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Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets

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Abstract

Deep sequencing of prokaryotic 16S rDNA regularly reveals thousands of microbial species thriving in many common habitats. It is still unknown how this huge microbial diversity, including many potentially competing organisms, may persist at a single site. One of plausible hypotheses is that a large number of spatially separated microcommunities exist within each complex habitat. Smaller subset of the species may exist in each microcommunity and actually interact with each other. We sampled two groups of microbial stalactites growing at a single acidic mine drainage outlet as a model of multiplicated, low-complexity microhabitat. Samples from six other sites were added for comparison. Both tRFLP and 16S rDNA pyrosequencing showed that microbial communities containing 6 to 51 species-level operational taxonomic units (OTU) inhabited all stalactites. Interestingly, most OTUs including the highly abundant ones unpredictably alternated regardless of physical and environmental distance of the stalactites. As a result, the communities clustered independently on sample site and other variables when using both phylogenetic dissimilarity and OTU abundance metrics. Interestingly, artificial communities generated by pooling the biota of several adjacent stalactites together clustered by the locality more strongly than when the stalactites were analyzed separately. The most probable interpretation is that each stalactite contains likely random selection from the pool of plausible species. Such degree of stochasticity in assembly of extremophilic microbial communities is significantly greater than commonly proposed and requires caution when interpreting microbial diversity.

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Acknowledgments

This work was supported by the Charles University in Prague (project GA UK 528613) and Charles University specific research grant no. SVV 260 208/2015.

We thank to Jan Černý for providing molecular biology laboratory, Petr Baldrian for providing the 454 sequencing facility and help with sample preparation, Jan Kotris for enabling prospection of the Zlaté Hory mine, Pavel Chaloupka for enabling prospection of the Lehnschafter mine, Tomáš Herben and Jana Škodová for the significant help with statistical methods, Petr Drahota for chemical analyses, and Johana Rotterová for thorough language correction.

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Correspondence to Lukáš Falteisek.

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Fig. S1

Appearance of the sampling sites. Scale bar: A, B, G = 1 m, C, D, E, F 10 = cm. a. ZH-A, Zlaté Hory. b. ZH-B, Zlaté Hory. c. MI, Lehnschafter mine, Mikulov. d. BS, Banská Štiavnica. e. ZH7, Zlaté Hory. f. KU, Kristýnov mine, Plzeň. g. ZH10, Zlaté Hory. (JPG 1648 kb)

Fig S2

a. Results of clustering of the microbial communities determined from presence/absence and abundance of principal OTUs using tree-building algorithms. b. UPGMA clustering of the microbial communities based on unweighted UniFrac metrics. Jackknife values higher than 50 % are shown at the nodes. (JPG 151 kb)

Table S1

Basic characteristics of the sequenced samples. Legend: water flow: 0—hanging drop, no dripping observed; 1—rare dripping; 2—intensive dripping; 3—continuous flow; OTU/80 % sequences—number of OTUs in the upper 80 % of sequences sorted by abundance. (DOC 50 kb)

Table S2

a. Results of identification of the OTUs by BLAST against the GenBank nt/nr database. The first identified BLAST hit is shown for each OTU. b. Distribution of the OTUs among the samples. c. Rarefaction curves showing coverage of the microbial diversity in the samples. Increment was 25 sequences per each step. (XLS 168 kb)

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Falteisek, L., Duchoslav, V. & Čepička, I. Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets. Microb Ecol 72, 163–174 (2016). https://doi.org/10.1007/s00248-016-0760-6

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