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Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition

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Abstract

Coniferous forest soils have an indispensable ecological role in the global cycles of nutrients on Earth. Despite the fact that microbial communities in this ecosystem were subject of multiple studies, the involvement of individual taxa in the processes of organic matter transformation and the functional roles of dominant and active bacteria are largely unknown. Here, we have performed a comprehensive isolation effort to obtain multiple dominant bacterial taxa from a Picea abies forest soil and provide their physiological characterization. This information allows us to link ecological traits with groups of microorganisms. In the study, conventional culture techniques at acidic pH and low-nutrient content led to the recovery of 299 bacterial isolates. The isolates represented operational taxonomic units (OTUs) that contained 20 and 32 % of all bacterial genomes detected in the litter and soil by 16S amplicon analysis, including some of those bacterial strains representing the most abundant and active OTUs. These included also several isolates of the still underexplored phylum of the Acidobacteria, all of them belonging to the subdivision 1 of the phylum. Acidobacterial isolates produced the widest range of enzymes among all isolates and highest enzyme activities in acidic conditions. Moreover, members of the Acidobacteria represented more than 50 % of the isolates able to grow on disaccharides produced during the breakdown of cellulose, chitin, and starch. Our results indicate that Acidobacteria may play an important ecological role by degrading polysaccharides of plant and fungal origin in the important ecosystems of acidic coniferous forests.

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Acknowledgments

This work was supported by the Czech Science Foundation (14-09040P), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA agreement no. 289949 (TRAINBIODIVERSE), and by the Research Concept of the Institute of Microbiology ASCR (RVO61388971).

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Authors and Affiliations

  1. Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Vídeňská 1083, 14220, Praha 4, Czech Republic

    Salvador Lladó, Lucia Žifčáková, Tomáš Větrovský, Ivana Eichlerová & Petr Baldrian

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  1. Salvador Lladó
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  2. Lucia Žifčáková
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  3. Tomáš Větrovský
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  4. Ivana Eichlerová
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Correspondence to Salvador Lladó.

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Figure S1

Phylogenetic tree of the partial 16S rRNA gene sequences showing the placement of bacterial isolates from the Picea abies forest litter and soil. The Neighbor-Joining tree was calculated from an alignment of 667 nucleotide positions using MEGA 6. Bootstrap values (1000 replicates) above 50% are shown next to the branches. The evolutionary distances were inferred using the Tamura-Nei method. GenBank accession numbers are displayed in parentheses. The bar indicates 0.05 substitutions per nucleotide position. (PPTX 31 kb)

Figure S2

Principal component analysis (PCA) biplot of data showing scores and the eleven most important variable vectors. Percent variability explained by each principal component is shown in parentheses after each axis legend. Red circles: Acidobacteria; green triangles: Bacteroidetes; blue triangle: Actinobacteria; yellow squares: Proteobacteria. (PPTX 67 kb)

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Lladó, S., Žifčáková, L., Větrovský, T. et al. Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition. Biol Fertil Soils 52, 251–260 (2016). https://doi.org/10.1007/s00374-015-1072-6

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