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Different substrates within a lake harbour connected but specialised microbial communities

  • Trends in Aquatic Ecology III
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Abstract

Natural water bodies contain physically interconnected habitats suitable for microbes, such as different water layers and substrates for biofilms. Yet, little is known on the extent to which microbial communities are shared between such habitats and whether differences and similarities are consistent between sites. Here we explicitly tested hypotheses on similarities between aquatic bacterial communities found floating in water, in association with daphnids and with copepods, within bottom sediments, and on littoral stones of a lake. Through high-throughput 16S rDNA amplicon sequencing, distinguishable patterns were retrieved between habitats. In particular, community composition was more similar between the two zooplankton taxa, between the two water depths, and was rather different in sediments, where a large fraction of the total diversity was present. Most bacterial taxa were restricted to one or few habitats, whereas only few were found as generalists on different habitats. Our results indicate a limited role of source–sink dynamics between habitats for aquatic bacteria. Similarly to patterns of diversity in larger organisms, community composition was different between habitats, potentially because of specific mechanisms creating and maintaining habitat filtering.

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Acknowledgments

This research has received funding from the IEF Marie Skłodowska-Curie Actions of the EU’s Horizon2020 program, Grant N° 655537 - RAVE. Sequencing was financed through the Laboratorio di Biodiversità Moleculare - Lifewatch Italy call and we particularly thank Graziano Pesole and Teresa De Filippis for their collaboration. We thank Birgit Stenzel and Giuliana Manfredini for the help with sampling and laboratory work, Cristiana Callieri and Roberto Bertoni for the valuable input on potential sampling stations and lake properties, Andrea Lami for advice on sediment sampling, and two anonymous reviewers for their helpful suggestions.

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  1. Microbial Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Largo Tonolli 50, 28922, Verbania, Italy

    Ester M. Eckert, Andrea Di Cesare, Gianluca Corno & Diego Fontaneto

  2. Water Research Institute, National Research Council of Italy (CNR-IRSA), Via Salaria Km 29,300, Monterotondo, 00015, Rome, Italy

    Stefano Amalfitano

  3. Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council of Italy (CNR-IBBE), Via Giovanni Amendola 165/A, 70126, Bari, Italy

    Caterina Manzari

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  1. Ester M. Eckert
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Electronic supplementary material

Below is the link to the electronic supplementary material.

10750_2019_4068_MOESM1_ESM.pdf

Supplementary material 1 (PDF 274 kb) Supplementary Fig. S1 Map of sampling scheme. Left box: Lake Maggiore, between Italy (IT) and Switzerland (CH), right box: location of the three sampling stations, A–C

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Supplementary material 2 (TXT 1242 kb) Supplementary Table S1 Raw OTU table for all replicates with summary of taxonomy for each OTU. Names of the sample report the station (A, B, or C), the habitat (e.g. water 10 m, copepods) and the replicate (a, b, or c)

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Supplementary material 3 (TXT 7 kb) Supplementary Table S2 Ten repetitions of the permutational analysis of variance (adonis) on Sorensen index (βsor) distance matrix to evaluate the contribution of sampling station (Place), habitat (Medium), and their interaction

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Supplementary material 4 (TXT 4 kb) Supplementary Table S3 Ten repetitions of nested analysis of variance (ANOVA) to test the effect of differences between habitats (Medium) and between sampling stations (Place) on α diversity

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Supplementary material 5 (TXT 7 kb) Supplementary Table S4 Ten repetitions of Tukey’s test for nested ANOVA differences between habitats on α diversity

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Supplementary material 6 (TXT 13 kb) Supplementary Table S5 Ten repetitions of generalised linear models (GLMs) considering quasi-Poisson distribution to test whether there was a connection between H-value and read number and B-value and read number

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Supplementary material 7 (TXT 10 kb) Supplementary Table S6 Ten repetitions of ANOVA with Tukey’s honestly significant differences post hoc test to evaluate differences in B-values between habitats

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Supplementary material 8 (TXT 10 kb) Supplementary Table S7 Ten repetitions of ANOVA with Tukey’s honestly significant differences post hoc test to evaluate differences in B-values between the 20 most abundant OTUs of each habitat

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Supplementary material 9 (TXT 14 kb) Supplementary Table S8 Summary of the taxonomy and abundance (read counts) of the OTUs assigned as generalists in each habitat

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Supplementary material 10 (TXT 44 kb) Supplementary Table S9 Summary of the taxonomy and abundance (read counts) of the OTUs assigned as specialists in each habitat

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Eckert, E.M., Amalfitano, S., Di Cesare, A. et al. Different substrates within a lake harbour connected but specialised microbial communities. Hydrobiologia 847, 1689–1704 (2020). https://doi.org/10.1007/s10750-019-04068-1

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  • Issue Date:

  • DOI: https://doi.org/10.1007/s10750-019-04068-1

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