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 genetika MeSH
- Actinobacteria genetika MeSH
- Chloroflexi genetika MeSH
- genom bakteriální genetika MeSH
- metagenom genetika MeSH
- metagenomika metody MeSH
- mikrobiota fyziologie MeSH
- nátěrové hmoty MeSH
- oxidy MeSH
- půdní mikrobiologie * MeSH
- sloučeniny manganu MeSH
- železo MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem 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 klasifikace genetika izolace a purifikace MeSH
- cévnaté rostliny MeSH
- DNA bakterií genetika MeSH
- fylogeneze MeSH
- genom bakteriální genetika MeSH
- lesy MeSH
- mastné kyseliny analýza MeSH
- metabolismus sacharidů genetika MeSH
- polysacharidy metabolismus MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S genetika MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- techniky typizace bakterií MeSH
- veřejné parky MeSH
- zastoupení bazí genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika 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 genetika MeSH
- Actinobacteria genetika MeSH
- Bacteroidetes genetika MeSH
- biodiverzita MeSH
- Chlorophyta genetika MeSH
- denaturační gradientová gelová elektroforéza MeSH
- ekosystém MeSH
- houby klasifikace genetika MeSH
- Proteobacteria genetika MeSH
- půda chemie MeSH
- půdní mikrobiologie MeSH
- RNA ribozomální genetika MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sinice genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Antarktida 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 genetika izolace a purifikace metabolismus MeSH
- biodegradace MeSH
- biotransformace MeSH
- fylogeneze MeSH
- lesy MeSH
- molekulární sekvence - údaje MeSH
- půdní mikrobiologie * MeSH
- rostliny metabolismus mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
