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

Volumn 9, Issue 12, 2014, Pages

  Li, Yuanyuan ^a   Wen, Hongyu ^b   Chen, Longqian ^a,c   Yin, Tingting ^b  

^a CHINA UNIVERSITY OF MINING AND TECHNOLOGY   (China)

^b JIANGSU NORMAL UNIVERSITY   (China)

^c UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

[No Author keywords available]

Indexed keywords

NITROGEN; PHOSPHORUS; BACTERIAL DNA; COAL; RNA 16S;

ACIDOBACTERIA; ACTINOBACTERIA; ARTICLE; BACTEROIDETES; BIOREMEDIATION; CHINA; CHLOROFLEXI; CHRONOSEQUENCE; COAL MINING; COMMUNITY STRUCTURE; CONTROLLED STUDY; GEOCHEMISTRY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PH; PHYSICAL CHEMISTRY; PLANCTOMYCETES; POLYMERASE CHAIN REACTION; POPULATION ABUNDANCE; PROTEOBACTERIA; PYROSEQUENCING; REVEGETATION; SOIL; BIODIVERSITY; GENETICS; MICROBIOLOGY; PHYLOGENY;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLOROFLEXI; CHLOROFLEXI (CLASS); FABACEAE; PLANCTOMYCETES; POACEAE; PROTEOBACTERIA;

BIODIVERSITY; CHINA; COAL; DNA, BACTERIAL; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

EID: 84918583961     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0115024     Document Type: Article

References (61)

1. Wang LP, Zhang WW, Guo GX, Qian KM, Huang XP (2009) Selection experiments for the optimum combination of AMF-plant-substrate for the restoration of coal mines. International Journal of Mining Science and Technology 19: 479-482.
2. Munshower FF (1994) Practical handbook of disturbed land revegetation. Lewis Publ., Boca Raton, Fl.
3. Harris JA, Birch P, Palmer J (1996) Land restoration and reclamation: Principles and practice. Addison Wesley Longman, Edinburg, UK.
4. Rana S, Stahl PD, Ingram LJ, Wick AF (2007) Soil microbial community recovery in reclaimed soil under different vegetation in Wyoming minelands. In: Thirty years of SMCRA and beyond: Proceedings of the 24th National Meetings of the American Society of Mining and Reclamation, Gillette, WY. 2-7 June 2007. Curran Assoc., Red Hook, NY. p. 653-661.
5. Mummey DL, Stahl PD, Buyer JS (2002) Soil microbiological properties 20 years after surface mine reclamation: spatial analysis of reclaimed and undisturbed sites. Soil Biol Biochem 34: 1717-1725.
6. Wick AF (2007) Soil aggregate and organic matter dynamics in reclaimed mine land soils. Ph.D. Diss. Univ. of Wyoming, Laramie (Diss. Abstr. 3278006).
7. Hahn AS, Quideau SA (2013) Long-term effects of organic amendments on the recovery of plant and soil microbial communities following disturbance in the Canadian boreal forest. Plant Soil 363: 331-344.
8. Claassens S, Rensburg PV, Rensburg LV (2006) Soil microbial community structure of coal mine discard under rehabilitation. Water Air Soil Pollut 174: 355-366.
9. Dangi SR, Stahl PD, Wick AF, Ingram LJ, Buyer JS (2012) Soil microbial community recovery in reclaimed soils on a surface coal mine site. Soil Sci Soc Am J 76: 915-924.
10. Li J, Pu L, Zhu M, Zhang J, Li P, et al. (2014) Evolution of soil properties following reclamation in coastal areas: A review. Geoderma 226-227: 130-139.
11. Cui J, Liu C, Li Z, Wang L, Chen X, et al. (2012) Long-term changes in topsoil chemical properties under centuries of cultivation after reclamation of coastal wetlands in the Yangtze Estuary, China. Soil Till Res 123: 50-60.
12. Anderson JD, Ingram LJ, Stahl PD (2008) Influence of reclamation management practices on microbial biomass carbon and soil organic carbon accumulation in semiarid mined lands of Wyoming. Appl Soil Ecol 40: 387-397.
13. Acosta-Martinez V, Dowd SE, Sun Y, Wester D, Allen V (2010) Pyrosequencing analysis for characterization of soil bacterial populations as affected by an integrated livestock-cotton production system. Appl Soil Ecol 45: 13-25.
14. Dimitriu PA, Prescott CE, Quideau SA, Grayston SJ (2010) Impact of reclamation of surface-mined boreal forest soils on microbial community composition and function. Soil Biol Biochem 42: 2289-2297.
15. Mukhopadhyay S, Maiti SK, Masto RE (2013) Use of Reclaimed Mine Soil Index (RMSI) for screening of tree species for reclamation of coal mine degraded land. Ecol Eng 57: 133-142.
16. Zhao Z, Bai Z, Zhang Z, Guo D, Li J, et al. (2012) Population structure and spatial distributions patterns of 17 years old plantation in a reclaimed spoil of Pingshuo opencast mine, China Ecol Eng 44: 147-151.
17. Fraterrigo JM, Turner MG, Pearson SM, Dixon P (2005) Effects of past land use on spatial heterogeneity of soil nutrients in southern Appalachian forests. Ecol Monogr 75: 215-230.
18. Gasch C, Huzurbazar S, Stahl P (2014) Measuring soil disturbance effects and assessing soil restoration success by examining distributions of soil properties. Applied Soil Ecology 76: 102-111.
19. Li J, Okin GS, Alvarez L, Epstein H (2010) Effects of land-use history on soil spatial heterogeneity of macro- and trace elements in the Southern Piedmont USA. Geoderm 156: 60-73.
20. Walker LR, Wardle DA, Bardgett RD, Clarkson BD (2010) The use of chronosequences in studies of ecological succession and soil development.J Ecol 98: 725-736.
21. Li YY, Chen LQ, Wen HY, Zhou TJ, Zhang T, et al. (2014) 454 Pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas. J Microbiol Biotechnol 24: 313-323.
22. Nelson DW, Sommers LE (1982) Total carbon, organic carbon, and organic matter. In: Page AL, Miller RH, Keeney DR, (eds, ) Methods of soil analysis. Madison: American Society of Agronomy and Soil Science Society of American.
23. Bremmer JM (1965) Inorganic forms of nitrogen. In: C.A. Black, editor, Methods of soil analysis: Part 2- Chemical and microbiological properties. Madison: American Society of Agronomy. pp.1149-1178.
24. Pan P, Kang Q, Li X (2003) Determination of total phosphorus in soil by ammonium molybdate spectrophotometry. Chin J Spectrosc Lab 20: 697-699.
25. Carson PL (1980) Recommended potassium test, p. 17-18. In, W. C. Dahnke, (ed., ), Recommended chemical soil test procedures for the North Central Region. Bulletin 499. North Dakota Agricultural Experiment Station, Fargo, ND.
26. Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, et al. (2012) The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery1,2,3,4. Am J Clin Nutr 96: 544-551.
27. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
28. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-41.
29. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
30. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
31. Jiang XT, Peng X, Deng GH, Sheng HF, Wang Y, et al. (2013) Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland. Microb Ecol 66: 96-104.
32. Etten EV (2005) Multivariate analysis of ecological data using CANOCO. Austral Ecol 30: 486-487.
33. Jami E, Israel A, Kotser A, Mizrahi I (2013) Exploring the bovine rumen bacterial community from birth to adulthood. The ISME Journal 7(6):1069-79.
34. Huson DH, Mitra S, Weber N, Ruscheweyh H, Schuster SC (2011). Integrative analysis of environmental sequences using MEGAN4. Genome Research 21: 1552-1560.
35. Sheik CS, Mitchell TW, Rizvi FZ, Rehman Y, Faisal M, et al. (2012) Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure. PLoS ONE 7(6): e40059.
36. Bastida F, Hernández T, Albaladejo J, García C (2013) Phylogenetic and functional changes in the microbial community of long-term restored soils under semiarid climate. Soil Biol Biochem 65: 12-21.
37. Chen LX, Li JT, Chen YT, Huang LN, Hua ZS, et al. (2013) Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ Microbiol 5(9):2431-2444.
38. Rastogi G, Osman S, Vaishampayan PA, Andersen GL, Stetler LD, et al. (2010) Microbial Diversity in Uranium Mining-Impacted Soils as Revealed by High-Density 16S Microarray and Clone Library. Microb Ecol 59: 94-108.
39. Huang LN, Zhou WH, Hallberg KB, Wan CY, Li J, et al. (2011) Spatial and temporal analysis of the microbial community in the tailings of a Pb-Zn mine generating acidic drainage. Appl Environ Microbiol 77: 5540-5544.
40. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
41. Qiu MH, Zhang RF, Xue C, Zhang SS, Li SQ, et al. (2012) Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil. Biol Fertil Soils 48: 807-816.
42. Kolton M, Harel Y M, Pasternak Z, Graber ER, Elad Y, et al. (2011) Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants.Appl Environ Microb 77: 4924-4930.
43. Tait E, Carman M, Sievert S M (2007) Phylogenetic diversity of bacteria associated with ascidians in Eel Pond (Woods Hole, Massachusetts, USA).J Exp Mar Biol Ecol 2007: 342: 138-146.
44. Kuffner M, Hai B, Rattei T, Melodelima C, Schloter M, et al. (2012) Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiol Ecol 82: 551-562.
45. 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.
46. 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.
47. Ye RW, Thomas SM (2001) Microbial nitrogen cycles; physiogogy, genmics and applications. Curr Opin Microbiol 4 (03):307-312.
48. Keil D, Meyer A, Berner D, Poll C, Schützenmeister A, 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.
49. Afrasayab S, Yasmin A, Hasnain S (2002) Characterization of some indigenous mercury resistant bacteria from polluted environment. Pak J Biol Sci 5: 792-799.
50. Lewis DE, White JR, Wafula D, Athar R, Dickerson T, et al. (2010) Soil functional diversity analysis of a bauxite-mined restoration chronosequence. Microb Ecol 59: 710-723.
51. Ingram LJ, Schuman GE, Stahl PD, Spackman LK (2005) Microbial respiration and organic carbon indicate nutrient cycling recovery in reclaimed soils. Soil Sci Soc Am J 69: 1737-1745.
52. Frost SM, Stahl PD, Williams SE (2001) Long-term reestablishment of Arbuscular mycorrhizal fungi in a drastically disturbed semiarid surface mine soil. Arid Land Res Manag 15: 3-12.
53. Poncelet DM, Cavender N, Cutright TJ, Senko JM (2014) An assessment of microbial communities associated with surface mining-disturbed overburden. Environ Monit Assess 3: 1917-1929.
54. Singh BK, Millard P, Whiteley AS, Murrell JC (2004) Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trend Microbiol 12: 386-393.
55. Sun Y, Li X, Mander Ü, He Y, Jia Y, et al. (2011) Effect of reclamation time and land use on soil properties in Changjiang River Estuary, China. Chin Geogr Sci 21: 403-416.
56. Xiao R, Bai J, Zhang H, Gao H, Liu X, et al. (2011) Changes of P, Ca, Al and Fe contents in fringe marshes along a pedogenic chronosequence in the Pearl River estuary, South China. Cont Shelf Res 31: 739-747.
57. Sheoran V, Sheoran AS, Poonia P (2010) Soil reclamation of abandoned mine land by revegetation: a review. International Journal of Soil, Sediment and Water 3: 1-4.
58. Li MS (2006) Ecological restoration of mineland with particular reference to the metalliferous mine wasteland in China: a review of research and practice. Sci Total Environ 357: 38-53.
59. Wu RP, Li H, Cao P (2009) Amelioration of weathered coal on soil physical, chemical properties and enzyme activities with vegetation restoration. Journal of Agro-Environment Science 28: 1855-1861.
60. Xu QF, Jiang PK, Wang HL (2010) Improvement of biochemical and biological properties of eroded red soil by artificial revegetation. J. Soil Sediment 10: 255-262.
61. Six J, Bossuyt H, Degryze S, Denef K (2004) A history of research on the link between aggregates, soil biota, and soil organic matter dynamics. Soil Till Res 79: 7-31.