ssu rrna sequence tags  (Pyrosequencing Inc)

Journal: mSphere

Article Title: Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential

doi: 10.1128/mSphere.00759-21

Figure Lengend Snippet: Abundances of real-time PCR-targeted coding regions in the candidate pal biosynthetic gene cluster in Antarctic ascidian samples. (A) Gene copies estimated for three targeted coding regions (acyltransferase AT1, 3-hydroxy-methyl-glutaryl coenzyme A synthase [HCS], and the condensation domain of a nonribosomal peptide synthase [NRPS]) in the candidate pal biosynthetic gene cluster surveyed over 63 DNA extracts derived from microbial cell preparations enriched from the Antarctic ascidian Synoicum adarenum. Nine samples were collected at each of seven sites: Bonaparte Point (Bon), Delaca Island (Del), Janus Island (Jan), Killer Whale Rocks (Kil), Laggard Island (Lag), Litchfield Island (Lit), and Norsel Point (Nor) . (B) Relationship between gene copy number for the three gene targets and the 16S rRNA gene ASV occurrences of Opitutaceae -related ASV_15 across a 63 S. adareanum microbial DNA sample set. Asterisks indicate samples Bon-1C-2011 and Del-2b-2011 that were selected for PacBio sequencing.

Article Snippet: Taxonomic attribution of the BGC was inferred using a real-time PCR strategy targeting three coding regions of the putative palmerolide A BGC spanning the length of the cluster (acyltransferase AT1, hydroxymethylglutaryl Co-A synthase [HCS], and the condensation domain of the nonribosomal peptide synthase NRPS; ) to assay a Synoicum microbiome collection of 63 samples that have been taxonomically classified using Illumina small-subunit (SSU) rRNA gene tag sequencing ( ).

Techniques: Real-time Polymerase Chain Reaction, Derivative Assay, PacBio Sequencing

Journal: bioRxiv

Article Title: Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential

doi: 10.1101/2021.05.05.442870

Figure Lengend Snippet: Abundances of real time PCR-targeted coding regions in the candidate pal biosynthetic gene cluster in Antarctic ascidian samples. (A) Gene copies estimated for three targeted coding regions (Acyltransferase, AT1; 3-hydroxy-methyl-glutaryl coenzyme A synthase, HCS; and the condensation domain of a non-ribosomal peptide synthase; NRPS) in the candidate pal biosynthetic gene cluster surveyed over 63 DNA extracts derived from microbial cell preparations enriched from the Antarctic ascidian Synoicum adarenum . Nine samples were collected at each of seven sites: Bon, Bonaparte Point; Del, Delaca Island; Jan, Janus Island, Kil, Killer Whale Rocks; Lag, Laggard Island, Lit, Litchfield Island; Nor, Norsel Point . (B) Relationship between gene copy number for the three gene targets and the 16S rRNA gene ASV occurrences of Opitutaceae-related ASV_15 across a 63 S. adareanum microbial DNA sample set. * indicates samples Bon-1C-2011 and Del-2b-2011 that were selected for PacBio sequencing.

Article Snippet: Taxonomic attribution of the BGC was inferred using a real time PCR strategy targeting three coding regions of the putative palmerolide A BGC spanning the length of the cluster (acyltransferase, AT1; hydroxymethylglutaryl Co-A synthase, HCS, and the condensation domain of the non-ribosomal peptide synthase NRPS, ) to assay a Synoicum microbiome collection of 63 samples that have been taxonomically classified using Illumina SSU rRNA gene tag sequencing ( ).

Techniques: Real-time Polymerase Chain Reaction, Derivative Assay, PacBio Sequencing

Journal: The ISME Journal

Article Title: Distinct microbial communities associated with buried soils in the Siberian tundra

doi: 10.1038/ismej.2013.219

Figure Lengend Snippet: Schematic drawings of one representative soil pit profile for each vegetation type (shrubby grass tundra: pit C, shrubby tussock tundra: pit D and shrubby lichen tundra: pit I). O, Oe, Oa, OA, A, AB: topsoil, BCg, Cg: subsoil. Ajj: buried topsoils, PF: permafrost (depth in cm below surface indicated in brackets). Location of buried topsoils (Ajj) is indicated and labeled with the corresponding sample ID. If sample IDs are missing, location of the soil sample was only reported in the soil pit description, but not included in the drawings. Bar charts show abundances of Bacteria and Fungi as bacterial and fungal SSU gene copy numbers g−1 dry soil (logarithmic scale). Supplementary Figures S3A–C provide information on SSU rRNA gene quantifications for all nine soil pits (three replicates per vegetation type, including the ones presented in this figure).

Article Snippet: None of the measured soil parameters were significantly correlated with species richness and diversity in subsoils. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3 caption a7 Prokaryotic ( a ) and fungal ( b ) community structure shown as relative abundance on phylum level and based on SSU rRNA gene Illumina tag sequencing and fungal ITS pyrosequencing, respectively.

Techniques: Labeling, Bacteria

Journal: The ISME Journal

Article Title: Distinct microbial communities associated with buried soils in the Siberian tundra

doi: 10.1038/ismej.2013.219

Figure Lengend Snippet: Fungal–bacterial (FB) ratios for the three different sampling sites as calculated from bacterial and fungal SSU rRNA gene copies g−1 dry soil. Small letters indicate significant differences between soil horizons as determined by one-way ANOVA and Tukey's HSD test.

Article Snippet: None of the measured soil parameters were significantly correlated with species richness and diversity in subsoils. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3 caption a7 Prokaryotic ( a ) and fungal ( b ) community structure shown as relative abundance on phylum level and based on SSU rRNA gene Illumina tag sequencing and fungal ITS pyrosequencing, respectively.

Techniques: Sampling

Journal: The ISME Journal

Article Title: Distinct microbial communities associated with buried soils in the Siberian tundra

doi: 10.1038/ismej.2013.219

Figure Lengend Snippet: Prokaryotic (a) and fungal (b) community structure shown as relative abundance on phylum level and based on SSU rRNA gene Illumina tag sequencing and fungal ITS pyrosequencing, respectively. ‘Others' include phyla with <0.5% relative abundance (see Supplementary Tables S2 and S3 in the supplementary for detailed information). Number of samples analyzed given in brackets.

Article Snippet: None of the measured soil parameters were significantly correlated with species richness and diversity in subsoils. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3 caption a7 Prokaryotic ( a ) and fungal ( b ) community structure shown as relative abundance on phylum level and based on SSU rRNA gene Illumina tag sequencing and fungal ITS pyrosequencing, respectively.

Techniques: Sequencing