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Zhang C, McIntosh KD, Sienkiewicz N, Stelzer EA, Graham JL, Lu J. Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States. WATER RESEARCH 2023; 235:119679. [PMID: 37011576 PMCID: PMC10123349 DOI: 10.1016/j.watres.2023.119679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Phytoplankton is the essential primary producer in fresh surface water ecosystems. However, excessive phytoplankton growth due to eutrophication significantly threatens ecologic, economic, and public health. Therefore, phytoplankton identification and quantification are essential to understanding the productivity and health of freshwater ecosystems as well as the impacts of phytoplankton overgrowth (such as Cyanobacterial blooms) on public health. Microscopy is the gold standard for phytoplankton assessment but is time-consuming, has low throughput, and requires rich experience in phytoplankton morphology. Quantitative polymerase chain reaction (qPCR) is accurate and straightforward with high throughput. In addition, qPCR does not require expertise in phytoplankton morphology. Therefore, qPCR can be a useful alternative for molecular identification and enumeration of phytoplankton. Nonetheless, a comprehensive study is missing which evaluates and compares the feasibility of using qPCR and microscopy to assess phytoplankton in fresh water. This study 1) compared the performance of qPCR and microscopy in identifying and quantifying phytoplankton and 2) evaluated qPCR as a molecular tool to assess phytoplankton and indicate eutrophication. We assessed phytoplankton using both qPCR and microscopy in twelve large freshwater rivers across the United States from early summer to late fall in 2017, 2018, and 2019. qPCR- and microscope-based phytoplankton abundance had a significant positive linear correlation (adjusted R2 = 0.836, p-value < 0.001). Phytoplankton abundance had limited temporal variation within each sampling season and over the three years studied. The sampling sites in the midcontinent rivers had higher phytoplankton abundance than those in the eastern and western rivers. For instance, the concentration (geometric mean) of Bacillariophyta, Cyanobacteria, Chlorophyta, and Dinoflagellates at the sampling sites in the midcontinent rivers was approximately three times that at the sampling sites in the western rivers and approximately 18 times that at the sampling sites in the eastern rivers. Welch's analysis of variance indicates that phytoplankton abundance at the sampling sites in the midcontinent rivers was significantly higher than that at the sampling sites in the eastern rivers (p-value = 0.013) but was comparable to that at the sampling sites in the western rivers (p-value = 0.095). The higher phytoplankton abundance at the sampling sites in the midcontinent rivers was presumably because these rivers were more eutrophic. Indeed, low phytoplankton abundance occurred in oligotrophic or low trophic sites, whereas eutrophic sites had greater phytoplankton abundance. This study demonstrates that qPCR-based phytoplankton abundance can be a useful numerical indicator of the trophic conditions and water quality in freshwater rivers.
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Affiliation(s)
- Chiqian Zhang
- Department of Civil and Environmental Engineering, College of Sciences and Engineering, Southern University and A&M College, Baton Rouge, LA 70813, United States
| | - Kyle D McIntosh
- Oak Ridge Institute for Science and Education at the United States Environmental Protection Agency's Office of Research and Development, Oak Ridge, TN 37830, United States
| | - Nathan Sienkiewicz
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States
| | - Erin A Stelzer
- U.S. Geological Survey, Columbus, OH 43229, United States
| | | | - Jingrang Lu
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, United States.
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2
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Klawonn I, Dunker S, Kagami M, Grossart HP, Van den Wyngaert S. Intercomparison of Two Fluorescent Dyes to Visualize Parasitic Fungi (Chytridiomycota) on Phytoplankton. MICROBIAL ECOLOGY 2023; 85:9-23. [PMID: 34854932 PMCID: PMC9849195 DOI: 10.1007/s00248-021-01893-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Fungal microparasites (here chytrids) are widely distributed and yet, they are often overlooked in aquatic environments. To facilitate the detection of microparasites, we revisited the applicability of two fungal cell wall markers, Calcofluor White (CFW) and wheat germ agglutinin (WGA), for the direct visualization of chytrid infections on phytoplankton in laboratory-maintained isolates and field-sampled communities. Using a comprehensive set of chytrid-phytoplankton model pathosystems, we verified the staining pattern on diverse morphological structures of chytrids via fluorescence microscopy. Empty sporangia were stained most effectively, followed by encysted zoospores and im-/mature sporangia, while the staining success was more variable for rhizoids, stalks, and resting spores. In a few instances, the staining was unsuccessful (mostly with WGA), presumably due to insufficient cell fixation, gelatinous cell coatings, and multilayered cell walls. CFW and WGA staining could be done in Utermöhl chambers or on polycarbonate filters, but CFW staining on filters seemed less advisable due to high background fluorescence. To visualize chytrids, 1 µg dye mL-1 was sufficient (but 5 µg mL-1 are recommended). Using a dual CFW-WGA staining protocol, we detected multiple, mostly undescribed chytrids in two natural systems (freshwater and coastal), while falsely positive or negative stained cells were well detectable. As a proof-of-concept, we moreover conducted imaging flow cytometry, as a potential high-throughput technology for quantifying chytrid infections. Our guidelines and recommendations are expected to facilitate the detection of chytrid epidemics and to unveil their ecological and economical imprint in natural and engineered aquatic systems.
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Affiliation(s)
- Isabell Klawonn
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.
- Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, 18119, Rostock, Germany.
| | - Susanne Dunker
- Department for Physiological Diversity, Helmholtz Centre for Environmental Research (UFZ), 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), 04103, Leipzig, Germany
| | - Maiko Kagami
- Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, 240-8502, Japan
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany
| | - Silke Van den Wyngaert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.
- WasserCluster Lunz, Biologische Station, Dr. Carl Kupelwieser Promenade 5, 3293, Lunz am See, Austria.
- Department of Biology, University of Turku, Vesilinnantie 5, 20014, Turku, Finland.
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3
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Tinnevelt GH, Lushchikova O, Augustijn D, Lochs M, Geertsma RW, Rijkeboer M, Kools H, Dubelaar G, Veen A, Buydens LMC, Jansen JJ. Water quality monitoring based on chemometric analysis of high-resolution phytoplankton data measured with flow cytometry. ENVIRONMENT INTERNATIONAL 2022; 170:107587. [PMID: 36274492 DOI: 10.1016/j.envint.2022.107587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/14/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
River water is an important source of Dutch drinking water. For this reason, continuous monitoring of river water quality is needed. However, comprehensive chemical analyses with high-resolution gas chromatography [GC]-mass spectrometry [MS]/liquid chromatography [LC]-MS are quite tedious and time consuming; this makes them poorly fit for routine water quality monitoring and, therefore, many pollution events are missed. Phytoplankton are highly sensitive and responsive to toxicity, which makes them highly usable for effect-based water quality monitoring. Flow cytometry can measure the optical properties of phytoplankton every hour, generating a large amount of information-rich data in one year. However, this requires chemometrics, as the resulting fingerprints need to be processed into information about abnormal phytoplankton behaviour. We developed Discriminant Analysis of Multi-Aspect CYtometry (DAMACY) to model the "normal condition" of the phytoplankton community imposed by diurnal, meteorological, and other exogenous influences. DAMACY first describes the cellular variability and distribution of phytoplankton in each measurement using principal component analysis, and then aims to find subtle differences in these phytoplankton distributions that predict normal environmental conditions. Deviations from these normal environmental conditions indicated abnormal phytoplankton behaviour that happened alongside pollution events measured with the GC/MS and LC/MS systems. Thus, our results demonstrate that flow cytometry in combination with chemometrics may be used for an automated hourly assessment of river water quality and as a near real-time early warning for detecting harmful known or unknown contaminants. Finally, both the flow cytometer and the DAMACY algorithm run completely autonomous and only requires maintenance once or twice per year. The warning system results may be uploaded automatically, so that drinking water companies may temporary stop pumping water whenever abnormal phytoplankton behaviour is detected. In the case of prolonged abnormal phytoplankton behaviour, comprehensive analysis may still be used to identify the chemical compound, its origin, and toxicity.
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Affiliation(s)
- Gerjen H Tinnevelt
- Radboud University, Institute for Molecules and Materials, (Analytical Chemistry), P.O. Box 9010, 6500 GL Nijmegen, the Netherlands; TI-COAST, Science Park 904, 1098 XH Amsterdam, the Netherlands.
| | - Olga Lushchikova
- Radboud University, Institute for Molecules and Materials, (Analytical Chemistry), P.O. Box 9010, 6500 GL Nijmegen, the Netherlands; TI-COAST, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Dillen Augustijn
- Radboud University, Institute for Molecules and Materials, (Analytical Chemistry), P.O. Box 9010, 6500 GL Nijmegen, the Netherlands; TI-COAST, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Mathijs Lochs
- Radboud University, Institute for Molecules and Materials, (Analytical Chemistry), P.O. Box 9010, 6500 GL Nijmegen, the Netherlands; TI-COAST, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Rinze W Geertsma
- Laboratory for Hydrobiological Analysis, Rijkswaterstaat (RWS), Zuiderwagenplein 2, 8224 AD Lelystad, the Netherlands
| | - Machteld Rijkeboer
- Laboratory for Hydrobiological Analysis, Rijkswaterstaat (RWS), Zuiderwagenplein 2, 8224 AD Lelystad, the Netherlands
| | - Harrie Kools
- CytoBuoy bv, Johan de Wittlaan 11, 3445 AG Woerden, the Netherlands
| | - George Dubelaar
- CytoBuoy bv, Johan de Wittlaan 11, 3445 AG Woerden, the Netherlands
| | - Arnold Veen
- CytoBuoy bv, Johan de Wittlaan 11, 3445 AG Woerden, the Netherlands
| | - Lutgarde M C Buydens
- Radboud University, Institute for Molecules and Materials, (Analytical Chemistry), P.O. Box 9010, 6500 GL Nijmegen, the Netherlands
| | - Jeroen J Jansen
- Radboud University, Institute for Molecules and Materials, (Analytical Chemistry), P.O. Box 9010, 6500 GL Nijmegen, the Netherlands
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Dunker S, Boyd M, Durka W, Erler S, Harpole WS, Henning S, Herzschuh U, Hornick T, Knight T, Lips S, Mäder P, Švara EM, Mozarowski S, Rakosy D, Römermann C, Schmitt‐Jansen M, Stoof‐Leichsenring K, Stratmann F, Treudler R, Virtanen R, Wendt‐Potthoff K, Wilhelm C. The potential of multispectral imaging flow cytometry for environmental monitoring. Cytometry A 2022; 101:782-799. [DOI: 10.1002/cyto.a.24658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/23/2022] [Accepted: 05/12/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Susanne Dunker
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research (UFZ) Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Matthew Boyd
- Department of Anthropology Lakehead University Thunder Bay Canada
| | - Walter Durka
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
| | - Silvio Erler
- Institute for Bee Protection, Julius Kühn Institute (JKI)‐Federal Research Centre for Cultivated Plants Braunschweig Germany
| | - W. Stanley Harpole
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research (UFZ) Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology, Martin Luther University Halle‐Wittenberg Halle Germany
| | - Silvia Henning
- Department of Experimental Aerosol and Cloud Microphysics Leibniz Institute for Tropospheric Research (TROPOS) Leipzig Germany
| | - Ulrike Herzschuh
- Alfred‐Wegner‐Institute Helmholtz Centre of Polar and Marine Research Polar Terrestrial Environmental Systems Potsdam Germany
- Institute of Environmental Sciences and Geography University of Potsdam Potsdam Germany
- Institute of Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Thomas Hornick
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research (UFZ) Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Tiffany Knight
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
- Institute of Biology, Martin Luther University Halle‐Wittenberg Halle Germany
| | - Stefan Lips
- Department of Bioanalytical Ecotoxicology Helmholtz‐Centre for Environmental Research – UFZ Leipzig Germany
| | - Patrick Mäder
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Computer Science and Automation Technische Universität Ilmenau Ilmenau Germany
- Faculty of Biological Sciences Friedrich‐Schiller‐University Jena Jena Germany
| | - Elena Motivans Švara
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
- Institute of Biology, Martin Luther University Halle‐Wittenberg Halle Germany
| | | | - Demetra Rakosy
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research (UFZ) Halle Germany
| | - Christine Römermann
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Ecology and Evolution Friedrich‐Schiller‐University Jena Jena Germany
| | - Mechthild Schmitt‐Jansen
- Department of Bioanalytical Ecotoxicology Helmholtz‐Centre for Environmental Research – UFZ Leipzig Germany
| | - Kathleen Stoof‐Leichsenring
- Alfred‐Wegner‐Institute Helmholtz Centre of Polar and Marine Research Polar Terrestrial Environmental Systems Potsdam Germany
| | - Frank Stratmann
- Department of Experimental Aerosol and Cloud Microphysics Leibniz Institute for Tropospheric Research (TROPOS) Leipzig Germany
| | - Regina Treudler
- Department of Dermatology, Venerology and Allergology University of Leipzig Medical Center Leipzig Germany
| | | | - Katrin Wendt‐Potthoff
- Department of Lake Research Helmholtz‐Centre for Environmental Research – UFZ Magdeburg Germany
| | - Christian Wilhelm
- Faculty of Life Sciences, Institute of Biology University of Leipzig Leipzig Germany
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5
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Rodríguez-Herrera J, Cabado AG, Bodelón G, Cunha SC, Pinto V, Fernandes JO, Lago J, Muñoz S, Pastoriza-Santos I, Sousa P, Gonçalves L, López-Cabo M, Pérez-Juste J, Santos J, Minas G. Methodological Approaches for Monitoring Five Major Food Safety Hazards Affecting Food Production in the Galicia-Northern Portugal Euroregion. Foods 2021; 11:84. [PMID: 35010210 PMCID: PMC8750003 DOI: 10.3390/foods11010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
The agri-food industry has historically determined the socioeconomic characteristics of Galicia and Northern Portugal, and it was recently identified as an area for collaboration in the Euroregion. In particular, there is a need for action to help to ensure the provision of safe and healthy foods by taking advantage of key enabling technologies. The goals of the FOODSENS project are aligned with this major objective, specifically with the development of biosensors able to monitor hazards relevant to the safety of food produced in the Euroregion. The present review addresses the state of the art of analytical methodologies and techniques-whether commercially available or in various stages of development-for monitoring food hazards, such as harmful algal blooms, mycotoxins, Listeria monocytogenes, allergens, and polycyclic aromatic hydrocarbons. We discuss the pros and cons of these methodologies and techniques and address lines of research for point-of-care detection. Accordingly, the development of miniaturized automated monitoring strategies is considered a priority in terms of health and economic interest, with a significant impact in several areas, such as food safety, water quality, pollution control, and public health. Finally, we present potential market opportunities that could result from the availability of rapid and reliable commercial methodologies.
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Affiliation(s)
- Juan Rodríguez-Herrera
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (IIM-CSIC), 36208 Vigo, Spain; (S.M.); (M.L.-C.)
| | - Ana G. Cabado
- ANFACO-CECOPESCA, Ctra. Colexio Universitario, 16, 36310 Vigo, Spain; (A.G.C.); (J.L.)
| | - Gustavo Bodelón
- CINBIO, Campus Universitario As Lagoas, Universidade de Vigo, 36310 Vigo, Spain; (G.B.); (I.P.-S.); (J.P.-J.)
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Sara C. Cunha
- LAQV-REQUIMTE, Laboratory of Bromatology and Hidrology, Department of Chemical Sciences, Facultaty of Pharmacy, University of Porto, Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; (S.C.C.); (J.O.F.); (J.S.)
| | - Vânia Pinto
- Center for MicroElectromechanical Systems (CMEMS-UMinho), University of Minho, 4800-058 Guimarães, Portugal; (V.P.); (P.S.); (L.G.); (G.M.)
| | - José O. Fernandes
- LAQV-REQUIMTE, Laboratory of Bromatology and Hidrology, Department of Chemical Sciences, Facultaty of Pharmacy, University of Porto, Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; (S.C.C.); (J.O.F.); (J.S.)
| | - Jorge Lago
- ANFACO-CECOPESCA, Ctra. Colexio Universitario, 16, 36310 Vigo, Spain; (A.G.C.); (J.L.)
| | - Silvia Muñoz
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (IIM-CSIC), 36208 Vigo, Spain; (S.M.); (M.L.-C.)
| | - Isabel Pastoriza-Santos
- CINBIO, Campus Universitario As Lagoas, Universidade de Vigo, 36310 Vigo, Spain; (G.B.); (I.P.-S.); (J.P.-J.)
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Paulo Sousa
- Center for MicroElectromechanical Systems (CMEMS-UMinho), University of Minho, 4800-058 Guimarães, Portugal; (V.P.); (P.S.); (L.G.); (G.M.)
| | - Luís Gonçalves
- Center for MicroElectromechanical Systems (CMEMS-UMinho), University of Minho, 4800-058 Guimarães, Portugal; (V.P.); (P.S.); (L.G.); (G.M.)
| | - Marta López-Cabo
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (IIM-CSIC), 36208 Vigo, Spain; (S.M.); (M.L.-C.)
| | - Jorge Pérez-Juste
- CINBIO, Campus Universitario As Lagoas, Universidade de Vigo, 36310 Vigo, Spain; (G.B.); (I.P.-S.); (J.P.-J.)
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - João Santos
- LAQV-REQUIMTE, Laboratory of Bromatology and Hidrology, Department of Chemical Sciences, Facultaty of Pharmacy, University of Porto, Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; (S.C.C.); (J.O.F.); (J.S.)
| | - Graça Minas
- Center for MicroElectromechanical Systems (CMEMS-UMinho), University of Minho, 4800-058 Guimarães, Portugal; (V.P.); (P.S.); (L.G.); (G.M.)
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RoŽanc J, Finšgar M, Maver U. Progressive use of multispectral imaging flow cytometry in various research areas. Analyst 2021; 146:4985-5007. [PMID: 34337638 DOI: 10.1039/d1an00788b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Multi-spectral imaging flow cytometry (MIFC) has become one of the most powerful technologies for investigating general analytics, molecular and cell biology, biotechnology, medicine, and related fields. It combines the capabilities of the morphometric and photometric analysis of single cells and micrometer-sized particles in flux with regard to thousands of events. It has become the tool of choice for a wide range of research and clinical applications. By combining the features of flow cytometry and fluorescence microscopy, it offers researchers the ability to couple the spatial resolution of multicolour images of cells and organelles with the simultaneous analysis of a large number of events in a single system. This provides the opportunity to visually confirm findings and collect novel data that would otherwise be more difficult to obtain. This has led many researchers to design innovative assays to gain new insight into important research questions. To date, it has been successfully used to study cell morphology, surface and nuclear protein co-localization, protein-protein interactions, cell signaling, cell cycle, cell death, and cytotoxicity, intracellular calcium, drug uptake, pathogen internalization, and other applications. Herein we describe some of the recent advances in the field of multiparametric imaging flow cytometry methods in various research areas.
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Affiliation(s)
- Jan RoŽanc
- University of Maribor, Faculty of Medicine, Institute of Biomedical Sciences, Taborska ulica 8, SI-2000 Maribor, Slovenia.
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7
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Conacher CG, Luyt NA, Naidoo-Blassoples RK, Rossouw D, Setati ME, Bauer FF. The ecology of wine fermentation: a model for the study of complex microbial ecosystems. Appl Microbiol Biotechnol 2021; 105:3027-3043. [PMID: 33834254 DOI: 10.1007/s00253-021-11270-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/11/2022]
Abstract
The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.
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Affiliation(s)
- C G Conacher
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - N A Luyt
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - R K Naidoo-Blassoples
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - D Rossouw
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - M E Setati
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - F F Bauer
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa.
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8
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Hofmann P, Clark A, Hoffmann P, Chatzinotas A, Harpole WS, Dunker S. Beyond nitrogen: phosphorus - estimating the minimum niche dimensionality for resource competition between phytoplankton. Ecol Lett 2021; 24:761-771. [PMID: 33590958 DOI: 10.1111/ele.13695] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 01/06/2023]
Abstract
The niche dimensionality required for coexistence is often discussed in terms of the number of limiting resources. N and P limitation are benchmarks for studying phytoplankton interactions. However, it is generally agreed that limitation by small numbers of resources cannot explain the high phytoplankton diversity observed in nature. Here, we parameterised resource competition models using experimental data for six phytoplankton species grown in monoculture with nine potential limiting resources. We tested predicted species biomass from these models against observations in two-species experimental mixtures. Uptake rates were similar across species, following the classic Redfield ratio. Model accuracy levelled out at around three to five resources suggesting the minimum dimensionality of this system. The models included the resources Fe, Mg, Na and S. Models including only N and P always performed poorly. These results suggest that high-dimensional information about resource limitation despite stoichiometric constraints may be needed to accurately predict community assembly.
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Affiliation(s)
- Peter Hofmann
- Department of Physiological Diversity, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany.,Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Adam Clark
- Department of Physiological Diversity, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany.,Institute of Biology, University of Graz, Holteigasse 6, Graz, 8010, Austria
| | - Petra Hoffmann
- Department of Physiological Diversity, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany.,Institute of Biology, University Leipzig, Talstr.33, Leipzig, 04103, Germany
| | - W Stanley Harpole
- Department of Physiological Diversity, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany.,Martin Luther University Halle-Wittenberg, Am Kirchtor 1, Halle (Saale), 06108, Germany
| | - Susanne Dunker
- Department of Physiological Diversity, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
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9
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Fukuba T, Fujii T. Lab-on-a-chip technology for in situ combined observations in oceanography. LAB ON A CHIP 2021; 21:55-74. [PMID: 33300537 DOI: 10.1039/d0lc00871k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The oceans sustain the global environment and diverse ecosystems through a variety of biogeochemical processes and their complex interactions. In order to understand the dynamism of the local or global marine environments, multimodal combined observations must be carried out in situ. On the other hand, instrumentation of in situ measurement techniques enabling biological and/or biochemical combined observations is challenging in aquatic environments, including the ocean, because biochemical flow analyses require a more complex configuration than physicochemical electrode sensors. Despite this technical hurdle, in situ analyzers have been developed to measure the concentrations of seawater contents such as nutrients, trace metals, and biological components. These technologies have been used for cutting-edge ocean observations to elucidate the biogeochemical properties of water mass with a high spatiotemporal resolution. In this context, the contribution of lab-on-a-chip (LoC) technology toward the miniaturization and functional integration of in situ analyzers has been gaining momentum. Due to their mountability, in situ LoC technologies provide ideal instrumentation for underwater analyzers, especially for miniaturized underwater observation platforms. Consequently, the appropriate combination of reliable LoC and underwater technologies is essential to realize practical in situ LoC analyzers suitable for underwater environments, including the deep sea. Moreover, the development of fundamental LoC technologies for underwater analyzers, which operate stably in extreme environments, should also contribute to in situ measurements for public or industrial purposes in harsh environments as well as the exploration of the extraterrestrial frontier.
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Affiliation(s)
- Tatsuhiro Fukuba
- Institute for Marine-Earth Exploration and Engineering, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho 2-15, Yokosuka, Kanagawa 237-0061, Japan.
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10
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Dunker S, Motivans E, Rakosy D, Boho D, Mäder P, Hornick T, Knight TM. Pollen analysis using multispectral imaging flow cytometry and deep learning. THE NEW PHYTOLOGIST 2021; 229:593-606. [PMID: 32803754 DOI: 10.1111/nph.16882] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/28/2020] [Indexed: 05/24/2023]
Abstract
Pollen identification and quantification are crucial but challenging tasks in addressing a variety of evolutionary and ecological questions (pollination, paleobotany), but also for other fields of research (e.g. allergology, honey analysis or forensics). Researchers are exploring alternative methods to automate these tasks but, for several reasons, manual microscopy is still the gold standard. In this study, we present a new method for pollen analysis using multispectral imaging flow cytometry in combination with deep learning. We demonstrate that our method allows fast measurement while delivering high accuracy pollen identification. A dataset of 426 876 images depicting pollen from 35 plant species was used to train a convolutional neural network classifier. We found the best-performing classifier to yield a species-averaged accuracy of 96%. Even species that are difficult to differentiate using microscopy could be clearly separated. Our approach also allows a detailed determination of morphological pollen traits, such as size, symmetry or structure. Our phylogenetic analyses suggest phylogenetic conservatism in some of these traits. Given a comprehensive pollen reference database, we provide a powerful tool to be used in any pollen study with a need for rapid and accurate species identification, pollen grain quantification and trait extraction of recent pollen.
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Affiliation(s)
- Susanne Dunker
- Helmholtz-Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig, 04318, Germany
- German Centre for Integrative Biodiversity Research - iDiv, Deutscher Platz 5a, Leipzig, 04103, Germany
| | - Elena Motivans
- German Centre for Integrative Biodiversity Research - iDiv, Deutscher Platz 5a, Leipzig, 04103, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Am Kirchtor 1, Halle (Saale), 06120, Germany
- Martin Luther University Halle-Wittenberg, Am Kirchtor 1, Halle (Saale), 06108, Germany
| | - Demetra Rakosy
- Helmholtz-Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig, 04318, Germany
- German Centre for Integrative Biodiversity Research - iDiv, Deutscher Platz 5a, Leipzig, 04103, Germany
| | - David Boho
- Software Engineering for Safety-Critical Systems Group, Technische Universität Ilmenau, Ilmenau, 98693, Germany
| | - Patrick Mäder
- Software Engineering for Safety-Critical Systems Group, Technische Universität Ilmenau, Ilmenau, 98693, Germany
| | - Thomas Hornick
- Helmholtz-Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig, 04318, Germany
- German Centre for Integrative Biodiversity Research - iDiv, Deutscher Platz 5a, Leipzig, 04103, Germany
| | - Tiffany M Knight
- German Centre for Integrative Biodiversity Research - iDiv, Deutscher Platz 5a, Leipzig, 04103, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Am Kirchtor 1, Halle (Saale), 06120, Germany
- Martin Luther University Halle-Wittenberg, Am Kirchtor 1, Halle (Saale), 06108, Germany
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11
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Langley B, Halloran PR, Power A, Rickaby REM, Chana P, Diver P, Thornalley D, Hacker C, Love J. A new method for isolating and analysing coccospheres within sediment. Sci Rep 2020; 10:20727. [PMID: 33244023 PMCID: PMC7692543 DOI: 10.1038/s41598-020-77473-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/06/2020] [Indexed: 11/25/2022] Open
Abstract
Size is a fundamental cellular trait that is important in determining phytoplankton physiological and ecological processes. Fossil coccospheres, the external calcite structure produced by the excretion of interlocking plates by the phytoplankton coccolithophores, can provide a rare window into cell size in the past. Coccospheres are delicate however and are therefore poorly preserved in sediment. We demonstrate a novel technique combining imaging flow cytometry and cross-polarised light (ISX+PL) to rapidly and reliably visually isolate and quantify the morphological characteristics of coccospheres from marine sediment by exploiting their unique optical and morphological properties. Imaging flow cytometry combines the morphological information provided by microscopy with high sample numbers associated with flow cytometry. High throughput imaging overcomes the constraints of labour-intensive manual microscopy and allows statistically robust analysis of morphological features and coccosphere concentration despite low coccosphere concentrations in sediments. Applying this technique to the fine-fraction of sediments, hundreds of coccospheres can be visually isolated quickly with minimal sample preparation. This approach has the potential to enable rapid processing of down-core sediment records and/or high spatial coverage from surface sediments and may prove valuable in investigating the interplay between climate change and coccolithophore physiological/ecological response.
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Affiliation(s)
- Beth Langley
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4RJ, UK
| | - Paul R Halloran
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4RJ, UK.
| | - Ann Power
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| | - Prabhjoat Chana
- Luminex B.V., Het Zuiderkruis 1, 5215 MV, 's-Hertogenbosch, The Netherlands
| | - Poppy Diver
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| | - David Thornalley
- Department of Geography, University College London, London, WC1H 9LG, UK
| | - Christian Hacker
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - John Love
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
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12
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Dunker S. Imaging Flow Cytometry for Phylogenetic and MorphologicallyBased Functional Group Clustering of a Natural Phytoplankton Community over 1 Year in an Urban Pond. Cytometry A 2020; 97:727-736. [PMID: 32472660 DOI: 10.1002/cyto.a.24044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/10/2022]
Abstract
Ponds are an insufficiently studied research object but represent a biodiversity hotspot and have a high value for ecosystem services like recreation, water retention, or angling. Especially urban ponds create a direct contact for citizens experiencing nature. But on the other side, these systems also suffer from several pressures caused by humans, for example, high nutrient and salt influxes or high temperatures. Phytoplankton organisms are a crucial part of ponds ecosystem and an understanding of community composition is crucial especially when eutrophication and high temperatures lead to dominance of unpleasant toxic cyanobacteria. With traditional microscopic methods for phytoplankton analysis, monitoring is not feasible with high spatial resolution and frequency. Therefore, a new approach of imaging flow cytometry to classify phytoplankton species in either taxonomic or morphologically based functional groups (MBFGs) is suggested. In this study, both classifications could be successfully applied to a natural phytoplankton community in an urban pond in Leipzig with minor modifications. Both classifications in combination provide a good mechanistic understanding of phytoplankton community dynamics. In addition, a great advantage of the measurements is the archivability of microscopic images allowing a comprehensive respective data analysis. Two examples of detailed trait and image analysis are demonstrated to investigate single-cell traits for cyanobacteria and chlorophytes/euglenophytes and to follow the fate of a cyanobacterial bloom affected by a fungal infection. © 2020 The Author. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Susanne Dunker
- Helmholtz-Centre for Environmental Research - UFZ, Department Physiological Diversity, Permoserstraße 15 Leipzig, 04318, Germany.,German Centre for Integrative Biodiversity Research - iDiv, Department Physiological Diversity, Deutscher Platz 5e, Leipzig, 04103, Germany
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13
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Hofmann P, Chatzinotas A, Harpole WS, Dunker S. Temperature and stoichiometric dependence of phytoplankton traits. Ecology 2019; 100:e02875. [DOI: 10.1002/ecy.2875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Peter Hofmann
- Department of Environmental Microbiology Helmholtz‐Centre for Environmental Research – UFZ Permoserstrasse 15 Leipzig 04318 Germany
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research – UFZ Permoserstrasse 15 Leipzig 04318 Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology Helmholtz‐Centre for Environmental Research – UFZ Permoserstrasse 15 Leipzig 04318 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e Leipzig 04103 Germany
| | - W. Stanley Harpole
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research – UFZ Permoserstrasse 15 Leipzig 04318 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e Leipzig 04103 Germany
- Martin Luther University Halle‐Wittenberg Am Kirchtor 1 Halle (Saale) 06108 Germany
| | - Susanne Dunker
- Department of Physiological Diversity Helmholtz‐Centre for Environmental Research – UFZ Permoserstrasse 15 Leipzig 04318 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e Leipzig 04103 Germany
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