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Melekhina EN, Belykh ES, Kanev VA, Taskaeva AA, Tarabukin DV, Zinovyeva AN, Velegzhaninov IO, Rasova EE, Baturina OA, Kabilov MR, Markarova MY. Soil Microbiome in Conditions of Oil Pollution of Subarctic Ecosystems. Microorganisms 2023; 12:80. [PMID: 38257907 PMCID: PMC10820038 DOI: 10.3390/microorganisms12010080] [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: 10/24/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest-tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50-80% of bacterial OTUs and 44-60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution.
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Affiliation(s)
- Elena N. Melekhina
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Elena S. Belykh
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Vladimir A. Kanev
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Anastasia A. Taskaeva
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Dmitry V. Tarabukin
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Aurika N. Zinovyeva
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Ilya O. Velegzhaninov
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Elena E. Rasova
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
| | - Olga A. Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Lavrentieva 8, 630090 Novosibirsk, Russia; (O.A.B.); (M.R.K.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Lavrentieva 8, 630090 Novosibirsk, Russia; (O.A.B.); (M.R.K.)
| | - Maria Yu. Markarova
- Institute of Biology, Komi Scientifc Center, Ural Branch of Russian Academy of Sciences (IB FRC Komi SC UB RAS), Kommunisticheskaya 28, 167982 Syktyvkar, Russia; (E.S.B.); (V.A.K.); (A.A.T.); (D.V.T.); (A.N.Z.); (I.O.V.); (E.E.R.); (M.Y.M.)
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Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic. Sci Rep 2021; 11:19620. [PMID: 34608182 PMCID: PMC8490368 DOI: 10.1038/s41598-021-98680-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
The present comprehensive study aimed to estimate the aftermath of oil contamination and the efficacy of removing the upper level of polluted soil under the conditions of the extreme northern taiga of northeastern European Russia. Soil samples from three sites were studied. Two sites were contaminated with the contents of a nearby sludge collector five years prior to sampling. The highly contaminated upper soil level was removed from one of them. The other was left for self-restoration. A chemical analysis of the soils was conducted, and changes in the composition of the soil zoocoenosis and bacterial and fungal microbiota were investigated. At both contaminated sites, a decrease in the abundance and taxonomic diversity of indicator groups of soil fauna, oribatid mites and collembolans compared to the background site were found. The pioneer eurytopic species Oppiella nova, Proisotoma minima and Xenyllodes armatus formed the basis of the microarthropod populations in the contaminated soil. A complete change in the composition of dominant taxonomic units was observed in the microbiota, both the bacterial and fungal communities. There was an increase in the proportion of representatives of Proteobacteria and Actinobacteria in polluted soils compared to the background community. Hydrocarbon-degrading bacteria-Alcanivorax, Rhodanobacter ginsengisoli, Acidobacterium capsulatum, and Acidocella-and fungi-Amorphotheca resinae abundances greatly increased in oil-contaminated soil. Moreover, among both bacteria and fungi, a sharp increase in the abundance of uncultivated organisms that deserve additional attention as potential oil degraders or organisms with a high resistance to oil contamination were observed. The removal of the upper soil level was partly effective in terms of decreasing the oil product concentration (from approximately 21 to 2.6 g/kg of soil) and preventing a decrease in taxonomic richness but did not prevent alterations in the composition of the microbiota or zoocoenosis.
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Novakovskiy AB, Kanev VA, Markarova MY. Long-term dynamics of plant communities after biological remediation of oil-contaminated soils in far north. Sci Rep 2021; 11:4888. [PMID: 33649460 PMCID: PMC7921116 DOI: 10.1038/s41598-021-84226-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/15/2021] [Indexed: 12/13/2022] Open
Abstract
We studied the long-term dynamics of plant communities after bio and phytoremediation of oil-polluted soils. Nine plots located in European Northeast and treated using various bioremediation methods were monitored from 2002 to 2014. Geobotanical descriptions (relevés) of each plot were performed in 2006 and 2014, and Grime’s theoretical CSR (competition–stress–ruderality) framework was used to assess the vegetation state and dynamics. We observed a clear shift of communities from pioneer (where ruderal species were prevalent) to stable (where competitor species were dominant) states. However, the remediation type did not significantly impact the vegetation recovery rate. After 12 years, all methods led to a 55–90% decrease in the oil content of the soil and a recovery of the vegetation cover. The plant communities contained mainly cereals and sedges which significantly differed from the original tundra communities before the oil spill. The control plot, treated only by mechanical cleaning, had minimum oil degradation rate (50%) and vegetation recovery rates, although, in CSR terms, its vegetation assemblage resembled the background community. Cereals (Agrostis gigantea, Deschampsia cespitosa, Phalaris arundinacea, and Poa pratensis), sedges (Carex canescens, Carex limosa, and Eriophorum vaginatum), and shrubs (Salix) were found to be the most effective species for phytoremediation, exhibiting high community productivity under the harsh northern conditions.
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Affiliation(s)
- A B Novakovskiy
- Institute of Biology Komi SC UB RAS, Kommunisticheskaya st., 28, Syktyvkar, Russia.
| | - V A Kanev
- Institute of Biology Komi SC UB RAS, Kommunisticheskaya st., 28, Syktyvkar, Russia
| | - M Y Markarova
- Institute of Biology Komi SC UB RAS, Kommunisticheskaya st., 28, Syktyvkar, Russia.,Federal Scientific Vegetable Center, Selektsionnaya st. 14, Odintsovo District, Moscow Region, Russia
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Kuyukina MS, Ivshina IB. Bioremediation of Contaminated Environments Using Rhodococcus. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-11461-9_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rhodococcus lactonase with organophosphate hydrolase (OPH) activity and His₆-tagged OPH with lactonase activity: evolutionary proximity of the enzymes and new possibilities in their application. Appl Microbiol Biotechnol 2013; 98:2647-56. [PMID: 24057406 DOI: 10.1007/s00253-013-5233-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/30/2013] [Accepted: 09/09/2013] [Indexed: 10/26/2022]
Abstract
Decontamination of soils with complex pollution using natural strains of microorganisms is a matter of great importance. Here we report that oil-oxidizing bacteria Rhodococcus erythropolis AC-1514D and Rhodococcus ruber AC-1513D can degrade various organophosphorous pesticides (OP). Cell-mediated degradation of five different OP is apparently associated with the presence of N-acylhomoserine lactonase, which is pronouncedly similar (46-50 %) to the well-known enzyme organophosphate hydrolase (OPH), a hydrolysis catalyst for a wide variety of organophosphorous compounds. Additionally, we demonstrated the high lactonase activity of hexahistidine-tagged organophosphate hydrolase (His6-OPH) with respect to various N-acylhomoserine lactones, and we determined the catalytic constants of His6-OPH towards these compounds. These experimental data and theoretical analysis confirmed the hypothesis about the evolutionary proximity of OPH and lactonases. Using Rhodococcus cells, we carried out effective simultaneous biodegradation of pesticide paraoxon (88 mg/kg) and oil hydrocarbon hexadecane (6.3 g/kg) in the soil. Furthermore, the discovered high lactonase activity of His6-OPH offers new possibilities for developing an efficient strategy of combating resistant populations of Gram-negative bacterial cells.
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Archegova IB, Khabibullina FM, Shubakov AA. Optimization of the purification of soil and water objects from oil using biosorbents. CONTEMP PROBL ECOL+ 2013. [DOI: 10.1134/s1995425512060042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Application of Rhodococcus in Bioremediation of Contaminated Environments. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Alonso-Gutiérrez J, Figueras A, Albaigés J, Jiménez N, Viñas M, Solanas AM, Novoa B. Bacterial communities from shoreline environments (costa da morte, northwestern Spain) affected by the prestige oil spill. Appl Environ Microbiol 2009; 75:3407-18. [PMID: 19376924 PMCID: PMC2687268 DOI: 10.1128/aem.01776-08] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 03/26/2009] [Indexed: 11/20/2022] Open
Abstract
The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics.
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MESH Headings
- Alkenes/metabolism
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Biodegradation, Environmental
- Biodiversity
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Geologic Sediments/microbiology
- Hydrocarbons, Aromatic/metabolism
- Mineral Oil
- Molecular Sequence Data
- Nucleic Acid Denaturation
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Spain
- Water Pollution, Chemical
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Zhukov DV, Murygina VP, Kalyuzhnyi SV. Kinetics of the degradation of aliphatic hydrocarbons by the bacteria Rhodococcus ruber and Rhodococcus erythropolis. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807060038] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ouyang W, Liu H, Murygina V, Yu Y, Xiu Z, Kalyuzhnyi S. Comparison of bio-augmentation and composting for remediation of oily sludge: A field-scale study in China. Process Biochem 2005. [DOI: 10.1016/j.procbio.2005.06.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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