Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy

Abstract

Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both in both aquatic and terrestrial systems. Despite their well‐known significance, their taxonomy remains problematic and is the subject of much research. Taxonomic issues of Cyanobacteria have consequently led to inaccurate curation within known reference databases, ultimately leading to problematic taxonomic assignment during diversity studies. Recent advances in sequencing technologies have increased our ability to characterize and understand microbial communities, leading to the generation of thousands of sequences that require taxonomic assignment. We herein propose CyanoSeq (https://zenodo.org/record/7569105), a database of cyanobacterial 16S rRNA gene sequences with curated taxonomy. The taxonomy of CyanoSeq is based on the current state of cyanobacterial taxonomy, with ranks from the domain to genus level. Files are provided for use with common naive Bayes taxonomic classifiers, such as those included in DADA2 or the QIIME2 platform. Additionally, FASTA files are provided for creation of de novo phylogenetic trees with (near) full‐length 16S rRNA gene sequences to determine the phylogenetic relationship of cyanobacterial strains and/or ASV/OTUs. The database currently consists of 5410 cyanobacterial 16S rRNA gene sequences along with 123 Chloroplast, Bacterial, and Vampirovibrionia (formally Melainabacteria) sequences.

Spatiotemporal diversity and community structure of cyanobacteria and associated bacteria in the large shallow subtropical Lake Okeechobee (Florida, United States)

“…A total of six ASVs corresponded to Microcystis ( Supplementary Figure S4 ), which may be several different species of Microcystis . Microcystis species are known to form microcystin-producing blooms within Lake Okeechobee ( Kinley-Baird et al, 2021 ; Pokrzywinski et al, 2022 ), however both microcystin and non-microcystin producing Microcystis species are known to occur and bloom in Florida ( Lefler et al, 2020 , 2022 , 2023 ). Furthermore, recent phylogenomic analyses supported several of the morphologically different species of Microcystis , each with various toxigenic potential ( Cai et al, 2023 ).…”

“…Taxonomic assignment of ASVs was based on a naïve Bayesian classifying method ( Wang et al, 2007 ) with CyanoSeq V1.2 ( Lefler et al, 2023 ) and SILVA 138.1 ( Quast et al, 2012 ) as the taxonomic databases. The CyanoSeq database was supplemented with 16S rRNA sequences from unialgal cyanobacterial cultures isolated from Lake Okeechobee and surrounding fresh waters housed in the Berthold Laughinghouse Culture Collection (BLCC) at the University of Florida – IFAS, Fort Lauderdale Research and Education Center (Davie, FL, United States).…”

Microbial Diversity Impacts Non-Protein Amino Acid Production in Cyanobacterial Bloom Cultures Collected from Lake Winnipeg

“…The forward and reverse reads were then merged, and chimeras removed. Taxonomy was assigned using CyanoSeq (v1.1.2), consisting of a curated cyanobacterial 16S rRNA database containing 5411 cyanobacterial sequences [ 76 ] and SILVA (v138.1), and a database containing more than 2 million 16S/18S rRNA bacterial, archaiac, and eukaryotic sequences [ 77 ]. Taxonomic assignments were performed at the bootstrap levels of 50, 80, and 95.…”

Metabarcoding reveals unique microbial mat communities and evidence of biogeographic influence in low‐oxygen, high‐sulfur sinkholes and springs

“…ASVs identified as chloroplast or mitochondria in the 16S dataset were removed. The SILVA database (release 138.1, Quast et al., 2013 ) appended with CyanoSeq (Lefler et al., 2023 ) was employed to assign taxonomy to the 16S ASVs. For the rbc L dataset, taxonomy was assigned using the curated reference database Diat.barcode (Rimet et al., 2019 ).…”