ABSTRACT

Here, we present the complete genome sequence of Nitrospina watsonii 347, a nitrite-oxidizing bacterium isolated from the Black Sea at a depth of 100 m. The genome has a length of 3,011,914 bp with 2,895 predicted coding sequences. Its predicted metabolism is similar to that of Nitrospina gracilis with differences in defense against reactive oxygen species.

ANNOUNCEMENT

Members of the family Nitrospinaceae within the phylum Nitrospinota constitute the prevalent nitrite oxidizers in the marine environment (1, 2). Here, we report the complete genome sequence of Nitrospina watsonii 347, which was isolated from an enrichment culture started in 1969 with a Black Sea water sample from a depth of 100 m and was described in 2014 (3).
N. watsonii was obtained as an active culture from the collection of nitrite-oxidizing bacteria at Hamburg University and grown in the dark at 28°C in a synthetic seawater medium (https://doi.org/10.17504/protocols.io.81wgby1zovpk/v1). Next, 3 mM nitrite was added to the culture and replenished whenever it was consumed completely.
DNA was isolated from the culture using the DNeasy blood and tissue kit (Qiagen). For short-read sequencing, libraries were prepared using the Nextera XT kit (Illumina), quality checked using the Agilent 2100 bioanalyzer with the high-sensitivity (HS) DNA kit, and quantified using a Qubit instrument with the double-stranded DNA (dsDNA) HS assay kit (Thermo Fisher Scientific Inc.). Paired-end sequencing of 2 × 300 bp was performed using the Illumina MiSeq sequencer with MiSeq reagent kit v3, producing 11,829,056 sequence pairs with an N50 value of 300 bp. For Nanopore library preparation, the ligation sequencing kit 1D (SQK-LSK108) and the native barcoding expansion kit (EXP-NBD104) were used (Oxford Nanopore Technologies). The libraries were loaded on a flow cell (R9.4.1) and run on a MinION device (Oxford Nanopore Technologies). Basecalling was done using albacore v2.1.10 with the basecalling model template_r9.4_450bps_5mer_raw.jsn (Oxford Nanopore Technologies). In total, 290,544 sequence reads were obtained with an N50 value of 8,228 bp. Manufacturer instructions were followed for all protocols.
Nanopore reads were assembled using canu v.1.8 (4) (options: genomeSize = 3.6m, stopOnReadQuality=false, stopOnLowCoverage = 5) and were subsequently mapped against the assembly using minimap2 with default settings (5) to polish the canu assembly with racon v1.3.1 (6). Illumina reads were trimmed and filtered using BBDuk from BBTools (DOE Joint Genome Institute, Walnut Creek, CA, USA; parameters used: k = 23 mink = 11 hdist = 1 ktrim=r tbo qtrim=rl trimq = 17 maq = 20 maxns = 0 minlen = 150 tossjunk=t). A hybrid assembly was then constructed with unicycler v0.4.4 (7), using the existing long-read assembly from canu. The resulting circular genome had a mean genome coverage of 54.32x and was centered around the origin of replication using the “start_gene” option with the dnaA gene of Nitrospina gracilis (CCQ89934.1) (8) and a minimum required BLAST identity of 60%.
The circular genome of Nitrospina watsonii 347 has a total length of 3,011,914 bp, with 2,895 predicted coding sequences based on the MicroScope annotation platform (9) and an average GC content of 57.16%. The genome contains 1 complete rRNA operon and in total 45 tRNA genes (1 to 5 for each of the 20 amino acids). The core metabolism is as described for Nitrospina gracilis 3/211 (8), but the organisms differ in their potential for defense against reactive oxygen species, as N. watsonii carries a superoxide reductase not identified in N. gracilis.

Data availability.

The annotated genome of Nitrospina watsonii 347 has been deposited at ENA under accession number ERZ13641452 (PRJEB56043). The version described in this paper is the first version. The accessions for the raw reads are ERR10676989 (long reads; Oxford Nanopore) and ERR10676991 (short reads; Illumina MiSeq).

ACKNOWLEDGMENTS

This research was funded by the Gravitation Program of the Dutch Ministry of Education, Culture and Science (SIAM grant 024.002.002) and the Netherlands Organization for Scientific Research (grants VI.Veni.192.086 and 016.Vidi.189.050).
The LABGeM (CEA/Genoscope and CNRS UMR8030) and the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within the MicroScope annotation platform. We thank Suzanne C. M. Haaijer for excellent help with cultivation.

REFERENCES

1.
Beman JM, Leilei Shih J, Popp BN. 2013. Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean. ISME J 7:2192–2205.
2.
Levipan HA, Molina V, Fernandez C. 2014. Nitrospina-like bacteria are the main drivers of nitrite oxidation in the seasonal upwelling area of the Eastern South Pacific (Central Chile ~36°S). Environ Microbiol Rep 6:565–573.
3.
Spieck E, Keuter S, Wenzel T, Bock E, Ludwig W. 2014. Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum “Nitrospinae.” Syst Appl Microbiol 37:170–176.
4.
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736.
5.
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100.
6.
Vaser R, Sović I, Nagarajan N, Šikić M. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27:737–746.
7.
Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595.
8.
Lücker S, Nowka B, Rattei T, Spieck E, Daims H. 2013. The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front Microbiol 4:27.
9.
Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C. 2009. MicroScope: a platform for microbial genome annotation and comparative genomics. Database 2009:bap021.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 12Number 418 April 2023
eLocator: e00078-23
Editor: Frank J. Stewart, Montana State University
PubMed: 36943084

History

Received: 2 February 2023
Accepted: 8 March 2023
Published online: 21 March 2023

Contributors

Authors

Linnea F. M. Kop
Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Vienna, Austria
University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
Eva Spieck
Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
Theo van Alen
Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
Geert Cremers
Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Vienna, Austria
Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands

Editor

Frank J. Stewart
Editor
Montana State University

Notes

The authors declare no conflict of interest.

Metrics & Citations

Metrics

Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy