DOI: 10.7291/d1mh4w
title: Genome sequence and characterization of a freshwater photoarsenotroph, Cereibacter azotoformans strain ORIO, isolated from sediments capable of cyclic light-dark arsenic oxidation and reduction

description: 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 sediment
 demonstrated the interconversion of arsenite and arsenate was dependent on
 light-dark cycling. arxA and arrA (arsenate respiratory reductase) genes
 were detected in the light-dark cycled sediment metagenomes suggesting
 syntrophic interactions among arsenotrophs. This work establishes
 Cereibacter azotoformans str. ORIO as a new model organism for studying
 photoarsenotrophy and light-dark arsenic biogeochemical cycling.
description: 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
description: 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
description: # 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 testing the effects of either arsenate or arsenite on aerobic growth. The csv file is read into the jupyter notebook (fig\_2\_growth\_curve\_dryad.ipynb) that renders the figures shown in Figure 2AB of the manuscript. * fig2C\_data\_dryad.csv: this data set contains the OD600nm values of a time course growth experiment testing how increasing levels of arsenite affect the anaerobic growth of *Cereibacter azotoformans* strain ORIO. The csv file is read into the jupyter notebook (fig\_2\_growth\_curve.ipynb) and renders Figure 2C of the manuscript. * fig4\_data\_dryad.csv: the data is used to produce Figure 4 of the manuscript. This was a microcosm experiment was done with three replicates containing Owens River sediments and Little Hot Creek water spiked with 50 µM arsenite. The three microcosms were first incubated in the dark, then shifted into the light, then shifted back to the dark, and finally shifted into the light. Over the time course of light shifting, arsenate and arsenite were measured by HPLC-ICPMS in each of the three replicate microcosms. The jupyter notebook, fig\_4\_light\_dark\_cycling\_dryad.ipynb can be used with figure4\_data\_dryad.csv to generate the plot shown in Figure 4 of the manuscript. # Sharing/Access information Links to publicly accessible locations of the various genome sequencing data (as described above): * [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA814312](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA814312) * [https://www.ncbi.nlm.nih.gov/bioproject/808117](https://www.ncbi.nlm.nih.gov/bioproject/808117) * [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_022227035.1/](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_022227035.1/) Data was derived from the following sources: * Laboratory experiments conducted in the Saltikov lab at UC Santa Cruz # Code/Software Python jupyter notebook scripts are provided for generating the plots in the figures: * fig\_2\_growth\_curve\_dryad.ipynb * fig\_4\_light\_dark\_cycling\_dryad.ipynb