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Genome Announc. 2017 July; 5(30): e00742-17.
Published online 2017 July 27. doi:  10.1128/genomeA.00742-17
PMCID: PMC5532844

Draft Genome Sequence of Pseudomonas syringae PDD-32b-74, a Model Strain for Ice-Nucleation Studies in the Atmosphere

ABSTRACT

We report here the whole genome sequence of Pseudomonas syringae PDD-32b-74, a gammaproteobacterium isolated from cloud water. This microorganism is equipped with ice-nucleation protein and biosurfactant genes that could potentially be involved in physicochemical processes in the atmosphere and clouds.

GENOME ANNOUNCEMENT

Atmospheric microorganisms can play a role in numerous atmospheric physicochemical processes, including cloud droplet formation, ice nucleation, and precipitation initiation (1,4). Among those microorganisms isolated from cloud water, bacteria affiliated with the genus Pseudomonas are the most abundant and frequent (5). P. syringae PDD-32b-74 was recovered by the culture of cloud water sampled in November 2009 from the meteorological station on Puy de Dôme Mountain in France (altitude of 1,465 m) on R2A agar medium incubated at 17°C under aerobic conditions. Once purified from the original colony, the strain was identified based on its 16S rRNA gene sequence (GenBank accession no. HQ256872). P. syringae PDD-32b-74 has the ability to produce siderophores to satisfy its iron requirements (6); it thus potentially interferes with cloud chemical reactivity. This strain has been found to be highly ice-nucleation positive (7, 8) and to produce biosurfactants known for facilitating its spread on surfaces (9). We report here the draft genome sequence of P. syringae PDD-32b-74 to allow for further investigation into the role of this bacterium in clouds, as well as its capacity to survive and adapt to atmospheric stresses.

Whole-genome shotgun sequencing (2 × 150 bp) was prepared using the Nextera DNA sample preparation kit (Illumina, San Diego, CA, USA) following the manufacturer’s user guide and sequenced on the Illumina MiSeq platform (MR DNA [Molecular Research] Shallowater, TX, USA). Sequence data files were filtered for quality using FastQC, trimmed using Prinseq-Lite (10), and then de novo assembled with SPAdes (11). A total of 49 contigs were generated with an average coverage of 22.6-fold. The average contig size was 116,408 bp, and the N50 contig size was 288,783 bp. The size of the assembled genome is 5,704,000 bp with a GC content of 59.1%, which is within the range of known values for Pseudomonas genomes (12).

The draft genome of P. syringae PDD-32b-74 was annotated using the RAST annotation server (http://rast.nmpdr.org). The genome contains 65 RNAs, 4 rRNAs, 57 tRNAs, and 4,934 protein-coding genes, of which 50% were assigned to a total of 520 SEED subsystems. Among these SEED subsystems, 181 were affiliated to stress response (79 to oxidative stress, 32 to osmotic stress, 5 to cold shock, 17 to heat shock, 29 detoxification, and the rest were unclassified). As expected from its phenotype, one ice-nucleation protein (INA_Z; 1,259 amino acids long) was detected in the genome content of P. syringae PDD-32b-74, as well as four protein-coding genes associated with dormancy and sporulation, two affiliated with the persistence of cells in the environment, and two associated with the spore core dehydration and sporulation processes. All of these could contribute to the survival of P. syringae PDD-32b-74 and influence some of the physicochemical processes happening in clouds.

Accession number(s).

This whole-genome shotgun project has been deposited in GenBank under accession number MTSA00000000.

ACKNOWLEDGMENTS

We thank Magali Abrantes for the DNA extraction of P. syringae PDD-32b-74. This study was funded by the BIOCAP Project, which is supported by the French National Research Agency (ANR).

Footnotes

Citation Besaury L, Amato P, Sancelme M, Delort AM. 2017. Draft genome sequence of Pseudomonas syringae PDD-32b-74, a model strain for ice-nucleation studies in the atmosphere. Genome Announc 5:e00742-17. https://doi.org/10.1128/genomeA.00742-17.

REFERENCES

1. Ariya PA, Amyot M 2004. New directions: the role of bioaerosols in atmospheric chemistry and physics. Atmos Environ 38:1231–1232. doi:.10.1016/j.atmosenv.2003.12.006 [Cross Ref]
2. Deguillaume L, Leriche M, Amato P, Ariya PA, Delort A-M, Pöschl U, Chaumerliac N, Bauer H, Flossmann AI, Morris CE 2008. Microbiology and atmospheric processes: chemical interactions of primary biological aerosols. Biogeosciences Discuss 5:841–870. doi:.10.5194/bgd-5-841-2008 [Cross Ref]
3. Möhler O, DeMott PJ, Vali G, Levin Z 2007. Microbiology and atmospheric processes: the role of biological particles in cloud physics. Biogeosciences 4:1059–1071. doi:.10.5194/bg-4-1059-2007 [Cross Ref]
4. DeMott PJ, Prenni AJ 2010. New directions: need for defining the numbers and sources of biological aerosols acting as ice nuclei. Atmos Environ 44:1944–1945. doi:.10.1016/j.atmosenv.2010.02.032 [Cross Ref]
5. Vaïtilingom M, Attard E, Gaiani N, Sancelme M, Deguillaume L, Flossmann AI, Amato P, Delort AM 2012. Long-term features of cloud microbiology at the Puy de Dôme (France). Atmos Environ 56:88–100. doi:.10.1016/j.atmosenv.2012.03.072 [Cross Ref]
6. Vinatier V, Wirgot N, Joly M, Sancelme M, Abrantes M, Deguillaume L, Delort AM 2016. Siderophores in cloud waters and potential impact on atmospheric chemistry: production by microorganisms isolated at the Puy de Dôme station. Environ Sci Technol 50:9315–9323. doi:.10.1021/acs.est.6b02335 [PubMed] [Cross Ref]
7. Joly M, Attard E, Sancelme M, Deguillaume L, Guilbaud C, Morris CE, Amato P, Delort AM 2013. Ice nucleation activity of bacteria isolated from cloud water. Atmos Environ 70:392–400. doi:.10.1016/j.atmosenv.2013.01.027 [Cross Ref]
8. Attard E, Yang H, Delort A-M, Amato P, Pöschl U, Glaux C, Koop T, Morris CE 2012. Effects of atmospheric conditions on ice nucleation activity of Pseudomonas. Atmos Chem Phys 12:10667–10677. doi:.10.5194/acp-12-10667-2012 [Cross Ref]
9. Renard P, Canet I, Sancelme M, Wirgot N, Deguillaume L, Delort AM 2016. Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants. Atmos Chem Phys 16:12347–12358. doi:.10.5194/acp-16-12347-2016 [Cross Ref]
10. Schmieder R, Edwards R 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864. doi:.10.1093/bioinformatics/btr026 [PMC free article] [PubMed] [Cross Ref]
11. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:.10.1089/cmb.2012.0021 [PMC free article] [PubMed] [Cross Ref]
12. Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW 2011. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 35:652–680. doi:.10.1111/j.1574-6976.2011.00269.x [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)