to short-term weather deterioration during the growing season in an alpine lake." Hydrobiologia 847, no. 2: 535-548.

Original research article
Published: 31 July 2019 in Frontiers in Microbiology
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Alpine lakes are considered pristine freshwater ecosystems and sensitive to direct and indirect changes in water temperature as induced by climate change. The bacterial plankton constitutes a key component in the water column and bacterial metabolic activity has direct consequences for water quality. In order to understand bacterial response to global temperature rise in five alpine lakes located in the Austrian Alps (1700–2188 m a.S.L.) water temperature was compared within a decadal period. Depth-integrated samples were characterized in community composition by 16S rDNA deep-amplicon sequencing early [56 ± 16 (SD) days after ice break up] and later (88 ± 16 days) in the growing season. Within the 10 years period, temperature rise was observed through reduced ice cover duration and increased average water temperature. During the early growing season, the average water temperature recorded between circulation in spring until sampling date (WAS), and the day of autumn circulation, as well as chemical composition including dissolved organic carbon influenced bacterial community composition. In contrast, only nutrients (such as nitrate) were found influential later in the growing season. Metabolic theory of ecology (MTE) was applied to explain the dependence of taxonomic richness on WAS in mathematical terms. The calculated activation energy exceeded the frequently reported prediction emphasizing the role of WAS during early growing season. Accordingly, the relative abundance of predicted metabolism related genes increased with WAS. Thus, the dominant influence of temperature after ice break up could be explained by overall climate change effects, such as a more intense warming in spring and an overall higher amplitude of temperature variation.

ACS Style

Yiming Jiang; Haiying Huang; Tianli Ma; Jinlong Ru; Stephan Blank; Rainer Kurmayer; Li Deng. Temperature Response of Planktonic Microbiota in Remote Alpine Lakes. Frontiers in Microbiology 2019, 10, 1714 .

AMA Style

Yiming Jiang, Haiying Huang, Tianli Ma, Jinlong Ru, Stephan Blank, Rainer Kurmayer, Li Deng. Temperature Response of Planktonic Microbiota in Remote Alpine Lakes. Frontiers in Microbiology. 2019; 10 ():1714.

Chicago/Turabian Style

Yiming Jiang; Haiying Huang; Tianli Ma; Jinlong Ru; Stephan Blank; Rainer Kurmayer; Li Deng. 2019. "Temperature Response of Planktonic Microbiota in Remote Alpine Lakes." Frontiers in Microbiology 10, no. : 1714.

Dataset
Published: 23 October 2018 in protocols.io
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ACS Style

Isabelle Domaizon; Rainer Kurmayer; Camolla Capelli; Cécile Chardon; Peter Hufnagl; Marine Vautier; Nico Salmaso. Lake plankton sample collection from the field for downstream molecular analysis (sterivex filtration + lysis buffer preservation) v1. protocols.io 2018, 1 .

AMA Style

Isabelle Domaizon, Rainer Kurmayer, Camolla Capelli, Cécile Chardon, Peter Hufnagl, Marine Vautier, Nico Salmaso. Lake plankton sample collection from the field for downstream molecular analysis (sterivex filtration + lysis buffer preservation) v1. protocols.io. 2018; ():1.

Chicago/Turabian Style

Isabelle Domaizon; Rainer Kurmayer; Camolla Capelli; Cécile Chardon; Peter Hufnagl; Marine Vautier; Nico Salmaso. 2018. "Lake plankton sample collection from the field for downstream molecular analysis (sterivex filtration + lysis buffer preservation) v1." protocols.io , no. : 1.

Journal article
Published: 03 July 2018 in Toxins
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The human health risks posed by exposure to cyanobacterial toxins such as microcystin (MC) through water and fish consumption remain poorly described. During the last two decades, coastal regions of Lake Victoria such as Nyanza Gulf (Kisumu Bay) have shown severe signs of eutrophication with blooms formed by Microcystis producing MC. In this study, the spatial variability in MC concentration in Kisumu Bay was investigated which was mostly caused by Microcystis buoyancy and wind drifting. Small fish (Rastrineobola argentea were examined for MC content by means of biological methods such as ELISA and protein phosphatase inhibition assay (PPIA) and partly by chemical-analytical methods such as LC-MS/MS. Overall, the MC content in small fish was related to the MC content observed in the seston. When comparing the MC content in the seston in relation to dry weight with the MC content in small fish the latter was found three orders of magnitude decreased. On average, the ELISA-determined MC contents exceeded the PPIA-determined MC contents by a factor of 8.2 ± 0.5 (SE) while the MC contents as determined by LC-MS/MS were close to the detection limit. Using PPIA, the MC content varied from 25–109 (mean 62 ± 7) ng/g fish dry weight in Kisumu Bay vs. 14 ± 0.8 ng MC/g in the more open water of L. Victoria at Rusinga channel. Drying the fish under the sun showed little effect on MC content, although increased humidity might indirectly favor photocatalyzed MC degradation.

ACS Style

Benard Mucholwa Simiyu; Steve Omondi Oduor; Thomas Rohrlack; Lewis Sitoki; Rainer Kurmayer. Microcystin Content in Phytoplankton and in Small Fish from Eutrophic Nyanza Gulf, Lake Victoria, Kenya. Toxins 2018, 10, 275 .

AMA Style

Benard Mucholwa Simiyu, Steve Omondi Oduor, Thomas Rohrlack, Lewis Sitoki, Rainer Kurmayer. Microcystin Content in Phytoplankton and in Small Fish from Eutrophic Nyanza Gulf, Lake Victoria, Kenya. Toxins. 2018; 10 (7):275.

Chicago/Turabian Style

Benard Mucholwa Simiyu; Steve Omondi Oduor; Thomas Rohrlack; Lewis Sitoki; Rainer Kurmayer. 2018. "Microcystin Content in Phytoplankton and in Small Fish from Eutrophic Nyanza Gulf, Lake Victoria, Kenya." Toxins 10, no. 7: 275.

20th iac symposium
Published: 21 August 2017 in Hydrobiologia
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In order to understand Chamaesiphon spp. evolution and ecological diversification, we investigated the phylogenetic differentiation of three morphospecies from field samples by means of single colony genetics. Individual colonies of three different morphospecies (C. starmachii, C. polonicus, C. geitleri,) were isolated from lotic gravel streams and their 16S rDNA nucleotide variability was analyzed. For a number of individual colonies, microscopical and ultrastructural analysis was also performed. A phylogenetic tree of all major lineages of the phylum of Cyanobacteria assigned all Chamaesiphon genotypes (1149–1176 bp) most closely with the family of Gomontiellaceae of the order Oscillatoriales. The sequences obtained from colonies assigned to C. starmachii (n = 21), C. polonicus (n = 9), and C. geitleri (n = 17) were found to reveal high average (3.5%) nucleotide diversity. No phylogenetic sub-branching in correspondence with morphology was observed suggesting that the three Chamaesiphon morphospecies did not represent monophyletic taxa. We could not attribute specific thylakoid ultrastructure to phylogenetic sub-branches; however, the observed parietally and loosely arranged thylakoids indicate that for the genus Chamaesiphon, the variability in thylakoid ultrastructure might have been underestimated. In summary, the high nucleotide diversity of the 16S rDNA gene implies phylogenetic diversity that corresponds little to morphological classification.

ACS Style

Rainer Kurmayer; Guntram Christiansen; Andreas Holzinger; Eugen Rott. Single colony genetic analysis of epilithic stream algae of the genus Chamaesiphon spp. Hydrobiologia 2017, 811, 61 -75.

AMA Style

Rainer Kurmayer, Guntram Christiansen, Andreas Holzinger, Eugen Rott. Single colony genetic analysis of epilithic stream algae of the genus Chamaesiphon spp. Hydrobiologia. 2017; 811 (1):61-75.

Chicago/Turabian Style

Rainer Kurmayer; Guntram Christiansen; Andreas Holzinger; Eugen Rott. 2017. "Single colony genetic analysis of epilithic stream algae of the genus Chamaesiphon spp." Hydrobiologia 811, no. 1: 61-75.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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With fast development and wide applications of next generation sequencing (NGS) technologies, pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the microbial community profiles. In this chapter we describe an approach for sequencing 16S rRNA gene amplicons for monitoring of (toxigenic) cyanobacteria and other prokaryotes in environmental samples. Our SOP is particular adapted for relative long amplicon size (~800bp) in order to achieve more accurate taxonomy assignment.

ACS Style

Li Deng; Stephan Blank; Rainer Kurmayer; Maxime Sweetlove; Dagmar Obbels; Elie Verleyen; Igor S. Pessi; Annick Wilmotte; Wim Vyverman. Monitoring of Toxigenic Cyanobacteria Using Next-Generation Sequencing Techniques. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 277 -299.

AMA Style

Li Deng, Stephan Blank, Rainer Kurmayer, Maxime Sweetlove, Dagmar Obbels, Elie Verleyen, Igor S. Pessi, Annick Wilmotte, Wim Vyverman. Monitoring of Toxigenic Cyanobacteria Using Next-Generation Sequencing Techniques. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():277-299.

Chicago/Turabian Style

Li Deng; Stephan Blank; Rainer Kurmayer; Maxime Sweetlove; Dagmar Obbels; Elie Verleyen; Igor S. Pessi; Annick Wilmotte; Wim Vyverman. 2017. "Monitoring of Toxigenic Cyanobacteria Using Next-Generation Sequencing Techniques." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 277-299.

Chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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ACS Style

Elke Dittmann; Anne Helena Ylinen; Vitor Ramos; Vitor Vasconcelos; Guntram Christiansen; Rainer Kurmayer. Nucleic Acid Extraction. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 135 -161.

AMA Style

Elke Dittmann, Anne Helena Ylinen, Vitor Ramos, Vitor Vasconcelos, Guntram Christiansen, Rainer Kurmayer. Nucleic Acid Extraction. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():135-161.

Chicago/Turabian Style

Elke Dittmann; Anne Helena Ylinen; Vitor Ramos; Vitor Vasconcelos; Guntram Christiansen; Rainer Kurmayer. 2017. "Nucleic Acid Extraction." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 135-161.

Chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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In this chapter details on PCR detection protocols and characterizing of PCR amplified gene fragments indicative of cyanotoxin synthesis are described. The SOP 6.1 describes a mcy gene genus‐general PCR linked to a subsequent RFLP discrimination step. The SOP 6.2 describes several mcyE/ndaF gene general primers indicative of microcystin/nodularin synthesis that are supposed to amplify all mcy/nda‐ gene containing cyanobacteria. In contrast SOP 6.3 describes a mcyE genus diagnostic PCR detecting specific genera only. SOP 6.4 describes PCR detection of anaC gene fragment and subsequent RFLP analysis. SOP 6.5 describes a PCR strategy to amplify a number of characteristic gene fragments indicative of saxitoxin synthesis. SOP 6.6 describes PCR amplification of the cyrJ gene indicative of cylindrospermopsin synthesis. A PCR protocol to amplify DNA fragments from rather low amounts (picogram) of template DNA originating from single filaments/colonies of toxigenic cyanobacteria is included (SOP 6.7). SOP 6.8 describes PCR linked to RFLP analysis amplifying larger but variable regions of microcystin biosynthesis genes to resolve the population genetic structure. Finally SOP 6.9 describes multiplex PCR detection including mcy gene fragments from food supplements.

ACS Style

Elke Dittmann; Anne Helena Ylinen; Kaarina Sivonen; Ilona Gągała; Joanna Mankiewicz-Boczek; Samuel Cirés; Andreas Ballot; Guntram Christiansen; Rainer Kurmayer; Vitor Ramos; Vitor Vasconcelos; Martin Saker. Conventional PCR. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 163 -203.

AMA Style

Elke Dittmann, Anne Helena Ylinen, Kaarina Sivonen, Ilona Gągała, Joanna Mankiewicz-Boczek, Samuel Cirés, Andreas Ballot, Guntram Christiansen, Rainer Kurmayer, Vitor Ramos, Vitor Vasconcelos, Martin Saker. Conventional PCR. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():163-203.

Chicago/Turabian Style

Elke Dittmann; Anne Helena Ylinen; Kaarina Sivonen; Ilona Gągała; Joanna Mankiewicz-Boczek; Samuel Cirés; Andreas Ballot; Guntram Christiansen; Rainer Kurmayer; Vitor Ramos; Vitor Vasconcelos; Martin Saker. 2017. "Conventional PCR." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 163-203.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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The prelims comprise: Half-Title PageTitle PageCopyright PageHans C.P. Matthijs (1951–2016): A passion for light and lifeTable of ContentsList of ContributorsAbout the EditorsAbout the BookPrefaceAcknowledgments

ACS Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. Front Matter. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 1 .

AMA Style

Rainer Kurmayer, Kaarina Sivonen, Annick Wilmotte, Nico Salmaso. Front Matter. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():1.

Chicago/Turabian Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. 2017. "Front Matter." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 1.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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After a brief historical overview on cyanotoxin research in general during the last decades the current knowledge on the genetic basis of cyanotoxin synthesis is summarized. In particular the biosynthetic pathways (the gene clusters and synthesis) of microcystin, cylindrospermopsin, saxitoxin and anatoxin-a as well as their evolutionary history are reviewed. It is important to note that genetic methods are only able to indicate the potential of toxin synthesis and do not provide information about actual toxin production and concentrations. Nevertheless there are potential applications in monitoring such as early warning and/or high throughput analysis. In the course of introducing into the application of the molecular tools an overview of the entire book structure is given and possible workflows as comprised among the individual chapters are highlighted.

ACS Style

Rainer Kurmayer; Kaarina Sivonen; Nico Salmaso. Introduction. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 1 -18.

AMA Style

Rainer Kurmayer, Kaarina Sivonen, Nico Salmaso. Introduction. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():1-18.

Chicago/Turabian Style

Rainer Kurmayer; Kaarina Sivonen; Nico Salmaso. 2017. "Introduction." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 1-18.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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In this chapter details on qPCR-based quantification of gene fragments indicative of cyanotoxin synthesis are described. In SOP 7.1 the protocols of qPCR assays of mcyE/mcyB/ndaF genes are provided. In the chapter's introductory text the principles of qPCR relative quantification, optimization and calibration of qPCR assays are reviewed, which are then described in detail in individual SOPs (7.2-7.4). In SOP 7.5 a protocol to quantify the transcript (cDNA) amounts of all the mcy genes part of the mcy gene cluster in Planktothrix is provided. SOP 7.6 and SOP 7.7 describe protocols to quantify sxtB or cyrJ genes in samples obtained from the environment. Finally SOP 7.8 provides a set of minimum information needed for qPCR data analysis used for toxigenic cyanobacteria.

ACS Style

Anne Helena Ylinen; Henna Savela; Kaarina Sivonen; Rainer Kurmayer. Quantitative PCR. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 205 -239.

AMA Style

Anne Helena Ylinen, Henna Savela, Kaarina Sivonen, Rainer Kurmayer. Quantitative PCR. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():205-239.

Chicago/Turabian Style

Anne Helena Ylinen; Henna Savela; Kaarina Sivonen; Rainer Kurmayer. 2017. "Quantitative PCR." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 205-239.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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ACS Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. Index. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 393 -402.

AMA Style

Rainer Kurmayer, Kaarina Sivonen, Annick Wilmotte, Nico Salmaso. Index. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():393-402.

Chicago/Turabian Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. 2017. "Index." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 393-402.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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ACS Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. Glossary. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 379 -391.

AMA Style

Rainer Kurmayer, Kaarina Sivonen, Annick Wilmotte, Nico Salmaso. Glossary. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():379-391.

Chicago/Turabian Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. 2017. "Glossary." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 379-391.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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ACS Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. Supplementary Tables. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 335 -378.

AMA Style

Rainer Kurmayer, Kaarina Sivonen, Annick Wilmotte, Nico Salmaso. Supplementary Tables. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():335-378.

Chicago/Turabian Style

Rainer Kurmayer; Kaarina Sivonen; Annick Wilmotte; Nico Salmaso. 2017. "Supplementary Tables." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 335-378.

Book chapter
Published: 30 June 2017 in Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
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In this chapter details of sampling and sample storage for DNA and RNA analysis are described. Since the sampling strategy and storage protocol are of decisive importance for subsequent analysis, downstream analysis using molecular tools should be defined before the sampling step. This chapter includes protocols to sample planktonic (SOP 2.1) and benthic (SOP 2.2) cyanobacteria as well as a protocol (SOP 2.3) for the isolation of individual filaments/colonies of cyanobacteria under the microscope. The representative sampling of food supplements (SOP 2.4) is described as well. To collect cells for RNA analysis a fast-harvest protocol using low vacuum filtration is described (SOP 2.5). Finally, the SOP 2.6 describes the collecting and recording of sample metadata.

ACS Style

Rainer Kurmayer; Guntram Christiansen; Konstantinos Kormas; Wim Vyverman; Elie Verleyen; Vitor Ramos; Vitor Vasconcelos; Nico Salmaso. Sampling and Metadata. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria 2017, 19 -42.

AMA Style

Rainer Kurmayer, Guntram Christiansen, Konstantinos Kormas, Wim Vyverman, Elie Verleyen, Vitor Ramos, Vitor Vasconcelos, Nico Salmaso. Sampling and Metadata. Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. 2017; ():19-42.

Chicago/Turabian Style

Rainer Kurmayer; Guntram Christiansen; Konstantinos Kormas; Wim Vyverman; Elie Verleyen; Vitor Ramos; Vitor Vasconcelos; Nico Salmaso. 2017. "Sampling and Metadata." Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria , no. : 19-42.