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.2023 Aug 22:14:1214631.
doi: 10.3389/fmicb.2023.1214631. eCollection 2023.

Phenotypic and genomic characterization ofBathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal classBathyarchaeia

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Phenotypic and genomic characterization ofBathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal classBathyarchaeia

Maria A Khomyakova et al. Front Microbiol..

Abstract

Bathyarchaeia are widespread in various anoxic ecosystems and are considered one of the most abundant microbial groups on the earth. There are only a few reports of laboratory cultivation ofBathyarchaeia, and none of the representatives of this class has been isolated in pure culture. Here, we report a sustainable cultivation of theBathyarchaeia archaeon (strain M17CTs) enriched from anaerobic sediment of a coastal lake. The cells of strain M17CTs were small non-motile cocci, 0.4-0.7 μm in diameter. The cytoplasmic membrane was surrounded by an S-layer and covered with an outermost electron-dense sheath. Strain M17CTs is strictly anaerobic mesophile. It grows at 10-45°C (optimum 37°C), at pH 6.0-10.0 (optimum 8.0), and at NaCl concentrations of 0-60 g l-1 (optimum 20 g l-1). Growth occurred in the presence of methoxylated aromatic compounds (3,4-dimethoxybenzoate and vanillate) together with complex proteinaceous substrates. Dimethyl sulfoxide and nitrate stimulated growth. The phylogenomic analysis placed strain M17CTs to BIN-L-1 genus-level lineage from the BA1 family-level lineage and B26-1 order-level lineage (former subgroup-8) within the classBathyarchaeia. The complete genome of strain M17CTs had a size of 2.15 Mb with a DNA G + C content of 38.1%. Based on phylogenomic position and phenotypic and genomic properties, we propose to assign strain M17CTs to a new species of a novel genusBathyarchaeum tardum gen. nov., sp. nov. within the classBathyarchaeia. This is the first sustainably cultivated representative ofBathyarchaeia. We propose under SeqCode the complete genome sequence of strain M17CTs (CP122380) as a nomenclatural type ofBathyarchaeum tardum, which should be considered as a type for the genusBathyarchaeum, which is proposed as a type for the familyBathyarchaeaceae, orderBathyarchaeales, and of the classBathyarchaeia.

Keywords: Methanocalculus; O-demethylase; anaerobic; archaea; methoxylated aromatic compounds; uncultured microorganisms.

Copyright © 2023 Khomyakova, Merkel, Mamiy, Klyukina and Slobodkin.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Growth dynamics of M17CTs cultivated with DMB (5mM). Culture was also supplemented with 0.1 g l−1 yeast extract, 0.20 ml 10 ml−1 (v/v) of sterilized sediment from a natural sample and antibiotics mixture of streptomycin and lincomycin (0.05 g l−1 each). 1.2 mM of DMB (blue line) was consumed, and 0.4 mM of DHB (red line) was produced (in addition to acetate and ethanol) during 2 months of cultivation. No DHB, acetate, or ethanol was detected in un-inoculated controls after 2 months of incubation. The doubling time was estimated to be 7.2 days.
Figure 2
Figure 2
Fluorescencein situ hybridization (FISH) image of strain M17CTs cultivated with DMB. For FISH, M17CTs cells were hybridized with aBathyarchaeia 16S rRNA targeted probe MCG493 (yellow fluorescence, right panel). After hybridization, the cells were counterstained with DAPI (blue fluorescence, left panel). Bar 1 μm.
Figure 3
Figure 3
Morphological characteristics of strain M17CTs. Electron micrographs of negatively stained cells showing(A) single cell of coccoid morphology with small areas of mucus on the surface of the cell;(B) chain of cells without surface appendages covered by unidentified common layer. Ultrathin section of(C) typical coccoid cells of strain M17CTs of regular shape;(D, E) dividing cells,(F) multiple cells of strain M17CTs and the single cell of the unidentified archaeon present in culture. CM—cytoplasmic membrane; SL—S-layer; OL—outermost surface layer. Bar 0.1 μm.
Figure 4
Figure 4
Phylogenomic placement of M17C-01Ts and M17C-73-01 MAGs based on(A) concatenated partial amino acid sequences of 122 archaeal single copy conserved marker genes with taxonomic designations according to the GTDB (Parks et al., 2018);(B) on 16S rRNA gene sequences. The “g_” stands for genus level, “f_”—for family level, and “o_”—order level. The trees were built using the IQ-TREE 2 program (Minh et al., 2020) with fast model selection via ModelFinder (Kalyaanamoorthy et al., 2017) and ultrafast bootstrap approximation (Minh et al., 2013) as well as approximate likelihood-ratio test for branches (Anisimova and Gascuel, 2006). Bootstrap consensus tree is shown with values placed at the nodes. Bar, 0.1 changes per position.
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References

    1. Alneberg J., Bjarnason B. S., Bruijn d. e., Schirmer I., Quick M., Ijaz J. U.Z., et al. . (2014). Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146. 10.1038/nmeth.3103 - DOI - PubMed
    1. Altschul S., Gish W., Miller W., Myers E., Lipman D. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. 10.1016/S0022-2836(05)80360-2 - DOI - PubMed
    1. Anisimova M., Gascuel O. (2006). Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 55, 539–552. 10.1080/10635150600755453 - DOI - PubMed
    1. Berben T., Forlano Bó F., In 't Zandt M. H., Yang S., Liebner S., Welte C. U. (2022). The Polar Fox Lagoon in Siberia harbours a community of Bathyarchaeota possessing the potential for peptide fermentation and acetogenesis. Anton Leeuw. Int. J. 115, 1229–1244. 10.1007/s10482-022-01767-z - DOI - PMC - PubMed
    1. Bolger A. M., Lohse M., Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170 - DOI - PMC - PubMed

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The study was supported by the Russian Science Foundation, project no. 22-24-00868.

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