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http://dx.doi.org/10.4014/jmb.1309.09001

454 Pyrosequencing Analysis of Bacterial Diversity Revealed by a Comparative Study of Soils from Mining Subsidence and Reclamation Areas  

Li, Yuanyuan (Jiangsu Key Laboratory for Resources and Environment Information Engineering, School of Environment and Spatial Informatics, China University of Mining and Technology)
Chen, Longqian (Jiangsu Key Laboratory for Resources and Environment Information Engineering, School of Environment and Spatial Informatics, China University of Mining and Technology)
Wen, Hongyu (School of Life Science, Jiangsu Normal University)
Zhou, Tianjian (Jiangsu Key Laboratory for Resources and Environment Information Engineering, School of Environment and Spatial Informatics, China University of Mining and Technology)
Zhang, Ting (Jiangsu Key Laboratory for Resources and Environment Information Engineering, School of Environment and Spatial Informatics, China University of Mining and Technology)
Gao, Xiali (School of Life Science, Jiangsu Normal University)
Publication Information
Journal of Microbiology and Biotechnology / v.24, no.3, 2014 , pp. 313-323 More about this Journal
Abstract
Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.
Keywords
454 Pyrosequencing; bacterial diversity; mining soil reclamation; soil organic matter; total nitrogen;
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1 Pernes-Debuyers A, Tessier D. 2004. Soil physical properties affected by long-term fertilization. Eur. J. Soil Sci. 55: 505-512.   DOI   ScienceOn
2 Kuffner M, Hai B, Rattei T, Melodelima C, Schloter M, Zechmeister-Boltenstern S, et al. 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.
3 Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N. 2010. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol. Lett. 307: 80-86.   DOI   ScienceOn
4 Lamb EG, Kennedy N, Siciliano SD. 2011. Effects of plant species richness and evenness on soil microbial community diversity and function. Plant Soil 338: 483-495.   DOI
5 Li J, Hong J, Xie Y, Wang H. 2010. Effects of different fertilization treatments on reclaimed soil microbial community structure in core-mining subsidence area. Acta Ecol. Sin. 30: 6193-6200.
6 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: 195-202.
7 Lin XG, Lu H. 2008. Scientific connotation and ecological service function of soil microbial diversity. Acta Pedol. Sin. 45: 892-895.
8 Liu F, Lu L. 2009. Progress in the study of ecological restoration of coal mining subsidence areas. J. Nat. Resour. 24: 613-616.
9 Mallarino AP, Borges R. 2006. Phosphorus and potassium distribution in soil following long-term deep-band fertilization in different tillage systems. Soil Sci. Soc. Am. J. 70: 702-707.   DOI   ScienceOn
10 Mitchell JS, Ruess RW. 2009. N fixing alder (Alnusviridis spp. fruti-cosa) effects on soil properties across a secondary successional chronosequence in interior Alaska. Biogeochemistry 95: 215-229.   DOI
11 He X, Su Y, Liang Y, Chen X, Zhu H, Wang K. 2012. Land reclamation and short-term cultivation change soil microbial communities and bacterial metabolic profiles. J. Sci. Food Agric. 92: 1103-1111.   DOI   ScienceOn
12 Garbeva P, Van Veen J A, V an E lsas J D. 2004. M icrobial diversity in soil: selection of microbial populations by plant and soil type and implications for soil suppressiveness. Annu. Rev. Phytopathol. 42: 243-270.   DOI   ScienceOn
13 Hou X, Wu J, Xu J. 2007. The influence of lead-bensulfuronmethyl complex pollution on soil microbial activities and community structure. China Environ. Sci. 27: 738-742.
14 Gomez E, Ferreras L, Toresani S. 2006. Soil bacterial functional diversity as influenced by organic amendment application. Bioresour. Technol. 97: 1484-1489.   DOI   ScienceOn
15 Janssen PH. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72: 1719-1728.   DOI   ScienceOn
16 Han XM, Wang R, Liu J, Wang MC, Zhou J, Guo WH. 2007. Effects of vegetation type on soil microbial community structure and catabolic diversity assessed by polyphasic methods in North China. J. Environ. Sci. 19: 1228-1234.   DOI   ScienceOn
17 Kaschuk G, Alberton O, Hungria M. 2010. Three decades of soil microbial biomass studies in Brazilian ecosystems: lessons learned about soil quality and indications for improving sustainability. Soil Biol. Biochem. 42: 11-13.
18 Kirk JL, Klironomos JN, Lee H, Trevors JT. 2005. The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil. Environ. Pollut. 133: 455-465.   DOI   ScienceOn
19 Kolton M, Harel YM, Pasternak Z, Graber ER, Elad Y, Cytryn E. 2011. Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl. Environ. Microbiol. 77: 4924- 4930.   DOI   ScienceOn
20 Chu H. 2007. Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol. Biochem. 39: 2971-2976.   DOI   ScienceOn
21 Diacono M, Montemurro F. 2010. Long-term effects of organic amendments on soil fertility. A review. Agron. Sustain. Dev. 30: 401-422.   DOI   ScienceOn
22 Dinamarca MA, Cereceda-Balic F, Fadic X, Seeger M. 2007. Analysis of striazine -degrading microbial communities in soils using most-probable-number enumeration and tetrazolium salt detection. Int. Microbiol. 10: 209-215.
23 Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.   DOI   ScienceOn
24 Fan W, Bai Z, Li H, Qiao J, Xu J. 2011. Effects of different vegetation restoration patterns and reclamation years on microbes in reclaimed soil. Trans. CSAE 27: 330-336.
25 Fortuna AM, Marsh TL, Honeycutt CW, Halteman WA. 2011. Use of primer selection and restriction enzymes to assess bacterial community diversity in an agricultural soil used for potato production via terminal restriction fragment length polymorphism. Appl. Microbiol. Biotechnol. 91: 1193-1202.   DOI
26 Chhabra S, Brazil D, Morrissey J, Burke J, O'Gara F, Dowling DN. 2013. Fertilization management affects the alkaline phosphatase bacterial community in barley rhizosphere soil. Biol. Fertil. Soils 49: 31-39.   DOI
27 Gans J, Wolinsky M, Dunbar J. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1389.   DOI   ScienceOn
28 Ganzert L, Lipski A, Hubberten HW, Wagner D. 2011. The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. Microb. Ecol. 76: 476-491.   DOI   ScienceOn
29 Bartelt-Ryser J, Joshi J, Schmid B, Brandl H, Balser T. 2005. Soil feedbacks of plant diversity on soil microbial communities and subsequent plant growth. Perspect. Plant Ecol. 7: 27-49.   DOI   ScienceOn
30 Belay A, Claassens AS, Wehner FC. 2002. Effect of direct nitrogen and potassium and residual phosph orus fertilizers on soil chemical properties, microbial components and maize yield under long-term crop rotation. Biol. Fertil. Soils 35: 420-427.   DOI
31 Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, Mira A. 2012. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am. J. Clin. Nutr. 96: 544-551.   DOI   ScienceOn
32 Afrasayab S, Yasmin A, Hasnain S. 2002. Characterization of some indigenous mercury resistant bacteria from polluted environment. Pak. J. Biol. Sci. 5: 792-799.   DOI
33 Cai ZC, Qin SW. 2006. Dynamics of crop yields and soil organic carbon in a long-term fertilization experiment in the Huang-Huai-Hai Plain of China. Geoderma 136: 708 -715.   DOI
34 Balachandar D, Raja P, Kumar K, Sundaram SP. 2007. Nonrhizobial nodulation in legumes. Biotechnol. Mol. Biol. Rev. 2: 49-57.
35 Cao X. 2007. Regulating mine land reclamation in developing countries: the case of China. Land Use Policy 24: 472-483.   DOI   ScienceOn
36 Ceja-Navarro JA, Rivera-Orduna FN, Patino-Zuniga L, Vila- Sanjurjo A, Crossa J, Govaerts B, Dendooven L. 2010. Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Appl. Environ. Microbiol. 76: 3685-3691.   DOI   ScienceOn
37 Chen L, Qiao G, Dong H, Ma W. 2012. Influence of soil bacterial diversity in the process of reclamation in Jungar open coal mine of Inner Mongolia. J. A rid L and Resour. Environ. 26: 120-125.
38 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 livestockcotton production system. Appl. Soil Ecol. 45: 13-25.   DOI   ScienceOn
39 Zhang J, Zhu T, Cai Z, Qin S, Müller C. 2012. Effects of long-term repeated mineral and organic fertilizer applications on soil nitrogen transformations. Eur. J. Soil Sci. 63: 75-85.   DOI   ScienceOn
40 Zhong W, Gu T, Wang W, Zhang B, Lin X, Huang Q, Shen W. 2010. The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil 326: 511-522.   DOI   ScienceOn
41 Zhuang X, Han Z, Bai Z, Zhuang G, Shim H. 2010. Progress in decontamination by halophilic microorganisms in saline wastewater and soil. Environ. Pollut. 158: 1119-1126.   DOI   ScienceOn
42 Stursová M, Baldrian P. 2011. Effects of soil properties and management on the activity of soil organic matter transforming enzymes and the quantification of soil-bound and free activity. Plant Soil 338: 99-110.   DOI
43 Suleiman AKA, Manoeli L, Boldo JT, Pereira MG, Roesch LFW. 2013. Shifts in soil bacterial community after eight years of land-use change. Syst. Appl. Microbiol. 36: 137-144.   DOI   ScienceOn
44 Vendan RT, Lee SH, Yu YJ, Rhee YH. 2012. Analysis of bacterial community in the ginseng soil using Denaturing gradient gel electrophoresis (DGGE). Indian J. Microbiol. 52: 286-288.   DOI   ScienceOn
45 Wallenius K, Rita H, Mikkonen A, Lappi K, Lindström K, Hartikainen H, et al. 2011. Effects of land use on the level, variation and spatial structure of soil enzyme activities and bacterial communities. Soil Biol. Biochem. 43: 1464-1473.   DOI   ScienceOn
46 Wei Y, Yu L, Zhang J, Yu Y, Deangelis DL. 2011. Relationship between vegetation restoration and soil microbial characteristics in degraded karst regions: a case study. Pedosphere 21: 132-138.   DOI   ScienceOn
47 Yu W, Su S, Lee C. 2008. A novel retrieval system for nearly complete microbial genomic fragments from soil samples. J. Microbiol. Methods 72: 197-205.   DOI   ScienceOn
48 Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, et al. 2010. Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl. Environ. Microbiol. 76: 6751-6759.   DOI   ScienceOn
49 Wilson DW, Sander LE. 1996. Total carbon, organic carbon, and organic matter. In Sparks DL (ed.). Methods of Soil Analysis: Part 3 - Chemical Methods. Soil Sci. Soc. Am. J. 1002- 1005.
50 Youssef N, Elshahed M. 2008. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias. J. Microbiol. Methods 75: 86-91.   DOI   ScienceOn
51 Qian K, Wang L, Li J. 2011. Variation of microbial activity in reclaimed soil in mining area. J. Ecol. Rural Environ. 27: 59-63.
52 Ren H, Lu Y, Yu Y, Zhou R, Sun W, Dai C, et al. 2011. Cloning and characterisation of a novel 2,4-dichlorophenol hydroxylase from a metagenomic library derived from polychlorinated biphenyl-contaminated soil. Biotechnol. Lett. 33: 1159-1167.   DOI
53 Rivas R, Willems A, Subba-Rao NS, Mateos PF, Dazzoc FB, Kroppenstedt RM, et al. 2003. Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India. Syst. Appl. Microbiol. 26: 47-53.   DOI   ScienceOn
54 Roesch LF, Fulthrope RR, Riva A, Casella G, Kent, AD, Daroub SM, et al. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1: 283-290.   DOI
55 Rousk J, Baath E, Brookes PC, Lauber CL, Caporaso JG, Knight R, Fierer N. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4: 1340-1351.   DOI   ScienceOn
56 Scherer-Lorenzen M, Pahnborg C, Prinz A, Schulze ED. 2003. The role of plant diversity and composition for nitrate leaching in grasslands. Ecology 84: 1539-1552.   DOI   ScienceOn
57 Moreno B, Vivas A, Nogales R, Macci C, Masciandaro G, Benitez E. 2009. Restoring biochemical activity and bacterial diversity in a trichloroethylene-contaminated soil: the reclamation effect of vermicomposted olive wastes. Environ. Sci. Pollut. Res. 16: 253-264.   DOI
58 Sengupta S, Haldar S, Choudhury SR. 2011. Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea. Antonie Van Leeuwenhoek 100: 161-170.   DOI
59 Spehn EM, Joshi J, Schmid B, Alphei J, Korner C. 2000. Plant diversity effects on soil heterotrophic activity in experimental grassland ecosystems. Plant Soil 224: 217-230.   DOI   ScienceOn
60 Morales S, Cosart T, Johnson J, Holben W. 2009. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters. Appl. Environ. Microbiol. 75: 668-675.   DOI   ScienceOn
61 Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, et al. 2011. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. Plos One 6: e17000.   DOI   ScienceOn
62 O'Neill T, Balks M, Stevenson B, Lopez-Martínez J, Aislabie J, Rhodes P. 2013. The short-term effects of surface soil disturbance on soil bacterial community structure at an experimental site near Scott Base, Antarctica. Polar Biol. 36: 985-996.   DOI   ScienceOn
63 Pan P, Kang Q, Li X. 2003. Determination of total phosphorus in soil by ammonium molybdate spectrophotometry. Chin. J. Spectrosc. Lab. 20: 697-699.
64 Peech M. 1945. Determination of exchangeable cations and exchange capacity of soils - rapid micromethods using centrifuge and spectrophotometer. Soil Sci. 59: 25-38.   DOI
65 Peralta RM, Ahn C, Gillevet PM. 2013. Characterization of soil bacterial community structure and physicochemical properties in created and natural wetlands. Sci. Total Environ. 443: 725-732.   DOI   ScienceOn
66 Shen W, Lin X, Gao N, Zhang H, Yin R, Shi W, Duan Z. 2008. Land use intensification affects soil microbial populations, functional diversity and related suppressiveness of cucumber Fusarium wilt in China's Yangtze River Delta. Plant Soil 306: 117-127.   DOI