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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39078161
mra00372-24
10.1128/mra.00372-24
mra.00372-24
Genome Sequences
genomics-and-proteomicsGenomics and ProteomicsComplete genome sequence of Sporomusa sphaeroides DSM 2875T isolated from mud of the Leine river and Sporomusa ovata DSM 2662T isolated from sugar beet leaf silage
Böer Tim 1
Lüschen Alina 1
https://orcid.org/0000-0002-8646-7925
Daniel Rolf 1 rdaniel@gwdg.de

https://orcid.org/0000-0002-2473-6202
Poehlein Anja 1
1 Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen , Göttingen, Germany
Editor Hudson André O. Rochester Institute of Technology , Rochester, New York, USA

Address correspondence to Rolf Daniel, rdaniel@gwdg.de
Tim Böer and Alina Lüschen contributed equally to this article. The author order was determined both alphabetically and in order of increasing seniority.

The authors declare no conflict of interest.

9 2024
30 7 2024
30 7 2024
13 9 e00372-2410 4 2024
13 5 2024
Copyright © 2024 Böer et al.
2024
Böer et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

We report the closed genome sequences of the acetogen Sporomusa sphaeroides ET (DSM 2875T) and of Sporomusa ovata H1T (DSM 2662T). The S. sphaeroides ET genome harbors a chromosome (4,956,256 bp) and a plasmid (59,087 bp). The genome of S. ovata H1T harbors one chromosome (5,433,971 bp).

KEYWORDS

Sporomusa sphaeroides
Sporomusa ovata
Wood-Ljungdahl pathway
acetogenic bacteria
Sporomusa
cover-dateSeptember 2024
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pmcANNOUNCEMENT

Sporomusa is an exclusively acetogenic genus, which grows autotrophically with H2 + CO2 and produces acetate as sole fermentation product. Sporomusa members attracted attention as efficient electrotrophic biocatalysts employed in microbial electrosynthesis for the production of biocommodities such as acetate or biofuels, simultaneously fixing the greenhouse gas CO2 (1, 2). However, the only currently available complete Sporomusa genome sequence is from Sporomusa termitida (3). We report the complete genome sequences of the Sporomusa type species Sporomusa sphaeroides ET (DSM 2875T) isolated from mud of the Leine river (Göttingen, Germany) and the type strain of Sporomusa ovata H1T (DSM 2662T) isolated from sugar beet leaf silage (Göttingen, Germany) (4).

Both strains were cultivated in 10 mL of DSM 311c medium as listed by the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany) under anaerobic conditions. Cells were inoculated from lyophilized stock cultures from the DSMZ in an anaerobic chamber and incubated in Hungate tubes at 35°C for 12 h without shaking. Cells were harvested by centrifugation at 18,000 × g for 5 min. For Illumina sequencing and Nanopore sequencing, separately grown cell cultures were used. DNA was isolated by using the Master-Pure Complete DNA and RNA purification kit (Epicentre, Madison, WI, USA) following the instructions for cell samples. Illumina sequencing was performed by the preparation of Illumina sequencing libraries using the Nextera XT DNA sample preparation kit and using a MiSeq system with v3 chemistry (2 × 300 bp, 600 cycles) following the instructions of the manufacturer (Illumina, San Diego, CA, USA). Nanopore sequencing libraries were prepared with 1.5 µg high-molecular-weight DNA using the ligation sequencing kit 1D2 (SQK-LSK308) for S. sphaeroides ET and the ligation sequencing kit 1D (SQK-LSK108) for S. ovata H1T as well as the native barcode expansion kit (EXP-NBD103) as recommended by the manufacturer (Oxford Nanopore Technologies, Oxford, UK). Nanopore sequencing was conducted for 72 h using the MinION device Mk1B, a SpotON flow cell R9.4.1 and the MinKNOW software (v1.10.11) as recommended by the manufacturer (Oxford Nanopore Technologies). Default parameters were used for all software unless otherwise specified. Base calling of Nanopore sequencing data was performed with the Albacore software (v2.0.1).

The following programs were used for genome assemblies: Trimmomatic (v0.36; LEADING: 3, TRAILING: 3, SLIDINGWINDOW:4:15, MINLEN:50) (5) and Unicycler (v0.4.0) (6). The Unicycler pipeline was used for the combined assembly of the Nanopore and the Illumina reads resulting in circular chromosomes for both genomes. Identification and trimming of the plasmid overlap was performed as part of the standard Unicycler pipeline. Genome annotations were performed with Prokka (v1.14.5) (7) and PGAP (v6.6) (8), and quality assessment of the final genome assemblies was conducted with CheckM2 (v1.0.2) (9). Protein-encoding genes containing selenocysteine (Sec) and pyrrolysine (Pyl) residues were manually identified and annotated. Details of sequencing and genome statistics of S. sphaeroides ET and S. ovata H1T are summarized in Table 1. The comparison of the Wood-Ljungdahl gene cluster of both strains (Fig. 1) was visualized with Clinker (v0.0.28) (10).

TABLE 1 Sequencing statistics and genome features of S. sphaeroides ET and S. ovata H1T

Feature	S. sphaeroides ET (DSM 2875T)	S. ovata H1T (DSM 2662T)	
Chromosome size (bp)	4,956,256	5,433,971	
Number of Illumina reads (250 bp)	4,388,306	2,924,484	
Number of Nanopore reads/mean length (bp)	50,628/3,746	50,548/3,260	
Nanopore reads N50 (bp)	6,797	5,646	
Chromosome mean coverage (Illumina/Nanopore)	232/27	145/30	
Plasmid size (bp)	59,087	–a	
Plasmid mean coverage (Illumina/Nanopore)	269/35	–	
GC content (%)	47	43	
Genes	4,656	5,314	
CDS	4,511	5,112	
Functional proteins	2,596	3,609	
Hypothetical proteins	1,915	1,503	
rRNAs (5S, 16S, 23S)	33 (10, 12, 11)	42 (15, 15, 12)	
tRNAs	111	160	
tmRNAs	1	1	
CheckM2:			
 Completeness score (%)	99.99	100	
 Contamination score (%)	1.19	7.57	
a "–", not present.

Fig 1 Comparison of the Wood-Ljungdahl cluster of S. sphaeroides DSM 2875T and S. ovata DSM 2662T. The following gene abbreviations were used: fchA, methenyl THF cyclohydrolase; folD, bifunctional cyclohydrolase/dehydrogenase; acsF, carbon monoxide dehydrogenase accessory protein; fhs, formyl THF synthetase; acsA, anaerobic carbon-monoxide dehydrogenase catalytic subunit; acsB, carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta; acsC, CoFeSP large subunit; acsV, corrinoid activation/regeneration protein; cooC, carbon monoxide dehydrogenase accessory protein; acsD, CoFeSP small subunit; acsE, methyl THF CoFeSP methyltransferase; hdrC, heterodisulfide oxidoreductase iron-sulfur cluster-binding subunit; hdrB, heterodisulfide reductase subunit B; hdrA, heterodisulfide reductase subunit A; mvhD, methyl-viologen-reducing hydrogenase delta subunit; metV, methylene THF reductase C-terminal catalytic subunit; metF, methylene THF reductase large subunit; hydC, electron bifurcating hydrogenase subunit HydC; hydB, electron bifurcating hydrogenase subunit HydB; hydA, electron bifurcating hydrogenase subunit HydA; pabA, aminodeoxychorismate/anthranilate synthase component 2; pabB, aminodeoxychorismate synthase component 1; ilvE, branched-chain-amino-acid aminotransferase; fdhD, sulfur carrier protein; moeA, molybdopterin molybdenumtransferase; tag, DNA-3-methyladenine glycosylase 1; gabR, HTH-type transcriptional regulatory protein GabR; mobB, molybdopterin-guanine dinucleotide biosynthesis adapter protein; fdhF, formate dehydrogenase H; hyfA, hydrogenase-4 component A; cooF, iron-sulfur protein; lutA, lactate utilization protein A; mobA, molybdenum cofactor guanylyltransferase; valS, valine--tRNA ligase; fpgS, folylpolyglutamate synthase; spoIIAB, anti-sigma F factor; rsxB, ion-translocating oxidoreductase complex subunit B; hndB, NADP-reducing hydrogenase subunit HndB; stnA, Sporomusa-type Nfn transhydrogenase subunit A; stnB, Sporomusa-type Nfn transhydrogenase subunit B; stnC, Sporomusa-type Nfn transhydrogenase subunit C.

ACKNOWLEDGMENTS

We acknowledge the support by the Open Access Publication Funds of the Göttingen University. Furthermore, we acknowledge the support of T.B. and A.L. by the “Deutsche Bundesstiftung Umwelt” (DBU; 20020/640 and 20022/016). R.D. and A.P. are grateful for support from the Bundesministerium für Bildung und Forschung (BMBF) for the project “Mikrobielle Biofabriken: THERMOSYNCON—Entwicklung thermophiler Mikroorganismen als Biokatalysatoren für die Umwandlung von Synthesegas zu Biobrennstoffen und Chemikalien" (grant number 031B0857C). The supporters had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank Melanie Heinemann for technical assistance.

DATA AVAILABILITY

Genome sequences were deposited under the GenBank accession numbers CP146991 and CP146992 (S. sphaeroides) and CP146301 (S. ovata). Raw read data were deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers SRR28314578 (Illumina) and SRR28314177 (Nanopore) for S. sphaeroides, and SRR28327341 (Illumina) and SRR28327318 (Nanopore) for S. ovata.
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