, Volume 13, Issue 2, pp 263–271 | Cite as

Archaeal and bacterial communities of heavy metal contaminated acidic waters from zinc mine residues in Sepetiba Bay

  • Welington I. Almeida
  • Ricardo P. Vieira
  • Alexander Machado CardosoEmail author
  • Cynthia B. Silveira
  • Rebeca G. Costa
  • Alessandra M. Gonzalez
  • Rodolfo Paranhos
  • João A. Medeiros
  • Flávia A. Freitas
  • Rodolpho M. Albano
  • Orlando B. Martins
Original Paper


Mining of metallic sulfide ore produces acidic water with high metal concentrations that have harmful consequences for aquatic life. To understand the composition and structure of microbial communities in acid mine drainage (AMD) waters associated with Zn mine tailings, molecular diversity of 16S genes was examined using a PCR, cloning, and sequencing approach. A total of 78 operational taxonomic units (OTUs) were obtained from samples collected at five different sites in and around mining residues in Sepetiba Bay, Brazil. We analyzed metal concentration, physical, chemical, and microbiological parameters related to prokaryotic diversity in low metal impacted compared to highly polluted environments with Zn at level of gram per liter and Cd–Pb at level of microgram per liter. Application of molecular methods for community structure analyses showed that Archaea and Bacteria groups present a phylogenetic relationship with uncultured environmental organisms. Phylogenetic analysis revealed that bacteria present at the five sites fell into seven known divisions, α-Proteobacteria (13.4%), β-Proteobacteria (16.3%), γ-Proteobacteria (4.3%), Sphingobacteriales (4.3%), Actinobacteria (3.2%) Acidobacteria (2.1%), Cyanobacteria (11.9%), and unclassified bacteria (44.5%). Almost all archaeal clones were related to uncultivated Crenarchaeota species, which were shared between high impacted and low impacted waters. Rarefaction curves showed that bacterial groups are more diverse than archaeal groups while the overall prokaryotic biodiversity is lower in high metal impacted environments than in less polluted habitats. Knowledge of this microbial community structure will help in understanding prokaryotic diversity, biogeography, and the role of microorganisms in zinc smelting AMD generation and perhaps it may be exploited for environmental remediation procedures in this area.


Acidophiles Systematics Ecology Phylogeny Archaea Biodiversity Ecology Molecular phylogeny and molecular biology Zinc mine 



We acknowledge the Genome Sequencing facilities core Johanna Döbereiner at IBqM/UFRJ, the Limnology Laboratory of UFRJ for access to liquid scintillator. We are grateful to João Paulo M. Torres and Valéria Magalhães for manuscript review. This work was supported by Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ), Coordenação de Aperfeiçoamento de Pessoal de Ensino Superior (CAPES), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  2. Amado Filho GM, Karez CS, Andrade LR, Yoneshigue-Valentin Y, Pfeiffer WC (1997) Effects on growth and accumulation of zinc in six seaweed species. Ecotoxicol Environ Saf 37:223–228PubMedCrossRefGoogle Scholar
  3. Amann RI, Stromley J, Devereux R, Key R, Stahl DA (1992) Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl Environ Microbiol 58:614–623PubMedGoogle Scholar
  4. Andrade L, Gonzalez AM, Araújo FV, Paranhos R (2003) Flow cytometry assessment of bacterioplankton in tropical marine environments. J Microbiol Methods 55:841–850PubMedCrossRefGoogle Scholar
  5. Bond PL, Druschel GK, Banfield JF (2000) Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems. Appl Environ Microb 66:4962–4971CrossRefGoogle Scholar
  6. Brãuer SL, Cadillo-Quiroz H, Yashiro E, Yavitt JB, Zinder SH (2006) Isolation of a novel acidiphilic methanogen from an acid peat bog. Nature 442:192–194PubMedCrossRefGoogle Scholar
  7. Cánovas CR, Olías M, Nieto JM, Sarmiento AM, Cerón JC (2007) Hydrogeochemical characteristics of the Tinto and Odiel Rivers (SW Spain). Factors controlling metal contents. Sci Total Environ 373:363–382PubMedCrossRefGoogle Scholar
  8. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443PubMedCrossRefGoogle Scholar
  9. Correa Junior JD, Allodi S, Amado-Filho GM, Farina M (2000) Zinc accumulation in phosphate granules of Ucides cordatus hepatopancreas. Braz J Med Biol Res 33:217–221PubMedCrossRefGoogle Scholar
  10. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 12:5685–5689CrossRefGoogle Scholar
  11. Dopson M, Baker-Austin C, Koppineed PR, Bond PL (2003) Growth in sulfidic mineral environments: metal resistance mechanism in acidophilic microorganisms. Microbiol 149:1959–1970CrossRefGoogle Scholar
  12. Edwards KJ, Bond PL, Gihring TM, Banfield JF (2000) An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:1796–1799PubMedCrossRefGoogle Scholar
  13. Edwing B, Hillier L, Wendl M, Green P (1998) Base-calling of automated sequencer traces using phred accuracy assessment. Gen Res 8:175–185Google Scholar
  14. Gasol JM, del Giorgio PA (2000) Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities. Sci Mar 64:197–224CrossRefGoogle Scholar
  15. Giovannoni SJ, Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 15:343–348CrossRefGoogle Scholar
  16. Grasshoff K, Kremling K, Erhardt M (1999) Methods of seawater analysis, 3rd edn. Wiley–VCH Verlag, Germany, p 600Google Scholar
  17. Hallberg KB, Coupland K, Kimura S, Johnson DB (2006) Macroscopic streamer growths in acidic, metal-rich mine waters in north wales consist of novel and remarkably simple bacterial communities. Appl Environ Microbiol 72:2022–2030PubMedCrossRefGoogle Scholar
  18. He Z, Xiao S, Xie X, Zhong H, Hu Y, Li Q, Gao F, Li G, Liu J, Qiu G (2007) Molecular diversity of microbial community in acid mine drainages of Yunfu sulfide mine. Extremophiles 11:305–314PubMedCrossRefGoogle Scholar
  19. He Z, Xiao S, Xie X, Hu Y (2008) Microbial diversity in acid mineral bioleaching systems of dongxiang copper mine and Yinshan lead–zinc mine. Extremophiles 12:225–234PubMedCrossRefGoogle Scholar
  20. Heck KL, van Belle G, Simberloff D (1975) Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56:1459–1461CrossRefGoogle Scholar
  21. Hurlbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577–586CrossRefGoogle Scholar
  22. Johnson DB (1998) Biodiversity and ecology of acidophilic microorganisms. FEMS Microb Ecol 27:307–317CrossRefGoogle Scholar
  23. Johnson DB, Rolfe S, Hallberg KB, Iversen E (2001) Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine. Environ Microbiol 3:630–637PubMedCrossRefGoogle Scholar
  24. Johnson DB, Hallberg KB (2003) The microbiology of acidic mine waters. Res Microbiol 154:466–473PubMedCrossRefGoogle Scholar
  25. Junior RGSL, Araújo FG, Maia MF, Pinto ASSB (2002) Evaluation of heavy metals in fish of the Sepetiba and Ilha Grande Bays, Rio de Janeiro, Brazil. Environ Res 89:171–179CrossRefGoogle Scholar
  26. Kamjunke N, Tittel J, Krumbeck H, Beulker C, Poerschmann J (2005) High heterotrophic bacterial production in acidic, iron-rich mining lakes. Microb Ecol 49:425–433PubMedCrossRefGoogle Scholar
  27. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120PubMedCrossRefGoogle Scholar
  28. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245PubMedCrossRefGoogle Scholar
  29. Lacerda LD, Pfeiffer WC, Fiszman M (1987) Heavy metal distribution, availability and fate in Sepetiba Bay, S.E. Brazil. Sci Total Environ 65:163–173CrossRefGoogle Scholar
  30. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175Google Scholar
  31. Lohr AJ, Laverman AM, Braster M, van Straalen NM, Roling WF (2006) Microbial communities in the world’s largest acidic volcanic lake, Kawah Ijen in Indonesia, and in the Banyupahit River originating from it. Microb Ecol 2:609–618CrossRefGoogle Scholar
  32. Maeda S, Sakaguchi T (1990) Accumulation and detoxification of toxic metal elements by algae. In: Akatsuka I (ed) Introduction to applied phycology. Acad Publish, The Netherlands, pp 109–136Google Scholar
  33. Molisani MM, Martins RV, Machado W, Paraquetti HHM, Bidone ED, Lacerda LD (2004) Environmental changes in Sepetiba Bay, SE Brazil. Reg Environ Change 4:17–27CrossRefGoogle Scholar
  34. Nicomrat D, Dick WA, Tuovinen OH (2006) Assessment of the microbial community in a constructed wetland that receives acid coal mine drainage. Microb Ecol 51:83–89PubMedCrossRefGoogle Scholar
  35. Nordstrom DK, Alpers CN (1999) Negative pH, efflorescent mineralogy, and consequences for environmental restoration at the Iron Mountain Superfund site, California. Proc Natl Acad Sci 96:3455–3468PubMedCrossRefGoogle Scholar
  36. Peplow D, Edmonds R (2005) The effects of mine waste contamination at multiple levels of biological organization. Ecol Eng 24:101–119CrossRefGoogle Scholar
  37. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Ann Rev Microbiol 57:369–394CrossRefGoogle Scholar
  38. Rühling A, Tyler G (1973) Heavy metal pollution and decomposition of spruce needle litter. Oikos 24:402–416CrossRefGoogle Scholar
  39. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  40. SEMADS (2001) Bacias Hidrográficas e Recursos Hídricos da Macroregião Ambiental 2 - Bacia da Baía de Sepetiba. Rio de Janeiro 1:79Google Scholar
  41. Singleton DR, Furlong MA, Ratbhun SL, Whitman WB (2001) Quantitative comparisons of 16S rRNA Gene Sequence Libraries from Environmental Samples. Appl Environ Microbiol 67:4374–4376PubMedCrossRefGoogle Scholar
  42. Smith DC, Azam F (1992) A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar Microb Food Webs 6:107–114Google Scholar
  43. Somerville CC, Knight IT, Straube WL, Colwell RR (1989) Simple rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol 55:548–554PubMedGoogle Scholar
  44. Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK (2001) Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol 67:5750–5760PubMedCrossRefGoogle Scholar
  45. Tan GL, Shu WS, Hallberg KB, Li F, Lan CY, Huang LN (2006) Cultivation-dependent and cultivation-independent characterization of the microbial community in acid mine drainage associated with acidic Pb/Zn mine tailings at Lechang, Guangdong, China. FEMS Microbiol Ecol 59:118–126PubMedGoogle Scholar
  46. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882CrossRefGoogle Scholar
  47. Tyler G (1974) Heavy metal pollution and soil enzymatic activity. Plant Soil 41:303–311CrossRefGoogle Scholar
  48. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 4:37–43CrossRefGoogle Scholar
  49. Urbach E, Kevin LV, Young L, Morse A, Larson GL, Giovannoni SJ (2001) Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol Oceanogr 46:557–572Google Scholar
  50. Vieira RP, Clementino MM, Cardoso AM, Oliveira DN, Albano RM, Gonzalez AM, Paranhos R, Martins OB (2007) Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil. Microb Ecol 54:460–468PubMedCrossRefGoogle Scholar
  51. Wendt-Potthoff K, Koschorreck M (2002) Functional groups and activities of bacteria in a highly acidic volcanic mountain stream and lake in Patagonia, Argentina. Microb Ecol 43:92–106PubMedCrossRefGoogle Scholar
  52. Yin H, Cao L, Qiu G, Wang D, Kellog L, Zhou J, Liu X, Dai Z, Ding J, Liu X (2008) Molecular diversity of 16S rRNA and gyrB genes in copper mines. Arch Microbiol 189:101–110PubMedCrossRefGoogle Scholar
  53. Zang HB, Yang MX, Shi W, Zheng Y, Sha T, Zhao ZW (2007) Bacterial diversity in mine tailings compared by cultivation and cultivation-independent methods and their resistance to lead and cadmium. Microb Ecol 54:702–712Google Scholar

Copyright information

© Springer 2008

Authors and Affiliations

  • Welington I. Almeida
    • 1
  • Ricardo P. Vieira
    • 1
    • 2
  • Alexander Machado Cardoso
    • 1
    • 4
    Email author
  • Cynthia B. Silveira
    • 1
  • Rebeca G. Costa
    • 1
  • Alessandra M. Gonzalez
    • 2
  • Rodolfo Paranhos
    • 2
  • João A. Medeiros
    • 3
  • Flávia A. Freitas
    • 5
  • Rodolpho M. Albano
    • 5
  • Orlando B. Martins
    • 1
  1. 1.Instituto de Bioquímica MédicaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
  2. 2.Instituto de BiologiaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
  3. 3.Instituto de QuímicaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
  4. 4.Centro Universitário Estadual da Zona OesteRio de JaneiroBrazil
  5. 5.Departamento de BioquímicaUniversidade do Estado do Rio de JaneiroRio de JaneiroBrazil

Personalised recommendations