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Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description

  • Environmental Microbiology
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Abstract

Rock varnish is a thin layer of Fe and Mn oxyhydroxides with embedded clay minerals that contain an increased Mn/Fe ratio compared to that of the Earth’s crust. Even if the study of rock varnish has important implications in several fields, the composition of epilithic bacterial communities and the distribution of taxa on varnish surfaces are still not wholly described. The aim of this study was (i) to identify the bacterial taxa which show the greatest variation between varnish and non-varnish environments, collected from the same rock, and (ii) to describe the morphology of epilithic communities through scanning electron microscopy (SEM). Triplicate samples of rock surfaces with varnish and triplicate samples without varnish were collected from five sites in Matsch Valley (South Tyrol, Italy). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing. Fifty-five ubiquitous taxa have been examined to assess variation between varnish and non-varnish. Cyanobacteria, Chloroflexi, Proteobacteria along with minor taxa such as Solirubrobacterales, Conexibaxter, and Rhodopila showed significant variations of abundance, diversity, or both responding to the ecology (presence/absence of varnish). Other taxa, such as the genus Edaphobacter, showed a more marked spatial variation responding to the sampling site. SEM images showed a multitude of bacterial morphologies and structures involved in the process of attachment and creation of a suitable environment for growth. The features emerging from this analysis suggest that the highly oxidative Fe and Mn-rich varnish environment favors anoxigenic autotrophy and establishment of highly specialized bacteria.

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Acknowledgments

We acknowledge the help of Kjell Jansson for his suggestions for SEM analysis, Boyke Bunk for bioinformatics, and Anders Andersson for his help in statistics. The present study was supported by the Erich-Ritter and the Herzog-Sellenberg Foundations within the Stifterverband für die Deutsche Wissenschaft within the EMERGE project (CUP I41J11000490007), and the grants from Liljevalchs fund, Stockholm University. English quality was edited by Dr. James Haile and Hilderd Crill.

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Authors and Affiliations

  1. Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 1, I-39100, Bozen-Bolzano, Italy

    Alfonso Esposito, Sonia Ciccazzo & Lorenzo Brusetti

  2. Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden

    Engy Ahmed & Sara J. M. Holmström

  3. Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, D-38124, Braunschweig, Germany

    Johannes Sikorski & Jörg Overmann

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  1. Alfonso Esposito
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Correspondence to Lorenzo Brusetti.

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Fig. SM1

Shannon (upper row) and Chao (lower row) diversity indices for Cyanobacteria, Solirubrobacterales and Conexibacter, and table with diversity indices values for each of the sites. (PPT 150 kb)

Fig. SM2

Bacterial community profile based on Illumina sequencing (on average 354494 reads per sample). Major (> 99.9 % of the reads) phyla, classes and orders are depicted. The table in the lower right quarter of the picture is a list of the other taxa divided according to their occurrence in one of the two environment or in both; the number of samples in which the taxa occur are given in the parenthesis. (PPT 385 kb)

Fig. SM3

Interactions between microbes and minerals: (A) structure analogous to figure 3G; with stone surface corrosion by filamentous bacteria from site 3 varnish; (B) filamentous forms colonizing a microfracture from non-varnish of site 4; (C) unknown structures from varnish of site 5; (D) unknown blood-cell like shapes from non-varnish of site 2; (E) cave buds of unknown origin from non-varnish sample of site 3; (F) putative rock-dwelling microcolonial fungi, from varnish of site 5; (G) analogous structure as in (F) plus enlargements of the biological structure (H-I) from varnish of site 3. (PPT 2333 kb)

Fig. SM4

Landscape pictures, extracellular structure and dividing cells: (A) micrometre thick coating on mineral surface from varnish of site 4; (B) landscape aspect of non-varnish samples of site 4; (C) filamentous form from varnish of site 3; (D) tetra-cocci with external slime from varnish of site 2; (E) coccal shape with external biofilms from varnish of site 3 and (F) varnish site 2; (G) coccal shapes adhering to the mineral surface, zoom from figure 2c; (H) reproducing bacteria from varnish of site 3 and (I) non-varnish of site 2. (PPT 2050 kb)

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Esposito, A., Ahmed, E., Ciccazzo, S. et al. Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description. Microb Ecol 70, 741–750 (2015). https://doi.org/10.1007/s00248-015-0617-4

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