, Volume 96, Issue 9, pp 1035–1042 | Cite as

Is the availability of different nutrients a critical factor for the impact of bacteria on subterraneous carbon budgets?

  • M. C. Portillo
  • E. Porca
  • S. Cuezva
  • J. C. Cañaveras
  • S. Sanchez-Moral
  • J. M. GonzalezEmail author
Original Paper


Bacteria thriving in underground systems, such as karsts, adapt to use a variety of nutrients. Most of these nutrients derive from superficial processes. This study shows that bacteria are able to differentially induce carbonate precipitation or dissolution depending on the availability of nutrients for growth. Different bacterial strains isolated from caves, representing the most common components of these microbial communities, were cultured with different carbon and nitrogen sources (e.g., acetate, glucose, peptone, humic acids) and induced changes in pH were measured during growth. Carbonate can either precipitate or dissolve during bacterial growth. The induction of carbonate precipitates or their dissolution as a function of consumption of specific carbon sources revealed the existence of an active nutrient cycling process in karsts and links nutrients and environmental conditions to the existence of a highly significant carbon sink in subterraneous environments.


Nutrient Carbonate precipitation Carbon sink Carbon budget Subterraneous environments 



This research was supported by CGL2006-11561/BTE project. All Altamira Cave Research Centre and Museum staff is acknowledged for their collaboration throughout the whole research period.


  1. Alonso-Zarza AM, Martin-Perez A (2008) Dolomite in caves: recent dolomite formation in oxic, non-sulfate environments. Castañar Cave, Spain. Sediment Geol 205:160–164. doi: 10.1016/j.sedgeo.2008.02.006 CrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. American Public Health Association (APHA) (1989) Standard Methods for the Examination of Water and Wastewater, 17th edn. APHA, Washington, DC, USAGoogle Scholar
  4. Barabesi C, Galizzi A, Mastromei G, Rossi M, Tamburini E, Perito B (2007) Bacillus subtilis gene cluster involved in calcium carbonate biomineralization. J Bacteriol 189:228–235. doi: 10.1128/JB.01450-06 PubMedCrossRefGoogle Scholar
  5. Barton HA, Northup DE (2007) Geomicrobiology in cave environments: past, current and future perspectives. J Caves Karst Stud 69:163–178Google Scholar
  6. Boquet E, Boronat A, Ramos-Cormenzana A (1973) Production of calcite (calcium carbonate) crystals by soil bacteria is a general phenomenon. Nature 246:527–529. doi: 10.1038/246527a0 CrossRefGoogle Scholar
  7. Braissant O, Verrecchia EP, Aragno M (2002) Is the contribution of bacteria to terrestrial carbon budget greatly underestimated? Naturwissenschaften 89:366–370. doi: 10.1007/s00114-002-0340-0 PubMedCrossRefGoogle Scholar
  8. Bruce JP, Frome M, Haites E, Janzen H, Lal R, Paustian K (1999) Carbon sequestration in soil. J Soil Water Conserv 54:382–389Google Scholar
  9. Butler JN (1982) Carbon dioxide equilibria and their applications. Addison-Wesley, Reading, pp 259Google Scholar
  10. Butler JL, Williams MA, Bottomley PJ, Myrold DD (2003) Microbial community dynamics associated with rhizosphere carbon flow. Appl Environ Microbiol 69:6793–6800. doi: 10.1128/AEM.69.11.6793-6800.2003 PubMedCrossRefGoogle Scholar
  11. Cañaveras JC, Sanchez-Moral S, Soler V, Saiz-Jimenez C (2001) Microorganisms and microbially induced fabrics in cave walls. Geomicrobiol J 18:223–240. doi: 10.1080/01490450152467769 CrossRefGoogle Scholar
  12. Cañaveras JC, Cuezva S, Sanchez-Moral S, Lario J, Laiz L, Gonzalez JM, Saiz-Jimenez C (2006) On the origin of fiber calcite crystals in moonmilk deposits. Naturwissenschaften 93:27–32. doi: 10.1007/s00114-005-0052-3 PubMedCrossRefGoogle Scholar
  13. Castanier S, Le Metayer-Levrel G, Perthuisot J-P (1999) Ca-carbonates precipitation and limestone genesis—the microbiogeologists point of view. Sediment Geol 126:9–23. doi: 10.1016/S0037-0738(99) 00028-7 CrossRefGoogle Scholar
  14. Chidthaisong M, Rosenstock B, Conrad R (1999) Measurement of monosaccharides and conversion of glucose to acetate in anoxic rice field soil. Appl Environ Microbiol 65:2350–2355PubMedGoogle Scholar
  15. Coates JD, Chakraborty R, O’Connor SM, Schmidt C, Thieme J (2000) The geochemical effects of microbial humic substances reduction. Acta Hydrochim Hydrobiol 28:420–427. doi: 10.1002/1521-401X(20017) 28:7 < 420::AID-AHEH420 > 3.0.CO;2-D CrossRefGoogle Scholar
  16. Cuezva S, Sanchez-Moral S, Saiz-Jimenez C, Cañaveras JC (2009) Microbial communities and associated mineral fabrics in Altamira Cave, Spain. Int J Speleol 38:83–92Google Scholar
  17. Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499. doi: 10.1073/pnas.142680199 PubMedCrossRefGoogle Scholar
  18. Douglas S, Beveridge TJ (1998) Mineral formation by bacteria in natural microbial communities. FEMS Microbiol Ecol 26:79–88. doi: 10.1111/j.1574-6941.1998.tb00494.x CrossRefGoogle Scholar
  19. Ehrlich HL (1998) Geomicrobiology: its significance for geology. Earth-Sci Rev 45:45–60. doi: 10.1016/S0012-8252(98) 00034-8 CrossRefGoogle Scholar
  20. Ferrer MR, Quevedo-Sarmiento J, Bejar V, Delgado R, Ramos-Cormenzana A, Rivadeneyra MA (1988) Calcium carbonate formation by Deleya halophila: effect of salt concentration and incubation temperature. Geomicrobiology 6:49–57. doi: 10.1080/01490458809377821 CrossRefGoogle Scholar
  21. Gadd GM (1999) Fungal production of citric and oxalic acid: importance in metal physiology and biochemical processes. Adv Microb Physiol 41:47–92. doi: 10.1016/S0065-2911(08) 60165-4 PubMedCrossRefGoogle Scholar
  22. Gombert P (2002) Role of karstic dissolution in global carbon cycle. Global Planet Change 33:177–184. doi: 10.1016/S0921-8181(02) 00069-3 CrossRefGoogle Scholar
  23. Gonzalez JM, Ortiz-Martinez A, Gonzalez-delValle MA, Laiz L, Saiz-Jimenez C (2003) An efficient strategy for screening large cloned libraries of amplified 16S rDNA sequences from complex environmental communities. J Microbiol Methods 55:459–463. doi: 10.1016/S0167-7012(03) 00171-4 PubMedCrossRefGoogle Scholar
  24. Gonzalez JM, Portillo MC, Saiz-Jimenez C (2005) Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy Lumber sequences from natural environments. Environ Microbiol 7:1024–1028. doi: 10.1111/j.1462-2920.2005.00779.x PubMedCrossRefGoogle Scholar
  25. Gonzalez JM, Portillo MC, Saiz-Jimenez C (2006) Metabolically active Crenarchaeota in Altamira Cave. Naturwissenschaften 93:42–45. doi: 10.1007/s00114-005-0060-3 PubMedCrossRefGoogle Scholar
  26. Hammes F, Verstraete W (2002) Key roles of pH and calcium metabolism in microbial carbonate precipitation. Rev Environ Sci Biotechnol 1:3–7. doi: 10.1023/A:1015135629155 CrossRefGoogle Scholar
  27. Jones DL (1998) Organic acids in the rhizosphere—a critical review. Plant Soil 205:25–44. doi: 10.1023/A:1004356007312 CrossRefGoogle Scholar
  28. Kowalski AS, Serrano-Ortiz P, Janssens IA, Sanchez-Moral S, Cuezva S, Domingo F, Were A, Alados-Arboledas L (2008) Can flux tower research neglect geochemical CO2 exchange? Agric For Meteorol 148:1045–1054. doi: 10.1016/j.agrformet.2008.02.004 CrossRefGoogle Scholar
  29. Madigan M, Martinko J, Parker J (2003) Brock biology of microorganisms. Prentice Hall, New JerseyGoogle Scholar
  30. Mattson ED, Bowman RS, Lindgren ER (2002) Electrokinetic ion transport through unsaturated soil: 2. Application to a heterogeneous field site. J Contam Hydrol 54:121–140. doi: 10.1016/S0169-7722(01) 00145-0 PubMedCrossRefGoogle Scholar
  31. Portillo MC, Gonzalez JM, Saiz-Jimenez C (2008) Metabolically active microbial communities of yellow and grey colonizations on the walls of Altamira Cave, Spain. J Appl Microbiol 104:681–691. doi: 10.1111/j.1365-2672.2007.03594.x PubMedCrossRefGoogle Scholar
  32. Portillo MC, Saiz-Jimenez C, Gonzalez JM (2009) Molecular characterization of total and metabolically active bacterial communities of “white colonizations” in Altamira Cave, Spain. Res Microbiol 160:41–47. doi: 10.1016/j.resmic.2008.10.002 PubMedCrossRefGoogle Scholar
  33. Portillo MC, Gonzalez JM (2009) Sulfate-reducing bacteria are common members of bacterial communities in Altamira Cave (Spain). Sci Total Environ 407:1114–1122PubMedGoogle Scholar
  34. Rivadeneyra MA, Delgado R, Delgado G, Del Moral A, Ferrer MR, Ramos-Cormenzana A (1994) Precipitation of carbonates by Bacillus sp. isolated from saline soils. Geomicrobiol J 11:174–184Google Scholar
  35. Saiz-Jimenez C, Hermosin B (1999) The nature of the organic matter present in dripping waters from Altamira Cave. J Anal Appl Pyrolysis 49:337–347. doi: 10.1016/S0165-2370(98) 00112-0 CrossRefGoogle Scholar
  36. Verrecchia EP (1990) Litho-diagenetic implications of the calcium oxalate–carbonate biogeochemical cycle in semiarid calcretes, Nazareth, Israel. Geomicrobiol J 8:87–99. doi: 10.1080/01490459009377882 CrossRefGoogle Scholar
  37. Verrecchia EP, Verrecchia KE (1994) Needle-fibercalcite: a critical review and a proposed classification. J Sediment Res 64:650–664Google Scholar
  38. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583. doi: 10.1073/pnas.95.12.6578 PubMedCrossRefGoogle Scholar
  39. Yates KK, Robbins LL (1999) Radioisotope tracer studies of inorganic carbon and Ca in microbiologically derived CaCO3. Geochim Cosmochim Acta 63:129–136. doi: 10.1016/S0016-7037(98) 00297-X CrossRefGoogle Scholar
  40. Zimmermann J, Gonzalez JM, Ludwig W, Saiz-Jimenez C (2005) Detection and phylogenetic relationships of a highly diverse uncultured acidobacterial community on paleolithic paintings in Altamira Cave using 23S rRNA sequence analyses. Geomicrobiol J 22:379–388. doi: 10.1080/01490450500248986 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • M. C. Portillo
    • 1
  • E. Porca
    • 1
  • S. Cuezva
    • 2
  • J. C. Cañaveras
    • 3
  • S. Sanchez-Moral
    • 2
  • J. M. Gonzalez
    • 1
    Email author
  1. 1.Instituto de Recursos Naturales y AgrobiologíaIRNAS–CSICSevillaSpain
  2. 2.Museo Natural de Ciencias NaturalesMNCN–CSICMadridSpain
  3. 3.Dep. Ciencias de la Tierra y del Medio Ambiente—Lab. Petrología AplicadaUniversidad de AlicanteAlicanteSpain

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