Skip to main content
SpringerLink
Log in

Abundance and Diversity of CO2-fixing Bacteria in Grassland Soils Close to Natural Carbon Dioxide Springs

  • Original Article
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Gaseous conditions at natural CO2 springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO2 concentrations ([CO2]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO2-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavešinci mofette, a natural CO2 spring which is known for very pure CO2 emissions, at different distances from the CO2 releasing vents, at locations that clearly differed in soil CO2 efflux (from 12.5 to over 200 μmol CO2 m−2 s−1 yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the “red-like” type of cbbL genes could be detected. In contrast, the “green-like” type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of “red-like” cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO2 concentrations. Furthermore, the diversity pattern of “red-like” cbbL genes changed depending on the CO2 regime. This indicates that only a part of the autotrophic CO2-fixing microbes could adapt to the very high CO2 concentrations and adverse life conditions that are governed by mofette gaseous regime.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  1. Carney KM, Hungate BA, Drake BG, Megonigal JP (2007) Altered soil microbial community at elevated CO2 leads to loss of soil carbon. . Proc Natl Acad Sci U S A 104(12):4990–4995

    Article  PubMed  CAS  Google Scholar 

  2. Cotrufo MF, Raschi A, Lanini M, Ineson P (1999) Decomposition and nutrient dynamics of Quercus pubescens leaf litter in a naturally enriched CO2 Mediterranean ecosystem. Funct Ecol 13(3):343–351

    Article  Google Scholar 

  3. Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and duplication of RubisCO genes in Eubacteria and plastids. Mol Biol Evol 13(6):873–882

    PubMed  CAS  Google Scholar 

  4. DeSantis TZ, Dubosarskiy I, Murray SR, Andersen GL (2003) Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics 19(12):1461–1468

    Article  PubMed  CAS  Google Scholar 

  5. Griffiths RI, Whiteley AS, O’Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66(12):5488–5491

    Article  PubMed  CAS  Google Scholar 

  6. Heukeshoven J, Dernick R (1988) Increased sensitivity for Coomassie staining of sodium dodecyl sulphate-polyacrylamide gels using PhatSystem Development Unit. Electrophoresis 9(1):60–61

    Article  PubMed  CAS  Google Scholar 

  7. Janitzky P (1986) Particle-size analysis. In: Singer MJ, Janitzky P (eds) Field and laboratory procedures used in a soil chronosequence study. vol. 1648. U.S. Geological Survey Bulletin, Washington, pp 11–16

    Google Scholar 

  8. Kaligarič M (2001) Vegetation responses to elevated CO2 from natural CO2 springs at Strmec (Radenci, Slovenia). Acta Biol Slov 44(1–2):31–38

    Google Scholar 

  9. Lee X, Wu HJ, Sigler J, Oishi C, Siccama T (2004) Rapid and transient response of soil respiration to rain. Glob Change Biol 10:1017–1026

    Article  Google Scholar 

  10. Maček I (2004) Root response of selected agriculturally important species to naturally elevated CO2 concentration. Doctoral Dissertation. Biotechnical Faculty, University of Ljubljana, Ljubljana

  11. Miltner A, Richnow HH, Kopinke FD, Kästner M (2004) Assimilation of CO2 by soil microorganisms and transformation into soil organic matter. Org Geochem 35(9):1015–1024

    Article  CAS  Google Scholar 

  12. Miltner A, Kopinke FD, Kindler R, Selesi D, Hartmann A, Kästner M (2005) Non-phototrophic CO2 fixation by soil microorganisms. Plant Soil 269:193–203

    Article  CAS  Google Scholar 

  13. Pfanz H, Vodnik D, Wittmann C, Aschan G, Raschi A (2004) Plants and geothermal CO2 exhalations—survival in and adaptation to a high CO2 environment. Prog Bot 65:499–538

    Google Scholar 

  14. Selesi D, Schmid M, Hartmann A (2005) Diversity of green-like and red-like ribulose 1.5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils. Appl Environ Microbiol 71(1):175–184

    Article  PubMed  CAS  Google Scholar 

  15. Selesi D, Pattis I, Schmid M, Kandeler E, Hartmann A (2007) Quantification of bacterial RubisCO genes in soils by cbbL targeted real-time PCR. J Microbiol Methods 69:497–503

    Article  PubMed  CAS  Google Scholar 

  16. Sharma S, Aneja M, Mayer J, Munch JC, Schloter M (2005) Characterisation of bacterial community structure in rhizosphere soil of grain legumes. Microbial Ecol 49(3):407–415

    Article  CAS  Google Scholar 

  17. Shiverly JM, van Keulen G, Meijer WG (1998) Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu Rev Microbiol 52:191–230

    Article  Google Scholar 

  18. SIST ISO 10390 (1996) Soil quality—determination of pH. ISO, Geneva

    Google Scholar 

  19. SIST ISO 11261 (1996) Soil quality—determination of total nitrogen. Modified Kjeldahl method. ISO, Geneva

    Google Scholar 

  20. Soil Survey Division Staff (1993) Soil survey manual. United States Department of Agriculture, Washington (D.C.), Handbook 18:139–143

  21. Tabita FR (1999) Microbial ribulose-1.5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynth Res 60:1–28

    Article  CAS  Google Scholar 

  22. Vodnik D, Pfanz H, Wittmann C, Maček I, Kastelec D, Turk B, Batič F (2002) Photosynthetic acclimation in plants growing near a carbon dioxide spring. Phyton-Annales rei Botanicae 42(3):239–244

    Google Scholar 

  23. Vodnik D, Šircelj H, Kastelec D, Maček I, Pfanz H, Batič F (2005) The effect of natural CO2 enrichment on the growth of maize. J Crop Improv 13(1/2):193–212

    Article  CAS  Google Scholar 

  24. Vodnik D, Kastelec D, Pfanz H, Maček I, Turk B (2006) Small-scale spatial variation in soil CO2 concentration in a natural carbon dioxide spring and some related plant responses. Geoderma 133(3–4):309–319

    Article  CAS  Google Scholar 

  25. Watson GMF, Tabita FR (1996) Regulation, unique gene organisation and unusual primary structure of carbon fixation genes from a marine phycoerythrin-containing cyanobacterium. Plant Mol Biol 32(6):1103–1115

    Article  PubMed  CAS  Google Scholar 

  26. Watson GMF, Tabita FR (1997) Microbial ribulose 1.5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. Minireview. FEMS Microbiol Lett 146:13–22

    Article  PubMed  CAS  Google Scholar 

  27. WBR (2006) World reference base for soil resources 2006. A framework for international classification, correlation and communication, World soil resources reports, vol. 103. 2nd edn. FAO, Rome

    Google Scholar 

Download references

Acknowledgments

This research was supported by the grant P4-0085 (ARRS, Republic of Slovenia), Scientific and Educational Foundation of the Republic of Slovenia, Public Fund and UL 327/45,24.112006 (SOCRATES/ERASMUS scholarship, U.V.). The authors would like to thank Mrs. Conny Galonska (Helmholtz Zentrum München) for technical assistance.

Author information

Authors and Affiliations

  1. Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia

    Urška Videmšek, Marjetka Suhadolc & Dominik Vodnik

  2. Institute of Soil Ecology, Helmholtz Zentrum München—German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany

    Alexandra Hagn, Viviane Radl & Michael Schloter

  3. Chair for Soil Science, Technical University of Munich, 85350, Freising-Weihenstephan, Germany

    Heike Knicker

  4. Institute of Soil Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85758, Oberschleissheim, Germany

    Michael Schloter

Authors
  1. Urška Videmšek
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alexandra Hagn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marjetka Suhadolc
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Viviane Radl
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Heike Knicker
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Michael Schloter
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Dominik Vodnik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael Schloter.

Additional information

Urška Videmšek, Alexandra Hagn, Michael Schloter, and Dominik Vodnik contributed equally to this study.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Videmšek, U., Hagn, A., Suhadolc, M. et al. Abundance and Diversity of CO2-fixing Bacteria in Grassland Soils Close to Natural Carbon Dioxide Springs. Microb Ecol 58, 1–9 (2009). https://doi.org/10.1007/s00248-008-9442-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-008-9442-3

Keywords

Search

Navigation