Abstract:

The data provided here show a draft genome sequence of Nitrosomonas sp. strain APG5, an ammonia-oxidizing bacterium isolated from beach sand. In 2008, Nitrosomonas sp. strain APG5 was isolated from a dry sand sample collected from Edmonds Ferry Dock Beach locates in the Puget Sound, which is historically and routinely contaminated by small oil spills due to heavy ship transportation including a state-run ferry system. The bacterium was isolated and characterized because no ammonia-oxidizing bacterium has been isolated from beach sand and deposited in public culture collections. It hinders the study of the ecological response of nitrification to oil spills and its impact on the marine nitrogen cycling. To get insights into marine nitrogen cycling, we determined a draft genome sequence of Nitrosomonas sp. strain APG5. The bacterium was deposited in public culture collections and the genome dataset is now in public.

Suggested Citation:

Urakawa, Hidetoshi; Lopez, Jose. 2019. Isolation and characterization of ammonia-oxidizing bacterium Nitrosomonas sp. strain APG5, Puget Sound, Washington, 2008-10-26. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-fnva-0v52

Publications:

Urakawa, H., Skutas, J., & Lopez, J. V. (2019). Draft Genome Sequence of Nitrosomonas sp. Strain APG5, a Betaproteobacterial Ammonia-Oxidizing Bacterium Isolated from Beach Sand. Microbiology Resource Announcements, 8(21). doi:10.1128/mra.01573-18

Purpose:

Together with ammonia-oxidizing archaea, ammonia-oxidizing bacteria (AOB) play important roles in both natural and artificial environments. However, AOB are sensitive to environmental stressors such as hydrocarbon contaminants and serve as valuable ecological indicators. We isolated, characterized and sequenced the genome of this bacterium to use it for future oil toxicity studies. Data obtained from pure cultures will be used to assess ecological responses and resilience of nitrifying communities to hydrocarbons. Nitrosomonas sp. strain APG5 was deposited in public culture collections (NCIMB 14870 = ATCC TSA-116) and available for all researchers.

Data Parameters and Units:

Organism/Name, Strain, CladeID, BioSample, BioProject, Assembly, Level, Size (Mb), GC %, Replicons, WGS, Scaffolds, Gene, Protein, Release Date, Modify Date, RefSeq, INSDC, rRNA, tRNA, Other RNA, Pseudogene.

Methods:

A draft genome sequence was obtained using the Illumina MiSeq platform, V2 with 2 × 250 bp paired-end reads (3,338,462 reads). Reads were assembled using the Unicycler on Galaxy v (https://usegalaxy.org/) and annotated with the RAST server and the NCBI Prokaryotic Genome Annotation Pipeline (Gene Mark S+ ver. 4.4).

Instruments:

The Illumina MiSeq platform at Nova Southeastern University was used for sequencing.

Error Analysis:

Global statistics are reported here. Total sequence length 3,751,701 Total assembly gap length 0 Gaps between scaffolds 0 Number of scaffolds 239 Scaffold N50 56,724 Scaffold L50 22 Number of contigs 239 Contig N50 56,724 Contig L50 22 Total number of chromosomes and plasmids: One chromosome and one plasmid (pAPG501, 14,708 bp) Number of component sequences (WGS) 239

Provenance and Historical References:

In last 20 years, only two Nitrosomonas species were deposited in public culture collections due to the difficulty of cultivation and maintenance of cultures.

Individual Files: