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Pipeline publication

[…] assembled using Code Aligner (CodonCode Corporation; www.codoncode.com) prior to phylogenetic analyses. Sequences were deposited in GenBank with accession numbers KJ636536-KJ636761., When not indicated otherwise, microbialite samples were collected near the water surface., Environmental 16S rRNA gene sequences retrieved from our samples were compared with sequences in the GenBank database (http://www.ncbi.nlm.nih.gov/) by BLAST (Altschul et al., ). We retrieved the closest sequences found in the database and included them in an alignment containing also sequences from the closest cultivated members and some representative sequences of major cyanobacterial taxa. Sequences were aligned using MUSCLE (Edgar, ). Ambiguously aligned positions and gaps were eliminated using Gblocks (Castresana, ). The resulting sequence alignments were used as input to build phylogenetic trees by approximate maximum likelihood using Fasttree (Price et al., ) with a General Time Reversible (GTR) model of sequence evolution, and taking among-site rate variation into account by using a four-category discrete approximation of a Γ distribution. ML bootstrap proportions were inferred using 1000 replicates. Trees were visualized with FigTree (http://tree.bio.ed.ac.uk/software/figtree/)., Samples of freshly collected aquaria biofilms and microbial mat samples were briefly rinsed in abundant distilled water to avoid the formation of extracellular precipitates upon drying, as previously described (Couradeau et al., , ). Then, small sample fragments were deposited onto on formvar-coated transmission electron microscopy (TEM) cupper microscopy grids and let dry. Scanning electron microscopy (SEM) analyses were performed using a Zeiss ultra 55 SEM equipped with a field emission gun. Images were collected in backscattered electron (BSE) mode with a Zeiss Ultra 55 FEG-SEM operating at 10 kV with a 30 μm aperture and a working di […]

Pipeline specifications

Software tools MUSCLE, Gblocks, FastTree, FigTree