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Semenova EM, Tourova TP, Babich TL, Logvinova EY, Sokolova DS, Loiko NG, Myazin VA, Korneykova MV, Mardanov AV, Nazina TN. Crude Oil Degradation in Temperatures Below the Freezing Point by Bacteria from Hydrocarbon-Contaminated Arctic Soils and the Genome Analysis of Sphingomonas sp. AR_OL41. Microorganisms 2023; 12:79. [PMID: 38257905 PMCID: PMC10818417 DOI: 10.3390/microorganisms12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to study the physiology and growth in oil at temperatures below 0 °C of four strains of bacteria of the genera Pseudomonas, Rhodococcus, Arthrobacter, and Sphingomonas-previously isolated from diesel-contaminated soils of the Franz Josef Land archipelago-as well as genomic analysis of the Sphingomonas sp. AR_OL41 strain. The studied strains grew on hydrocarbons at temperatures from -1.5 °C to 35 °C in the presence of 0-8% NaCl (w/v). Growth at a negative temperature was accompanied by visual changes in the size of cells as well as a narrowing of the spectrum of utilized n-alkanes. The studied strains were psychrotolerant, degraded natural biopolymers (xylan, chitin) and n-alkanes of petroleum, and converted phosphates into a soluble form. The ability to degrade n-alkanes is rare in members of the genus Sphingomonas. To understand how the Sphingomonas sp. AR_OL41 strain has adapted to a cold, diesel-contaminated environment, its genome was sequenced and analyzed. The Illumina HiSeq 2500 platform was used for AR_OL41 genome strain sequencing. The genome analysis of the AR_OL41 strain showed the presence of genes encoding enzymes of n-alkane oxidation, pyruvate metabolism, desaturation of membrane lipids, and the formation of exopolysaccharides, confirming the adaptation of the strain to hydrocarbon pollution and low habitat temperature. Average nucleotide identity and digital DNA-DNA hybridization values for genomes of the AR_OL41 strain with that of the phylogenetically relative Sphingomonas alpine DSM 22537T strain were 81.9% and 20.9%, respectively, which allows the AR_OL41 strain to be assigned to a new species of the genus Sphingomonas. Phenomenological observations and genomic analysis indicate the possible participation of the studied strains in the self-purification of Arctic soils from hydrocarbons and their potential for biotechnological application in bioremediation of low-temperature environments.
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Affiliation(s)
- Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Ekaterina Y. Logvinova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Nataliya G. Loiko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Vladimir A. Myazin
- Institute of North Industrial Ecology Problems–Subdivision of the Federal Research Centre “Kola Science Centre of Russian Academy of Science”, 184209 Apatity, Russia;
- Agrarian and Technological Institute, People’s Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Maria V. Korneykova
- Institute of North Industrial Ecology Problems–Subdivision of the Federal Research Centre “Kola Science Centre of Russian Academy of Science”, 184209 Apatity, Russia;
- Agrarian and Technological Institute, People’s Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
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Namsaraev Z, Kozlova A, Tuzov F, Krylova A, Izotova A, Makarov I, Bezgreshnov A, Melnikova A, Trofimova A, Kuzmin D, Patrushev M, Toshchakov S. Biogeographic Analysis Suggests Two Types of Planktonic Prokaryote Communities in the Barents Sea. BIOLOGY 2023; 12:1310. [PMID: 37887020 PMCID: PMC10604488 DOI: 10.3390/biology12101310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the Psychrobacter, Sulfitobacter and Polaribacter genera were dominant in samples from both types of communities. The first type of community was also dominated by members of Halomonas, Pseudoalteromonas, Planococcaceae and an unclassified representative of the Alteromonadaceae family. The second type of community also had a significant proportion of Nitrincolaceae, SAR92, SAR11 Clade I, NS9, Cryomorphaceae and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.
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Affiliation(s)
- Zorigto Namsaraev
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Aleksandra Kozlova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Tuzov
- Department of Oceanology, Faculty of Geography, Lomonosov Moscow State University, 119991 Moscow, Russia
- All-Russian Research Institute for Civil Defense and Emergencies, 121352 Moscow, Russia
| | - Anastasia Krylova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anna Izotova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Andrei Bezgreshnov
- Arctic and Antarctic Research Institute, 199397 Saint Petersburg, Russia
| | - Anna Melnikova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anna Trofimova
- Department of Geography and Hydrometeorology, Higher School of Natural Sciences and Technologies, Northern (Arctic) Federal University, 163002 Arkhangelsk, Russia
| | - Denis Kuzmin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Maksim Patrushev
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Stepan Toshchakov
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
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