# Complete genome sequence of a marine Pseudoalteromonas bacterial strain

Eric Manirakiza, Timothée Chaumier, Leïla Tirichine

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Eric Manirakiza, Timothée Chaumier, Leïla Tirichine. Complete genome sequence of a marine Pseudoalteromonas bacterial strain. Microbiology Resource Announcements, 2024, 14 (1), 10.1128/mra.00975-24. hal-05174200

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Distributed under a Creative Commons Attribution 4.0 International License
# Complete genome sequence of a marine *Pseudoalteromonas* bacterial strain

Eric Manirakiza,¹ Timothée Chaumier,¹ Leïla Tirichine¹,²

**AUTHOR AFFILIATIONS** See affiliation list on p. 3.

**ABSTRACT** *Pseudoalteromonas* is an abundant bacterial genera, found ubiquitously, including in extreme environments. Its broad metabolic capacity enables unique associations with various organisms. Using PacBio sequencing, we generated the complete genome sequence of a marine *Pseudoalteromonas*, revealing two circular chromosomes and one putative plasmid. The genome data are accessible at https://BacBrowse.univ-nantes.fr.

**KEYWORDS** *Pseudoalteromonas*, prokaryotes-eukaryotes interactions, active compounds, biofilm

*Pseudoalteromonas* species are a group of gamma proteobacteria exclusively isolated from marine waters worldwide (1). These species are often found in extreme environments, including cold habitats and deep-sea sediments (2–4). Interestingly, *Pseudoalteromonas* species are frequently associated with eukaryotic organisms such as sponges, tunicates, and various marine algae, and play a role in controlling harmful dinoflagellate blooms (5–9). This genus forms biofilm and produces active compounds (10, 11). The ecological success and diverse associations of this genus reveal its potential as a vast reservoir of active metabolites, making it highly relevant for both fundamental and applied research. The genus *Pseudoalteromonas* is classified into pigmented and non-pigmented clades, with pigmented species often linked to a higher propensity for natural product synthesis (12–14). Despite the identification of over 2,000 species, the full extent of the genus diversity remains largely unexplored.

Here, we report the complete genome sequences of a pigmented *Pseudoalteromonas* sourced from the National Collection of Industrial Microorganisms (NCIMB_1079) as *Pseudomonas fluorescens*. This discrepancy has been reported to NCIMB. *Pseudoalteromonas* (1,079 NCIMB) was isolated on 12 October 1962, from sea water, 16 km East South East of Aberdeen in the United Kingdom (latitude 57°6'15"N, longitude 1°44'15"W). The salinity of sea water at the sampling site was 34.7‰ (15). Upon isolation, the strain was plated on Anderson's marine medium (16). Upon purchase in October 2019, the strain was stored as a glycerol stock at -80°C. Cells were cultured in liquid Luria-Bertani (LB) medium at 30°C with shaking at 180 rpm for 48 h. DNA was extracted using the MagAttract High Molecular Weight DNA Kit (Cat. no. 67563) following the manufacturer's instructions. Genomic DNA was sheared with Covaris g-TUBES at 4,000 RPM. The DNA libraries were prepared without size selection using SMRTbell Express Template Prep Kit 2.0 protocol following the Pacific Biosciences Procedure. DNA was sequenced by Genome Quebec using the Pacific Biosciences Sequel platform with Circular Consensus Sequencing (CCS). SmrtLink v8.0 was used to monitor run QC, demultiplex reads, remove adapter sequences, and generate subreads filtered for minimum read quality. CCS reads were generated from subreads with CCS 6.4.0 and assembled with Canu (v2.2) (17). Genome coverage was 118.11×, with an estimated size of 4.5 Mb (Table 1, Fig. 1). Among the three contigs, two were identified as chromosomes and the third as a

Editor Julie C. Dunning Hotopp, University of Maryland School of Medicine, Baltimore, Maryland, USA

Address correspondence to Leïla Tirichine, tirichine-l@univ-nantes.fr.

The authors declare no conflict of interest.

See the funding table on p. 3.

Received 9 September 2024

Accepted 12 November 2024

Published 10 December 2024

Copyright © 2024 Manirakiza et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
<figure><img src="image_2.png" /><figcaption>FIG 1 Graphical circular map of the large chromosome (A), small chromosome (B), and plasmid (C) of *Pseudoalteromonas* sp. Blue arrows represent coding sequences. GC content is shown in brown (values outside the circle represent GC content that deviates from the average, either higher or lower). tRNA and rRNA are represented in red and yellow, respectively. GC skew is depicted in pink to represent positive values and in purple to represent negative values.</figcaption></figure>

plasmid. The large chromosome, small chromosome, and plasmid display overlaps at their ends measuring 15.4, 14.2, and 16.4 kb, respectively. The identification of plasmids was performed using two plasmid prediction tools: PlasmidHunter (v1.4) (18) and PLASMe (v1.1) (19). These tools predicted a plasmid with a length of 86,689 bp (Fig. 1). Gene annotation and functional assignment were performed using anvi'o v7.1 (20). Additional gene annotations were performed with DFAST 1.2.20 (21), Prokka (v1.14.6) (22) with compliant parameter and EggNOG (v2.1.12) (23). For all softwares, default parameters were used except where otherwise noted. The parameters -m [diamond] and
<table><caption>TABLE 1 Genome features of *Pseudoalteromonas* bacterial strain</caption><thead><tr><th></th><th>Pseudoalteromonas</th></tr></thead><tbody><tr><td>Number of subreads</td><td>1,472,349</td></tr><tr><td>N<sub>50</sub> of subreads</td><td>7,745</td></tr><tr><td>Number of CCS reads</td><td>76,463</td></tr><tr><td>N<sub>50</sub> of CCS reads (bp)</td><td>8,902</td></tr><tr><td>Average length of CCS reads</td><td>7,015.55</td></tr><tr><td>Genome size (bp)</td><td>4,512,622</td></tr><tr><td>Number of contigs</td><td>3</td></tr><tr><td>Mean genome coverage</td><td>118.11x</td></tr><tr><td>Contamination<sup>a</sup></td><td>0</td></tr><tr><td>Completeness (%)<sup>a</sup></td><td>100</td></tr><tr><td>GC content (%)</td><td>39.4</td></tr><tr><td>Coding region (%)</td><td>88.1</td></tr><tr><td>Average length CR (bp)</td><td>977.47</td></tr><tr><td>Intergenic region (%)</td><td>12.2</td></tr><tr><td>Average length IR (bp)</td><td>168.08</td></tr><tr><td>Total repeats</td><td>231</td></tr><tr><td>Total tRNAs</td><td>106</td></tr><tr><td>Total rRNAs</td><td>25</td></tr><tr><td>Total pseudogenes</td><td>436</td></tr></tbody></table>

pfam_realign [realign] were used for EggNOG. The assembled genome is available on BacBrowse (https://BacBrowse.univ-nantes.fr).

## ACKNOWLEDGMENTS

This study was supported by Connect Talent EpiAlg grant from Région Pays de la Loire to L.T. The authors thank Udita Chandola for DNA extraction. We are grateful to the Genomics Core Facility GenoA, member of Biogenouest and France Genomique and to the Bioinformatics Core Facility BiRD, member of Biogenouest and Institut Français de Bioinformatique (IFB) (ANR-11-INBS-0013) for the use of their resources and their technical support.

L.T. conceived, designed, and supervised the study. E.M. performed the bioinformatics analysis. T.C. contributed to the bioinformatics analysis. L.T. wrote the manuscript with input from E.M. and T.C. All authors read and approved the manuscript.

## AUTHOR AFFILIATIONS

## AUTHOR ORCIDs

Timothée Chaumier http://orcid.org/0009-0008-7923-1683

Leïla Tirichine http://orcid.org/0000-0002-9491-4414

## FUNDING

<table><thead><tr><th>Funder</th><th>Grant(s)</th><th>Author(s)</th></tr></thead><tbody><tr><td>Conseil Régional des Pays de la Loire (Région Pays de la Loire)</td><td>EpiAlg</td><td>Leïla Tirichine</td></tr><tr><td>Agence Nationale de la Recherche (ANR)</td><td>Epicycle</td><td>Leïla Tirichine</td></tr></tbody></table>

<footnote><sup>a</sup>Genome contamination and completeness were determined using CheckM (24).</footnote>

<footnote n="1">¹Nantes Université, Nantes, France</footnote>

<footnote n="2">²Institute for Marine and Antarctic Studies (IMAS), Ecology and Biodiversity Centre, University of Tasmania, Hobart, Tasmania, Australia</footnote>
## AUTHOR CONTRIBUTIONS

Eric Manirakiza, Formal analysis, Methodology, Writing - review and editing | Timothée Chaumier, Data curation, Formal analysis, Methodology, Writing - review and editing | Leïla Tirichine, Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Writing - original draft, Writing - review and editing

## DATA AVAILABILITY

The genome sequences of *Pseudoalteromonas* sp., has been deposited in GenBank under the Bioproject PRJNA1101843. The genome assembly and sequencing raw reads have been deposited in the NCBI Sequence Read Archive under accession numbers ASM4056769v1 and SRR28815868, respectively.

## REFERENCES

1. Enger O, Nygaard H, Solberg M, Schei G, Nielsen J, Dundas I. 1987. Characterization of Alteromonas denitrificans sp. nov. Int J Syst Bacteriol 37:416-421. https://doi.org/10.1099/00207713-37-4-416

2. Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. 2021. The art of adapting to extreme environments: the model system *Pseudoalteromonas*. Phys Life Rev 36:137-161. https://doi.org/10.1016/j.plifev.2019.04.003

3. Qin Q-L, Li Y, Zhang Y-J, Zhou Z-M, Zhang W-X, Chen X-L, Zhang X-Y, Zhou B-C, Wang L, Zhang Y-Z. 2011. Comparative genomics reveals a deep-sea sediment-adapted life style of *Pseudoalteromonas* sp. SM9913. ISME J 5:274-284. https://doi.org/10.1038/ismej.2010.103

4. Bian F, Xie B-B, Qin Q-L, Shu Y-L, Zhang X-Y, Yu Y, Chen B, Chen X-L, Zhou B-C, Zhang Y-Z. 2012. Genome sequences of six *Pseudoalteromonas* strains isolated from Arctic sea ice. J Bacteriol 194:908-909. https://doi.org/10.1128/JB.06427-11

5. Ivanova EP, Kiprianova EA, Mikhailov VV, Levanova GF, Garagulya AD, Gorshkova NM, Yumoto N, Yoshikawa S. 1996. Characterization and identification of marine *Alteromonas nigriciens* strains and emendation of the description. Int J Syst Bacteriol 46:223-228. https://doi.org/10.1099/00207713-46-1-223

6. Ivanova EP, Kiprianova EA, Mikhailov VV, Levanova GF, Garagulya AD, Gorshkova NM, Vysotskii MV, Nicolau DV, Yumoto N, Taguchi T, Yoshikawa S. 1998. Phenotypic diversity of *Pseudoalteromonas citrea* from different marine habitats and emendation of the description. Int J Syst Bacteriol 48:247-256. https://doi.org/10.1099/00207713-48-1-247

7. Holmström C, James S, Neilan BA, White DC, Kjelleberg S. 1998. *Pseudoalteromonas tunicata* sp. nov., a bacterium that produces antifouling agents. Int J Syst Bacteriol 48:1205-1212. https://doi.org/10.1099/00207713-48-4-1205

8. Egan S, Thomas T, Holmström C, Kjelleberg S. 2000. Phylogenetic relationship and antifouling activity of bacterial epiphytes from the marine alga *Ulva lactuca*. Environ Microbiol 2:343-347. https://doi.org/10.1046/j.1462-2920.2000.00107.x

9. Lovejoy C, Bowman JP, Hallegraeff GM. 1998. Algicidal effects of a novel marine *Pseudoalteromonas* isolate (class proteobacteria, gamma subdivision) on harmful algal bloom species of the genera *Chattonella*, *Gymnodinium*, and *Heterosigma*. Appl Environ Microbiol 64:2806-2813. https://doi.org/10.1128/AEM.64.8.2806-2813.1998

10. Casillo A, Lanzetta R, Parrilli M, Corsaro MM. 2018. Exopolysaccharides from marine and marine extremophilic bacteria: structures, properties, ecological roles and applications. Mar Drugs 16:69. https://doi.org/10.3390/md16020069

11. Skovhus TL, Ramsing NB, Holmström C, Kjelleberg S, Dahllöf I. 2004. Real-time quantitative PCR for assessment of abundance of *Pseudoalteromonas* species in marine samples. Appl Environ Microbiol 70:2373-2382. https://doi.org/10.1128/AEM.70.4.2373-2382.2004

12. Egan S, James S, Holmström C, Kjelleberg S. 2002. Correlation between pigmentation and antifouling compounds produced by *Pseudoalteromonas tunicata*. Environ Microbiol 4:433-442. https://doi.org/10.1046/j.1462-2920.2002.00322.x

13. Holmström C, Kjelleberg S. 1999. Marine *Pseudoalteromonas* species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol Ecol 30:285-293. https://doi.org/10.1111/j.1574-6941.1999.tb00656.x

14. Bowman JP. 2007. Bioactive compound synthetic capacity and ecological significance of marine bacterial genus *pseudoalteromonas*. Mar Drugs 5:220-241. https://doi.org/10.3390/md504220

15. A. JIW. 1962. Heterotrophic bacteria of North sea water, Glasgow

16. Brown AE. 2019. Benson's microbiological applications: laboratory manual in general microbiology. In T. E. M.-H. Education

17. 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. https://doi.org/10.1101/gr.215087.116

18. Tian R, Imanian B. 2023. PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning. Bioinformatics. https://doi.org/10.1101/2023.02.01.526640

19. Tang X, Shang J, Ji Y, Sun Y. 2023. PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer. Nucleic Acids Res 51:e83. https://doi.org/10.1093/nar/gkad578

20. Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, et al. 2021. Community-led, integrated, reproducible multi-omics with anvi'o. Nat Microbiol 6:3-6. https://doi.org/10.1038/s41564-020-00834-3

21. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. 2016. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 35:173-184. https://doi.org/10.12938/bmfh.16-003

22. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068-2069. https://doi.org/10.1093/bioinformatics/btu153

23. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. 2021. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Bioinformatics. https://doi.org/10.1101/2021.06.03.446934

24. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043-1055. https://doi.org/10.1101/gr.186072.114