Skip to main content
SpringerLink
Log in

Microbial ecology and geochemistry of soils containing iron pans

  • Original Article
  • Published:
Environmental Geology

Abstract

Soils in New Zealand, and elsewhere, often contain substantial zones of ferro-manganese concretions and pans (laterally continuous layers) that can affect soil quality and management. Soils containing concretions and pans from Southland, New Zealand, were investigated to determine links between microbial ecology and geochemistry. Three soil profiles were sampled at 100-mm intervals to a depth of 1 m and then assayed for nine different populations of bacteria using selective media. Geochemical analysis was performed on the soils at the same intervals, and on shallow groundwater from nearby wells. The largest concentrations of iron (Fe) and manganese (Mn) coincide with concretions. Nitrogen (N) and carbon (C) are not correlated with Fe and Mn but may be depleted due to bacterial metabolism. Fe and Mn concentrations in groundwater are low, suggesting that the source of these elements in the concretions and pans is in situ weathering rather than groundwater. Numbers of iron oxidising organisms increase where concretions and pans are encountered, but manganese-oxidising organisms decrease. Heterotrophic, sulphur-oxidising, and anaerobic populations have relatively consistent numbers at all depths within the profiles. Fifty organisms were selected for phylogenetic characterisation, of which only Pseudomonas sp. is known to have significant interactions with Fe and Mn. These results suggest a link between concretion development and iron-oxidising microbial populations.

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

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Boogerd FC, De-Vrind JPM (1987) Manganese oxidation by Leptothrix discophora. J Bacteriol 169(2):489–494

    CAS  PubMed  Google Scholar 

  • Boogerd FC, De-Vrind JPM (1987) Manganese oxidation by Leptothrix discophora. J Bacteriol 169(2):489–494Brock TD, Madigan MT (eds) (1991) Biology of microorganisms. Prentice Hall, Englewood Cliffs

    Google Scholar 

  • Caccavo F, Coates JD, Rossello-Mora RA, Ludwig W, Schleifer KH, Lovley DR, Mcinerney MJ (1996) Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacteria. Arch Microbiol 165:370–376

    Article  CAS  PubMed  Google Scholar 

  • Caccavo F, Coates JD, Rossello-Mora RA, Ludwig W, Schleifer KH, Lovley DR, Mcinerney MJ (1996) Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacteria. Arch Microbiol 165:370–376Christensen H, Hansen M, Sorensen J (1999) Counting and size classification of active soil bacteria by fluoresence in situ hybridisation with an rRNA oligonucleotide probe. Appl Environ Microb 65(4):1753–1761

    CAS  PubMed  Google Scholar 

  • Caccavo F, Coates JD, Rossello-Mora RA, Ludwig W, Schleifer KH, Lovley DR, Mcinerney MJ (1996) Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacteria. Arch Microbiol 165:370–376Christensen H, Hansen M, Sorensen J (1999) Counting and size classification of active soil bacteria by fluoresence in situ hybridisation with an rRNA oligonucleotide probe. Appl Environ Microb 65(4):1753–1761Corkill FM (1932) Invercargill water supply. Proc N Z Soc Civil Eng 18:230–262

    Google Scholar 

  • Caccavo F, Coates JD, Rossello-Mora RA, Ludwig W, Schleifer KH, Lovley DR, Mcinerney MJ (1996) Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacteria. Arch Microbiol 165:370–376Christensen H, Hansen M, Sorensen J (1999) Counting and size classification of active soil bacteria by fluoresence in situ hybridisation with an rRNA oligonucleotide probe. Appl Environ Microb 65(4):1753–1761Corkill FM (1932) Invercargill water supply. Proc N Z Soc Civil Eng 18:230–262Cuthbertson JR (1882) On a source of water supply for Invercargill. Trans N Z Inst 14:121–122

    Google Scholar 

  • Caccavo F, Coates JD, Rossello-Mora RA, Ludwig W, Schleifer KH, Lovley DR, Mcinerney MJ (1996) Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacteria. Arch Microbiol 165:370–376Christensen H, Hansen M, Sorensen J (1999) Counting and size classification of active soil bacteria by fluoresence in situ hybridisation with an rRNA oligonucleotide probe. Appl Environ Microb 65(4):1753–1761Corkill FM (1932) Invercargill water supply. Proc N Z Soc Civil Eng 18:230–262Cuthbertson JR (1882) On a source of water supply for Invercargill. Trans N Z Inst 14:121–122Ehrlich HL (1996) Chapter 8: Geomicrobial interactions with iron and manganese. In: Geomicrobiology, 3rd edn. Marcel Dekker, New York, pp 276–293

  • Emiliani F, Gonzalez De Paira SM (1998) Bacteriological quality of Bendetti Lake (Santo Tome, Santa Fe Province, Argentina) and associated environmental variables. Argent Microbiol Rev 30:30–38

    CAS  Google Scholar 

  • Emiliani F, Gonzalez De Paira SM (1998) Bacteriological quality of Bendetti Lake (Santo Tome, Santa Fe Province, Argentina) and associated environmental variables. Argent Microbiol Rev 30:30–38Ferris FG, Tazaki K and others (1989) Iron oxides in acid mine drainage environments and their association with bacteria. Chem Geol 74(3–4):321–330

    Google Scholar 

  • Fortin D, Ferris FG (1998) Precipitation of iron, silica, and sulfate on bacterial cell surfaces. Geomicrobiol J 15(4):309–324

    CAS  Google Scholar 

  • Fortin D, Ferris FG (1998) Precipitation of iron, silica, and sulfate on bacterial cell surfaces. Geomicrobiol J 15(4):309–324Fortin D, Ferris FG and others (1997) Surface-mediated mineral development by bacteria. Rev Mineral 35:161–180

    CAS  Google Scholar 

  • Fortin D, Ferris FG (1998) Precipitation of iron, silica, and sulfate on bacterial cell surfaces. Geomicrobiol J 15(4):309–324Fortin D, Ferris FG and others (1997) Surface-mediated mineral development by bacteria. Rev Mineral 35:161–180Gamo M, Shoji T (1999) A method for profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources. Appl Environ Microbiol 65:4419–4424

    CAS  PubMed  Google Scholar 

  • Fortin D, Ferris FG (1998) Precipitation of iron, silica, and sulfate on bacterial cell surfaces. Geomicrobiol J 15(4):309–324Fortin D, Ferris FG and others (1997) Surface-mediated mineral development by bacteria. Rev Mineral 35:161–180Gamo M, Shoji T (1999) A method for profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources. Appl Environ Microbiol 65:4419–4424Ghiorse WC (1984) Biology of iron and manganese-depositing bacteria. Annu Rev Microbiol 38:515–550

    CAS  PubMed  Google Scholar 

  • Fortin D, Ferris FG (1998) Precipitation of iron, silica, and sulfate on bacterial cell surfaces. Geomicrobiol J 15(4):309–324Fortin D, Ferris FG and others (1997) Surface-mediated mineral development by bacteria. Rev Mineral 35:161–180Gamo M, Shoji T (1999) A method for profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources. Appl Environ Microbiol 65:4419–4424Ghiorse WC (1984) Biology of iron and manganese-depositing bacteria. Annu Rev Microbiol 38:515–550Glasauer S, Langley S and others (2001) Sorption of Fe (hydr)oxides to the surface of Shewanella putrefaciens: cell-bound fine-grained minerals are not always formed de novo. Appl Environ Microbiol 67(12):5544–5550

    Article  CAS  PubMed  Google Scholar 

  • Fortin D, Ferris FG (1998) Precipitation of iron, silica, and sulfate on bacterial cell surfaces. Geomicrobiol J 15(4):309–324Fortin D, Ferris FG and others (1997) Surface-mediated mineral development by bacteria. Rev Mineral 35:161–180Gamo M, Shoji T (1999) A method for profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources. Appl Environ Microbiol 65:4419–4424Ghiorse WC (1984) Biology of iron and manganese-depositing bacteria. Annu Rev Microbiol 38:515–550Glasauer S, Langley S and others (2001) Sorption of Fe (hydr)oxides to the surface of Shewanella putrefaciens: cell-bound fine-grained minerals are not always formed de novo. Appl Environ Microbiol 67(12):5544–5550Harrison APJ (1984) The acidophillic thiobacilli and other acidophillic bacteria that share their habitat. Annu Rev Microbiol 38:265–292

    Article  CAS  PubMed  Google Scholar 

  • Fortin D, Ferris FG (1998) Precipitation of iron, silica, and sulfate on bacterial cell surfaces. Geomicrobiol J 15(4):309–324Fortin D, Ferris FG and others (1997) Surface-mediated mineral development by bacteria. Rev Mineral 35:161–180Gamo M, Shoji T (1999) A method for profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources. Appl Environ Microbiol 65:4419–4424Ghiorse WC (1984) Biology of iron and manganese-depositing bacteria. Annu Rev Microbiol 38:515–550Glasauer S, Langley S and others (2001) Sorption of Fe (hydr)oxides to the surface of Shewanella putrefaciens: cell-bound fine-grained minerals are not always formed de novo. Appl Environ Microbiol 67(12):5544–5550Harrison APJ (1984) The acidophillic thiobacilli and other acidophillic bacteria that share their habitat. Annu Rev Microbiol 38:265–292Hewitt AE (1998) New Zealand soil classification, 2nd edn. Landcare Research Science Series No 1. Manaaki Whenua Press, New Zealand

    Google Scholar 

  • Hughes B (2001) Southland. In: Rosen MR, White PA (eds) Groundwaters of New Zealand. New Zealand Hydrological Society. Caxton Press, Christchurch, pp 481–485

  • Hungate RE (1969) A roll tube method for the cultivation of strict anaerobes. Methods Microbiol 3B:117–132

    CAS  Google Scholar 

  • Hungate RE (1969) A roll tube method for the cultivation of strict anaerobes. Methods Microbiol 3B:117–132Ingledew WJ (1982) Thiobacillus ferrooxidans the bioenergetics of an acidophilic chemolithotroph. Biochim Biophys Acta 683:89–117

    CAS  PubMed  Google Scholar 

  • Hungate RE (1969) A roll tube method for the cultivation of strict anaerobes. Methods Microbiol 3B:117–132Ingledew WJ (1982) Thiobacillus ferrooxidans the bioenergetics of an acidophilic chemolithotroph. Biochim Biophys Acta 683:89–117Keis S, Bennett CF, Ward VK, Jones DT (1995) Taxonomy and phylogeny of industrial solvent producing Clostridia. Int J Syst Bacteriol 45:693–705

    CAS  PubMed  Google Scholar 

  • Hungate RE (1969) A roll tube method for the cultivation of strict anaerobes. Methods Microbiol 3B:117–132Ingledew WJ (1982) Thiobacillus ferrooxidans the bioenergetics of an acidophilic chemolithotroph. Biochim Biophys Acta 683:89–117Keis S, Bennett CF, Ward VK, Jones DT (1995) Taxonomy and phylogeny of industrial solvent producing Clostridia. Int J Syst Bacteriol 45:693–705Konhauser KO (1997) Bacterial iron biomineralisation in nature. FEMS Microbiol Rev 20(3–4):315–326

  • Kusel K, Dorsch T, Acker G, Stackebrandt E (1999) Microbial reduction of Fe(III) in acidic sediments: isolation of Acidiphilium cryptum JF-5 capable of coupling the reduction of Fe(III) to the oxidation of glucose. Appl Environ Microbiol 65(8):3633–3640

    PubMed  Google Scholar 

  • Kusel K, Dorsch T, Acker G, Stackebrandt E (1999) Microbial reduction of Fe(III) in acidic sediments: isolation of Acidiphilium cryptum JF-5 capable of coupling the reduction of Fe(III) to the oxidation of glucose. Appl Environ Microbiol 65(8):3633–3640Lovley DR, Phillips EJP (1986) Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl Environ Microbiol 51(4):683–9

    CAS  Google Scholar 

  • Kusel K, Dorsch T, Acker G, Stackebrandt E (1999) Microbial reduction of Fe(III) in acidic sediments: isolation of Acidiphilium cryptum JF-5 capable of coupling the reduction of Fe(III) to the oxidation of glucose. Appl Environ Microbiol 65(8):3633–3640Lovley DR, Phillips EJP (1986) Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl Environ Microbiol 51(4):683–9Mo H (2000) Drinking-water standards for New Zealand, 2000. National Drinking-Water Standards Review Expert Working Group for the Ministry of Health, Wellington

    Google Scholar 

  • Myers CR, Nealson KH (1988) Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240:1319–1321

    CAS  Google Scholar 

  • Myers CR, Nealson KH (1988) Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240:1319–1321Newman DK, Kennedy EK, Coates JD, Ahmann D, Ellis DJ, Lovley DR, Morel FMM (1997) Dissimilatory arsenate and sulfate reduction in Desulfotomaculum auripigmentum sp. nov. Arch Microbiol 168:380–388

    CAS  PubMed  Google Scholar 

  • Myers CR, Nealson KH (1988) Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240:1319–1321Newman DK, Kennedy EK, Coates JD, Ahmann D, Ellis DJ, Lovley DR, Morel FMM (1997) Dissimilatory arsenate and sulfate reduction in Desulfotomaculum auripigmentum sp. nov. Arch Microbiol 168:380–388Okazaki M, Sugita T, Shimizu M, Ohode K, Iwamoto K, De-Vrind-De-Jong EW, De-Vrind JPM, Corstjens PLAM (1997) Partial purification and characterisation of manganese-oxidizing factors of Pseudomonas fluorescens GB-1. Appl Environ Microbiol 63(12):4793–4799

    CAS  PubMed  Google Scholar 

  • Myers CR, Nealson KH (1988) Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240:1319–1321Newman DK, Kennedy EK, Coates JD, Ahmann D, Ellis DJ, Lovley DR, Morel FMM (1997) Dissimilatory arsenate and sulfate reduction in Desulfotomaculum auripigmentum sp. nov. Arch Microbiol 168:380–388Okazaki M, Sugita T, Shimizu M, Ohode K, Iwamoto K, De-Vrind-De-Jong EW, De-Vrind JPM, Corstjens PLAM (1997) Partial purification and characterisation of manganese-oxidizing factors of Pseudomonas fluorescens GB-1. Appl Environ Microbiol 63(12):4793–4799Rosen MR (2001) Hydrochemistry of New Zealand's Aquifers. In: Rosen MR, White PA (eds) Groundwaters of New Zealand. New Zealand Hydrological Society, Caxton Press, Christchurch, pp 77–110

  • Schwertmann U, Fitzpatrick R-W (1992) Iron minerals in surface environments. In: Skinner H-C-W, Fitzpatrick R-W (eds) Biomineralization processes of iron and manganese; modern and ancient environments. Catena Supplement 21. Catena Verlag, Cremlingen-Destedt, Germany, pp 7–30

  • Smith S A, Tuovinen OH (1985) Environmental analysis of iron-precipitating bacteria in groundwater and wells. Ground Water Monitor Rev 5:45–52

    CAS  Google Scholar 

  • Smith S A, Tuovinen OH (1985) Environmental analysis of iron-precipitating bacteria in groundwater and wells. Ground Water Monitor Rev 5:45–52Tannock GW, Munro K, Harmsen HJM, Welling GW, Smart J, Gopal PK (2000) Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 66(6):2578–2588

    CAS  PubMed  Google Scholar 

  • Smith S A, Tuovinen OH (1985) Environmental analysis of iron-precipitating bacteria in groundwater and wells. Ground Water Monitor Rev 5:45–52Tannock GW, Munro K, Harmsen HJM, Welling GW, Smart J, Gopal PK (2000) Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 66(6):2578–2588Taylor AL, Galloway JL (2000) Soils of the Dipton West District. Topoclimate South Scientific Report 37. Crops for Southland, Invercargill, New Zealand

    Google Scholar 

  • Timmis KN, Stahl D (1999) The birth of environmental microbiology. Environ Microbiol 1:187–188

    Article  CAS  PubMed  Google Scholar 

  • Timmis KN, Stahl D (1999) The birth of environmental microbiology. Environ Microbiol 1:187–188Urrutia MM, Beveridge TJ (1994) Formation of fine-grained metal and silicate precipitates on a bacterial surface (Bacillus subtilis). Chem Geol 116(3–4):261-280

  • Vojak PWL, Edwards C, Jones MV (1985) A note on enumeration of manganese-oxidizing bacteria in estuarine water and sediment samples. J Appl Bacteriol 59:375–379

    CAS  Google Scholar 

  • Vojak PWL, Edwards C, Jones MV (1985) A note on enumeration of manganese-oxidizing bacteria in estuarine water and sediment samples. J Appl Bacteriol 59:375–379Weeber J, Brown L, White P, Russell W, Thorpe H, Hughes B (2001): A history of groundwater in New Zealand. In: Rosen MR, White PA (eds) Groundwaters of New Zealand. New Zealand Hydrological Society. Caxton Press, Christchurch, pp 5–44

  • Wielinga B, Lucy JK, Moore JN, Seastone OF, Gannon JE (1999) Microbiological and geochemical characterisation of fluvially deposited mine tailings. Appl Environ Microbiol 65(4):1548–1555

    PubMed  Google Scholar 

  • Wielinga B, Lucy JK, Moore JN, Seastone OF, Gannon JE (1999) Microbiological and geochemical characterisation of fluvially deposited mine tailings. Appl Environ Microbiol 65(4):1548–1555Winkelmann G (1991) CRC Handbook of microbial iron chelates. CRC Press, Boca Raton

    Google Scholar 

  • Woese CR (1996) Whither microbiology? Phylogenetic trees. Curr Opin Biol 6(9):1060–1063

    CAS  Google Scholar 

  • Woese CR (1996) Whither microbiology? Phylogenetic trees. Curr Opin Biol 6(9):1060–1063Zeikus JG, Hegge PW, Anderson MA (1979) Thermoanaerobium brockii gen. and sp. nov., a new chemoorganotrophic, caldoactive, anaerobium bacterium. Arch Microbiol 122:41–48

    CAS  Google Scholar 

Download references

Acknowledgments

We would like to thank Dr. Gregory Cook for assistance in all aspects of this project. Special thanks to Professor Gerald Tannock and Karen Munro for the work on the DGGE profiles, and Dr. Helen McIntyre and Dr. Stef Kies for advice on optimising molecular biology techniques. Thanks also to Brian Daly from Landcare Research, Palmerston North, and John Hunt from Spectrachem for analytical chemistry work and Amy Taylor from Topoclimate South. Special thanks to Mo Turnbull for dreaming up the project and arranging funding for the work. Without this none of this would have happened.

Author information

Author notes

  1. C. R. Anderson

    Present address: CMB-Microbiology, Göteborgs Universitet, Box 462, 405 30 , Göteborg, Sweden

Authors and Affiliations

  1. Institute of Geological & Nuclear Sciences Limited, New Zealand

    C. R. Anderson, I. M. Turnbull & M. R. Rosen

Authors
  1. C. R. Anderson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. I. M. Turnbull
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. R. Rosen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to C. R. Anderson.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Anderson, C.R., Turnbull, I.M. & Rosen, M.R. Microbial ecology and geochemistry of soils containing iron pans. Env Geol 45, 209–220 (2003). https://doi.org/10.1007/s00254-003-0868-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00254-003-0868-0

Keywords

Search

Navigation