4 research outputs found

    Design and Evaluation of Illumina MiSeq Compatible 18S rRNA Gene Primers for Improved Characterization of Mixed Phototrophic Communities

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    A systematic analysis of the most commonly amplified 18S rRNA hypervariable regions and the effect that PCR/sequencing bias has on community representation. The V4 and V8-V9 hypervariable regions were amplified for seven mock communities and for freshwater, marine, and wastewater samples to compare the sequenced community structure to theoretical communities and validate these results with environmental samples. This project contains mothur script files for analyzing the data

    Comparable nutrient uptake across diel cycles from three distinct algal communities

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    Three algal communities cultured from inocula sourced from geographically distinct locations within the continental United States were maintained under identical sequencing-batch growth conditions in photobioreactors and sampled over 82 days. Communities were sequenced via both V4 and V8-V9 18S rRNA gene sequencing. Mothur and R were used to analyze sequencing data and to describe and compare community dynamics within and between communities. This project includes both mothur and R script files used to analyze the data

    A combined culture-dependent and culture-independent approach highlights the prevalence of diverse manganese(II)-oxidizing bacteria in drinking water systems.

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    <p>16S rRNA pyrosequencing data from the Ann Arbor Drinking Water system for samples collected from June 2010 to August 2011. The dataset includes six files:</p> <p>1. marcus.dwtp.fasta and marcus.dwds.fasta: unique fasta sequences that are quality trimmed and chimera free for the drinking water treatment plant (dwtp) and distribution system (dwds). The sequences were aligned to the SILVA seed alignment available through mothur, filtered, and and degapped prior to blastn analyses as described in the manuscript.</p> <p>2. marcus.dwtp.names and marcus.dwds.names: names file generated by mothur and linked to the fasta files for the dwtp and dwds.</p> <p>3. marcus.dwtp.groups and marcus.dwds.groups: groups file generated by mothur and linked to the dwtp and dwds specific fasta and names files. The group file relates each sequence to the sampling location and sampling timepoint associated with it. Specifically, the format is "location.timepoint". Timepoints range from Jun10-Aug11 which are from June 2010 to August 2011. The sampling locations include numeric values in the marcus.dwds.groups file with 1-13 as locations in the drinking water distribution system, while the locations in the marcus.dwtp.groups file are r,w,i,f,e,re which refer to sampling locations in the river (source water), well (source water), filter influent, filter bed, filter effluent, and final reservoir - all of which were collected in the drinking water treatment plant.</p

    Figure 1/S1: Ribosomal protein alignment - Metagenomic Evidence for the Presence of Comammox Nitrospira-like bacteria in a Drinking Water System

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    <p>Alignment used to construct RAxML (1) based maximum likelihood phylogenetic tree corresponding to the radial cladogram in Figure 1A in the main manuscript and annotated tree in the supplementary material Figure S1. 16 syntetic ribosomal proteins (2) were aligned separately with correponding sequence from the Nitrospira metagenome bin using muscle (3) . Each protein alignment was trimmed using trimal with the gappyout flag (4) and the trimmed alingments were concantenated to create a superalignment using FasconCAT (5). </p> <p> </p> <p>1. Stamatakis A. 2014. RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 30: 1312-1313. doi: 10.1093/bioinformatics/btu033.</p> <p>2. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 4. doi: 10.1038/ncomms3120</p> <p>3. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797</p> <p>4. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973. doi: 10.1093/bioinformatics/btp348</p> <p>5. Kück P, Meusemann K. 2010. FASconCAT: Convenient handling of data matrices. Molecular Phylogenetics and Evolution 56:1115-1118.</p> <p> </p
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