1
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Martens N, Ehlert E, Putri W, Sibbertsen M, Schaum CE. Organic compounds drive growth in phytoplankton taxa from different functional groups. Proc Biol Sci 2024; 291:20232713. [PMID: 38320614 PMCID: PMC10846936 DOI: 10.1098/rspb.2023.2713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Phytoplankton are usually considered autotrophs, but an increasing number of studies show that many taxa are able also to use organic carbon. Acquiring nutrients and energy from different sources might enable an efficient uptake of required substances and provide a strategy to deal with varying resource availability, especially in highly dynamic ecosystems such as estuaries. In our study, we investigated the effects of 31 organic carbon sources on the growth (proxied by differences in cell counts after 24 h exposure) of 17 phytoplankton strains from the Elbe estuary spanning four functional groups. All of our strains were able to make use of at least 1 and up to 26 organic compounds for growth. Pico-sized green algae such as Mychonastes, as well as the nano-sized green alga Monoraphidium in particular were positively affected by a high variety of substances. Reduced light availability, typically appearing in turbid estuaries and similar habitats, resulted in an overall poorer ability to use organic substances for growth, indicating that organic carbon acquisition was not primarily a strategy to deal with darkness. Our results give further evidence for mixotrophy being a ubiquitous ability of phytoplankton and highlight the importance to consider this trophic strategy in research.
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Affiliation(s)
- Nele Martens
- Institute of Marine Ecosystem and Fishery Science, Olbersweg 24, 22767 Hamburg, Germany
| | - Emilia Ehlert
- Institute of Marine Ecosystem and Fishery Science, Olbersweg 24, 22767 Hamburg, Germany
| | - Widhi Putri
- Institute of Marine Ecosystem and Fishery Science, Olbersweg 24, 22767 Hamburg, Germany
| | - Martje Sibbertsen
- Institute of Marine Ecosystem and Fishery Science, Olbersweg 24, 22767 Hamburg, Germany
| | - C.-Elisa Schaum
- Institute of Marine Ecosystem and Fishery Science, Olbersweg 24, 22767 Hamburg, Germany
- Center for Earth System Research and Sustainability, Bundesstraße 53–55, 20146 Hamburg, Germany
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2
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Dirren-Pitsch G, Bühler D, Salcher MM, Bassin B, Le Moigne A, Schuler M, Pernthaler J, Posch T. FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates. Front Microbiol 2022; 13:1070232. [PMID: 36578568 PMCID: PMC9790926 DOI: 10.3389/fmicb.2022.1070232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.
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Affiliation(s)
- Gianna Dirren-Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland,*Correspondence: Gianna Dirren-Pitsch,
| | - Dominique Bühler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Michaela M. Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budĕjovice, Czechia
| | - Barbara Bassin
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Alizée Le Moigne
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Martina Schuler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
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3
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Zufiaurre A, Felip M, Camarero L, Sala-Faig M, Juhanson J, Bonilla-Rosso G, Hallin S, Catalan J. Bacterioplankton seasonality in deep high-mountain lakes. Front Microbiol 2022; 13:935378. [PMID: 36187988 PMCID: PMC9519062 DOI: 10.3389/fmicb.2022.935378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.
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Affiliation(s)
- Aitziber Zufiaurre
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Área de Biodiversidad, Gestión ambiental de Navarra-Nafarroako Ingurumenkudeaketa (GAN-NIK), Pamplona-Iruñea, Navarra, Spain
| | - Marisol Felip
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Camarero
- Centre d’Estudis Avançats de Blanes (CEAB), CSIC, Blanes, Catalonia, Spain
| | - Marc Sala-Faig
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Jaanis Juhanson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - German Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jordi Catalan
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- CSIC, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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4
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Wu C, Chao Y, Shu L, Qiu R. Interactions between soil protists and pollutants: An unsolved puzzle. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128297. [PMID: 35077968 DOI: 10.1016/j.jhazmat.2022.128297] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Soil protists are essential but often overlooked in soils, although they play crucial functional roles in the terrestrial ecosystem. While soil protists have drawn increased attention to their functional role in soils, their interaction with soil pollutants remains unresolved. This review provides a first overview of the current understanding of interactions between soil protists and major pollutants (heavy metals, organic pollutants, nanoparticles, and soil pathogens). We summarize how soil pollutants affect protists and vice versa, showing that we are just beginning to understand their complex interactions. In addition, we identify five research gaps, including hidden diversity, adaptive mechanisms, species interactions, soil bioindicators and environmental applications, and we hope that our review will help promote and build research guidelines for the future. In conclusion, a better understanding of soil pollutant-protist interactions will significantly increase our knowledge of the pollution ecology in the soil and how soil organisms respond and adapt to environmental pollution, which will contribute to the bioremediation and environmental applications of protists in soil.
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Affiliation(s)
- Chenyuan Wu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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5
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Liu K, Ng HYT, Gao Z, Liu H. Selective Feeding of a Mixotrophic Dinoflagellate (Lepidodinium sp.) in Response to Experimental Warming and Inorganic Nutrient Imbalance. Front Microbiol 2022; 13:805306. [PMID: 35516439 PMCID: PMC9063636 DOI: 10.3389/fmicb.2022.805306] [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: 10/30/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Mixotrophic protists are widely observed in the aquatic ecosystems, while how they respond to inorganic nutrient imbalance and ocean warming remains understudied. We conducted a series of experiments on a mixotrophic dinoflagellate Lepidodinium sp. isolated from subtropical coastal waters to investigate the combined effect of temperature and medium nitrate to phosphate ratio (N:P ratio) on the ingestion activities of mixotrophic protists. We found Lepidodinium sp. displayed selective feeding behaviour with a higher ingestion rate on high-N prey (N-rich Rhodomonas salina) when the ambient inorganic N:P ratio was equal to or below the Redfield ratio. The Chesson selectivity index α increased with increasing temperature, suggesting that warming exacerbated the selective feeding of Lepidodinium sp. Under inorganic nitrogen sufficient conditions (N:P ratio = 64), no selective feeding was observed at 25 and 28°C, while it occurs at 31°C, which also indicates that warming alters the feeding behaviour of Lepidodinium sp. In addition, our results revealed that the total ingestion rate of Lepidodinium sp. under the condition with normal inorganic nutrients (Redfield ratio) was significantly lower than that under nutrient-imbalanced conditions, which indicates that Lepidodinium sp. developed compensatory feeding to balance their cellular stoichiometry and satisfy their growth. Our study is the first attempt on revealing the selective feeding behaviours of mixotrophic protists on prey under different inorganic nutrient environments and rising temperatures, which will contribute to our understanding of the response of marine plankton food web to projected climate changes.
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Affiliation(s)
- Kailin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Herrick Yin-To Ng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Zuyuan Gao
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- State Key Laboratory of Marine Pollution, Hong Kong SAR, China
- *Correspondence: Hongbin Liu,
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6
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Cerbin S, Pérez G, Rybak M, Wejnerowski Ł, Konowalczyk A, Helmsing N, Naus-Wiezer S, Meima-Franke M, Pytlak Ł, Raaijmakers C, Nowak W, Bodelier PLE. Methane-Derived Carbon as a Driver for Cyanobacterial Growth. Front Microbiol 2022; 13:837198. [PMID: 35432228 PMCID: PMC9010870 DOI: 10.3389/fmicb.2022.837198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ13C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, 13C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.
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Affiliation(s)
- Slawek Cerbin
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- *Correspondence: Slawek Cerbin,
| | - Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Michał Rybak
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Łukasz Wejnerowski
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Adam Konowalczyk
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Nico Helmsing
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Suzanne Naus-Wiezer
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Łukasz Pytlak
- Montanuniversität Leoben, Applied Geosciences and Geophysics, Leoben, Austria
| | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Witold Nowak
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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7
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Schoenle A, Hohlfeld M, Hermanns K, Mahé F, de Vargas C, Nitsche F, Arndt H. High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans. Commun Biol 2021; 4:501. [PMID: 33893386 PMCID: PMC8065057 DOI: 10.1038/s42003-021-02012-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.
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Affiliation(s)
- Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
| | - Manon Hohlfeld
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Karoline Hermanns
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Frédéric Mahé
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Colomban de Vargas
- CNRS, Sorbonne Université, Station Biologique de Roscoff, UMR7144, ECOMAP-Ecology of Marine Plankton, Roscoff, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara GOSEE, Paris, France
| | - Frank Nitsche
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
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8
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Piwosz K, Mukherjee I, Salcher MM, Grujčić V, Šimek K. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology. Front Microbiol 2021; 12:640066. [PMID: 33746931 PMCID: PMC7970053 DOI: 10.3389/fmicb.2021.640066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.
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Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
- Centre ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Michaela M. Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Vesna Grujčić
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
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9
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Traboni C, Calbet A, Saiz E. Effects of prey trophic mode on the gross-growth efficiency of marine copepods: the case of mixoplankton. Sci Rep 2020; 10:12259. [PMID: 32704097 PMCID: PMC7378051 DOI: 10.1038/s41598-020-69174-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/08/2020] [Indexed: 11/11/2022] Open
Abstract
Copepod reproductive success largely depends on food quality, which also reflects the prey trophic mode. As such, modelling simulations postulate a trophic enhancement to higher trophic levels when mixotrophy is accounted in planktonic trophodynamics. Here, we tested whether photo-phagotrophic protists (mixoplankton) could enhance copepod gross-growth efficiency by nutrient upgrading mechanisms compared to obligate autotrophs and heterotrophs. To validate the hypothesis, we compared physiological rates of the copepod Paracartia grani under the three functional nutrition types. Ingestion and egg production rates varied depending on prey size and species, regardless of the diet. The gross-growth efficiency was variable and not significantly different across nutritional treatments, ranging from 3 to 25% in the mixoplanktonic diet compared to autotrophic (11–36%) and heterotrophic (8–38%) nutrition. Egg hatching and egestion rates were generally unaffected by diet. Overall, P. grani physiological rates did not differ under the tested nutrition types due to the large species-specific variation within trophic mode. However, when we focused on a single species, Karlodinium veneficum, tested as prey under contrasting trophic modes, the actively feeding dinoflagellate boosted the egestion rate and decreased the copepod gross-growth efficiency compared to the autotrophic ones, suggesting possible involvement of toxins in modulating trophodynamics other than stoichiometric constraints.
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Affiliation(s)
- Claudia Traboni
- Institut de Ciéncies del Mar (ICM-CSIC), Psg. Marítim Barceloneta 37-49, 08003, Barcelona, Spain. .,Laboratoire d'Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, CP221, Boulevard du Triomphe, 1050, Brussels, Belgium.
| | - Albert Calbet
- Institut de Ciéncies del Mar (ICM-CSIC), Psg. Marítim Barceloneta 37-49, 08003, Barcelona, Spain
| | - Enric Saiz
- Institut de Ciéncies del Mar (ICM-CSIC), Psg. Marítim Barceloneta 37-49, 08003, Barcelona, Spain
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10
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Llorens-Marès T, Catalan J, Casamayor EO. Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:135929. [PMID: 31863999 DOI: 10.1016/j.scitotenv.2019.135929] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/15/2019] [Accepted: 12/02/2019] [Indexed: 05/20/2023]
Abstract
High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.
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Affiliation(s)
- Tomas Llorens-Marès
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC, Acc. Cala St Francesc 14, E-17300 Blanes, Catalonia, Spain
| | - Jordi Catalan
- CREAF - CSIC, Campus UAB, Edifici C, 08193 Cerdanyola del Vallès, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC, Acc. Cala St Francesc 14, E-17300 Blanes, Catalonia, Spain.
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11
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Herber J, Klotz F, Frommeyer B, Weis S, Straile D, Kolar A, Sikorski J, Egert M, Dannenmann M, Pester M. A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ Microbiol 2019; 22:212-228. [PMID: 31657089 DOI: 10.1111/1462-2920.14840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022]
Abstract
Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.
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Affiliation(s)
- Janina Herber
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Franziska Klotz
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Dietmar Straile
- Limnological Institute, University of Konstanz, Mainaustraße 252, Constance, 78464, Germany
| | - Allison Kolar
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Johannes Sikorski
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany.,Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany.,Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, Braunschweig, 38106, Germany
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12
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Santi I, Tsiola A, Dimitriou PD, Fodelianakis S, Kasapidis P, Papageorgiou N, Daffonchio D, Pitta P, Karakassis I. Prokaryotic and eukaryotic microbial community responses to N and P nutrient addition in oligotrophic Mediterranean coastal waters: Novel insights from DNA metabarcoding and network analysis. MARINE ENVIRONMENTAL RESEARCH 2019; 150:104752. [PMID: 31326679 DOI: 10.1016/j.marenvres.2019.104752] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
The effects of the abrupt input of high quantities of dissolved inorganic nitrogen and phosphorus on prokaryotic and eukaryotic microbial plankton were investigated in an attempt to simulate the nutrient disturbances caused by eutrophication and climate change. Two nutrient levels were created through the addition of different quantities of dissolved nutrients in a mesocosm experiment. During the developed blooms, compositional differences were found within bacteria and microbial eukaryotes, and communities progressed towards species of faster metabolisms. Regarding the different nutrient concentrations, different microbial species were associated with each nutrient treatment and community changes spanned from the phylum to the operational taxonomic unit (OTU) level. Network analyses revealed important differences in the biotic connections developed: more competitive relationships were established in the more intense nutrient disturbance and networks of contrasting complexity were formed around species of different ecological strategies. This work highlights that sudden disturbances in water column chemistry lead to the development of entirely different microbial food webs with distinct ecological characteristics.
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Affiliation(s)
- Ioulia Santi
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), PO Box 2214, Heraklion, 71003, Crete, Greece; Department of Biology, University of Crete, Voutes Campus, Heraklion, 71003, Crete, Greece
| | - Anastasia Tsiola
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), PO Box 2214, Heraklion, 71003, Crete, Greece; Department of Biology, University of Crete, Voutes Campus, Heraklion, 71003, Crete, Greece
| | - Panagiotis D Dimitriou
- Department of Biology, University of Crete, Voutes Campus, Heraklion, 71003, Crete, Greece
| | - Stilianos Fodelianakis
- Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Panagiotis Kasapidis
- Institute of Marine Biology, Biotechnology & Aquaculture, Hellenic Centre for Marine Research, PO Box 2214, 71003, Heraklion, Crete, Greece
| | - Nafsika Papageorgiou
- Department of Biology, University of Crete, Voutes Campus, Heraklion, 71003, Crete, Greece
| | - Daniele Daffonchio
- Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Paraskevi Pitta
- Institute of Oceanography, Hellenic Centre for Marine Research (HCMR), PO Box 2214, Heraklion, 71003, Crete, Greece.
| | - Ioannis Karakassis
- Department of Biology, University of Crete, Voutes Campus, Heraklion, 71003, Crete, Greece
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13
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Abstract
Ammonia-oxidizing archaea (AOA) from the phylum Thaumarchaeota are ubiquitous in marine ecosystems and play a prominent role in carbon and nitrogen cycling. Previous studies have suggested that, like all microbes, thaumarchaea are infected by viruses and that viral predation has a profound impact on thaumarchaeal functioning and mortality, thereby regulating global biogeochemical cycles. However, not a single virus capable of infecting thaumarchaea has been reported thus far. Here we describe the isolation and characterization of three Nitrosopumilus spindle-shaped viruses (NSVs) that infect AOA and are distinct from other known marine viruses. Although NSVs have a narrow host range, they efficiently infect autochthonous Nitrosopumilus strains and display high rates of adsorption to their host cells. The NSVs have linear double-stranded DNA genomes of ∼28 kb that do not display appreciable sequence similarity to genomes of other known archaeal or bacterial viruses and could be considered as representatives of a new virus family, the "Thaspiviridae." Upon infection, NSV replication leads to inhibition of AOA growth, accompanied by severe reduction in the rate of ammonia oxidation and nitrite reduction. Nevertheless, unlike in the case of lytic bacteriophages, NSV propagation is not associated with detectable degradation of the host chromosome or a decrease in cell counts. The broad distribution of NSVs in AOA-dominated marine environments suggests that NSV predation might regulate the diversity and dynamics of AOA communities. Collectively, our results shed light on the diversity, evolution, and potential impact of the virosphere associated with ecologically important mesophilic archaea.
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14
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De Corte D, Paredes G, Yokokawa T, Sintes E, Herndl GJ. Differential Response of Cafeteria roenbergensis to Different Bacterial and Archaeal Prey Characteristics. MICROBIAL ECOLOGY 2019; 78:1-5. [PMID: 30448922 DOI: 10.1007/s00248-018-1293-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
In the marine environment, the abundance of Bacteria and Archaea is either controlled bottom-up via nutrient availability or top-down via grazing. Heterotrophic nanoflagellates (HNF) are mainly responsible for prokaryotic grazing losses besides viral lysis. However, the grazing specificity of HNF on specific bacterial and archaeal taxa is under debate. Bacteria and Archaea might have different nutritive values and surface properties affecting the growth rates of HNF. In this study, we offered different bacterial and archaeal strains with different morphologic and physiologic characteristics to Cafeteria roenbergensis, one of the most abundant and ubiquitous species of HNF in the ocean. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains, and two fast growing marine Bacteria (Pseudoalteromonas sp. and Marinobacter sp.) were fed to Cafeteria cultures. Cafeteria roenbergensis exhibited high growth rates when feeding on Pseudoalteromonas sp., Marinobacter sp., and Nitrosopumilus adriaticus, while the addition of the other strains resulted in minimal growth. Taken together, our data suggest that the differences in growth of Cafeteria roenbergensis associated to grazing on different thaumarchaeal and bacterial strains are likely due to the subtle metabolic, cell size, and physiological differences between different bacterial and thaumarchaeal taxa. Moreover, Nitrosopumilus adriaticus experienced a similar grazing pressure by Cafeteria roenbergensis as compared to the other strains, suggesting that other HNF may also prey on Archaea which might have important consequences on the global biogeochemical cycles.
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Affiliation(s)
- Daniele De Corte
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Gabriela Paredes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Taichi Yokokawa
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, 1790 AB, Den Burg, The Netherlands
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15
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Cohen Y, Pasternak Z, Johnke J, Abed‐Rabbo A, Kushmaro A, Chatzinotas A, Jurkevitch E. Bacteria and microeukaryotes are differentially segregated in sympatric wastewater microhabitats. Environ Microbiol 2019; 21:1757-1770. [DOI: 10.1111/1462-2920.14548] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 01/20/2019] [Accepted: 01/28/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Yossi Cohen
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem Rehovot, 76100 Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem Rehovot, 76100 Israel
| | - Julia Johnke
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZ Permoserstrasse 15, Leipzig, 04318 Germany
| | - Alfred Abed‐Rabbo
- Faculty of ScienceBethlehem University, Palestinian National Authority, Bethlehem, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein‐Goren, The Department of Biotechnology Engineering, Faculty of Engineering SciencesBen‐Gurion University of the Negev P.O. Box 653, Beer‐Sheva Israel
- The Ilse Katz Centre for Meso and Nanoscale Science and TechnologyBen‐Gurion University of the Negev Beer‐Sheva Israel
| | - Antonis Chatzinotas
- Department of Environmental MicrobiologyHelmholtz 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
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem Rehovot, 76100 Israel
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16
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Ballen-Segura M, Catalan J, Felip M. Experimental evidence of the quantitative relationship between the prokaryote ingestion rate and the food vacuole content in mixotrophic phytoflagellates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:704-710. [PMID: 30259678 DOI: 10.1111/1758-2229.12696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/04/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
The verification that many phytoflagellates ingest prokaryotes has changed the view of the microbial loop in aquatic ecosystems. Still, progress is limited because the phagotrophic activity is difficult to quantify in natural assemblages. Linking the food vacuole content in protist with the ingestion rate of prokaryotes would provide a crucial step forward. In this study, using the catalysed reporter deposition - fluorescence in situ hybridization protocol (CARD-FISH), which allows the visualization of labelled prokaryotes inside protists without relying on incubation procedures, we experimentally relate the food vacuole content of prokaryotes (Vc ) to the population-averaged ingestion rates (Ir ) estimated using bacteria-size fluorescent microspheres. The two variables relate according to the equation Ir = 7.52 Vc 0.9 , which indicates a prokaryote half-life of about 6 min in the protist vacuole. Five mixotrophic flagellate species from natural and culture populations were evaluated seven times during 24 h; they provided a broad range of average vacuole content (0.01 to 2.02 prokaryote protist-1 ) and ingestion rates (0.18 to 23 prokaryote protist-1 h-1 ). Consequently, the relationship found can be applied to quantify the mixotrophy activity in a large variety of field and experimental studies.
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Affiliation(s)
- Miguel Ballen-Segura
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC. Accés Cala Sant Francesc, 14. 17300, Blanes, Catalonia, Spain
- Escuela de Ciencias Exactas e Ingenierias, Universidad Sergio Arboleda, Calle 74 #, 14-14, Bogotá, Colombia
| | - Jordi Catalan
- CREAF, Campus UAB, Edifici C, 08193, Cerdanyola del Vallès, Catalonia, Spain
- CSIC, Campus UAB, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Marisol Felip
- CREAF, Campus UAB, Edifici C, 08193, Cerdanyola del Vallès, Catalonia, Spain
- Departament BECCA i Centre de Recerca d'Alta Muntanya, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
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