Actinomycetes Rhodococcus ruber – Key and Universal Bioxidizers of Gaseous Alkanes C₂−C₄

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Abstract

In recent years, there has been an increasing interest of researchers in microorganisms capable of oxidizing higher gaseous homologues of methane (ethane, propane, n-butane). Among propane- and butane-oxidizing bacteria, representatives of Rhodococcus ruber attract special attention; they can easily adapt to extreme environmental conditions and have significant potential for biotechnology. The review emphasizes the importance of R. ruber as a bioindicator of oil and gas fields and a component of microbial consortia for the degradation of hydrocarbons and other xenobiotics. Data on natural substrates and ecological niches of gas-oxidizing Rhodococcus are presented, their morphological and physiological features are described. Their role in biogeochemical cycles and the potential for industrial use are discussed. As a result of the analysis of functional genes and enzyme systems of gaseous hydrocarbon (C2−C4) catabolism, the key stages of propane oxidation in Rhodococcus were identified and the role of propanotrophy in the bioremediation potential of R. ruber was revealed. The need for further research to understand the mechanisms of adaptation of these microorganisms to anthropogenic impact was substantiated.

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About the authors

I. B. Ivshina

Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences; Perm National Research State University

Author for correspondence.
Email: ivshina@iegm.ru
Russian Federation, Perm, 614081; Perm, 614990

M. S. Kuyukina

Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences; Perm National Research State University

Email: ivshina@iegm.ru
Russian Federation, Perm, 614081; Perm, 614990

A. V. Krivoruchko

Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences; Perm National Research State University

Email: ivshina@iegm.ru
Russian Federation, Perm, 614081; Perm, 614990

E. A. Tyumina

Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences; Perm National Research State University

Email: ivshina@iegm.ru
Russian Federation, Perm, 614081; Perm, 614990

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3. Fig. 1. Scanning electron microscopy of R. ruber IEGM 333 and IEGM 565 cells grown on a mineral medium in a propane atmosphere (Ivshina et al., 2021): a ‒ strain IEGM 333, the arrow indicates the germination of the progenitor coccobacillary cell; b ‒ strain 333, the arrow indicates a filamentous branching cell; c ‒ strain 333, cells with laterally located growth processes; d ‒ strain IEGM 565, the arrow indicates the exfoliation of a fragment of the “old” peptide glycan from the cell surface.

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4. Fig. 2. Scanning electron microscopy of R. ruber IEGM 333 cells grown on a mineral medium in a propane atmosphere (Ivshina et al., 1982, 2021; Ivshina et al., 2021, 2024a): a ‒ cone-shaped outgrowths are shown by an arrow; b ‒ cells separating by cleavage. The arrow indicates ring-shaped protrusions dividing the cell into two zones: the old mother cell with a strong cell wall and the new daughter cell of a smaller diameter with a thin elastic layer.

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5. Fig. 3. Ultrathin sections of R. ruber cells grown on a mineral medium in an atmosphere of propane (a-c, d, f) and n-butane (d) (Ivshina et al., 1982, 2021; Ivshina et al., 2024a): a ‒ strain IEGM 73; b ‒ strain IEGM 565; c ‒ strain IEGM 333; d ‒ strain IEGM 342; e ‒ strain IEGM 342. N – nucleoid; IMS – intracytoplasmic membrane system; B – polyphosphate granules; G – lipid inclusions; EPS – electron-dense inclusions; FC – cytoplasmic fragmentation; OS – rounded structures; MK – microcapsule; RKS – cell wall proliferation; MV – microvesicles.

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6. Fig. 4. Soluble diiron-containing monooxygenases of R. ruber strains from the Regional Profiled Collection of Alkanotrophic Microorganisms (acronym of the IEGM collection, http://www.iegmcol.ru/): a – organization of loci with genes encoding monooxygenases MO-I and MO-II (numbers show the length of genes and spacers between genes in nucleotides; lengths of peptide chains in amino acid residues are given in brackets; arrows point to overlaps between genes of 3 nucleotides in length; ? – hypothetical proteins; filled sectors – propane metabolism genes; unfilled sectors – genes not directly associated with propane metabolism); b – phylogram constructed on the basis of nucleotide sequences of the α-subunit of protein A of monooxygenases MO-I and MO-II; c – a phylogram constructed based on the amino acid sequences of the α-subunit of protein A of monooxygenases MO-I and MO-II. Phylograms were obtained using the Clustal Omega program (Madeira et al., 2024). The scales on the phylograms show the evolutionary distances between the sequences. The names of the branches include the strain number and information about the location of the gene in the genome of this strain. The genomes of the strains listed in the legend to Fig. S2 were used for the analysis.

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