Desulfosporosinus infrequens


Citation

Formal styling
Desulfosporosinus infrequens Hausmann et al., 2019 (valid 2024)
Effective publication
Hausmann et al., 2019
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:zukezao3 (validated)
Cannonical URL
https://seqco.de/i:32296

Nomenclature

Rank
Species
Syllabication
in.fre'quens
Etymology
L. masc. adj. infrequens, infrequent
Nomenclatural type
NCBI Assembly: GCA_900290375.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
MAG SbF1 obtained from a wetland in Germany. A major driver of sulfate reduction in experimental microcosms established with acidic soil from the Schlöppnerbrunnen II fen (Bavaria, Germany).

The population genome of the low-abundance Desulfosporosinus species was obtained by coassembly and differential coverage binning of metagenomes obtained from native peat soil and 13C-labeled fractions of a DNA-stable isotope probing experiment of the same peatland (see Fig. S1in the supplemental material) (29). The high-quality metagenome-assembled genome (MAG) SbF1 had a size of 5.3 Mbp (on 971 scaffolds), a G+C content of 42.6%, a CheckM-estimated completeness of 98.0%, a potential residual contamination of 3.9%, and 10% strain heterogeneity. Besides 16S and 23S rRNA genes, SbF1 carried 6,440 protein-coding genes (CDS), five 5S rRNA gene copies, 59 tRNAs, and 37 other ncRNAs, making a total of 6,543 predicted genomic features. The genome size and G+C content were in the same range as observed for genomes of cultured Desulfosporosinus species (3.0 to 5.9 Mbp and 42 to 44%, respectively) (3034). Scaffolds containing rRNA genes had a higher coverage than the average coverage of all scaffolds (Fig. S1), indicating multiple rrn operon copies, as is known from genomes of other Desulfosporosinus species (on average, 9.3 rrn operons; range, 8 to 11) (35).

Based on its phylogenetic placement and novel ecophysiological behavior, we propose that Desulfosporosinus sp. MAG SbF1 represents a novel species with the proposed name Desulfosporosinus infrequens” sp. nov. (in.fre′quens. L. adj. infrequens, rare, referring to its low relative abundance). Based on its genome-derived metabolic potential and support from metatranscriptomics,Desulfosporosinus infrequens” is capable of complete oxidation of acetate, propionate, and lactate with sulfate as the electron acceptor, with further potential for oxidation of molecular hydrogen (Fig. 1).
Notes
This taxon was previously known as MAG SbF1.
Classification
Bacteria » Bacillota » Clostridia » Eubacteriales » Peptococcaceae » Desulfosporosinus » Desulfosporosinus infrequens
Parent
Desulfosporosinus gtdb

Genomics

Accession
NCBI Assembly:GCA_900290375.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 98.0%
  • Contamination: 3.9%
  • Quality: 78.5
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 77.0%)
  • tRNAs for 20 amino acids
Source
Other features
  • G+C Content: 42.6%
  • Coding Density: 82.2%
  • Codon Table: 11
  • N50: 11,065 bp
  • Contigs: 971
  • Largest Contig: 94,466 bp
  • Assembly Length: 5,321,430 bp
  • Ambiguous Assembly Fraction: 0.027%
Submitter comments
Sampling of peat soil from the acidic peatland Schlöppnerbrunnen II (Germany), DNA-stable isotope probing (DNA-SIP), total nucleic acid extraction, metagenome sequencing and assembly, and coverage-based binning were described previously (5, 16, 29). In brief, DNA from native peat soil (10- to 20-cm depth) and DNA pooled from 16 13C-enriched fractions (density, 1.715 to 1.726 g ml−1) of a previous DNA-SIP experiment with soil from the same site (16) was sequenced using the Illumina HiSeq 2000 system. DNA-SIP was performed after a 120-day incubation (again, 10- to 20-cm depth) that was periodically amended with small dosages of sulfate and first a mixture of unlabeled formate, acetate, propionate, and lactate for 2 weeks and thereafter a mixture of 13C-labeled formate, acetate, propionate, and lactate (all in the lower-micromolar range) (16). Raw reads were quality filtered, trimmed, and coassembled (native soil, 385 million reads; DNA-SIP, 576 million reads) using the CLC Genomics Workbench 5.5.1 (CLC Bio). Differential coverage binning was applied to extract the Desulfosporosinus metagenome-assembled genome (MAG) (75). As expected (16), the Desulfosporosinus MAG was of low abundance in the native soil with an average coverage of 0.026 while enriched in the SIP sample with an average coverage of 34 (detailed per scaffold in Table S1b). A side effect of sequencing a DNA-SIP sample is an apparent G+C content skew, which was normalized arbitrarily to improve binning using the following formula (29, 76): (coverage/G+C content9) × 1015.
Scaffolds containing the 16S and 23S rRNA genes were successfully identified using paired-end linkage data (75). Completeness, contamination, and strain heterogeneity were estimated using CheckM 1.0.6 (77).
Phylogenomic analysis of the Desulfosporosinus MAG was based on a concatenated set of 34 phylogenetically informative marker genes as defined by reference 77 and the Bayesian phylogeny inference method PhyloBayes using the CAT-GTR model (78). 16S rRNA gene-based phylogeny was inferred using the ARB SILVA database r126 as a reference (79), the SINA aligner (80), and the substitution model testing and maximum likelihood treeing method IQ-TREE (81). Pairwise 16S rRNA gene sequence identities were calculated with T-Coffee 11 (82). Pairwise average nucleic and amino acid identities (ANI and AAI, respectively) (37) between protein-encoding genes of the Desulfosporosinus MAG and reference genomes were calculated as described previously (29).
Automated checks
Complete
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Metadata

Outside links and data sources
Search sequences
Local history
Registered by
Loy, Alexander 4 months ago
Submitted by
Loy, Alexander 4 months ago
Curators
Endorsed by
Palmer, Marike 4 months ago
Validated by
Palmer, Marike 4 months ago

Publications
2

Citation Title
Oren, Garrity, 2022, International Journal of Systematic and Evolutionary Microbiology CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa
Hausmann et al., 2019, mBio Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member
Effective publication



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