Rock varnish is a microbial habitat, characterised by thin (5-500 μm) and shiny coatings of iron (Fe) and manganese (Mn) oxides associated with clay minerals. This structure is well studied by geologists, and recently there have been reports about the taxonomical composition of its microbiome. In this study, we investigated the rock varnish microbiome using shotgun metagenomics together with analyses of elemental composition, lipid and small molecule biomarkers, and rock surface analyses to explore the biogeography of microbial communities and their functional features. We report taxa and encoded functions represented in metagenomes retrieved from varnish or non-varnish samples, additionally, eight nearly complete genomes have been reconstructed spanning four phyla (Acidobacteria, Actinobacteria, Chloroflexi and TM7). The functional and taxonomic analyses presented in this study provide new insights into the ecosystem dynamics and survival strategies of microbial communities inhabiting varnish and non-varnish rock surfaces.

• MeSH
• Acidobacteria genetics   MeSH
• Actinobacteria genetics   MeSH
• Chloroflexi genetics   MeSH
• Genome, Bacterial genetics   MeSH
• Metagenome genetics   MeSH
• Metagenomics methods   MeSH
• Microbiota physiology   MeSH
• Paint MeSH
• Oxides MeSH
• Soil Microbiology * MeSH
• Manganese Compounds MeSH
• Iron MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

During the course of a study assessing the bacterial diversity of a coniferous forest soil (pH 3.8) in the Bohemian Forest National Park (Czech Republic), we isolated strain S15(T) which corresponded to one of the most abundant soil OTUs. Strain S15(T) is represented by Gram-negative, motile, rod-like cells that are 0.3-0.5μm in diameter and 0.9-1.1μm in length. Its pH range for growth was 3-6, with optimal conditions found at approximately 4-5. It can grow at temperatures between 20°C and 28°C, with optimum growth at 22-24°C. Its respiratory quinone is MK-8, and its main fatty acid is iso-C15:0 (73.7%). The G+C DNA content was 58.2mol%. According to the 16S rRNA gene sequence analysis, strain S15(T) belongs to subdivision 1 of the phylum Acidobacteria, being affiliated to the cluster of Acidipila rosea AP8(T) and Acidobacterium capsulatum ATCC 51196(T). Analysis of the S15(T) genome revealed the presence of 404 genes that are involved in carbohydrate metabolism, which indicates the metabolic potential to degrade polysaccharides of plant and fungal origin. Based on genotypic and phenotypic characteristics, the strain S15(T) represents a new genus and species within the family Acidobacteriaceae, for which the name Silvibacterium bohemicum gen. nov., sp. nov. is proposed (type strain S15(T)=LMG 28607(T)=CECT 8790(T)).

• MeSH
• Acidobacteria classification   genetics   isolation & purification   MeSH
• Tracheophyta MeSH
• DNA, Bacterial genetics   MeSH
• Phylogeny MeSH
• Genome, Bacterial genetics   MeSH
• Forests MeSH
• Fatty Acids analysis   MeSH
• Carbohydrate Metabolism genetics   MeSH
• Polysaccharides metabolism   MeSH
• Soil Microbiology * MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Base Sequence MeSH
• Sequence Analysis, DNA MeSH
• Bacterial Typing Techniques MeSH
• Parks, Recreational MeSH
• Base Composition genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH

The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematoda were present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations.

• MeSH
• Acidobacteria genetics   MeSH
• Actinobacteria genetics   MeSH
• Bacteroidetes genetics   MeSH
• Biodiversity MeSH
• Chlorophyta genetics   MeSH
• Denaturing Gradient Gel Electrophoresis MeSH
• Ecosystem MeSH
• Fungi classification   genetics   MeSH
• Proteobacteria genetics   MeSH
• Soil chemistry   MeSH
• Soil Microbiology MeSH
• RNA, Ribosomal genetics   MeSH
• Base Sequence MeSH
• Sequence Analysis, DNA MeSH
• Cyanobacteria genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Antarctic Regions MeSH

Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55(T), which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55(T) include Bryocella elongata SN10(T) (95.4% identity), Acidicapsa ligni WH120(T) (95.2% identity), and Telmatobacter bradus TPB6017(T) (95.0% identity), revealing that strain S55(T) should be classified within the phylum Acidobacteria, subdivision 1. Strain S55(T) is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55(T) corresponds to a new genus within the phylum Acidobacteria; thus, we propose the name Terracidiphilus gabretensis gen. nov., sp. nov. (strain S55(T) = NBRC 111238(T) = CECT 8791(T)). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55(T) also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55(T) being expressed in the forest soil, especially during winter. Our results suggest an important contribution of T. gabretensis S55(T) in the carbon cycle in the Picea abies coniferous forest.

• MeSH
• Acidobacteria genetics   isolation & purification   metabolism   MeSH
• Biodegradation, Environmental MeSH
• Biotransformation MeSH
• Phylogeny MeSH
• Forests MeSH
• Molecular Sequence Data MeSH
• Soil Microbiology * MeSH
• Plants metabolism   microbiology   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Changes in the abundance of bacteria and fungi and in the composition of bacterial communities during primary succession were investigated in a brown coal mine deposit area near Sokolov, the Czech Republic, using phospholipid fatty acids analysis, microarray and 16S rRNA gene sequencing. The study considered a chronosequence of sites undergoing spontaneous succession: 6-, 12-, 21- and 45-year-old and a 21-year-old site revegetated with Alnus glutinosa. During succession, organic carbon and the total nitrogen content increased while the pH and the C/N ratio decreased. Microbial biomass and bacterial diversity increased until 21 years and decreased later; bacteria dominated over fungi in the initial and late phases of succession. Bacterial community composition of the 6-year-old site with no vegetation cover largely differed from the older sites, especially by a higher content of Gammaproteobacteria, Cyanobacteria and some Alphaproteobacteria. Bacteria belonging to the genera Acidithiobacillus, Thiobacillus and related taxa, the CO(2) and N(2) fixers, dominated the community at this site. In the later phases, bacterial community development seemed to reflect more the changes in soil nutrient content and pH than vegetation with a decrease of Actinobacteria and an increase of Acidobacteria. The site revegetated with A. glutinosa resembled the 45-year-old primary succession site and exhibited an even lower pH and C/N ratio, indicating that recultivation is able to accelerate soil development.

• MeSH
• Acidobacteria MeSH
• Actinobacteria genetics   growth & development   MeSH
• Alphaproteobacteria genetics   growth & development   MeSH
• Bacteria classification   genetics   growth & development   MeSH
• Biodiversity MeSH
• Biomass MeSH
• DNA, Bacterial analysis   MeSH
• Nitrogen analysis   metabolism   MeSH
• Phylogeny MeSH
• Genes, rRNA MeSH
• Fungi genetics   growth & development   MeSH
• Molecular Sequence Data MeSH
• Environmental Monitoring MeSH
• Soil chemistry   MeSH
• Soil Microbiology MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Base Sequence MeSH
• Cyanobacteria genetics   growth & development   MeSH
• Coal Mining MeSH
• Coal MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH