Genome sequence and characterization of a freshwater photoarsenotroph, Cereibacter azotoformans strain ORIO, isolated from sediments capable of cyclic light-dark arsenic oxidation and reduction

A freshwater photosynthetic arsenite-oxidizing bacterium, Cereibacter azotoformans strain ORIO, was isolated from Owens River, CA, USA.  The waters from Owens River are elevated in arsenic and serve as the headwaters to the Los Angeles Aqueduct.  The complete genome sequence of strain ORIO is 4.8 Mb genome (68 % G+C content) and comprises 2 chromosomes and 6 plasmids. Taxonomic analysis placed ORIO within the Cereibacter genus (formerly Rhodobacter). The ORIO genome contains arxB2AB1CD (encoding an arsenite oxidase), arxXSR (regulators), and several ars arsenic resistance genes all co-localized on a 136 kb plasmid, named pORIO3. Phylogenetic analysis of ArxA, the molybdenum-containing arsenite oxidase catalytic subunit, demonstrated photoarsenotrophy is likely to occur within members of the Alphaproteobacteria. ORIO is a mixotroph, oxidizes arsenite to arsenate photoheterotrophically, and expresses arxA in cultures grown with arsenite. Further ecophysiology studies with Owens River sedi..., The published paper describes data generation and collection.  Briefly the methods include:

Enrichment cultring of anoxygenic photosynthetic microbes
Growth curve analyses
Arsenic analyses by HPLC-ICPMS (Thermo X-Series2 ICP-MS and Hamilton PRP-X-100 HPLC column for arsenic speciation)
Genomic DNA sequencing by MiSeq and Oxford Nanopore
Metagenomic DNA sequencing by Oxford Nanopore
, The manuscript describes specific workflows and pipelines.  Briefly the software includes:

Oxford Nanopore Guppy v5.0.17
Assembly using PATRIC, now called BACTERIAL AND VIRAL BIOINFORMATICS RESOURCE CENTER https://www.bv-brc.org/
ToulligQC v2.1.1
Racon
Phylogeny using custom R script that can be found at https://github.com/csaltikov/arsenotrophy_phylogeny.
Various python scripts for producing data visualizations in the manuscript
, # Genome sequence and characterization of a freshwater photoarsenotroph, *Cereibacter azotoformans* strain ORIO

# Dataset contents include:

Sediment metagenomes from Owens River, an arsenic-rich freshwater environment in California (USA):

* [https://www.ncbi.nlm.nih.gov/bioproject/814312](https://www.ncbi.nlm.nih.gov/bioproject/814312): Genome sequencing and assembly for 12 MAGs and 3 SRA of the Oxford Nanopore Minion raw data.

The *Cereibacter azotoformans* str. ORIO genome sequencing assembly and raw data:

* [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_022227035.1/](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_022227035.1/): all the information regrading the ORIO genome can be found through this link at the NCBI. The refSeq is GCF\_022227035.1. The BioSample ID is SAMN20253214. The SRA is SAMN20253214.

Growth curve data:

* fig2AB\_data\_dryad.csv: contains the mean OD600nm values of a time course growth experiment conducted with *Cereibacter azotoformans* strain ORIO t...