Browse > Article
http://dx.doi.org/10.4491/eer.2018.040

Bacterial community analysis of stabilized soils in proximity to an exhausted mine  

Park, Jae Eun (Department of Environmental Science and Engineering, Ewha Womans University)
Lee, Byung-Tae (Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST))
Kim, Byung-Yong (Bioinformatcis Research Institute, Chun Lab, Inc.)
Son, Ahjeong (Department of Environmental Science and Engineering, Ewha Womans University)
Publication Information
Environmental Engineering Research / v.23, no.4, 2018 , pp. 420-429 More about this Journal
Abstract
Soil stabilization is a soil remediation technique that reduces the mobility of heavy metals in soils. Although it is a well-established technique, it is nonetheless essential to perform a follow-up chemical assessment via a leaching test to evaluate the immobilization of heavy metals in the soil matrix. Unfortunately, a standard chemical assessment is not sufficient for evaluation of the biological functional state of stabilized soils slated for agricultural use. Therefore, it is useful to employ a pyrosequencing-based microbial community analysis for the purpose. In this study, a recently stabilized site in the proximity of an exhausted mine was analyzed for bacterial diversity, richness, and relative abundance as well as the effect of environmental factors. Based on the Shannon and Chao1 indices and rarefaction curves, the results showed that the stabilized layer exhibited lower bacterial diversity than control soils. The prevalence of dominant bacterial populations was examined in a hierarchical manner. Relatively high abundances of Proteobacteria and Methylobacter tundripaludum were observed in the stabilized soil. In particular, there was substantial abundance of the Methylobacter genus, which is known for its association with heavy metal contamination. The study demonstrated the efficacy of (micro)biological assessment for aiding in the understanding and post-management of stabilized soils.
Keywords
Bacterial community analysis; Heavy metal; Methylobacter; Pyrosequencing; Soil stabilization;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Mamindy-Pajany Y, Hurel C, Geret F, Romeo M, Marmier N. Comparison of mineral-based amendments for ex-situ stabilization of trace elements (As, Cd, Cu, Mo, Ni, Zn) in marine dredged sediments: A pilot-scale experiment. J. Hazard. Mater. 2013;252:213-219.
2 MCIE. Mine pollution prevention plan (2007-2012). Release copy of MCIE, Korea. 2006.
3 MKE. Mine pollution prevention plan (2011-2016). Release copy of MKE, Korea, 2011.
4 U.S. EPA. SW-846 Test Method 9081: Cation-exchange capacity of soils (Sodium Acetate). 1986.
5 ASTM. ASTM D7348-08: Standard test methods for loss on ignition (LOI) of solid combustion residues. 2013.
6 KMOE. Standard method for soil pollution. Korea Ministry of Environment. 2002.
7 Chun J, Kim KY, Lee JH, Choi Y. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol. 2010;10:101.   DOI
8 Hur M, Kim Y, Song HR, Kim JM, Choi YI, Yi H. Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Appl. Environ. Microbiol. 2011;77:7611-7619.   DOI
9 Kim BS, Kim JN, Yoon SH, Chun J, Cerniglia CE. Impact of enrofloxacin on the human intestinal microbiota revealed by comparative molecular analysis. Anaerobe 2012;18:310-320.   DOI
10 Chao A. Nonparametric estimation of the number of classes in a community. Scand. J. Stat. 1984;11:265-270.
11 Shannon CE. The mathematical theory of communication. 1963, MD Comput, 14 (1997). p. 306-317.
12 Miranda J, Andrade E, Lopez-suarez A, Ledesma TR, Cahill A, Wakabayashi PH. A receptor model for atmospheric aerosols from a southwestern site in Mexico City. Atmos. Environ. 1996;30:3471-3479.   DOI
13 Diaz RV, Aldape F, Flores MJ. Identification of airborne particulate sources, of samples collected in Ticoman, Mexico, using PIXE and multivariate analysis. Nucl. Instrum. Methods Phys. Res. Sect. B-Beam Interact. Mater. Atoms 2002;189:249-253.   DOI
14 Gong M, Wu L, Bi XY, et al. Assessing heavy-metal contamination and sources by GIS-based approach and multivariate analysis of urban-rural topsoils in Wuhan, central China. Environ. Geochem. Health 2010;32:59-72.   DOI
15 Hudson RR, Boos DD, Kaplan NL. A statistical test for detecting population subdivision. Mol. Biol. Evol. 1992;9:138-151.
16 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X: Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876-4882.   DOI
17 Hall TA. Bioedit: A user-friendly biological sequence alignment editor and analysis. Nucleic Acids Symp. Ser. 1999;41:95-98.
18 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 2013;30:2725-2729.   DOI
19 Chodak M, Golebiewski M, Morawska-Ploskonka J, Kuduk K, Niklinska M. Diversity of microorganisms from forest soils differently polluted with heavy metals. Appl. Soil Ecol. 2013;64:7-14.   DOI
20 Sheik CS, Mitchell TW, Rizvi FZ, et al. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure. PLoS ONE 2012;7:e40059.   DOI
21 Zhu JY, Zhang JX, Li Q, et al. Phylogenetic analysis of bacterial community composition in sediment contaminated with multiple heavy metals from the Xiangjiang River in China. Mar. Pollut. Bull. 2013;70:134-139.   DOI
22 Atlas SA, Kleinert HD, Camargo MJ, et al. Purification, sequencing and synthesis of natriuretic and vasoactive rat atrial peptide. Nature 1984;309:717-719.   DOI
23 Golebiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wrobel B. 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb. Ecol. 2014;67:635-647.   DOI
24 Yin HQ, Niu JJ, Ren YH, et al. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination. Sci. Rep. 2015;5:14266.   DOI
25 Chen LX, Li JT, Chen YT, et al. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ. Microbiol. 2013;15:2431-2444.   DOI
26 Daquiado AR, Kuppusamy S, Kim SY, et al. Pyrosequencing analysis of bacterial community diversity in long-term fertilized paddy field soil. Appl. Soil Ecol. 2016;108:84-91.   DOI
27 Abbasian F, Palanisami T, Megharaj M, Naidu R, Lockington R, Ramadass K. Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by meta-genomics analysis. Biotechnol. Prog. 2016;32:638-648.   DOI
28 Nies DH. Microbial heavy-metal resistance. Appl. Microbiol. Biotechnol. 1999;51:730-750.   DOI
29 Bosecker K. Bioleaching: Metal solubilization by microorganisms. FEMS Microbiol. 1997;20:591-604.   DOI
30 Lee JS, Chon HT, Kim KW. Human risk assessment of As, Cd, Cu and Zn in the abandoned metal mine site. Environ. Geochem. Health 2005;27:185-191.   DOI
31 Melaku S, Dams L, Moens L. Determination of trace elements in agricultural soil samples by inductively coupled plasma-mass spectrometry: Microwave acid digestion versus aqua regia extraction. Anal. Chim. Acta 2005;543:117-123.   DOI
32 Kim J, Koo SW, Kim JY, et al. Influence of acid mine drainage on microbial communities in stream and groundwater samples at Guryong Mine, South Korea. Environ. Geol. 2009;58:1567-1574.   DOI
33 Schippers A, Breuker A, Blazejak A, Bosecker K, Kock D, Wright TL. The biogeochemistry and microbiology of sulfidic mine waste and bioleaching dumps and heaps, and novel Fe(II)-oxidizing bacteria. Hydrometallurgy 2010;104:342-350.   DOI
34 Ondruschka J, Bley T. Biosorption of environmentally relevant heavy metals on selected biomaterials for wastewater treatment. Eng. Life Sci. 2003;3:215-218.   DOI
35 Wartiainen I, Hestnes AG, McDonald IR, Svenning MM. Methylobacter tundripaludum sp nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78 degrees N). Int. J. Syst. Evol. Microbiol. 2006;56:109-113.   DOI
36 Bussmann I, Rahalkar M, Schink B. Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygen. FEMS Microbiol. Ecol. 2006;56:331-344.   DOI
37 Rajkumar M, Ae N, Freitas H. Endophytic bacteria and their potential to enhance heavy metal phytoextraction. Chemosphere 2009;77:153-160.   DOI
38 Guo G, Zhou Q, Ma LQ. Availability and assessment of fixing additives for the in situ remediation of heavy metal contaminated soils: A review. Environ. Monit. Assess. 2006;116:513-528.   DOI
39 Lee JS, Lee SW, Chon HT, Kim KW. Evaluation of human exposure to arsenic due to rice ingestion in the vicinity of abandoned Myungbong Au-Ag mine site, Korea. J. Geochem. Explor. 2008;96:231-235.   DOI
40 Brookes PC, McGrath SP. Effects of metal toxicity on the size of the soil microbial biomass. J. Soil Sci. 1984;35:341-346.   DOI
41 Jung MC, Thornton I. Heavy metal contamination of soils and plants in the vicinity of a lead-zinc mine, Korea. Appl. Geochem. 1996;11:53-59.   DOI
42 Ok YS, Lim JE, Moon DH. Stabilization of Pb and Cd contaminated soils and soil quality improvements using waste oyster shells. Environ. Geochem. Health 2011;33:83-91.   DOI
43 Razo I, Carrizales L, Castro J, Diaz-Barriga F, Monroy M. Arsenic and heavy metal pollution of soil, water and sediments in a semi-arid climate mining area in Mexico. Water Air Soil Pollut. 2004;152:129-152.   DOI
44 Kumpiene J, Lagerkvist A, Maurice C. Stabilization of As, Cr, Cu, Pb, and Zn in soil using amendments: A review. Waste Manage. 2008;28:215-225.   DOI
45 Ko MS, Kim JY, Bang S, Lee JS, Ko JI, Kim KW. Stabilization of the As-contaminated soil from the metal mining areas in Korea. Environ. Geochem. Health 2012;34:143-149.   DOI
46 Knapp CW, Fowle DA, Kulczycki E, Roberts JA, Graham DW. Methane monooxygenase gene expression mediated by methanobactin in the presence of mineral copper sources. Proc. Natl. Acad. Sci. USA 2007;104:12040-12045.   DOI
47 Choi DW, Antholine WE, Do YS, et al. Effect of methanobactin on the activity and electron paramagnetic resonance spectra of the membrane-associated methane monooxygenase in Methylococcus capsulatus Bath. Microbiology 2005;151:3417-3426.   DOI
48 Kim HJ, Graham DW, DiSpirito AA, et al. Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria. Science 2004;305:1612-1615.   DOI
49 Balasubramanian R, Rosenzweig AC. Copper methanobactin: A molecule whose time has come. Curr. Opin. Chem. Biol. 2008;12:245-249.   DOI