Abstract
Bacteria of the phylum Verrucomicrobiota colonize a wide spectrum of terrestrial and aquatic habitats. One of the ecosystems where verrucomicrobia represent a significant part of the indigenous microbial community are wetlands. All earlier published information regarding phylogenetic diversity of verrucomicrobia in wetlands, however, refers to raised bogs, while verrucomicrobial diversity in fens remains poorly explored. In this study, we performed a comparative diversity analysis of Verrucomicrobiota in six fens of Vologda region. Nucleotide sequences of verrucomicrobia comprised 4 to 7% of all 16S rRNA gene reads retrieved from the examined peat samples. The most abundant groups were represented by members of the families Pedosphaeraceae, Opitutaceae and the order Chtoniobacterales, as well as the as-yet-uncultivated order-candidate S-BQ2-57. Numerical correlation between the relative abundance of well-represented taxa and peat characteristics was determined.
We’re sorry, something doesn't seem to be working properly.
Please try refreshing the page. If that doesn't work, please contact support so we can address the problem.
REFERENCES
Beier, S., Witzel, K.P., and Marxsen, J., Bacterial community composition in Central European running waters examined by temperature gradient gel electrophoresis and sequence analysis of 16S rRNA genes, Appl. Environ. Microbiol., 2008, vol. 74, pp. 188–199. https://doi.org/1128/AEM.00327-07
Bergmann, G.T., Bates, S.T., Eilers, K.G., Lauber, C.L., Caporaso, J.G., Walters, W.A., Knight, R., and Fierer, N., The under-recognized dominance of Verrucomicrobia in soil bacterial communities, Soil Biol. Biochem., 2011, vol. 43, pp. 1450–1455. https://doi.org/1016/j.soilbio.2011.03.012
Caporaso, J., Kuczynski, J., and Stombaugh, J., QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 2010, vol. 7, pp. 335–336. https://doi.org/1038/nmeth0510-335
Chiang, E., Schmidt, M.L., Berry, M.A., Biddanda, B.A., Burtner, A., Johengen, T.H., Palladino, D., and Denef, V.J., Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats, PLoS One, 2018, vol. 13, p. e0195112. https://doi.org/1371/journal.pone.0206396
Chin, K.J., Liesack, W., and Janssen, P.H., Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division “Verrucomicrobia” isolated from rice paddy soil, Int. J. Syst. Evol. Microbiol., 2001, vol. 51, pp. 1965–1968. https://doi:1099/00207713-51-6-1965
de Bont, J.A.M., Staley, J.T., and Pankratz, H.S., Isolation and description of a non-motile, fusiform, stalked bacterium, a representatieve of a new genus, Antonie van Leeuwenhoek, 1970, vol. 36, pp. 397–407. https://doi.org/1007/BF02069040
Dedysh, S.N., Beletsky, A. V, Ivanova, A.A., Danilova, O.V, Begmatov, S., Kulichevskaya, I.S., Mardanov, A.V, and Ravin, N. V., Peat-inhabiting Verrucomicrobia of the order Methylacidiphilales do not possess methanotrophic capabilities, Microorganisms, 2021, vol. 9, p. 2566. https://doi.org/3390/microorganisms9122566
Dedysh, S.N., Beletsky, A.V., Ivanova, A.A., Kulichevskaya, I.S., Suzina, N.E., Philippov, D.A., Rakitin, A.L., Mardanov, A.V., and Ravin, N.V., Wide distribution of Phycisphaera-like planctomycetes from WD2101 soil group in peatlands and genome analysis of the first cultivated representative, Environ. Microbiol., 2020, vol. 23, pp. 1510–1526. https://doi.org/1111/1462-2920.15360
Freitas, S., Hatosy, S., Fuhrman, J.A., Huse, S.M., Mark Welch, D.B., Sogin, M.L., and Martiny, A.C., Global distribution and diversity of marine Verrucomicrobia, ISME J., 2012, vol. 6, pp. 1499–1505. https://doi.org/1038/ismej.2012.3
Gómez-Gallego, C., Pohl, S., Salminen, S., De Vos, W.M., and Kneifel, W., Akkermansia muciniphila: a novel functional microbe with probiotic properties, Benef. Microbes, 2016, vol. 7, pp. 571–584. https://doi.org/3920/BM2016.0009
Hardman, Y. and Henrici, A.T., Studies of freshwater bacteria, J. Bacteriol., 1939, vol. 37, pp. 97–105.
Hedlund, B.P., Gosink, J.J., and Staley, J.T., Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter, Antonie van Leeuwenhoek., 1997, vol. 72, pp. 29–38. https://doi.org/1023/A:1000348616863
Ivanova, A.A., Beletsky, A.V., Rakitin, A.L., Kadnikov, V.V., Philippov, D.A., Mardanov, A.V., Ravin, N.V., and Dedysh, S.N., Closely located but totally distinct: highly contrasting prokaryotic diversity patterns in raised bogs and eutrophic fens, Microorganisms, 2020, vol. 8, p. 484. https://doi.org/3390/microorganisms8040484
Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K., MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, pp. 1547–1549. https://doi.org/1093/molbev/msy096
Rast, P., Glöckner, I., Boedeker, C., Jeske, O., Wiegand, S., Reinhardt, R., Schumann, P., Rohde, M., Spring, S., Glöckner, F.O., Jogler, C., and Jogler, M., Three novel species with peptidoglycan cell walls form the new genus Lacunisphaera gen. nov. in the family Opitutaceae of the Verrucomicrobial Subdivision 4, Front. Microbiol., 2017, vol. 8, p. 202. https://doi.org/3389/fmicb.2017.00202.
Schmitz, R.A., Peeters, S.H., Versantvoort, W., Picone, N., Pol, A., Jetten, M.S.M., and Op Den Camp, H.J.M., Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles, FEMS Microbiol. Rev., 2021, vol. 45, p. fuab007. https://doi.org/1093/FEMSRE/FUAB007
Shieh, W.Y. and Jean, W.D., Alterococcus agarolyticus, gen.nov., sp.nov., a halophilic thermophilic bacterium capable of agar degradation, Can. J. Microbiol., 1998, vol. 44, pp. 637–645. https://doi.org/1139/cjm-44-7-637
Funding
This work was financially supported by the Ministry of Science and Higher Education of the Russian Federation.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
ETHICS APPROVAL AND CONSENT TO PARTICIPATE
This work does not contain any studies involving human and animal subjects.
CONFLICT OF INTEREST
The authors of this work declare that they have no conflicts of interest.
Additional information
Publisher’s Note.
Pleiades Publishing remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Ivanova, A.A., Dedysh, S.N. Phylogenetic Diversity of Verrucomicrobiota in Fens of Northern Russia. Microbiology 92 (Suppl 1), S7–S11 (2023). https://doi.org/10.1134/S0026261723603573
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0026261723603573