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Water chemistry is known to be one of the most important factors controlling species composition of many macro-organisms in wetlands. It is unclear to what extent micro-organisms respond to water chemistry as compared to chemistry-mediated substratum structure. We explored how the assemblages of different groups of micro-organisms in bryophyte tufts of spring-fens were determined by water chemistry and substratum structure. The aim was to compare unicellular autotrophic diatoms, unicellular heterotrophic testate amoebae and multicellular heterotrophic monogonont rotifers. Assemblages of all three groups showed a strong compositional gradient correlated with water pH and conductivity, calcium concentration and dominance of Sphagnum. While a second strong gradient in species composition of diatoms and testate amoebae was explained by factors such as substratum structure and water content, that of rotifers remained unexplained. Unlike the other two groups, testate amoeba assemblages were significantly determined by phosphates. Nitrates and iron were important species composition determinants for diatoms. Rotifers differed from the other groups in that they did not respond significantly to silica, iron or nutrients. When variation caused by substratum characteristics and water chemistry were partitioned out, testate amoebae were controlled more by substratum, while rotifers and diatoms were controlled more by water chemistry. Variation explained by individual effects of substratum or water chemistry, as compared to shared effects, was much lower for rotifers than for testate amoebae and diatoms. Our results show that, in semi-terrestrial ecosystems, pH and calcium concentrations are generally the main drivers of variation in species composition of unicellular and multicellular microorganisms, mirroring well described patterns for macro-organisms, providing support for general ecological hypotheses. Other water chemistry variables differed between shell-forming and other organisms, and between autotrophic and heterotrophic organisms. Even though water chemistry variables controlled the structure of the bryophyte tufts that acted as substratum for the micro-organisms, both water chemistry and bryophyte structure effects were independently significant for diatoms and testate amoebae. On the other hand, no effects of either substratum characteristics or water chemistry were found for rotifers. This was because their species composition is not influenced by chemical factors, apart from pH and calcium, which both strongly influence the occurrence of Sphagnum HÁJKOVÁ, Petra, Jindřiška BOJKOVÁ, Markéta FRÁNKOVÁ, Věra OPRAVILOVÁ, Michal HÁJEK, Kateřina KINTROVÁ, and Michal HORSÁK. 2011. “Disentangling the Effects of Water Chemistry and Substratum Structure on Moss-Dwelling Unicellular and Multicellular Micro-Organisms in Spring-Fens”. Journal of Limnology 70 (s1):54-64. https://doi.org/10.4081/jlimnol.2011.s1.54. More Citation Formats ACM ACS APA ABNT Chicago Harvard MLA Turabian Vancouver Download Citation Endnote/Zotero/Mendeley (RIS) BibTeX Downloads Download data is not yet available. Citations List of Cited By : Hordeumgeniculatumin the Pannonian Basin: Ecological requirements and grassland vegetation on salt-affected soils P. Eliáš, D. Dítě, R. Šuvada, V. Píš, I. 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