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Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers.

التفاصيل البيبلوغرافية
العنوان: Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers.
المؤلفون: Gross M; Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany., Dunthorn M; Natural History Museum, University of Oslo, Oslo, Norway., Mauvisseau Q; Natural History Museum, University of Oslo, Oslo, Norway., Stoeck T; Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany.
المصدر: Environmental microbiology [Environ Microbiol] 2024 Apr; Vol. 26 (4), pp. e16619.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Blackwell Science Country of Publication: England NLM ID: 100883692 Publication Model: Print Cited Medium: Internet ISSN: 1462-2920 (Electronic) Linking ISSN: 14622912 NLM ISO Abbreviation: Environ Microbiol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Oxford : Blackwell Science, 1999-
مواضيع طبية MeSH: Gene Dosage*, Polymerase Chain Reaction/methods ; Paramecium tetraurelia/genetics ; Ciliophora/genetics ; Ciliophora/classification ; Genes, rRNA ; RNA, Ribosomal/genetics ; DNA, Protozoan/genetics
مستخلص: Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour-intensive, time-consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per-cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per-cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.
(© 2024 The Authors. Environmental Microbiology published by John Wiley & Sons Ltd.)
References: Ahsan, R., Blanche, W. & Katz, L.A. (2022) Macronuclear development in ciliates, with a focus on nuclear architecture. The Journal of Eukaryotic Microbiology, 69, e12898.
Amman, F., Markt, R., Endler, L., Hupfauf, S., Agerer, B., Schedl, A. et al. (2022) Viral variant‐resolved wastewater surveillance of SARS‐CoV‐2 at national scale. Nature Biotechnology, 40, 1814–1822.
Gifford, D.J. & Caron, D.A. (2000) Sampling, preservation, enumeration and biomass of marine protozooplankton. In: Harris, R., Wiebe, P., Lenz, J., Skjoldal, H.‐R. & Huntley, M. (Eds.) ICES zooplankton methodology manual. London: Elsevier, pp. 193–221.
Aury, J.M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B.M. et al. (2006) Global trends of whole‐genome duplications revealed by the ciliate Paramecium tetraurelia. Nature, 444, 171–178.
Berger, J.D. (1988) The cell cycle and regulation of cell mass and macronuclear DNA content. In: Paramecium. Berlin; Heidelberg: Springer‐Verlag, pp. 97–119.
Boscaro, V., Rossi, A., Vannini, C., Verni, F., Fokin, S.I. & Petroni, G. (2017) Strengths and biases of high‐throughput sequencing data in the characterization of freshwater ciliate microbiomes. Microbial Ecology, 73, 865–875.
Cao, Y., Yu, M., Dong, G., Chen, B. & Zhang, B. (2020) Digital PCR as an emerging tool for monitoring of microbial biodegradation. Molecules, 25, 706.
Caron, D.A., Countway, P.D., Jones, A.C., Kim, D.Y. & Schnetzer, A. (2011) Marine protistan diversity. Annual Review of Marine Science, 4, 467–493.
Castellanos‐Rizaldos, E., Paweletz, C., Song, C., Oxnard, G.R., Mamon, H., Jänne, P.A. et al. (2015) Enhanced ratio of signals enables digital mutation scanning for rare allele detection. The Journal of Molecular Diagnostics, 17, 284–292.
Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D. & Zhang, J. (2015) Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: applications, microbes and future research needs. Biotechnology Advances, 33, 745–755.
Costas, B.A., McManus, G., Doherty, M. & Katz, L.A. (2007) Use of species‐specific primers and PCR to measure the distributions of planktonic ciliates in coastal waters. Limnology and Oceanography: Methods, 5, 163–173.
De Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R. et al. (2015) Eukaryotic plankton diversity in the sunlit ocean. Science, 348, 2023.
Dirren‐Pitsch, G., Bühler, D., Salcher, M.M., Bassin, B., Le Moigne, A., Schuler, M. et al. (2022) FISHing for ciliates: catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates. Frontiers in Microbiology, 13, 4807.
Doi, H., Takahara, T., Minamoto, T., Matsuhashi, S., Uchii, K. & Yamanaka, H. (2015) Droplet digital polymerase chain reaction (PCR) outperforms real‐time PCR in the detection of environmental DNA from an invasive fish species. Environmental Science & Technology, 49, 5601–5608.
Drews, F., Boenigk, J. & Simon, M. (2022) Paramecium epigenetics in development and proliferation. The Journal of Eukaryotic Microbiology, 69, e12914.
Drews, F., Salhab, A., Karunanithi, S., Cheaib, M., Jung, M., Schulz, M.H. et al. (2022) Broad domains of histone marks in the highly compact Paramecium macronuclear genome. Genome Research, 32, 710–725.
Dunthorn, M., Klier, J., Bunge, J. & Stoeck, T. (2012) Comparing the hyper‐variable V4 and V9 regions of the small subunit rRNA gene for assessment of ciliate environmental diversity. The Journal of Eukaryotic Microbiology, 59, 185–187.
Dunthorn, M., Stoeck, T., Clamp, J., Warren, A. & Mahé, F. (2014) Ciliates and the rare biosphere: a review. The Journal of Eukaryotic Microbiology, 61, 404–409.
Engberg, J. & Pearlman, R.E. (1972) The amount of ribosomal RNA genes in Tetrahymena pyriformis in different physiological states. European Journal of Biochemistry, 26, 393–400.
Filker, S., Gimmler, A., Dunthorn, M., Mahé, F. & Stoeck, T. (2015) Deep sequencing uncovers protistan plankton diversity in the Portuguese ria Formosa solar saltern ponds. Extremophiles, 19, 283–295.
Findly, R.C. & Gall, J.G. (1978) Free ribosomal RNA genes in paramecium are tandemly repeated. Proceedings of the National Academy of Sciences, 75, 3312–3316.
Foissner, W. (2008) Protist diversity and distribution: some basic considerations. Biodiversity and Conservation, 17, 235–242.
Foissner, W., Chao, A. & Katz, L.A. (2008) Diversity and geo‐graphic distribution of ciliates (Protista: Ciliophora). Biodiversity and Conservation, 17, 345–363.
Forster, D., Dunthorn, M., Mahé, F., Dolan, J.R., Audic, S., Bass, D. et al. (2016) Benthic protists: the under‐charted majority. FEMS Microbiology Ecology, 92, 1–11.
Forster, D., Filker, S., Kochems, R., Breiner, H.‐W., Cordier, T., Pawlowski, J. et al. (2019) A comparison of different ciliate metabarcode genes as bioindicators for environmental impact assessments of salmon aquaculture. The Journal of Eukaryotic Microbiology, 66, 294–308.
Frantal, D., Agatha, S., Beisser, D., Boenigk, J., Darienko, T., Dirren‐Pitsch, G. et al. (2022) Molecular data reveal a cryptic diversity in the genus Urotricha (Alveolata, Ciliophora, Prostomatida), a key player in freshwater lakes, with remarks on morphology, food preferences, and distribution. Frontiers in Microbiology, 12, 787290.
Fu, R. & Gong, J. (2017) Single cell analysis linking ribosomal (r)DNA and rRNA copy numbers to cell size and growth rate provides insights into molecular protistan ecology. The Journal of Eukaryotic Microbiology, 64, 885–896.
Galluzzi, L., Penna, A., Bertozzini, E., Vila, M., Garcés, E. & Magnani, M. (2004) Development of a real‐time PCR assay for rapid detection and quantification of Alexandrium minutum (a dinoflagellate). Applied and Environmental Microbiology, 70, 1199–1206.
Gimmler, A., Korn, R., De Vargas, C., Audic, S. & Stoeck, T. (2016) The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates. Scientific Reports, 6, 1–13.
Godhe, A., Asplund, M.E., Härnström, K., Saravanan, V., Tyagi, A. & Karunasagar, I. (2008) Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real‐time PCR. Applied and Environmental Microbiology, 74, 7174–7182.
Gong, J., Dong, J., Liu, X. & Massana, R. (2013) Extremely high copy numbers and polymorphisms of the rRNA gene operon estimated from single cell analysis of oligotrich and peritrich ciliates. Protist, 164, 369–379.
Gong, W. & Marchetti, A. (2019) Estimation of 18S gene copy number in marine eukaryotic plankton using a next‐generation sequencing approach. Frontiers in Marine Science, 6, 219.
Griffin, J.L. & Spoon, D.M. (1976) Natural preservation of corpses of Paramecium aurelia in cultures of a suctorian. Transactions of the American Microscopical Society, 95, 637–645.
Hiillos, A.L., Thonig, A. & Knott, K.E. (2021) Droplet digital PCR as a tool for investigating dynamics of cryptic symbionts. Ecology and Evolution, 11, 17381–17396.
Hindson, B.J., Ness, K.D., Masquelier, D.A., Belgrader, P., Heredia, N.J., Makarewicz, A.J. et al. (2011) High‐throughput droplet digital PCR system for absolute quantitation of DNA copy number. Analytical Chemistry, 83, 8604–8610.
Hindson, C.M., Chevillet, J.R., Briggs, H.A., Gallichotte, E.N., Ruf, I.K., Hindson, B.J. et al. (2013) Absolute quantification by droplet digital PCR versus analog real‐time PCR. Nature Methods, 10, 1003–1005.
Hu, G., Huang, K., Zhou, W., Wang, R., Zhao, W., Zou, H. et al. (2023) Comparison of droplet digital PCR and real‐time quantitative PCR for quantitative detection of the parasitic ciliate Ichthyophthirius multifiliis in the water environment. Journal of Fish Diseases, 46, 357–367.
Hunter, M.E., Dorazio, R.M., Butterfield, J.S.S., Meigs‐Friend, G., Nico, L.G. & Ferrante, J.A. (2017) Detection limits of quantitative and digital PCR assays and their influence in presence–absence surveys of environmental DNA. Molecular Ecology Resources, 17, 221–229.
Jones, M., Williams, J., Gärtner, K., Phillips, R., Hurst, J. & Frater, J. (2014) Low copy target detection by droplet digital PCR through application of a novel open access bioinformatic pipeline, ‘definetherain’. Journal of Virological Methods, 202, 46–53.
Jousson, O., Pretti, C., Di Bello, D. & Cognetti‐Varriale, A.M. (2005) Non‐invasive detection and quantification of the parasitic ciliate Ichthyophthirius multifiliis by real‐time PCR. Diseases of Aquatic Organisms, 65, 251–255.
Kassambara, A. (2023a) ggpubr: ‘ggplot2’ based publication ready plots. R package version 0.6.0. Available at: https://CRAN.R-project.org/package=ggpubr.
Kassambara, A. (2023b) rstatix: pipe‐friendly framework for basic statistical tests. R package version 0.7.2. Available at: https://CRAN.R-project.org/package=rstatix.
Kemp, P.F., Cole, J.J., Sherr, B.F. & Sherr, E.B. (1993) Handbook of methods in aquatic microbial ecology. Boca Raton, FL: CRC Press.
Kim, S.J. & Min, G.S. (2009) Optimization of DNA extraction from a single living ciliate for stable and repetitive PCR amplification. Animal Cells and Systems, 13, 351–356.
Kuhn, R., Böllmann, J., Krahl, K., Bryant, I.M. & Martienssen, M. (2017) Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples. Journal of Microbiological Methods, 143, 78–86.
Lara, E., Berney, C., Harms, H. & Chatzinotas, A. (2007) Cultivation‐independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon‐polluted soil. FEMS Microbiology Ecology, 62, 365–373.
Lavrinienko, A., Jernfors, T., Koskimäki, J.J., Pirttilä, A.M. & Watts, P.C. (2021) Does intraspecific variation in rDNA copy number affect analysis of microbial communities? Trends in Microbiology, 29, 19–27.
Lee, H.G., Kim, H.M., Min, J., Park, C., Jeong, H.J., Lee, K. et al. (2020) Quantification of the paralytic shellfish poisoning dinoflagellate Alexandrium species using a digital PCR. Harmful Algae, 92, 101726.
Liu, X. & Gong, J. (2012) Revealing the diversity and quantity of peritrich ciliates in environmental samples using specific primer‐based PCR and quantitative PCR. Microbes and Environments, 27, 497–503.
Logares, R., Mangot, J.F. & Massana, R. (2015) Rarity in aquatic microbes: placing protists on the map. Research in Microbiology, 166, 831–841.
Lynn, D.H. & Montagnes, D.H. (1991) Global production of heterotrophic marine planktonic ciliates. In: Reid, P.C., Turley, C.M. & Burkill, P.H. (Eds.) Protozoa and their role in marine processes. Berlin: Springer, pp. 281–307.
Lynn, D.H. (2008) The ciliated protozoa: characterization, classification, and guide to the literature, 3rd edition. Berlin: Springer.
López‐García, P., Rodríguez‐Valera, F., Pedrós‐Alió, C. & Moreira, D. (2001) Unexpected diversity of small eukaryotes in deep‐sea Antarctic plankton. Nature, 409, 603–607.
Madic, J., Zocevic, A., Senlis, V., Fradet, E., Andre, B., Muller, S. et al. (2016) Three‐color crystal digital PCR. Biomolecular Detection and Quantification, 10, 34–46.
Mangot, J.F., Forn, I., Obiol, A. & Massana, R. (2018) Constant abundances of ubiquitous uncultured protists in the open sea assessed by automated microscopy. Environmental Microbiology, 20, 3876–3889.
Massana, R., Terrado, R., Forn, I., Lovejoy, C. & Pedrós‐Alió, C. (2006) Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. Environmental Microbiology, 8, 1515–1522.
Mauvisseau, Q., Davy‐Bowker, J., Bulling, M., Brys, R., Neyrinck, S., Troth, C. et al. (2019) Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate. Scientific Reports, 9, 1–9.
Montagnes, D.J., Wilson, D., Brooks, S.J., Lowe, C. & Campey, M. (2002) Cyclical behaviour of the tide‐pool ciliate Strombidium oculatum. Aquatic Microbial Ecology, 28, 55–68.
Morin, F., Panova, M.A.Z., Schweizer, M., Wiechmann, M., Eliassen, N., Sundberg, P. et al. (2023) Hidden aliens: application of digital PCR to track an exotic foraminifer across the Skagerrak (North Sea) correlates well with traditional morphospecies analysis. Environmental Microbiology, 25, 2321–2337.
Müller, H., Schöne, A., Pinto‐Coelho, R.M., Schweizer, A. & Weisse, T. (1991) Seasonal succession of ciliates in lake constance. Microbial Ecology, 21, 119–138.
Netzer, R., Ribičić, D., Aas, M., Cavé, L., & Dhawan, T. (2021). Absolute quantification of priority bacteria in aquaculture using digital PCR. Journal of Microbiological Methods, 183, 106171. Available from: https://doi.org/10.1016/j.mimet.2021.106171.
Nolte, V., Pandey, R.V., Jost, S., Medinger, R., Ottenwälder, B., Boenigk, J. et al. (2010) Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Molecular Ecology, 19, 2908–2915.
Oksanen, J., Simpson, G., Blanchet, F., Kindt, R., Legendre, P., Minchin, P. et al. (2022) Vegan: community ecology package. R package version 2.6‐4. Available at: https://CRAN.R-project.org/package=vegan.
Oladi, M., Leontidou, K., Stoeck, T. & Shokri, M.R. (2022) Environmental DNA‐based profiling of benthic bacterial and eukaryote communities along a crude oil spill gradient in a coral reef in the Persian Gulf. Marine Pollution Bulletin, 184, 114143.
Oliverio, A.M., Power, J.F., Washburne, A., Cary, S.C., Stott, M.B. & Fierer, N. (2018) The ecology and diversity of microbial eukaryotes in geothermal springs. ISME J, 12, 1918–1928.
Ottesen, E.A., Hong, J.W., Quake, S.R. & Leadbetter, J.R. (2006) Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science, 314, 1464–1467.
Pitsch, G., Bruni, E.P., Forster, D., Qu, Z., Sonntag, B., Stoeck, T. et al. (2019) Seasonality of planktonic freshwater ciliates: are analyses based on V9 regions of the 18S rRNA gene correlated with morphospecies counts? Frontiers in Microbiology, 10, 248.
Porter, K.G., Pace, M.L. & Battey, J.F. (1979) Ciliate protozoans as links in freshwater planktonic food chains. Nature, 277, 563–565.
Preer, L.B., Rudman, B., Pollack, S. & Preer, J.R.J. (1999) Does ribosomal DNA get out of the micronuclear chromosome in Paramecium tetraurelia by means of a rolling circle? Molecular and Cellular Biology, 19(11), 7792–7800.
Prescott, D.M. (1994) The DNA of ciliated protozoa. Microbiological Reviews, 58, 233–267.
Qu, Z., Forster, D., Bruni, E.P., Frantal, D., Kammerlander, B., Nachbaur, L. et al. (2021) Aquatic food webs in deep temperate lakes: key species establish through their autecological versatility. Molecular Ecology, 30, 1053–1071.
Santoferrara, L., Burki, F., Filker, S., Logares, R., Dunthorn, M. & McManus, G.B. (2020) Perspectives from ten years of protist studies by high‐throughput metabarcoding. The Journal of Eukaryotic Microbiology, 67, 612–622.
Santoferrara, L.F. & McManus, G.B. (2020) Diversity and biogeography as revealed by morphologies and DNA sequences: tintinnid ciliates as an example. In: Teodósio, M.A. & Barbosa, A.B. (Eds.) Zooplankton ecology. Boca Raton: CRC Press, pp. 85–118.
Santoferrara, L.F. (2019) Current practice in plankton metabarcoding: optimization and error management. Journal of Plankton Research, 41, 571–582.
Santoferrara, L.F., Grattepanche, J.D., Katz, L.A. & Mcmanus, G.B. (2016) Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers? ISME J, 10, 1779–1790.
Singer, D., Seppey, C.V.W., Lentendu, G., Dunthorn, M., Bass, D., Belbahri, L. et al. (2021) Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. Environment International, 146, 106262.
Sommer, U., Adrian, R., De Senerpont Domis, L., Elser, J.J., Gaedke, U., Ibelings, B. et al. (2012) Beyond the plankton ecology group (PEG) model: mechanisms driving plankton succession. Annual Review of Ecology, Evolution, and Systematics, 43, 429–448.
Staley, Z.R., Boyd, R.J., Shum, P. & Edge, T.A. (2018) Microbial source tracking using quantitative and digital PCR to identify sources of fecal contamination in stormwater, river water, and beach water in a Great Lakes area of concern. Applied and Environmental Microbiology, 84, e01634.
Stoeck, T., Bass, D., Nebel, M., Christen, R., Jones, M.D., Breiner, H.W. et al. (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology, 19, 21–31.
Stoeck, T., Breiner, H.W., Filker, S., Ostermaier, V., Kammerlander, B. & Sonntag, B. (2014) A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage‐specific barcode markers in microbial ecology. Environmental Microbiology, 16, 430–444.
Stoeck, T., Przybos, E. & Dunthorn, M. (2014) The D1‐D2 region of the large subunit ribosomal DNA as barcode for ciliates. Molecular Ecology Resources, 14, 458–468.
Tamura, K., Stecher, G. & Kumar, S. (2021) MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38, 3022–3027.
Taniguchi, A., Onishi, H. & Eguchi, M. (2011) Quantitative PCR assay for the detection of the parasitic ciliate Cryptocaryon irritans. Fisheries Science, 77, 607–613.
Tiwari, A., Ahmed, W., Oikarinen, S., Sherchan, S.P., Heikinheimo, A., Jiang, G. et al. (2022) Application of digital PCR for public health‐related water quality monitoring. Science of the Total Environment, 837, 155663.
Torres‐Machorro, A.L., Hernández, R., Cevallos, A.M. & López‐Villaseñor, I. (2010) Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? FEMS Microbiology Reviews, 34, 59–86.
Tsang, H.H., Domingos, J.A., Westaway, J.A.F., Kam, M.H.Y., Huerlimann, R. & Bastos Gomes, G. (2021) Digital droplet pcr‐based environmental dna tool for monitoring cryptocaryon irritans in a marine fish farm from Hong Kong. Diversity, 13, 350.
Utermöhl, H. (1931) Neue Wege in der quantitativen Erfassung des Plankton. Verhandlungen – Internationale Vereinigung Fur Theoretische Und Angewandte Limnologie, 5, 567–596.
Vogelstein, B. & Kinzler, K.W. (1999) Digital PCR. Proceedings of the National Academy of Sciences, 96, 9236–9241.
Wang, C., Zhang, T., Wang, Y., Katz, L.A., Gao, F. & Song, W. (2017) Disentangling sources of variation in SSU rRNA gene sequences from single cell analyses of ciliates: impact of copy number variation and experimental error. Proceedings of the Royal Society B: Biological Sciences, 284, 20170425.
Wang, Y., Jiang, Y., Liu, Y., Li, Y., Katz, L.A., Gao, F. et al. (2020) Comparative studies on the polymorphism and copy number variation of mtSSU rRNA gene in ciliates (Protista, Ciliophora): implications for phylogenetic, environmental, and ecological research. Microorganisms, 8, 316.
Wang, Y., Wang, C., Jiang, Y., Katz, L.A., Gao, F. & Yan, Y. (2019) Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. Science China. Life Sciences, 62, 203–214.
Weisse, T. & Montagnes, D.J.S. (2022) Ecology of planktonic ciliates in a changing world: concepts, methods, and challenges. The Journal of Eukaryotic Microbiology, 69, e12879.
Weisse, T. & Sonntag, B. (2016) Ciliates in planktonic food webs: communication and adaptive response. In: Witzany, G. & Nowacki, M. (Eds.) Biocommunication of ciliates. Cham: Springer International Publishing, pp. 351–372.
Weisse, T. (2014) Ciliates and the rare biosphere—community ecology and population dynamics. The Journal of Eukaryotic Microbiology, 61, 419–433.
Weisse, T. (2017) Functional diversity of aquatic ciliates. European Journal of Protistology, 61, 331–358.
Weisse, T., Anderson, R., Arndt, H., Calbet, A., Hansen, P.J. & Montagnes, D.J.S. (2016) Functional ecology of aquatic phagotrophic protists – concepts, limitations, and perspectives. European Journal of Protistology, 55, 50–74.
Whale, A.S., De Spiegelaere, W., Trypsteen, W., Nour, A.A., Bae, Y.K., Benes, V. et al. (2020) The digital MIQE guidelines update: minimum information for publication of quantitative digital PCR experiments for 2020. Clinical Chemistry, 66, 1012–1029.
Wickham, H. & Seidel, D. (2022) Scales: scale functions for visualization. Available at: https://scales.r-lib.org, https://github.com/r-lib/scales.
Wickham, H. (2016) ggplot2: elegant graphics for data analysis. New York: Springer‐Verlag.
Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L.D., François, R. et al. (2019) Welcome to the tidyverse. Journal of Open Source Software, 4, 1686.
Worden, A.Z., Follows, M.J., Giovannoni, S.J., Wilken, S., Zimmerman, A.E. & Keeling, P.J. (2015) Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science, 347, 1257594.
Yang, R., Paparini, A., Monis, P. & Ryan, U. (2014) Comparison of next‐generation droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of cryptosporidium oocysts in faecal samples. International Journal for Parasitology, 44, 1105–1113.
Yarimizu, K., Sildever, S., Hamamoto, Y., Tazawa, S., Oikawa, H., Yamaguchi, H. et al. (2021) Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR. Harmful Algae, 103, 102008.
Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S. & Madden, T.L. (2012) Primer‐BLAST: a tool to design target‐specific primers for polymerase chain reaction. BMC Bioinformatics, 13, 134.
Zhu, F., Massana, R., Not, F., Marie, D. & Vaulot, D. (2005) Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiology Ecology, 52, 79–92.
Zingel, P., Agasild, H., Karus, K., Buholce, L. & Nõges, T. (2019) Importance of ciliates as food for fish larvae in a shallow sea bay and a large shallow lake. European Journal of Protistology, 67, 59–70.
Šimek, K., Grujčić, V., Nedoma, J., Jezberová, J., Šorf, M., Matoušů, A. et al. (2019) Microbial food webs in hypertrophic fishponds: omnivorous ciliate taxa are major protistan bacterivores. Limnology and Oceanography, 64, 2295–2309.
Šlapeta, J., Moreira, D. & López‐García, P. (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proceedings of the Royal Society B: Biological Sciences, 272, 2073–2081.
معلومات مُعتمدة: ST0414/13-3 Deutsche Forschungsgemeinschaft
المشرفين على المادة: 0 (RNA, Ribosomal)
0 (DNA, Protozoan)
تواريخ الأحداث: Date Created: 20240422 Date Completed: 20240429 Latest Revision: 20240429
رمز التحديث: 20240501
DOI: 10.1111/1462-2920.16619
PMID: 38649189
قاعدة البيانات: MEDLINE
الوصف
تدمد:1462-2920
DOI:10.1111/1462-2920.16619