Abstract
Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.
Similar content being viewed by others
Availability of data and material
Not applicable.
Code availability
Not applicable.
References
Abbas SZ, Rafatullah M, Hossain K, Ismail N, Tajarudin HA, Khalil HA (2018) A review on mechanism and future perspectives of cadmium-resistant bacteria. Int J Sci Environ Technol 15(1):243–262. https://doi.org/10.1007/s13762-017-1400-5
Achal V, Pan X, Fu Q, Zhang D (2012) Biomineralization based remediation of As (III) contaminated soil by Sporosarcina ginsengisoli. J Hazard Mater 201:178–184. https://doi.org/10.1016/j.jhazmat.2011.11.067
Adiansyah J, Rosano M, Vink S, Keir G (2015) A framework for a sustainable approach to mine tailings management: Disposal strategies. J Clean Prod 108:1050–1062. https://doi.org/10.1016/j.jclepro.2015.07.139
Afrasayab S, Yasmin A, Hasnain S (2002) Characterization of some indigenous mercury resistant bacteria from polluted environment. Pak J Biol Sci 5:792–799. https://doi.org/10.3923/pjbs.2002.792.797
Angelo RT, Cringan MS, Chamberlain DL, Stahl AJ, Haslouer SG, Goodrich CA (2007) Residual effects of lead and zinc mining on freshwater mussels in the Spring River Basin (Kansas, Missouri, and Oklahoma, USA). Sci Total Environ 384:467–496. https://doi.org/10.1016/j.scitotenv.2007.05.045
Ashauer R, Hintermeister A, O'Connor I, Elumelu M, Hollender J, Escher BI (2012) Significance of xenobiotic metabolism for bioaccumulation kinetics of organic chemicals in Gammarus pulex. Environ Sci Technol 46(6):3498–508. Erratum in: Environ Sci Technol 46(8):4682. https://doi.org/10.1021/es204611h
Auld RR, Mykytczuk NC, Leduc LG, Merritt TJ (2017) Seasonal variation in an acid mine drainage microbial community. Can J Microbiol 63(2):137–152. https://doi.org/10.1139/cjm-2016-0215
Ayangbenro AS, Babalola OO (2017) A new strategy for heavy metal polluted environments: a review of microbial biosorbents. Int J Environ Res Public Health 14(1):94. https://doi.org/10.3390/ijerph14010094
Aznar-Sánchez J, García-Gómez J, Velasco-Muñoz J, Carretero-Gómez A (2018) Mining waste and its sustainable management: advances in worldwide research. Minerals 8(7):284. https://doi.org/10.3390/min8070284
Bae W, Mehra RK, Mulchandani A, Chen W (2001) Genetic engineering of Escherichia coli for enhanced uptake and bioaccumulation of mercury. Appl Environ Microbiol 67(11):5335–5338. https://doi.org/10.1128/AEM.67.11.5335-5338.2001
Banning NC, Gleeson DB, Grigg AH, Grant CD, Andersen GL et al (2011) Soil microbial community successional patterns during forest ecosystem restoration. Appl Environ Microbiol 77:6158–6164. https://doi.org/10.1128/AEM.00764-11
Barbosa LP et al (2014) Nickel, manganese and copper removal by a mixed consortium of sulfate reducing bacteria at a high COD/sulfate ratio. World J Microbiol Biotechnol 30:2171–2180. https://doi.org/10.1007/s11274-013-1592-x
Beasley FC, Vinés ED, Grigg JC, Zheng Q, Liu S, Lajoie GA, Murphy ME, Heinrichs DE (2009) Characterization of staphyloferrin A biosynthetic and transport mutants in Staphylococcus aureus. Mol Microbiol 72(4):947–963. https://doi.org/10.1111/j.1365-2958.2009.06698.x
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
Belimov A, Hontzeas N, Safronova V, Demchinskaya S, Piluzza G, Bullitta S, Glick B (2005) Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.). Soil Biol Biochem 37:241–250. https://doi.org/10.1016/j.soilbio.2004.07.033
Bier RL, Wernegreen JJ, Vilgalys RJ, Ellis JC, Bernhardt ES (2020) Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage. Limnol Oceanogr 65:S277–S292. https://doi.org/10.1002/lno.11301
Bomberg M, Mäkinen J, Salo M, Kinnunen P (2019) High diversity in iron cycling microbial communities in acidic, iron-rich water of the Pyhäsalmi mine, Finland. Geofluids. https://doi.org/10.1155/2019/7401304
Brantner JS, Senko JM (2014) Response of soil-associated microbial communities to intrusion of coal mine-derived acid mine drainage. Environ Sci Technol 48(15):8556–8563. https://doi.org/10.1021/es502261u
Cao XF, Liu LP (2015) Using microorganisms to facilitate phytoremediation in mine tailings with multi heavy metals. Adv Mater Res Trans Tech Publ 437–440
Catalan LJ, Buset KC, Yin G (2002) Reactivity of oxidized sulfidic mine tailings during lime treatment. Environ Sci Technol 36:2766–2771. https://doi.org/10.1021/es011150s
Chao Y, Liu W, Chen Y et al (2016) Structure, Variation, and co-occurrence of soil microbial communities in abandoned sites of a rare earth elements mine. Environ Sci Technol 50(21):11481–11490. https://doi.org/10.1021/acs.est.6b02284
Chen LX, Li JT, Chen YT, Huang LN, Hua ZS, Hu M, Shu WS (2013) Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ Microbiol 15(9):2431–2444. https://doi.org/10.1111/1462-2920.12114
Chen LX, Huang LN, Méndez-García C, Kuang JL, Hua ZS, Liu J, Shu WS (2016) Microbial communities, processes and functions in acid mine drainage ecosystems. CurrOpin Biotechnol 38:150–158. https://doi.org/10.1016/j.copbio.2016.01.013
Chen J, Mo L, Zhang Z, Nan J, Xu D, Chao L, Bao Y (2019) Evaluation of the ecological restoration of a coal mine dump by exploring the characteristics of microbial communities. Appl Soil Ecol. https://doi.org/10.1016/j.apsoil.2019.103430
Cłapa T, Narożna D, Siuda R, Borkowski A, Selwet M, Mądrzak C (2019) Diversity of bacterial communities in the acid mine drainage ecosystem of an abandoned polymetallic mine in Poland. Pol J Environ Stud https://doi.org/10.15244/pjoes/91785
Coelho LM, Rezende HC, Coelho LM, de Sousa PA, Melo DF, Coelho NM (2015) Bioremediation of polluted waters using microorganisms. Adv Bioremed Wastewater Pollut Soil 10: 60770 https://doi.org/10.5772/60770
Costa BZ, da Rodrigues VD, Oliveira VM, de Ottoboni LMM, Marsaioli AJ (2016) Enzymatic potential of heterotrophic bacteria from a neutral copper mine drainage. Braz J Microbiol 47(4):846–852. https://doi.org/10.1016/j.bjm.2016.07.004
Costa OY, Raaijmakers JM, Kuramae EE (2018) Microbial extracellular polymeric substances: ecological function and impact on soil aggregation. Front Microbiol 9:1636. https://doi.org/10.3389/fmicb.2018.01636
Dave BP, Dube HC (2000) Regulation of siderophore production by iron Fe(III) in certain fungi and fluorescent pseudomonads. Indian J Exp Biol 38(3):297–299
Deng J, Yin Y, Zhu W, Zhou Y (2020) Response of soil environment factors and microbial communities to phytoremediation with Robinia pseudoacacia in an open-cut magnesite mine. Land Degrad Dev 31(16):2340–2355. https://doi.org/10.1002/ldr.3599
Dey S, Paul AK (2013) Evaluation of in vitro reduction of hexavalent chromium by cell-free extract of Arthrobacter sp. SUK 1201. British Microbiol Res J 3(3):325–338. https://doi.org/10.9734/BMRJ/2013/3726
Dey S, Paul AK (2016) Evaluation of chromate reductase activity in the cell-free culture filtrate of Arthrobacter sp. SUK 1201 isolated from chromite mine overburden. Chemosphere 156:69–75. https://doi.org/10.1016/j.chemosphere.2016.04.101
Dixit R, Malaviya D, Pandiyan K, Singh UB, Sahu A, Shukla R, Singh BP, Rai JP, Sharma PK, Lade H, Paul D (2015) Bioremediation of heavy metals from soil and aquatic environment: an overview of principles and criteria of fundamental processes. Sustainability 7(2):2189–2212. https://doi.org/10.3390/su7022189
Edmunds WM, Cook JM, Darling WG, Kinniburgh DG, Miles DL, Bath AH, Andrews JN (1987) Baseline geochemical conditions in the Chalk aquifer, Berkshire, UK: a basis for groundwater quality management. Appl Geochem 2(3):251–274. https://doi.org/10.1016/0883-2927(87)90042-4
Ezeokoli OT, Bezuidenhout CC, Maboeta MS, Khasa DP, Adeleke RA (2020) Structural and functional differentiation of bacterial communities in post-coal mining reclamation soils of South Africa: bioindicators of soil ecosystem restoration. Sci Rep 10(1):1–14. https://doi.org/10.1038/s41598-020-58576-5
Fabisch M, Beulig F, Akob DM, Küsel K (2013) Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations. Front Microbiol 4:390. https://doi.org/10.3389/fmicb.2013.00390
Fernandes CC, Kishi LT, Lopes EM, Omori WP, Souza JAMD, Alves LMC, Lemos EGDM (2018) Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine. Braz J Microbiol 49:489–502. https://doi.org/10.1016/j.bjm.2017.12.006
Fomina M, Gadd GM (2014) Biosorption: current perspectives on concept, definition and application. Bioresour Technol 160:3–14. https://doi.org/10.1016/j.biortech.2013.12.102
Freedman Z, Zak DR (2015) Soil bacterial communities are shaped by temporal and environmental filtering: Evidence from a long-term chronosequence. Environ Microbiol 17:3208–3218. https://doi.org/10.1111/1462-2920.12762
Glick BR, Todorovic B, Czarny J, Cheng Z, Duan J, McConkey B (2007) Promotion of plant growth by bacterial ACC deaminase. Crit Rev Plant Sci 26:227–242. https://doi.org/10.1080/07352680701572966
Golyshina OV (2011) Environmental, biogeographic, and biochemical patterns of archaea of the family Ferroplasmaceae. Appl Environ Microbiol 77(15):5071. https://doi.org/10.1128/AEM.00726-11
Golyshina OV, Bargiela R, Golyshin PN (2019) Cuniculiplasmataceae, their ecogenomic and metabolic patterns, and interactions with “ARMAN.” Extremophiles 23(1):1–7. https://doi.org/10.1007/s00792-018-1071-2
Grawunder A, Merten D, Büchel G (2014) Origin of middle rare earth element enrichment in acid mine drainage-impacted areas. Environ Sci Poll Res. https://doi.org/10.1007/s11356-013-2107-x
Ho A, Kerckhof FM, Luke C, Reim A, Krause S, Boon N, Bodelier PLE (2013) Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. Environ Microbiol Rep 5:335–345. https://doi.org/10.1111/j.1758-2229.2012.00370.x
Huang X, Yin Z, Wu S, Qi X, He Q, Zhang Q, Zhang H (2011) Graphene-based materials: synthesis, characterization, properties, and applications. Small 7(14):1876–1902. https://doi.org/10.1002/smll.201002009
Huang LN, Kuang JL, Shu WS (2016) Microbial ecology and evolution in the acid mine drainage model system. Trends Microbiol 24(7):581–593. https://doi.org/10.1016/j.tim.2016.03.004
Humphries MS, McCarthy TS, Pillay L (2017) Attenuation of pollution arising from acid mine drainage by a natural wetland on the Witwatersrand. S Afr J Sci 113(1–2): 1–9. https://doi.org/10.17159/sajs.2017/20160237
Ianeva OD (2009) Mechanisms of bacteria resistance to heavy metals. Mikrobiol Z71(6):54–65
Javanbakht V, Alavi SA, Zilouei H (2014) Mechanisms of heavy metal removal using microorganisms as biosorbent. Water Sci Technol 69(9):1775–1787. https://doi.org/10.2166/wst.2013.718
Ji H, Zhang Y, Bararunyeretse P, Li H (2018) Characterization of microbial communities of soils from gold mine tailings and identification of mercury-resistant strain. Ecotox Environ Safe 165:182–193. https://doi.org/10.1016/j.ecoenv.2018.09.011
Johnson DB, Hallberg KB, Hedrich S (2014) Uncovering a microbial enigma: isolation and characterization of the streamer-generating, iron-oxidizing, acidophilic bacterium “Ferrovum myxofaciens.” Appl Environ Microbiol 80(2):672–680. https://doi.org/10.1128/AEM.03230-13
Kadnikov VV, Ivasenko DA, Beletsky AV, Mardanov AV, Danilova EV, Pimenov NV, Ravin NV (2016) Effect of metal concentration on the microbial community in acid mine drainage of a polysulfide ore deposit. Microbiology 85(6):745–751. https://doi.org/10.1134/S0026261716060126
Kang C-H, Kwon Y-J, So J-S (2016) Bioremediation of heavy metals by using bacterial mixtures. Ecol Eng 89:64–69. https://doi.org/10.1016/j.ecoleng.2016.01.023
Keil D, Meyer A, Berner D, Poll C et al (2011) Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils. FEMS Microbiol Ecol 77:95–106. https://doi.org/10.1111/j.1574-6941.2011.01091.x
Kisková J, Perháčová Z, Vlčko L, Sedláková J, Kvasnová S, Pristaš P (2018) The bacterial population of neutral mine drainage water of Elizabeth’s Shaft (Slovinky, Slovakia). Curr Microbiol 75(8):988–996. https://doi.org/10.1007/s00284-018-1472-6
Konhauser K, Riding R (2012) Bacterial biomineralization. Fund of Geobiol. Blackwell. 105–130
Kuang JL, Huang LN, Chen LX, HuaZS LSJ, Hu M, Shu WS (2013) Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. The ISME J 7(5):1038–1050. https://doi.org/10.1038/ismej.2012.139
Kunoh T, Suzuki T, Shiraishi T, Kunoh H, Takada J (2015) Treatment of Leptothrix cells with ultrapure water poses a threat to their viability. Biology 4(1):50–66. https://doi.org/10.3390/biology4010050
Lal S, Ratna S, Said OB, Kumar R (2018) Biosurfactant and exopolysaccharide- assisted rhizobacterial technique for the remediation of heavy metal contaminated soil: an advancement in metal phytoremediation technology. Environ Technol Innov 10:243–263. https://doi.org/10.1016/j.eti.2018.02.011
Lee DJ, Liu X, Weng HL (2014) Sulfate and organic carbon removal by microbial fuel cell with sulfate-reducing bacteria and sulfide oxidising bacteria anodic biofilm. Biores Technol 156:14–19. https://doi.org/10.1016/j.biortech.2013.12.129
Lewis DE, Chauhan A, White JR, Overholt W, Green SJ et al (2012) Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica. Microb Ecol 64:738–749. https://doi.org/10.1007/s00248-012-0020-3
Li Y, Wen H, Chen L, Yin T (2014) Succession of bacterial community structure and diversity in soil along a chronosequence of reclamation and re-vegetation on coal mine spoils in China. PloS One 9(12):e115024. https://doi.org/10.1371/journal.pone.0115024
Li J, Liu F, Chen J (2016) The effects of various land reclamation scenarios on the succession of soil bacteria, archaea, and fungi over the short and long term. Front Ecol Evol. https://doi.org/10.3389/fevo.2016.00032
Li B, Cao Y, Guan X, Li Y, Hao Z, Hu W, Chen L (2019) Microbial assessments of soil with a 40-year history of reclaimed wastewater irrigation. Sci Total Environ 651:696–705. https://doi.org/10.1016/j.scitotenv.2018.09.193
Liebner S, Harder J, Wagner D (2008) Bacterial diversity and community structure in polygonal tundra soils from Samoylov Island, Lena Delta, Siberia. Int Microbiol 11(3):195–202
Lindsay MBJ, Condon PD, Jambor JL, Lear KG, Blowes DW, Ptacek CJ (2009) Mineralogical, geochemical, and microbial investigation of a sulfide-rich tailings deposit characterized by neutral drainage. Appl Geochem 24:2212–2221
Liu J, Li C, Jing J, Zhao P, Luo Z, Cao M, Chai B (2018a) Ecological patterns and adaptability of bacterial communities in alkaline copper mine drainage. Water Res 133:99–109. https://doi.org/10.1016/j.watres.2018.01.014
Liu L, Li W, Song W, Guo M (2018b) Remediation techniques for heavy metal-contaminated soils: Principles and applicability. Sci Total Environ 633:206–219. https://doi.org/10.1016/j.scitotenv.2018.03.161
Lovley DR, Phillips EJ (1994) Reduction of chromate by Desulfovibrio vulgaris and Its c(3) cytochrome. Appl Environ Microbiol 60:726–728
Lukhele T, Selvarajan R, Nyoni H, Mamba BB, Msagati TAM (2019) Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis. Extremophiles 23(6):719–734. https://doi.org/10.1007/s00792-019-01130-7
Ma Z, Chen K, Li Z, Bi J, Huang L (2016) Heavy metals in soils and road dusts in the mining areas of Western Suzhou, China: a preliminary identification of contaminated sites. J Soils Sediments 16:204–214. https://doi.org/10.1007/s11368-015-1208-1
Marques AP, Rangel AO, Castro PM (2009) Remediation of heavy metal contaminated soils: phytoremediation as a potentially promising clean-up technology. Crit Rev Environ Sci Technol 39:622–654. https://doi.org/10.1080/10643380701798272
Maurer B, Müller A, Keller-Schierlein W, Zähner H. Stoffwechselprodukte von Mikroorganismen (1968) Ferribactin, einSiderochromaus Pseudomonas fluorescens Migula Metabolic products of microorganisms Ferribactin, a siderochrome from Pseudomonas fluorescens Migula. Arch Mikrobiol 60(4):326–39. https://doi.org/10.1007/BF00408553
McGowen S, Basta N, Brown G (2001) Use of diammonium phosphate to reduce heavy metal solubility and transport in smelter-contaminated soil. J Environ Qual 30:493–500. https://doi.org/10.2134/jeq2001.302493x
Meier S, Borie F, Bolan N, Cornejo P (2012) Phytoremediation of metal-polluted soils by arbuscular mycorrhizal fungi. Crit Rev Environ Sci Technol 42:741–775. https://doi.org/10.1080/10643389.2010.528518
Mesa V, Gallego JL, González-Gil R, Lauga B, Sánchez J, Méndez-García C, Peláez AI (2017) Bacterial, archaeal, and eukaryotic diversity across distinct microhabitats in an acid mine drainage. Front Microbiol 8:1756. https://doi.org/10.3389/fmicb.2017.01756
Mishra A, Malik A (2013) Recent advances in microbial metal bioaccumulation. Crit Rev Environ Sci Technol 43(11):1162–1222. https://doi.org/10.1080/10934529.2011.627044
Moore CH, Foster LA, Gerbig DG Jr, Dyer DW, Gibson BW (1995) Identification of alcaligin as the siderophore produced by Bordetella pertussis and B. bronchiseptica. J Bacteriol 177(4):1116–8. https://doi.org/10.1128/jb.177.4.1116-1118.1995
Moreno FN, Anderson CW, Stewart RB, Robinson BH (2004) Phytoremediation of mercury-contaminated mine tailings by induced plant-mercury accumulation. Environ Pract 6:165–175. https://doi.org/10.1017/S1466046604000274
Motesharezadeh B, Kamal-poor S, Alikhani HA, Zariee M, Azimi S (2017) Investigating the effects of plant growth promoting bacteria and Glomus Mosseae on cadmium phytoremediation by Eucalyptus camaldulensis L. Pollution 3(4): 575–588. https://doi.org/10.22059/poll.2017.62774
Mummey DL, Stahl PD, Buyer JS (2002) Microbial biomarkers as an indicator of ecosystem recovery following surface mine reclamation. Appl Soil Ecol 21:251–259. https://doi.org/10.1016/S0929-1393(02)00090-2
Narayanan M, Ranganathan M, Kandasamy G et al (2021) Evaluation of interaction among indigenous rhizobacteria and Vigna unguiculata on remediation of metal-containing abandoned magnesite mine tailing. Arch Microbiol 203:1399–1410. https://doi.org/10.1007/s00203-020-02115-3
Navas M, Pérez-Esteban J, Torres MA, Hontoria C, Moliner A (2020) Taxonomic and functional analysis of soil microbial communities in a mining site across a metal(loid) contamination gradient. Eur J Soil Sci. https://doi.org/10.1111/ejss.12979
Nayak AK, Panda SS, Basu A, Dhal NK (2018) Enhancement of toxic Cr(VI), Fe, and other heavy metals phytoremediation by the synergistic combination of native Bacillus cereus strain and Vetiveria zizanioides L. Int J Phytoremediat 20:682–691. https://doi.org/10.1080/15226514.2017.1413332
Noinaj N, Guillier M, Barnard TJ, O’Brien S, Hodgson DJ, Buckling A (2014) Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa. Proc Biol Sci 281(1787):20140858
Nonnoi F, Chinnaswamy A, García de la Torre VS, De la Pena TC, Lucas MM, Pueyo JJ (2012) Metal tolerance of rhizobial strains isolated from nodules of herbaceous legumes (Medicago spp. and Trifolium spp.) growing in mercury-contaminated soils. Appl Soil Ecol 61:49–59. https://doi.org/10.1016/j.apsoil.2012.06.004
Ojuederie OB, Babalola OO (2017) Microbial and plant-assisted bioremediation of heavy metal polluted environments: a review. Int J Environ Res Public Health 14(12):1504. https://doi.org/10.3390/ijerph14121504
Ozdemir S, Oduncu MK, Kilinc E, Soylak M (2017) Resistance, bioaccumulation and solid phase extraction of uranium (VI) by Bacillus vallismortis and its UV-vis spectrophotometric determination. J Environ Radioact 171:217–225. https://doi.org/10.1016/j.jenvrad.2017.02.021
Pal C, Asiani K, Arya S, Rensing C, Stekel DJ, Larsson DGJ, Hobman JL (2017) Metal resistance and its association with antibiotic resistance. Adv Microb Physiol 70:261–313. https://doi.org/10.1016/bs.ampbs.2017.02.001
Parks JM, Johs A, Podar M, Bridou R, Hurt RA Jr, Smith SD, Tomanicek SJ, Qian Y, Brown SD, Brandt CC, Palumbo AV, Smith JC, Wall JD, Elias DA, Liang L (2013) The genetic basis for bacterial mercury methylation. Science 339(6125):1332–1335. https://doi.org/10.1126/science.1230667
Pereira LB, Vicentini R, Ottoboni LM (2015) Characterization of the co re microbiota of the drainage and surrounding soil of a Brazilian copper mine. Genet Mol Biol 38(4):484–489. https://doi.org/10.1590/S1415-475738420150025
Plumlee GS, Smith KS, Montour MR, Ficklin WH, Mosier EL (1999) Geologic controls on the composition of natural waters and mine waters draining diverse mineral-deposit types. Environm Geochem Mineral Depos Rev Econom Geol 6:373–432
Prakash D, Gabani P, Chandel AK, Ronen Z, Singh OV (2013) Bioremediation: a genuine technology to remediate radionuclides from the environment. Microb Biotechnol 6:349–360. https://doi.org/10.1111/1751-7915.12059
Rafique M, Haque K, Hussain T, Amna C, Javed H (2017) Biochemical Talk in the Rhizoshperic Microbial Community for Phytoremediation. Nova Science Publishers, NY, ISBN 978-1-53611-047-0
Rajkumar M, Ae N, Prasad MN, Freitas H (2010) Potential of siderophore-producing bacteria for improving heavy metal phytoextraction. Trends Biotechnol 28(3):142–149. https://doi.org/10.1016/j.tibtech.2009.12.002
Ray S, Dey K (2020) Coal mine water drainage: the current status and challenges. J Inst Eng India Ser D 101:165–172. https://doi.org/10.1007/s40033-020-00222-5
Reis MP, Barbosa FAR, Chartone-Souza E, Nascimento AMA (2013) The prokaryotic community of a historically mining-impacted tropical stream sediment is as diverse as that from a pristine stream sediment. Extremophiles 17(301–309):37. https://doi.org/10.1007/s00792-013-0517-9
Romanowicz KJ, Freedman ZB, Upchurch RA, Argiroff WA, Zak DR (2016) Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: The influence of pH and soil moisture. FEMS Microbiol Ecol 92:1–9. https://doi.org/10.1093/femsec/fiw149
Roth H, Gallo S, Badger P, Hillwig M (2019) Changes in microbial communities of a passive coal mine drainage bioremediation system. Can J Microbiol 65(10):775–782. https://doi.org/10.1139/cjm-2018-0612
Saha M, Sarkar S, Sarkar B, Sharma BK, Bhattacharjee S, Tribedi P (2016) Microbial siderophores and their potential applications: a review. Environ Sci Pollut Res Int 23(5):3984–3999. https://doi.org/10.1007/s11356-015-4294-0
Searle LJ, Méric G, Porcelli I, Sheppard SK, Lucchini S (2015) Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli. PLoS One 10(3):e0117906. https://doi.org/10.1371/journal.pone.0117906
Shahhosseini M, Ardejani FD, Baafi E (2017) Geochemistry of rare earth elements in a neutral mine drainage environment, Anjir Tangeh, northern Iran. Intl J Coal Geol 183:120–135. https://doi.org/10.1016/j.coal.2017.10.004
Sharma R, Rishi MS, Lata R (2013) Monitoring and assessment of soil quality near Kashlog limestone mine at Darlaghat district Solan, Himachal Pradesh, India. J Environ Earth Sci 3:1–40
Shin MN, Shim J, You Y, Myung H, Bang KS, Cho M, Kamala-Kannan S, Oh BT (2012) Characterization of lead resistant endophytic Bacillus sp. MN3-4 and its potential for promoting lead accumulation in metal hyperaccumulator Alnus firma. J Hazard Mater 199–200:314–320. https://doi.org/10.1016/j.jhazmat.2011.11.010
Silver S, Phung LT (2005) Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl Environ Microbiol 71(2):599–608. https://doi.org/10.1128/AEM.71.2.599-608.2005
Singh BK, Bardgett RD, Smith P, Reay DS (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat Rev Microbiol 8:779–790. https://doi.org/10.1038/nrmicro2439
Skinner HCW (2005) Biominerals. Mineral Mag 69(5):621–641
Smeaton CM, Fryer BJ, Weisener CG (2009) Intracellular precipitation of Pb by Shewanella putrefaciens CN32 during the reductive dissolution of Pb-jarosite. Environ Sci Technol 43(21):8086–8091. https://doi.org/10.1021/es901629c
Sun W, Sun X, Li B, Xu R, Young LY, Dong Y, Wang Q (2020) Bacterial response to sharp geochemical gradients caused by acid mine drainage intrusion in a terrace: Relevance of C, N, and S cycling and metal resistance. Environ Int 138:105601. https://doi.org/10.1016/j.envint.2020.105601
Teixeira LAJ, Berton RS, Coscione AR, Saes LA (2011) Biosolids application on banana production: soil chemical properties and plant nutrition. Appl Environ Soil Sci. https://doi.org/10.1155/2011/238185
Thakare M, Sarma H, Datar S, Roy A, Pawar P, Gupta K, Prasad R (2021) Understanding the holistic approach to plant-microbe remediation technologies for removing heavy metals and radionuclides from soil. Curr Res in Biotechnol 3:84–98. https://doi.org/10.1016/j.crbiot.2021.02.004
Tomczyk-Żak K, Kaczanowski S, Drewniak Ł, Dmoch Ł, Sklodowska A, Zielenkiewicz U (2013) Bacteria diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine. Sci Total Environ 461:330–340. https://doi.org/10.1016/j.scitotenv.2013.04.087
Ullah A, Heng S, Munis MFH, Fahad S, Yang X (2015) Phytoremediation of heavy metals assisted by plant growth promoting (PGP) bacteria: a review. Environ Exp Bot 117:28–40. https://doi.org/10.1016/j.envexpbot.2015.05.001
Valentín-Vargas A, Root RA, Neilson JW, Chorover J, Maier RM (2014) Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment. Sci Total Environ 500:314–324. https://doi.org/10.1016/j.scitotenv.2014.08.107
Winkelmann G (2002) Microbial siderophore-mediated transport. Biochem Soc Trans 30(4):691–696. https://doi.org/10.1042/bst0300691
Wu SC, Cheung KC, Luo YM, Wong MH (2006) Effects of inoculation of plant growth-promoting rhizobacteria on metal uptake by Brassica juncea. Environ Pollut 140:124–135. https://doi.org/10.1016/j.envpol.2005.06.023
Wu Y, Li Y, Zheng C, Zhang Y, Sun Z (2013) Organic amendment application influence soil organism abundance in saline alkali soil. Eur J Soil Biol 54:32–40. https://doi.org/10.1016/j.ejsobi.2012.10.006
Yancey RJ, Finkelstein RA (1981) Siderophore production by pathogenic Neisseria spp. Infect Immun 32(2):600–608
Yang J, Rawat S, Stemmler TL, Rosen BP (2010) Arsenic binding and transfer by the ArsD As(III) metallochaperone. Biochemistry 49(17):3658–3666. https://doi.org/10.1021/bi100026a
Yang P, Zhou XF, Wang LL, Li QS, Zhou T, Chen YK, Zhao ZY, He BY (2018) Effect of phosphate-solubilizing bacteria on the mobility of insoluble cadmium and metabolic analysis. Int J Environ Res Public Health 15(7):1330. 10.3390%2Fijerph15071330
Ye RW, Thomas SM (2001) Microbial nitrogen cycles; physiology, genomics and applications. Curr Opin Microbiol 4(03):307–312. https://doi.org/10.1016/s1369-5274(00)00208-3
Zhang X, Tang S, Wang M, Sun W, Xie Y, Peng H, Zhong A, Liu H, Zhang X, Yu H, Giesy JP, Hecker M (2019) Acid mine drainage affects the diversity and metal resistance gene profile of sediment bacterial community along a river. Chemosphere 217:790–799. https://doi.org/10.1016/j.chemosphere.2018.10.210
Zhang QM et al (2014) Effects of fomesafen on soil enzyme activity, microbialpopulation, and bacterial community composition. Environ Monit Assess 186:2801–2812. https://doi.org/10.1007/s10661-013-3581-9
Zinger L, Lejon DP, Baptist F, Bouasria A, Aubert S, Geremia RA et al (2011) Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape. PLoS One 6:e19950. https://doi.org/10.1371/journal.pone.0019950
Funding
Not applicable.
Author information
Authors and Affiliations
Contributions
The manuscript has been planned and written by Satarupa Dey.
Corresponding author
Ethics declarations
Conflict of interest
Not applicable.
Ethics approval
Not applicable.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Dey, S. Indigenous microbial populations of abandoned mining sites and their role in natural attenuation. Arch Microbiol 204, 251 (2022). https://doi.org/10.1007/s00203-022-02861-6
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-02861-6