{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T03:38:45Z","timestamp":1790048325520,"version":"4.0.1"},"reference-count":102,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T00:00:00Z","timestamp":1766707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012190","name":"Ministry of Science and Higher Education of the Russian Federation","doi-asserted-by":"publisher","award":["FSSF-2024-0023"],"award-info":[{"award-number":["FSSF-2024-0023"]}],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"publisher"}]},{"name":"RSF project","award":["#23-17-00118"],"award-info":[{"award-number":["#23-17-00118"]}]},{"name":"RUDN University Scientific Projects Grant System","award":["202414-2-000"],"award-info":[{"award-number":["202414-2-000"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Long-standing and chronic soil pollution in the Polar Regions is the most persistent. Simultaneous contamination with petroleum products and heavy metals puts additional load on the soil microbial community. The purpose of this work was to determine the composition of prokaryotes in the soils of Mount Kaskama with long-standing contamination with petroleum products and heavy metals (Murmansk region, Russia) and outside this zone and the potential ability of bacteria to participate in the self-purification of these soils. Using high-throughput sequencing of 16S rRNA gene V3\u2013V4 fragments, an increase in the proportion of bacteria of the phyla Pseudomonadota, Verrucomicrobiota, Cyanobacteriota, and Bacillota was shown with an increase in soil contamination. Bacteria of the genera Bacillus, Caballeronia, Cytobacillus, Paenibacillus, Paraburkholderia, Pseudomonas, and Rhodanobacter were isolated from soil samples. Bacteria of the genus Paenibacillus capable of hydrocarbon oxidation and iron reduction were isolated from the subsurface contaminated layers. Under aerobic conditions, Fe(II) oxidation by bacteria of the genus Pseudomonas and biodegradation of hydrocarbons by isolated bacteria are possible. The isolated strains grew at low temperatures, used diesel fuel components, and were resistant to Cu(II), Ni(II), and Pb(II). The data obtained indicates the adaptation of bacterial communities to environmental conditions and the ability to participate in the process of soil self-healing.<\/jats:p>","DOI":"10.3390\/microorganisms14010055","type":"journal-article","created":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T07:52:59Z","timestamp":1766994779000},"page":"55","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Bacterial Diversity of Arctic Soils with Long-Standing Pollution by Petroleum Products and Heavy Metals"],"prefix":"10.3390","volume":"14","author":[{"given":"Ekaterina M.","family":"Semenova","sequence":"first","affiliation":[{"name":"Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7638-4325","authenticated-orcid":false,"given":"Tamara L.","family":"Babich","sequence":"additional","affiliation":[{"name":"Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2422-4423","authenticated-orcid":false,"given":"Diyana S.","family":"Sokolova","sequence":"additional","affiliation":[{"name":"Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4155-3416","authenticated-orcid":false,"given":"Vladimir A.","family":"Myazin","sequence":"additional","affiliation":[{"name":"Institute of North Industrial Ecology Problems\u2013Subdivision of the Federal Research Centre \u201cKola Science Centre of Russian Academy of Science\u201d, 184209 Apatity, Russia"},{"name":"Agrarian and Technological Institute, People\u2019s Friendship University of Russia (RUDN University), 117198 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6167-1567","authenticated-orcid":false,"given":"Maria V.","family":"Korneykova","sequence":"additional","affiliation":[{"name":"Institute of North Industrial Ecology Problems\u2013Subdivision of the Federal Research Centre \u201cKola Science Centre of Russian Academy of Science\u201d, 184209 Apatity, Russia"},{"name":"Agrarian and Technological Institute, People\u2019s Friendship University of Russia (RUDN University), 117198 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6586-2467","authenticated-orcid":false,"given":"Tamara N.","family":"Nazina","sequence":"additional","affiliation":[{"name":"Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Yergeau, E., Sanschagrin, S., Beaumier, D., and Greer, C.W. (2012). Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0030058"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Pandolfo, E., Barra Caracciolo, A., and Rolando, L. (2023). Recent advances in bacterial degradation of hydrocarbons. Water, 15.","DOI":"10.3390\/w15020375"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/j.envpol.2017.01.079","article-title":"Bacterial community shift and hydrocarbon transformation during bioremediation of short-term petroleum-contaminated soil","volume":"223","author":"Wu","year":"2017","journal-title":"Environ. Pollut."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1021\/es0305149","article-title":"Hydrocarbon spills on Antarctic soils: Effects and management","volume":"38","author":"Aislabie","year":"2004","journal-title":"Environ. Sci. Technol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1111\/1758-2229.12680","article-title":"Microbial diversity and biogeography in Arctic soils","volume":"10","author":"Malard","year":"2018","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Garousin, H., Pourbabaee, A.A., Alikhani, H.A., and Yazdanfar, N. (2021). A combinational strategy mitigated old\u2013aged petroleum contaminants: Ineffectiveness of biostimulation as a bioremediation technique. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.642215"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1134\/S1064229315120054","article-title":"Seasonal dynamics of the microbiome of chernozems of the long\u2013term agrochemical experiment in Kamennaya Steppe","volume":"48","author":"Chernov","year":"2015","journal-title":"Eurasian Soil Sci."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Namsaraev, Z., Bobrik, A., Kozlova, A., Krylova, A., Rudenko, A., Mitina, A., Saburov, A., Patrushev, M., Karnachuk, O., and Toshchakov, S. (2023). Carbon emission and biodiversity of Arctic soil microbial communities of the Novaya Zemlya and Franz Josef Land Archipelagos. Microorganisms, 11.","DOI":"10.3390\/microorganisms11020482"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Korneykova, M.V., Myazin, V.A., Fokina, N.V., Chaporgina, A.A., Nikitin, D.A., and Dolgikh, A.V. (2023). Structure of microbial communities and biological activity in tundra soils of the Euro-Arctic region (Rybachy peninsula, Russia). Microorganisms, 11.","DOI":"10.3390\/microorganisms11051352"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1134\/S0026261721060138","article-title":"Microbial diversity of hydrocarbon-contaminated soils of the Franz Josef land Archipelago","volume":"90","author":"Semenova","year":"2021","journal-title":"Microbiology"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"11250","DOI":"10.1007\/s11356-014-3122-2","article-title":"Bioremediation treatment of hydrocarbon\u2013contaminated Arctic soils: Influencing parameters","volume":"21","author":"Naseri","year":"2014","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Yap, H.S., Zakaria, N.N., Zulkharnain, A., Sabri, S., Gomez\u2013Fuentes, C., and Ahmad, S.A. (2021). Bibliometric analysis of hydrocarbon bioremediation in cold regions and a review on enhanced soil bioremediation. Biology, 10.","DOI":"10.3390\/biology10050354"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"941810","DOI":"10.4061\/2011\/941810","article-title":"Microbial degradation of petroleum hydrocarbon contaminants: An overview","volume":"2011","author":"Das","year":"2011","journal-title":"Biotechnol. Res. Int."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Kumar, V., Kumar, M., and Prasad, R. (2018). Microbial Action on Hydrocarbons, Springer.","DOI":"10.1007\/978-981-13-1840-5"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3463","DOI":"10.1016\/S0045-6535(98)00575-X","article-title":"Biodegradation of diesel oil by cold-adapted microorganisms in presence of sodium dodecyl sulfate","volume":"38","author":"Margesin","year":"1999","journal-title":"Chemosphere"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3230","DOI":"10.1128\/AEM.66.8.3230-3233.2000","article-title":"Metabolic activity of permafrost bacteria below the freezing point","volume":"66","author":"Rivkina","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_17","first-page":"385","article-title":"Psychrophilic microorganisms: Challenges for life","volume":"4","author":"Collins","year":"2006","journal-title":"EMBO Rep."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Semenova, E.M., Tourova, T.P., Babich, T.L., Logvinova, E.Y., Sokolova, D.S., Loiko, N.G., Myazin, V.A., Korneykova, M.V., Mardanov, A.V., and Nazina, T.N. (2024). 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, 12.","DOI":"10.3390\/microorganisms12010079"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"24346","DOI":"10.1007\/s11356-017-0076-1","article-title":"Resistance of aerobic microorganisms and soil enzyme response to soil contamination with Ekodiesel Ultra fuel","volume":"24","author":"Borowik","year":"2017","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1021\/es00002a033","article-title":"Effect of aging of chemicals in soil on their biodegradability and extractability","volume":"29","author":"Hatzinger","year":"1995","journal-title":"Environ. Sci. Technol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.agee.2011.12.020","article-title":"Aging effect of petroleum hydrocarbons in soil under different attenuation conditions","volume":"149","author":"Tang","year":"2012","journal-title":"Agric. Ecosyst. Environ."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Timmis, K.N. (2010). Toxicity of hydrocarbons to microorganisms. Handbook of Hydrocarbon and Lipid Microbiology, Springer.","DOI":"10.1007\/978-3-540-77587-4"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Tang, H., Xiang, G., Xiao, W., Yang, Z., and Zhao, B. (2024). Microbial mediated remediation of heavy metals toxicity: Mechanisms and future prospects. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1420408"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1146\/annurev.mi.47.100193.001403","article-title":"Dissimilatory metal reduction","volume":"47","author":"Lovley","year":"1993","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_25","unstructured":"Kumar, P., Gurjar, B.R., and Govil, J.N. (2017). Biodegradation and Bioremediation. Environmental Science and Engineering, Studium Press."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.3389\/fmicb.2018.01985","article-title":"Microbial community and in situ bioremediation of groundwater by nitrate removal in the zone of a radioactive waste surface repository","volume":"9","author":"Safonov","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Saha, L., Tiwari, J., Bauddh, K., and Ma, Y. (2021). Recent developments in microbe-plant-based bioremediation for tackling heavy metal-polluted soils. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.731723"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s42269-023-01006-z","article-title":"Microbial bioremediation as a tool for the removal of heavy metals","volume":"47","author":"Hassan","year":"2023","journal-title":"Bull. Natl. Res. Cent."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"130038","DOI":"10.1016\/j.chemosphere.2021.130038","article-title":"Synergistic effect of ACC deaminase producing Pseudomonas sp. TR15a and siderophore producing Bacillus aerophilus TR15c for enhanced growth and copper accumulation in Helianthus annuus L","volume":"276","author":"Kumar","year":"2021","journal-title":"Chemosphere"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1111\/j.1574-6968.1998.tb12998.x","article-title":"Sulfate-reducing bacterium grows with Cr (VI), U (VI), Mn (IV), and Fe (III) as electron acceptors","volume":"162","author":"Tebo","year":"1998","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"3743","DOI":"10.1128\/AEM.66.9.3743-3749.2000","article-title":"Direct and Fe (II)-mediated reduction of technetium by Fe (III)-reducing bacteria","volume":"66","author":"Lloyd","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3752","DOI":"10.1128\/aem.60.10.3752-3759.1994","article-title":"Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism","volume":"60","author":"Caccavo","year":"1994","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s00203-016-1286-5","article-title":"An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater","volume":"199","author":"Mohapatra","year":"2017","journal-title":"Arch. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1289\/ehp.5840","article-title":"Impact of metals on the biodegradation of organic pollutants","volume":"111","author":"Sandrin","year":"2003","journal-title":"Environ. Health Perspect."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1016\/j.soilbio.2010.05.002","article-title":"Relative impact of soil, metal source and metal concentration on bacterial community structure and community tolerance","volume":"42","author":"Macdonald","year":"2010","journal-title":"Soil Biol. Biochem."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Liu, X., Hu, X., Cao, Y., Pang, W., Huang, J., Guo, P., and Huang, L. (2019). Biodegradation of phenanthrene and heavy metal removal by acid-tolerant Burkholderia fungorum FM\u20132. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00408"},{"key":"ref_37","first-page":"406598","article-title":"Effect of soil texture on remediation of hydrocarbons\u2013contaminated soil at El\u2013Minia District, Upper Egypt","volume":"2012","author":"Mohamed","year":"2012","journal-title":"ISRN Chem. Eng."},{"key":"ref_38","first-page":"1130","article-title":"Bioremediation of oil-polluted cultivated soils in the Euro-Arctic region","volume":"1","author":"Evdokimova","year":"2012","journal-title":"J. Environ. Sci. Eng."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Dell\u2019Anno, F., Brunet, C., van Zyl, L.J., Trindade, M., Golyshin, P.N., Dell\u2019Anno, A., Ianora, A., and Sansone, C. (2020). Degradation of hydrocarbons and heavy metal reduction by marine bacteria in highly contaminated sediments. Microorganisms, 8.","DOI":"10.3390\/microorganisms8091402"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"9864","DOI":"10.1021\/acs.est.1c01113","article-title":"Soil buffering capacity can be used to optimize biostimulation of psychrotrophic hydrocarbon remediation","volume":"55","author":"Mamet","year":"2021","journal-title":"Environ. Sci. Technol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"103054","DOI":"10.1016\/j.jece.2019.103054","article-title":"Monitoring the biodegradation of TPH and PAHs in refinery solid waste by biostimulation and bioaugmentation","volume":"7","author":"Zeneli","year":"2019","journal-title":"J. Environ. Chem. Eng."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1007\/s10653-021-01059-x","article-title":"The effect of combined pollution by PAHs and heavy metals on the topsoil microbial communities of Spolic Technosols of the lake Atamanskoe, Southern Russia","volume":"44","author":"Gorovtsov","year":"2022","journal-title":"Environ. Geochem. Health"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Myazin, V.A., Korneykova, M.V., Chaporgina, A.A., Fokina, N.V., and Vasilyeva, G.K. (2021). The effectiveness of biostimulation, bioaugmentation and sorption-biological treatment of soil contaminated with petroleum products in the Russian Subarctic. Microorganisms, 9.","DOI":"10.3390\/microorganisms9081722"},{"key":"ref_44","unstructured":"Shishov, L.L., Tonkonogov, V.D., Lebedeva, I.I., and Gerasimova, M.I. (2004). Classification and Diagnostics of Soils in Russia, Smolensk. (In Russian)."},{"key":"ref_45","unstructured":"IUSS Working Group WRB (2014). World Reference Base for Soil Resources 2014: International Soil Classification System for Naming Soils and Creating Legends for Soil Maps, FAO. World Soil Resources Reports No. 106."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1134\/S0026261706010127","article-title":"The properties of hydrocarbon oxidizing bacteria isolated from the oilfields of Tatarstan, Western Siberia, and Vietnam","volume":"75","author":"Borzenkov","year":"2006","journal-title":"Microbiology"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/aem.49.1.1-7.1985","article-title":"A new medium for the enumeration and subculture of bacteria from potable water","volume":"9","author":"Reasoner","year":"1985","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1134\/S1062359007030041","article-title":"A method for cultivation of microorganisms oxidizing iron and manganese in bottom sediments of Lake Baikal","volume":"34","author":"Zakharova","year":"2007","journal-title":"Biol. Bull."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1128\/aem.51.4.683-689.1986","article-title":"Organic matter mineralization with reduction of ferric iron in anaerobic sediments","volume":"51","author":"Lovley","year":"1986","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_50","first-page":"245","article-title":"\u00dcber das vitamin B12\u2014Bed\u00fcrfnis phototropher Schweferelbakterien","volume":"55","author":"Pfennig","year":"1966","journal-title":"Arch. Microbiol."},{"key":"ref_51","unstructured":"Stackebrandt, E., and Goodfellow, M. (1991). 16S\/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics, John Wiley & Sons."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"fiw018","DOI":"10.1093\/femsec\/fiw018","article-title":"Microbial diversity in European alpine permafrost and active layers","volume":"92","author":"Frey","year":"2016","journal-title":"FEMS Microbol. Ecol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"Pruesse","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: Highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and applications. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"W566","DOI":"10.1093\/nar\/gkv468","article-title":"ClustVis: A web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap","volume":"43","author":"Metsalu","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_60","first-page":"1","article-title":"Past: Paleontological Statistics Software Package for education and data analysis","volume":"4","author":"Hammer","year":"2001","journal-title":"Palaeontol. Electron."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Heberle, H., Meirelles, G.V., da Silva, F.R., Telles, G.P., and Minghim, R. (2015). InteractiVenn: A web-based tool for the analysis of sets through Venn diagrams. BMC Bioinform., 16.","DOI":"10.1186\/s12859-015-0611-3"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Koyama, A., Wallenstein, M.D., Simpson, R.T., and Moore, J.C. (2014). Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils. Front. Microbiol., 5.","DOI":"10.3389\/fmicb.2014.00516"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1111\/mec.13978","article-title":"Temporal dynamics of microbial communities in microcosms in response to pollutants","volume":"26","author":"Jiao","year":"2017","journal-title":"Mol. Ecol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1038\/ismej.2014.151","article-title":"Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site","volume":"8","author":"Mukherjee","year":"2014","journal-title":"ISME J."},{"key":"ref_65","first-page":"141","article-title":"Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine soils","volume":"41","author":"Whyte","year":"2002","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"3085","DOI":"10.1128\/AEM.69.6.3085-3092.2003","article-title":"Characterization of hydrocarbon\u2013degrading microbial populations in contaminated and pristine alpine soils","volume":"69","author":"Margesin","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1099\/ijs.0.013250-0","article-title":"Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria","volume":"60","author":"Kulichevskaya","year":"2010","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1111\/j.1574-6941.2012.01381.x","article-title":"Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils","volume":"82","author":"Rawat","year":"2012","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"de Chaves, M.G., Silva, G.G.Z., Rossetto, R., Edwards, R.A., Tsai, S.M., and Navarrete, A.A. (2019). Acidobacteria subgroups and their metabolic potential for carbon degradation in sugarcane soil amended with vinasse and nitrogen fertilizers. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01680"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"3113","DOI":"10.1128\/AEM.02012-06","article-title":"Acidobacteria phylum sequences in uranium\u2013contaminated subsurface sediments greatly expand the known diversity within the phylum","volume":"73","author":"Barns","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Ga\u0142\u0105zka, A., Grz\u0105dziel, J., Ga\u0142\u0105zka, R., Ukalska\u2013Jaruga, A., Strzelecka, J., and Smreczak, B. (2018). Genetic and functional diversity of bacterial microbiome in soils with long term impacts of petroleum hydrocarbons. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01923"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1099\/ijs.0.009209-0","article-title":"Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov., two acidophilic, psychrotolerant members of the Alphaproteobacteria from acidic northern wetlands","volume":"59","author":"Belova","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"e00867-20","DOI":"10.1128\/mSystems.00867-20","article-title":"Insights into the metabolism and evolution of the genus Acidiphilium, a typical acidophile in acid mine drainage","volume":"5","author":"Li","year":"2020","journal-title":"mSystems"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1007\/s00792-013-0566-0","article-title":"Acidocella aromatica sp. nov.: An acidophilic heterotrophic alphaproteobacterium with unusual phenotypic traits","volume":"17","author":"Jones","year":"2013","journal-title":"Extremophiles"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1023\/A:1016762613272","article-title":"Metal and antibiotic resistance traits in Bradyrhizobium sp. (cajanus) isolated from soil receiving oil refinery wastewater","volume":"17","author":"Ahmad","year":"2001","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"W\u0142odarczyk, A., Lirski, M., Fogtman, A., Koblowska, M., Bidzi\u0144ski, G., and Matlakowska, R. (2018). The oxidative metabolism of fossil hydrocarbons and sulfide minerals by the lithobiontic microbial community inhabiting deep subterrestrial Kupferschiefer Black Shale. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.00972"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1134\/S0026261721060096","article-title":"Microbial degraders of petroleum and polycyclic aromatic hydrocarbons from sod-podzolic soil","volume":"90","author":"Manucharova","year":"2021","journal-title":"Microbiology"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Banasiewicz, J., Gumowska, A., Ho\u0142ubek, A., and Orzechowski, S. (2025). Adaptations of the genus Bradyrhizobium to selected elements, heavy metals and pesticides present in the soil environment. Curr. Issues Mol. Biol., 47.","DOI":"10.3390\/cimb47030205"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1007\/s10532-024-10073-6","article-title":"Biodegradation of a complex hydrocarbon mixture and biosurfactant production by Burkholderia thailandensis E264 and an adapted microbial consortium","volume":"35","author":"Ouvrard","year":"2024","journal-title":"Biodegradation"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Pulschen, A.A., Bendia, A.G., Fricker, A.D., Pellizari, V.H., Galante, D., and Rodrigues, F. (2017). Isolation of uncultured bacteria from Antarctica using long incubation periods and low nutritional media. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2017.01346"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1134\/S000368382103008X","article-title":"Role of bacteria of the genus Pseudomonas in the sustainable development of agricultural systems and environmental protection (Review)","volume":"57","author":"Korshunova","year":"2021","journal-title":"Appl. Biochem. Microbiol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/s00792-005-0498-4","article-title":"Bioremediation of hydrocarbon-contaminated polar soils","volume":"10","author":"Aislabie","year":"2006","journal-title":"Extremophiles"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"2057","DOI":"10.1099\/ijsem.0.003431","article-title":"Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies","volume":"69","author":"Dobritsa","year":"2019","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Ara, I., Moriuchi, R., Dohra, H., Kimbara, K., Ogawa, N., and Shintani, M. (2023). Isolation and genomic analysis of 3-chlorobenzoate-degrading bacteria from soil. Microorganisms, 11.","DOI":"10.3390\/microorganisms11071684"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"133123","DOI":"10.1016\/j.jhazmat.2023.133123","article-title":"Responses of a polycyclic aromatic hydrocarbon-degrading bacterium, Paraburkholderia fungorum JT-M8, to Cd (II) under P\u2013limited oligotrophic conditions","volume":"465","author":"Li","year":"2024","journal-title":"J. Hazard. Mater."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"2810","DOI":"10.1099\/ijs.0.65018-0","article-title":"Rhodanobacter ginsengisoli sp. nov. and Rhodanobacter terrae sp. nov., isolated from soil cultivated with Korean ginseng","volume":"57","author":"Weon","year":"2007","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1038\/ismej.2009.154","article-title":"Metagenomic insights into evolution of a heavy metal\u2013contaminated groundwater microbial community","volume":"4","author":"Hemme","year":"2010","journal-title":"ISME J."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Prakash, O., Green, S.J., Singh, P., Jasrotia, P., and Kostka, J.E. (2021). Stress-related ecophysiology of members of the genus Rhodanobacter isolated from a mixed waste contaminated subsurface. Front. Environ. Sci. Eng., 15.","DOI":"10.1007\/s11783-020-1315-0"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"14437","DOI":"10.1007\/s11356-018-1604-3","article-title":"Surfactant-enhanced biodegradation of crude oil by mixed bacterial consortium in contaminated soil","volume":"25","author":"Xu","year":"2018","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"19620","DOI":"10.1038\/s41598-021-98680-8","article-title":"Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic","volume":"11","author":"Melekhina","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.biotechadv.2008.11.002","article-title":"Biosorbents for heavy metals removal and their future","volume":"27","author":"Wang","year":"2009","journal-title":"Biotechnol. Adv."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1139\/cjm-2014-0803","article-title":"Heavy metal resistance in Gram-negative bacteria isolated from Kongsfjord, Arctic","volume":"61","author":"Neethu","year":"2015","journal-title":"Can. J. Microbiol."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"152953","DOI":"10.1016\/j.scitotenv.2022.152953","article-title":"Co-response of Fe-reducing\/oxidizing bacteria and Fe species to the dynamic redox cycles of natural sediment","volume":"815","author":"Chen","year":"2022","journal-title":"Sci. Total. Environ."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/s41396-019-0527-4","article-title":"Syntrophic growth of alkaliphilic anaerobes controlled by ferric and ferrous minerals transformation coupled to acetogenesis","volume":"14","author":"Zavarzina","year":"2020","journal-title":"ISME J."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1007\/BF00290916","article-title":"Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals","volume":"159","author":"Lovley","year":"1993","journal-title":"Arch. Microbiol."},{"key":"ref_96","first-page":"005808","article-title":"Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays","volume":"73","author":"Lipski","year":"2023","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Saavedra-Tralma, D., Gaete, A., Merino-Guzm\u00e1n, C., Parada-Ib\u00e1\u00f1ez, M., N\u00e1jera-de Ferrari, F., and Jofr\u00e9-Fern\u00e1ndez, I. (2025). Functional and genomic evidence of L-arginine-dependent bacterial nitric oxide synthase activity in Paenibacillus nitricinens sp. nov. Biology, 14.","DOI":"10.3390\/biology14060733"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1099\/00207713-52-1-131","article-title":"PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene-degrading bacterium from the rhizosphere of salt marsh plants","volume":"52","author":"Daane","year":"2002","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"8001","DOI":"10.1128\/AEM.01844-12","article-title":"Fe(III) reduction and U(VI) immobilization by Paenibacillus sp. strain 300A, isolated from Hanford 300A subsurface sediments","volume":"78","author":"Ahmed","year":"2012","journal-title":"Environ. Microbiol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.biortech.2013.02.013","article-title":"Optimization and characterization of polysaccharide-based bioflocculant produced by Paenibacillus elgii B69 and its application in wastewater treatment","volume":"134","author":"Li","year":"2013","journal-title":"Bioresour. Technol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/s12934-016-0603-7","article-title":"Current knowledge and perspectives of Paenibacillus: A review","volume":"15","author":"Grady","year":"2016","journal-title":"Microb. Cell Fact."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"68692","DOI":"10.1007\/s11356-022-20581-8","article-title":"Cadmium resistance, microbial biosorptive performance and mechanisms of a novel biocontrol bacterium Paenibacillus sp. LYX\u20131","volume":"29","author":"Luo","year":"2022","journal-title":"Environ. Sci. Pollut. Res. Int."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/1\/55\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T08:08:19Z","timestamp":1766995699000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/1\/55"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,26]]},"references-count":102,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["microorganisms14010055"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14010055","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,26]]}}}