Abstract
This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by “P-type ATPases,” “cation diffusion facilitators,” and “heavy metal efflux-resistance nodulation cell division (HME-RND).” Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All data generated or analyzed during this study are included in this published article and its supplementary information file.
References
Alvarez A, Saez JM, Costa JSD, Colin VL, Fuentes MS, Cuozzo SA, Benimeli CS, Polti MA, Amoroso MJ (2017) Actinobacteria: current research and perspectives for bioremediation of pesticides and heavy metals. Chemosphere 166:41–62. https://doi.org/10.1016/j.chemosphere.2016.09.070
Beattie RE, Henke W, Campa MF, Hazen TC, McAliley LR, Campbell JH (2018) Variation in microbial community structure correlates with heavy-metal contamination in soils decades after mining ceased. Soil Biol Biochem 126:57–63. https://doi.org/10.1016/j.soilbio.2018.08.011
Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsène-Ploetze F, Gallien S, Lauga B, Casiot C, Calteau A, Vallenet D, Bonnefoy V, Bruneel O, Chane-Woon-Ming B, Cleiss-Arnold J, Duran R, Elbaz-Poulichet F, Fonknechten N, Giloteaux L, Halter D, Koechler S, Marchal M, Mornico D, Schaeffer C, Smith AAT, Van-Dorsselaer A, Weissenbach J, Medigue C, Le-Paslier D (2011) Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. ISME J 5:1735–1747. https://doi.org/10.1038/ismej.2011.51
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Bouyoucos GJ (1962) Hydrometer method improved for making particle size analyses of soils. Agron J 54:464–465. https://doi.org/10.2134/agronj1962.00021962005400050028x
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624. https://doi.org/10.1038/ismej.2012.8
Chen Y, Jiang Y, Huang H, Mou L, Ru J, Zhao J, Xiao S (2018) Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments. Sci Total Environ 637–638:1400–1412. https://doi.org/10.1016/j.scitotenv.2018.05.109
Chen J, Li J, Zhang H, Shi W, Liu Y (2019) Bacterial heavy-metal and antibiotic resistance genes in a copper tailing dam area in northern China. Front Microbiol 10(1916):1–12. https://doi.org/10.3389/fmicb.2019.01916
Chong CW, Convey P, Pearce DA, Tan IKP (2012) Assessment of soil bacterial communities on Alexander Island (in the maritime and continental Antarctic transitional zone). Polar Biol 35:387–399. https://doi.org/10.1007/s00300-011-1084-0
Drewniak L, Krawczyk PS, Mielnicki S, Adamska D, Sobczak A, Lipinski L, Burec-Drewniak W, Sklodowska A (2016) Physiological and metagenomic analyses of microbial mats involved in self-purification of mine waters contaminated with heavy metals. Front Microbiol 7(1252):1–18. https://doi.org/10.3389/fmicb.2016.01252
Feng G, Xie T, Wang X, Bail J, Tang L, Zhao H, Wei W, Wang M, Zhao Y (2018) Metagenomic analysis of microbial community and function involved in cd-contaminated soil. BMC Microbiol 18(11):1–13. https://doi.org/10.1186/s12866-018-1152-5
Gillan DC (2016) Metal-resistance systems in cultivated bacteria: are they found in complex communities? Curr Opin Biotechnol 38:123–130. https://doi.org/10.1016/j.copbio.2016.01.012
Gołębiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B (2014) 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb Ecol 67:635–647. https://doi.org/10.1007/s00248-013-0344-7
Guo FF, Yang W, Jiang W, Geng S, Peng T, Li JL (2012) Magnetosomes eliminate intracellular reactive oxygen species in Magnetospirillum gryphiswaldense MSR-1. Environ Microbiol 14:1722–1729. https://doi.org/10.1111/j.1462-2920.2012.02707.x
Hemmat-Jou MH, Safari-Sinegani AA, Mirzaie-Asl A, Tahmourespour A (2018) Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. Ecotoxicology 27:1281–1291. https://doi.org/10.1007/s10646-018-1981-x
Hu Q, Guo X, Liang Y, Hao X, Ma L, Yin H, Liu X (2015) Comparative metagenomics reveals microbial community differentiation in a biological heap leaching system. Res Microbiol 166:1–10. https://doi.org/10.1016/j.resmic.2015.06.005
Jackson ML (1958) Soil chemical analysis, vol 85. Prentice-Hall Inc, Englewood Cliffs, pp 251–252. https://doi.org/10.1002/jpln.19590850311
Jacquiod S, Cyriaque V, Riber L, Abu Al-soud W, Gillan DC, Wattiez R, Sørensen SJ (2018) Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome. J Hazard Mater 344:299–307. https://doi.org/10.1016/j.jhazmat.2017.09.046
Jia Y, Huang H, Zhong M, Wang FH, Zhang LM, Zhu YG (2013) Microbial arsenic methylation in soil and rice rhizosphere. Environ Sci Technol 47:3141–3148. https://doi.org/10.1021/es303649v
Kermanshahi K, Ghazifard R, Tavakoli A (2007) Identification of bacteria resistant to heavy metals in the soils of Isfahan Province. Iran J Sci Technol (Sci) 31(1):7–16
Lefèvre CT, Bazylinskib DA (2013) Ecology, diversity, and evolution of magnetotactic bacteria. Microbiol. Mol Biol Rev 77:497–526. https://doi.org/10.1128/MMBR.00021-13
Li X, Bond PL, Van-Nostrand JD, Zhou J, Huang L (2015) From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization. Sci Rep 5:12978. https://doi.org/10.1038/srep12978
Li X, Bond PL, Huang L (2017) Diversity of as metabolism functional genes in Pb-Zn mine tailings. Pedosphere 27:630–637. https://doi.org/10.1016/S1002-0160(17)60357-6
Lindsay WL, Norvell WA (1978) Development of a DTPA soil test for zinc, iron, manganese, and copper. Soil Sci Soc Am J 42(3):421–428. https://doi.org/10.2136/sssaj1978.03615995004200030009x
Lohsse A, Ullrich S, Katzmann E, Borg S, Wanner G, Richter M, Voigt B, Schweder T, Schüler D (2011) Functional analysis of the magnetosome island in Magnetospirillum gryphiswaldense: the mamAB operon is sufficient for magnetite biomineralization. PLoS One 6:e25561. https://doi.org/10.1371/journal.pone.0025561
Luo JM, Bai YH, Liang JS, Qu JH (2014) Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil. PLoS One 9:e108185. https://doi.org/10.1371/journal.pone.0108185
Ma Q, Qu YY, Zhang XW, Shen WL, Liu ZY, Wang JW, Zhang ZJ, Zhou JT (2015) Identification of the microbial community composition and structure of coal-mine wastewater treatment plants. Microbiol Res 175:1–5. https://doi.org/10.1016/j.micres.2014.12.013
Martínez-Iňigo MJ, Pérez-Sanz A, Ortiz I, Alonso J, Alarcόn R, García P, Lobo MC (2009) Bulk soil and rhizosphere bacterial community PCR-DGGE profiles and β-galactosidase activity as indicators of biological quality in soils contaminated by heavy metals and cultivated with Silene vulgaris (Moench) Garcke. Chemosphere 75:1376–1381. https://doi.org/10.1016/j.chemosphere.2009.03.014
McKenzie N, Yue S, Liu X, Ramsay BA, Ramsay JA (2014) Biodegradation of naphthenic acids in oils sands process waters in an immobilized soil/sediment bioreactor. Chemosphere 109:164–172. https://doi.org/10.1016/j.chemosphere.2014.02.001
Miller CD, Pettee B, Zhang C, Pabst M, McLean JE, Anderson AJ (2009) Copper and cadmium: responses in Pseudomonas putida KT2440. Lett Appl Microbiol 49:775–783. https://doi.org/10.1111/j.1472-765X.2009.02741.x
Mohammadian E, Babai-Ahari A, Arzanlou M, Oustan S, Khazaei SH (2017) Tolerance to heavy metals in filamentous fungi isolated from contaminated mining soils in the Zanjan Province, Iran. Chemosphere 185:290–296
Murat D, Quinlan A, Vali H, Komeili A (2010) Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. Proc Natl Acad Sci U S A 107:5593–5598. https://doi.org/10.1073/pnas.0914439107
Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D’haeseleer P, Woyke T, Kyrpides NC (2011) Complete genome sequence of Thioalkalivibrio sp. K90mix. Stand Genomic Sci 5:341–355. https://doi.org/10.4056/sigs.2315092
N’Guessan AL, Elifantz H, Nevin KP, Mouser PJ, Methe B, Woodard TL, Manley K, Williams KH, Wilkins MJ, Larsen JT, Long PE, Lovley DR (2010) Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer. ISME J 4:253–266. https://doi.org/10.1038/ismej.2009.115
Namiki T, Hachiya T, Tanaka H, Sakakibara Y (2012) MetaVelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 40:e155. https://doi.org/10.1093/nar/gks678
Neilands JB (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270:26723–26726. https://doi.org/10.1074/jbc.270.45.26723
Oksanen J, Kindt R, Legendre P, O'Hara B (2007) Package “Vegan”. University of Oulu, Oulu
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2013) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 206:14–D214. https://doi.org/10.1093/nar/gkt1226
Oves M, Saghir-Khan M, Huda-Qari A, Nadeen-Felemban M, Almeelbi T (2016) Heavy metals: biological importance and detoxification strategies. J Bioremediat Biodegrad 7:1–15. https://doi.org/10.4172/2155-6199.1000334
Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124. https://doi.org/10.1093/bioinformatics/btu494
Pereira LB, Vicentini R, Ottoboni LMM (2014) Changes in the bacterial community of soil from a neutral mine drainage channel. PLoS One 9(5):e96605. https://doi.org/10.1371/journal.pone.0096605
Pester M, Schleper C, Wagner M (2011) The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol 14:300–306. https://doi.org/10.1016/j.mib.2011.04.007
R Development Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna ISBN 3-900051-07-0. https://www.r-project.org/
Raiesi F, Sadeghi E (2019) Interactive effect of salinity and cadmium toxicity on soil microbial properties and enzyme activities. Ecotoxicol Environ Saf 168:221–229
Redmile-Gordon M, Chen L (2017) Zinc toxicity stimulates microbial production of extracellular polymers in a copiotrophic acid soil. Int Biodeterior Biodegradation 119:413–418. https://doi.org/10.1016/j.ibiod.2016.10.004
Renella G, Mench M, Landi L, Nannipieri P (2005) Microbial activity and hydrolase synthesis in long-term Cd-contaminated soils. Soil Biol Biochem 37:133–139. https://doi.org/10.1016/j.soilbio.2004.06.015
Richards LA (1954) Diagnosis and improvement of saline and alkaline soils. USDA Agricultural Handbook No. 60, USA. https://doi.org/10.1097/00010694-195408000-00012
Romaniuk K, Ciok A, Decewicz P, Uhrynowski W, Budzik K, Nieckarz M, Pawlowska J, Zdanowski MK, Bartosik D, Dziewit L (2018) Insight into heavy metal resistome of soil psychrotolerant bacteria originating from King George Island (Antarctica). Polar Biol 41:1319–1333. https://doi.org/10.1007/s00300-018-2287-4
Sentchilo V, Mayer AP, Guy L, Miyazaki R, Tringe SG, Barry K, Malfatti S, Goessmann A, Robinson-Rechavi M, Meer JRVD (2013) Community-wide plasmid gene mobilization and selection. ISME J 7:1173–1186. https://doi.org/10.1038/ismej.2013.13
Sposito G, Luud J, Change AC (1982) Trace metal chemistry in arid zone field soils amended with sewage sludge: I. Fractionation of Ni, Cu, Zn, Cd, and Pb in solid phases. Soil Sci Soc Am J 46:260–264. https://doi.org/10.2136/sssaj1982.03615995004600020009x
Studer RA, Dessailly BH, Orengo CA (2013) Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochem J 449:581–594. https://doi.org/10.1042/BJ20121221
Tahmasbian I, Safari-Sinegani AA, Nguyen TTN, Che R, Phan TD, Bai SH (2017) Application of manures to mitigate the harmful effects of electrokinetic remediation of heavy metals on soil microbial properties in polluted soils. Environ Sci Pollut Res 24:26485–26496. https://doi.org/10.1007/s11356-017-0281-y
Tang H, Shi X, Wang X, Hao H, Zhang XM, Zhang LP (2016) Environmental controls over Actinobacteria communities in ecological sensitive Yanshan Mountains zone. Front Microbiol 7:1–13. https://doi.org/10.3389/fmicb.2016.00343
Thomas JC, Oladeinde A, Kieran TJ, Finger-Jr JW, Bayona-Vasquez NJ, Cartee JC, Beasley JC, Seaman JC, McArthur JV, Rhodes-Jr OE, Glenn TC (2020) Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River site. Microb Biotechnol 13(4):1179–1200. https://doi.org/10.1111/1751-7915.13578
Uebe R, Schüler D (2016) Magnetosome biogenesis in magnetotactic bacteria. Nat Rev Microbiol 14:621–637. https://doi.org/10.1038/nrmicro.2016.99
Ullrich S, Schüler D (2010) Cre-lox-based method for generation of large deletions within the genomic magnetosome island of Magnetospirillum gryphiswaldense. Appl Environ Microbiol 76:2439–2444. https://doi.org/10.1128/AEM.02805-09
US Environmental Protection Agency (1999) Analytical methods support document for arsenic in drinking water. U.S. EPA, Office of Water, Targeting and Analysis Branch. EPA-815-R-00-010
Vance ED, Brookes PC, Jenkinson DS (1987) Microbial biomass measurements in forest soils-determination of Kc values and tests of hypotheses to explain the failure of the chloroform fumigation incubation method in acid soils. Soil Biol Biochem 19:689–696. https://doi.org/10.1016/0038-0717(87)90050-2
Walkley A (1947) A critical examination of a rapid method for determining organic carbon in soils-effect of variations in digestion conditions and of inorganic soil constituents. Soil Sci Soc Am J 63:251–264. https://doi.org/10.1097/00010694-194704000-00001
Wang H, Zeng Y, Guo C, Bao Y, Lu G, Reinfelder JR, Dang Z (2018) Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem. Sci Total Environ 616:107–116. https://doi.org/10.1016/j.scitotenv.2017.10.224
Welch BL (1947) The generalization of Student’s problem when several different population variances are involved. Biometrika. 34:28–35. https://doi.org/10.2307/2332510
Wu YW, Simmons BA, Singer SW (2016) MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32:605–607. https://doi.org/10.1093/bioinformatics/btv638
Xu K, Zhang H, Blumwald E, Xia T (2010) A novel plant vacuolar Na+/H+ antiporter gene evolved by DNA shuffling confers improved salt tolerance in yeast. J Biol Chem 285:22999–23006. https://doi.org/10.1074/jbc.M109.073783
Yadav AN, Sharma D, Gulati S, Singh S, Dey R, Pal KK, Kaushik R, Saxena AK (2015) Haloarchaea endowed with phosphorus solubilization attribute implicated in phosphorus cycle. Sci Rep 5:7–28. https://doi.org/10.1038/srep12293
Yan L, Da H, Zhanga S, Lópezb VM, Wanga W (2017) Bacterial magnetosome and its potential application. Microbiol Res 203:19–28. https://doi.org/10.1016/j.micres.2017.06.005
Zalaghi R, Safari-Sinegani AA (2014) The importance of different forms of Pb on diminishing biological activities in a calcareous soil. Chem Ecol 30:446–462. https://doi.org/10.1080/02757540.2013.871271
Zhu W, Lomsadze A, Borodovsky M (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38:e132. https://doi.org/10.1093/nar/gkq275
Author information
Authors and Affiliations
Contributions
Material preparation, major field studies, and lab facilities were performed by Ali Akbar Safari-Sinegani, Asghar Mirzaie-Asl, and Arezoo Tahmourespour. Iman Tahmasbian provided sequencing experiments. Data collection, analysis, and interpretation were performed by Mohammad Hossein Hemmat-Jou and Rongxiao Che. The first draft of the manuscript was written by Mohammad Hossein Hemmat-Jou and Rongxiao Che, then revised by Ali Akbar Safari-Sinegani, Asghar Mirzaie-Asl, and Arezoo Tahmourespour, and finally, all authors commented on previous versions of the manuscript. English checking was performed by Iman Tahmasbian. All authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare that they have no competing interests.
Ethical approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Additional information
Responsible editor: Robert Duran
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(DOCX 838 kb)
Rights and permissions
About this article
Cite this article
Hemmat-Jou, M.H., Safari-Sinegani, A.A., Che, R. et al. Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil. Environ Sci Pollut Res 28, 4845–4856 (2021). https://doi.org/10.1007/s11356-020-10824-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11356-020-10824-x