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Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach

Abstract

Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.

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References

  • Akob DM, Mills HJ, Ghiring TM, Kerkhof L, Stucki JW, Anastacio AS, Chin KJ, Kusel K, Palumbo AV, Watson DB, Kostka JE (2008) Functional diversity and electron donor dependence of microbial populations capable of U(VI) reduction in radionuclide-contaminated subsurface sediments. Appl Environ Microbiol 74:3159–3170

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Aust Ecol 26:32–46

    Google Scholar 

  • Bowman B, Kim M, Cho YJ, Korlach J (2015) Long-read, single molecule, real-time (SMRT) DNA sequencing for metagenomic applications. In: Izard J, Rivera MC (eds) Metagenomics for microbiology, 1st edn. Elsevier, London, p 25–38

    Chapter  Google Scholar 

  • Bray JR, Curtis JT (1957) An ordination of upland forest communities of southern Wisconsin. Ecol Monogr 27:325–349

    Article  Google Scholar 

  • Briceno G, Fuentes MS, Palma G, Jorquera MA, Amoroso MJ, Diez MC (2012) Chlorpyrifos biodegradation and 3,5,6-trichloro-2-pyridinol production by Actinobacteria isolated from soil. Int Biodeter Biodegr 73:1–7

    Article  CAS  Google Scholar 

  • Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72:6288–6298

    Article  CAS  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Cavaletti L, Monciardini P, Bamonte R, Schumann P, Rohde M, Sosio M, Donadio S (2006) New lineage of filamentous, spore-forming, Gram-positive bacteria from soil. Appl Environ Microbiol 72:4360–4369

    Article  CAS  Google Scholar 

  • Chain P, Lamerdin J, Larimer F, Regala W, Lao V, Land M, Hauser L, Hooper A, Klotz M, Norton J, Sayavedra-Soto L, Arciero D, Hommes N, Whittaker M, Arp D (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol 185:2759–2773

    Article  CAS  Google Scholar 

  • Chang YJ, Land M, Hauser L, Chertkov O, GlavinaDelRio T, Nolan M, Copeland A, Tice H, Cheng JF, Lucas S, Han C, Goodwin L, Pitluck S, Lvanova N, Ovchinikova G et al. (2011) Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacterra cemifertypestrain (SOSP1-21T). Stand Genom Sci 5:97–111

    Article  CAS  Google Scholar 

  • Chien C, Kuo Y, Chen C, Hung C, Yeh C, Yeh W (2008) Microbial diversity of soil bacteria in agricultural field contaminated with heavy metals. J Environ Sci 20:359–363

    Article  CAS  Google Scholar 

  • Chodak M, Gołebiewski M, Justyna MP, Katarzyna K, Maria N (2013) Diversity of microorganisms from forest soils differently polluted with heavy metals. Appl Soil Ecol 64:7–14

    Article  Google Scholar 

  • Chodak M, Gołebiewski M, Justyna MP, Katarzyna K, Maria N (2015) Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress. Ann Microbiol 65:1627–1637

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Das R, Kazy SK (2014) Microbial diversity, community composition and metabolic potential in hydrocarbon contaminated oily sludge: prospects for in situ bioremediation. Environ Sci Pollut Res 31:7369–7389

    Article  Google Scholar 

  • Deng L, Zeng G, Fan C, Lu L, Chen X, Chen M, Wu H, He X, Yan He (2015) Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil. Appl Microbiol Biotechnol 99:8259–8269

    Article  CAS  Google Scholar 

  • Ellis RJ, Morgan P, Weightman AJ, Fry JC (2003) Cultivation dependent and independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69:3223–3230

    Article  CAS  Google Scholar 

  • Epelde L, Lanzen A, Blanco F, Urich T, Garbisu C (2015) Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine. FEMS Microbiol Ecol 91:1–11

    Article  Google Scholar 

  • Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL (2013) Reconstructing the microbial diversity and function of pre-agricultural Tallgrass Prairie soils in the United States. Science 342:621–624

    Article  CAS  Google Scholar 

  • Fulladosa E, Murat JC, Villaescusa I (2005) Study on the toxicity of binary equitoxic mixtures of metals using the luminescent bacteria Vibrio fischeri as a biological target. Chemosphere 58:551–557

    Article  CAS  Google Scholar 

  • Galperin MY (2008) New feel for new phyla. Environ Microbiol 10:1927–1933

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Halter D, Cordi A, Gribaldo S, Gallien S, Goulhen-Chollet F, Heinrich-Salmeron A, Carapito C, Pagnout C, Montaut D, Seby F, Dorsselaer AV, Schaeffer C, Bertin PN, Bauda P, Arsene-Ploetze F (2011) Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments. Res Microbiol 162:877–887

    Article  CAS  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685

    Article  CAS  Google Scholar 

  • Hedlund BP (2011) Phylum XXIII Verrucomicrobia phyl nov. In: Krieg NR, Staley JT, Hedlund BP, Paster BJ, Ward N, Ludwig W (eds) Bergey’s Manual of Systematic Bacteriology, vol 4. Springer, New York, p 795–841

  • Hollister EB, Brooks JP, Gentry TJ (2015) Bioinformation and ’omic approaches for characterization of environmental microorganisms. In: Pepper IL, Gerba CP, Gentry TJ (eds) Environmental microbiology, 3rd edn. Elsevier, San Diego, p 482–505

    Chapter  Google Scholar 

  • Holtan-Hartwig L, Bechmann M, Høyås TR, Linjordet R, Bakken LR (2002) Heavy metals tolerance of soil denitrifying communities: N2O dynamics. Soil Biol Biochem 34:1181–1190

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Hudson T (2012) Living with Earth, an introduction to environmental geology. Pearson Prentice Hall, New Jersey

    Google Scholar 

  • Kandeler E, Tscherko D, Bruce KD, Stemmer M, Hobbs PJ, Bardgett RD, Amelung W (2000) Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil. Biol Fertil Soils 32:390–400

    Article  CAS  Google Scholar 

  • Kaur G, Sharma R, Singh K, Sharma PK (2015) Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India. 3 Biotech 5:727–734

    Article  Google Scholar 

  • Kielak AM, Barreto CC, Kowalchuk GA, Veen JA, Kuramae EE (2016) The ecology of Acidobacteria: moving beyond genes and genomes. Front Microbiol 7:1–16

    Google Scholar 

  • Kim H, Nishiyama M, Kunito T, Senoo K, Kawahara K, Murakami K, Oyaizu H (1998) High population of Sphingomonas species on plant surface. J Appl Microbiol 85:731–736

    Article  Google Scholar 

  • Koch IH, Gich F, Dunfield PF, Overmann J (2008) Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int J Syst Evol Microbiol 58:1114–1122

    Article  CAS  Google Scholar 

  • Lee KC, Webb RI, Janssen PH, Sangwan P, Romeo T, Staley JT, Fuerst JA (2009) Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes. BMC Microbiol 9:1–10

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Margesin R, Shivaji S (2015) Pedobacter. In: Whitman WB (ed) Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc.: Innsbruck, Austria, in association with Bergey’s Manual Trust, p 1–17

  • McCoy DD, Cetin A, Hausinger RP (1992) Characterization of urease from Sporosarcina ureae. Arch Microbiol 157:411–416

    Article  CAS  Google Scholar 

  • Meisinger DB, Zimmermann J, Ludwig W, Schleifer KH, Wanner G, Schmid M, Bennett PC, Engel AS, Lee NM (2007) In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophic ally based cave ecosystem (Lower Kane Cave, WY, USA). Environ Microbiol 9:1523–1534

    Article  CAS  Google Scholar 

  • Mendes LW, Tsai SM (2018) Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil. Antonie Van Leeuwenhoek 111:101–114

    Article  Google Scholar 

  • Nannipieri P, Pietramellara G, Renella G (2014) Omics in soil science. Caister Academic, Portland

    Google Scholar 

  • Navarro-Noya YE, Jan-Roblero J, González-Chávez MC, Hernández-Gama R, Hernández-Rodríguez C (2010) Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils. Antonie Van Leeuwenhoek 97:335–0349

    Article  CAS  Google Scholar 

  • Nielsen S, Minchin T, Kimber S, Zwieten L, Gilbert J, Munroe P, Joseph S, Thomas T (2014) Comparative analysis of the microbial communities in agricultural soil amended with enhanced biochars or traditional fertilizers. Agric Ecosyst Environ 191:73–82

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Paul D, Pandey G, Meier C, Meer JR, Jain RK (2006) Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation. FEMS Microbiol Ecol 57:116–127

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • R Development Core Team (2016) R: A Language and Environment for Statistical Computing. RFoundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0

  • Ramos JL (2004) Pseudomonas: genomics, life style and molecular architecture, vol 1. Springer Science+Business Media: Granada, Spain

  • Rastogi G, Osman S, Vaishampayan PA, Andersen GL, Stetler LD, Sani RK (2010) Microbial diversity in uranium mining impacted soils as revealed by high-density 16S microarray and clone library. Microb Ecol 59:94–108

    Article  CAS  Google Scholar 

  • Rivera MC, Izard J (2015) Promises and prospects of microbiome studies. In: Izard J, Rivera MC (eds) Metagenomics for microbiology, 1st edn. Elsevier, London, p 144–159

    Chapter  Google Scholar 

  • Robertson LA, Kuenen JG (2006) The genus Thiobacillus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, 3rd edn. Springer, New York, p 812–827

    Chapter  Google Scholar 

  • Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12:1–12

    Article  Google Scholar 

  • Sandaa RA, Torsvik V, Enger O, Daae FL, Castberg T, Hahn D (1999) Analysis of bacterial communities in heavy metal contaminated soils at different levels of resolution. FEMS Microbiol Ecol 30:237–251

    Article  CAS  Google Scholar 

  • Sheik CS, Mitchell TW, Rizvi FZ, Rehman Y, Faisal M, Hasnain S, Mclnerny MJ, Krumholz LR (2012) Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure. PLoS ONE 7(6):e40059

    Article  CAS  Google Scholar 

  • Singleton F, Peacock W, Coleman W (2012) Solirubrobacter. In: Whitman WB (ed) Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc: New Jersey, United States, in association with Bergey’s Manual Trust, p 1–5

  • Sobolev D, Begonia MFT (2008) Effects of heavy metal contamination upon soil microbes: lead-induced changes in general and denitrifying microbial communities as evidenced by molecular markers. Int J Environ Res Public Health 5:450–456

    Article  CAS  Google Scholar 

  • Spain AM, Krumholz LR, Elshahed MS (2009) Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J 3:992–1000

    Article  CAS  Google Scholar 

  • Spang A, Poehlein A, Offre P, Zumbragel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T et al. (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 14:3122–3145

    Article  CAS  Google Scholar 

  • Spring S, Schulze R, Overmann J, Schleifer KH (2000) Identification and characterization of ecologically significant prokaryotes in the sediment of fresh water lakes, molecular and cultivation studies. FEMS Microbiol Rev 24:573–590

    Article  CAS  Google Scholar 

  • Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748–4755

    Article  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Tebo BM, Davis RE, Anitori RP, Connell LB, Schiffman P, Staudigel H (2015) Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica. Front Microbiol 6:1–14

    Article  Google Scholar 

  • Teske A, Nelson DC (2006) The genera Beggiatoa and Thioploca. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes. A handbook on the biology of bacteria, 3rd edn. Springer, New York, p 784–810

  • Thies JE (2015) Molecular approaches to studying the soil biota, Elsevier. In: Paul EA (ed) Soil microbiology, ecology, and biochemistry, 4th edn. Academic Press, New York, p 151–185

    Chapter  Google Scholar 

  • Touceda-Gonzalez M, Brader G, Antonielli L, Ravindran VB, Waldner G, Friesl-Hanl W, Corretto E, Campisano A, Pancher M, Sessitsch A (2015) Combined amendment of immobilizers and the plant growth-promoting strain Burkholderia phytofirmans PsJN favours plant growth and reduces heavy metal uptake. Soil Biol Biochem 91:140–150

    Article  CAS  Google Scholar 

  • Wang J, Chen MH, Lv YY, Jiang YW, Qiu LH (2016) Edaphobacter dinghuensis sp. nov., an acidobacterium isolated from lower subtropical forest soil. Int J Syst Evol Microbiol 66:276–282

    Article  CAS  Google Scholar 

  • Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D et al. (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046–2056

    Article  CAS  Google Scholar 

  • Wiegel J (2006) The genus Xanthobacter. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds.) The prokaryotes, a handbook on the biology of bacteria, 3rd edn. Springer, New York, p 290–314

  • 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

    Google Scholar 

  • Yan X, Luo X, Zhao M (2016) Metagenomic analysis of microbial community in uranium-contaminated soil. Appl Microbiol Biotechnol 100:299–310

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K (2003) Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53:1155–1163

    Article  CAS  Google Scholar 

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Hemmat-Jou, M.H., Safari-Sinegani, A.A., Mirzaie-Asl, A. et al. Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. Ecotoxicology 27, 1281–1291 (2018). https://doi.org/10.1007/s10646-018-1981-x

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Keywords

  • Metagenomics
  • Sequencing
  • Archaea
  • Diversity
  • Heavy metals
  • Iran