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Prosthecodimorpha staleyi gen. nov., sp. nov., Novel Prosthecate Bacteria within the Family Ancalomicrobiaceae and Reclassification of the Polyphyletic Genus Prosthecomicrobium

Microbiology volume 91, pages 479–488 (2022)Cite this article

Abstract

An isolate of prosthecate bacteria was isolated from the takyr soil of a rice field on the Akdala massif (Kazakhstan) and designated as strain 22T. Strain 22T was represented by gram-negative, aerobic, motile, oxidase and catalase-positive bacteria. Cells of this strain formed numerous prosthecae extending in different directions from the cell surface. Bacteria had a dimorphic life cycle, with two different morphological types of cells. The prosthecae may be short (i.e., less than 1.0 µm long) or long (i.e., more than 2.0 µm long). Cells reproduced by budding and grew within the pH range of 6.5–8.5 and at 28–30°C. Major cellular fatty acids were C18:1 ω7, C16:0, C19:1 branched, and C16:1 ω7. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain 22T shared the highest gene sequence similarity with Prosthecomicrobium hirschii 16T (99.9%) and formed a common branch on the phylogenomic tree with P. hirschii 16T and Siculibacillus lacustris SA-279T. This branch was only distantly related to the phylogenetic lineage defined by the type species of the genus Prosthecomicrobium, P. pneumaticum ATCC 23633T, thus indicating a polyphyletic nature of the genus Prosthecomicrobium. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 22T and the most closely related species P. hirschii 16T were 93.6 and 47.6%, respectively, and were below the threshold accepted for species demarcation. Based on the results of phylogenetic analysis, strains 22T and 16T should be assigned to the Ancalomicrobiaceae family, with introduction of a novel genus Prosthecodimorpha gen. nov. The G + C content of the genome of strain 22T was 61.9%. Strain 22T represented a novel species in a novel genus, for which the name Prosthecodimorpha staleyi gen. nov., sp. nov. is proposed, with the type strain 22T (=VKM B-3576T = UQM 41461T = DSMZ 113594T).

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ACKNOWLEDGMENTS

Bioinformatic analysis was performed using computing resources at the SciBear OU (https://sci-bear.com/).

Funding

The work was supported by the Ministry of Science and Higher Education of the Russian Federation.

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Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia

    L. Vasilyeva, Y. Berestovskaya & N. Pimenov

  2. SciBear OU, 10115, Tallinn, Estonia

    D. Grouzdev

  3. Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia

    V. Koziaeva

  4. Gubkin Russian State University of Oil and Gas, 119071, Moscow, Russia

    A. Novikov

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  1. L. Vasilyeva
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Vasilyeva, L., Grouzdev, D., Koziaeva, V. et al. Prosthecodimorpha staleyi gen. nov., sp. nov., Novel Prosthecate Bacteria within the Family Ancalomicrobiaceae and Reclassification of the Polyphyletic Genus Prosthecomicrobium. Microbiology 91, 479–488 (2022). https://doi.org/10.1134/S0026261722601105

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  • DOI: https://doi.org/10.1134/S0026261722601105

Keywords:

  • prosthecate bacteria
  • Prosthecodimorpha
  • Prosthecomicrobium
  • Ancalomicrobiaceae
  • Hyphomicrobiaceae
  • Kaistiaceae
  • Hyphomicrobiales
  • rice field
  • dimorphic life cycle