Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: (a) Leaf-like thallus visualization of bacteria on a cross-section by 3D reconstruction of FISH image stacks. Eubacteria (red) and Alphaproteobacteria (yellow) were found widespread on both, the upper and the lower cortex, while Betaproteobacteria (pink) were less abundant and locally contained. Fungal hyphae (blue) and algae located under the upper cortex (green) were visualized without specific FISH probes, due to the naturally occurring fluorescence of the internal structures. (b) Model of the lichen symbiosis depicting the functional network of the participants. The model includes relevant functions of the colonizing bacteria, which are derived from metagenomic/metaproteomic analysis, as well as cultivation-dependent experiments.

Article Snippet: Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Bacteria, Algae, Fluorescence, Functional Assay, Derivative Assay

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: Principal Coordinates Analysis (PCoA) including 20 publicly available metagenomic datasets from MG-RAST and the Lobaria metagenome (red dot). All datasets were compared with subsytems and calculated using normalized values and the Bray-Curtis distance matrix. Single metagenomes from different biomes are labeled with their MG-RAST accession numbers and grouped in colored ellipses. The full colour version of this figure is available at ISME Journal online.

Article Snippet: Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Labeling

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: Functional recovery of the bacterial lichen microbiome metagenome on the metaproteomic level using Voronoi treemaps. The protein sequences were compared with metagenomic contigs by BLAST and then functionally characterized using HMMER3 and TIGRFAMs. Upper panel shows all functions covered by the metagenome (third level) and the respective subroles (second level) and main roles (first level). The mainrole labels are shown. On the lower panel, metaproteomic coverage is shown (blue cells: functions present only in the metagenome; grey cells: functions present in both metagenome and metaproteome).

Article Snippet: Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Functional Assay

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: (a) Leaf-like thallus visualization of bacteria on a cross-section by 3D reconstruction of FISH image stacks. Eubacteria (red) and Alphaproteobacteria (yellow) were found widespread on both, the upper and the lower cortex, while Betaproteobacteria (pink) were less abundant and locally contained. Fungal hyphae (blue) and algae located under the upper cortex (green) were visualized without specific FISH probes, due to the naturally occurring fluorescence of the internal structures. (b) Model of the lichen symbiosis depicting the functional network of the participants. The model includes relevant functions of the colonizing bacteria, which are derived from metagenomic/metaproteomic analysis, as well as cultivation-dependent experiments.

Article Snippet: Quality control and assembly of Illumina reads Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Fluorescence, Functional Assay, Derivative Assay

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: Principal Coordinates Analysis (PCoA) including 20 publicly available metagenomic datasets from MG-RAST and the Lobaria metagenome (red dot). All datasets were compared with subsytems and calculated using normalized values and the Bray-Curtis distance matrix. Single metagenomes from different biomes are labeled with their MG-RAST accession numbers and grouped in colored ellipses. The full colour version of this figure is available at ISME Journal online.

Article Snippet: Quality control and assembly of Illumina reads Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Labeling

Journal: The ISME Journal

Article Title: Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

doi: 10.1038/ismej.2014.138

Figure Lengend Snippet: Functional recovery of the bacterial lichen microbiome metagenome on the metaproteomic level using Voronoi treemaps. The protein sequences were compared with metagenomic contigs by BLAST and then functionally characterized using HMMER3 and TIGRFAMs. Upper panel shows all functions covered by the metagenome (third level) and the respective subroles (second level) and main roles (first level). The mainrole labels are shown. On the lower panel, metaproteomic coverage is shown (blue cells: functions present only in the metagenome; grey cells: functions present in both metagenome and metaproteome).

Article Snippet: Quality control and assembly of Illumina reads Illumina HiSeq 2000 paired-end metagenomic DNA sequencing reads (GATC Biotech) were initially quality-checked using the FastQC program.

Techniques: Functional Assay