Research Article: Incubation and grazing effects on spirotrich ciliate diversity inferred from molecular analyses of microcosm experiments

Date Published: May 6, 2019

Publisher: Public Library of Science

Author(s): Jean-David Grattepanche, Doris L. Juarez, Cameah C. Wood, George B. McManus, Laura A. Katz, Ute Risse-Buhl.


We used an experimental approach of analyzing marine microcosms to evaluate the impact of both predation (top-down) and food resources (bottom-up) on spirotrich ciliate communities. To assess the diversity, we used two molecular methods–denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (HTS). We carried out two types of experiments to measure top-down (adult copepods as predators) and bottom-up effects (phytoplankton as food resources) on the spirotrich ciliates. We observed both strong incubation effects (untreated controls departed from initial assessment of diversity) and high variability across replicates within treatments, particularly for the bottom-up experiments. This suggests a rapid community turn-over during incubation and differential susceptibility to the effects of experimental manipulation. Despite the variability, our analyses reveal some broad patterns such as (1) increasing adult copepod predator abundance had a greater impact on spirotrich ciliates than on other microbial eukaryotes; (2) there was no evidence for strong food selection by the dominant spirotrich ciliates.

Partial Text

The planktonic food web is the base of aquatic ecosystems, and hence strongly impacts the productivity and health of approximately two thirds of our planet. Diversity within the planktonic food web is great: prokaryotes recycling dissolved organic matter and small phytoplankton are eaten by heterotrophic microeukaryotes such as nanoflagellates and ciliates [1–3]. These predators and larger phytoplankton serve in their turn as prey for larger organisms, such as larger ciliates, dinoflagellates, and small metazoans including copepods, which are themselves consumed by larger invertebrates and fish [1, 2, 4]. Given these complex interactions, disentangling dynamics in planktonic food webs is difficult but essential for understanding both ecosystem function and health [5–7].

Although there was variability in the responses to the treatments in our various microcosms, some broad conclusions can be made. Overall, we found that ciliates were preferentially grazed by copepods, compared to other eukaryotes. The lack of clear reproducibility within our biological replicates suggest that the community was heterogeneous at very small scales (the size of our bag was around 500mL) or that the community responded ‘randomly’ to confinement. While surprising, this is in agreement with previous in situ observations failing to clearly relate spirotrich [54, 55, 71] and microbial eukaryote diversity [94, 95] to environmental parameters.




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