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      Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen

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          Abstract

          The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 μm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 μm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s00248-024-02344-9.

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          Fitting Linear Mixed-Effects Models Usinglme4

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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                ingrid.sassenhagen@io-warnemuende.de
                Journal
                Microb Ecol
                Microb Ecol
                Microbial Ecology
                Springer US (New York )
                0095-3628
                1432-184X
                18 January 2024
                18 January 2024
                2024
                : 87
                : 1
                : 33
                Affiliations
                [1 ]Department of Ecology and Genetics/Limnology, Uppsala University, ( https://ror.org/048a87296) Uppsala, Sweden
                [2 ]Biological Oceanography, Institute for Baltic Sea Research in Warnemünde, Seestraße 15, Rostock, 18119 Germany
                Article
                2344
                10.1007/s00248-024-02344-9
                10796478
                38236289
                327296cb-1310-4a2e-b41d-17930397007a
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 10 August 2023
                : 3 January 2024
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100004200, Olle Engkvists Stiftelse;
                Award ID: 146-300-188
                Award ID: 146-300-188
                Award Recipient :
                Funded by: Uppsala University
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                Research
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                © Springer Science+Business Media, LLC, part of Springer Nature 2024

                Microbiology & Virology
                predator–prey interaction,urotricha pseudofurcata,grazing experiment,humic lakes

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