Science China Earth Sciences

, Volume 62, Issue 11, pp 1719–1729 | Cite as

Microaerobic Fe(II) oxidation coupled to carbon assimilation processes driven by microbes from paddy soil

  • Xiaomin Li
  • Shan Mou
  • Yating Chen
  • Tongxu Liu
  • Jun Dong
  • Fangbai LiEmail author
Research Paper


Microaerobic Fe(II) oxidation process at neutral pH, driven by microbes can couple to carbon assimilation process in iron-rich freshwater and marine environments; however, few studies report such coupled processes in paddy soil of the critical zone in South China. In this study, rhizosphere soil from flooded paddy field was used as the inoculum to enrich the microaerophilic Fe(II)-oxidizing bacteria (FeOB) in gradient tubes with different Fe(II) substrates (FeS and FeCO3) and 13C-biocarbonate as inorganic carbon source to track the carbon assimilation. Kinetics of Fe(II) oxidation and biomineralization were analyzed, and the composition and abundance of the microbial community were profiled using 16S rRNA gene-based high-throughput sequencing. Results showed that microbial cell bands were formed 0.5–1.0 cm below the medium surface in the inoculated tubes with Fe(II) substances, while no cell band was found in the non-inocula controls. The protein concentrations in the cell bands reached the highest values at 18.7–22.9 mg mL-1 on 6 d in the inocula tubes with Fe(II) substrates. A plateau of the yields of 13C-biocarbonate incorporation was observed during 6–15 d at 0.44–0.54% and 1.61–1.98% in the inocula tubes with FeS and FeCO3, respectively. The inocula tube with FeS showed a higher Fe(II) oxidation rate of 0.156 mmol L-1 d-1 than that with FeCO3 (0.106 mmol L-1 d-1). Analyses of X-ray diffraction and scanning electron microscopy with energy-dispersive X-ray spectroscopy revealed that amorphous iron oxide was formed on the surface of rod-shaped bacteria after Fe(II) oxidation. Relative to the agar only control, the abundances of Clostridium and Pseudogulbenkiania increased in the inocula tube with FeS, while those of Vogesella, Magnetospirillum, Solitalea, and Oxalicibacterium increased in the inocula tube with FeCO3, all of which might be the potential microaerophilic FeOB in paddy soil. The findings in this study suggest that microbes that couple microaerobic Fe(II) oxidation to carbon assimilation existed in the paddy soil, which provides an insight into the iron-carbon coupling transformation under microaerobic conditions in the critical zone of the iron-rich red soil.


Microaerobic Fe(II) oxidation Paddy soil Carbon assimilation Microorganism 



We sincerely thank the reviewers for their constructive comments and suggestions. This work was supported by the National Natural Science Foundation of China (Grant Nos. 41571130052, 41701295 & 41271263), and the Guangdong Natural Science Funds for Distinguished Young Scholars (Grant No. 2017A030306010).


  1. Bai J F, Lin X G, Dai J, Hua J F, Qin H, Hu J L, Wang Y M, Zhang C L, Wang J W, Yuan W Y. 2015. Improving arsenic mobility concentration from As-polluted soils by the functional strains. Sci China Earth Sci, 58: 1420–1426CrossRefGoogle Scholar
  2. Bates S T, Berg-Lyons D, Caporaso J G, Walters W A, Knight R, Fierer N. 2011. Examining the global distribution of dominant archaeal populations in soil. ISME J, 5: 908–917CrossRefGoogle Scholar
  3. Bazylinski D A, Frankel R B. 2004. Magnetosome formation in prokaryotes. Nat Rev Microbiol, 2: 217–230CrossRefGoogle Scholar
  4. Benz M, Brune A, Schink B. 1998. Anaerobic and aerobic oxidation of ferrous iron at neutral pH by chemoheterotrophic nitrate-reducing bacteria. Arch Microbiol, 169: 159–165CrossRefGoogle Scholar
  5. Borch T, Kretzschmar R, Kappler A, Cappellen P V, Ginder-Vogel M, Voegelin A, Campbell K. 2009. Biogeochemical redox processes and their impact on contaminant dynamics. Environ Sci Technol, 44: 15–23CrossRefGoogle Scholar
  6. Chen X P, Zhu Y G, Xia Y, Shen J P, He J Z. 2008. Ammonia-oxidizing archaea: Important players in paddy rhizosphere soil? Environ Microbiol, 10: 1978–1987CrossRefGoogle Scholar
  7. Chen Y, Li F, Li X. 2016. Diversity and biomineralization of microaerophilic iron-oxidizing bacteria in paddy soil (in Chinese). Ecol Environ Sci, 25: 547–554Google Scholar
  8. Edwards K J, Rogers D R, Wirsen C O, McCollom T M. 2003. Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic alpha- and gamma-proteobacteria from the deep sea. Appl Environ Microbiol, 69: 2906–2913CrossRefGoogle Scholar
  9. Emerson D. 2012. Biogeochemistry and microbiology of microaerobic Fe (II) oxidation. Biochm Soc Trans, 40: 1211–1216CrossRefGoogle Scholar
  10. Emerson D, Fleming E J, McBeth J M. 2010. Iron-oxidizing bacteria: An environmental and genomic perspective. Annu Rev Microbiol, 64: 561–583CrossRefGoogle Scholar
  11. Emerson D, Floyd M M. 2005. Enrichment and isolation of iron-oxidizing bacteria at neutral pH. Methods Enzymol, 397: 112–123CrossRefGoogle Scholar
  12. Emerson D, Moyer C L. 1997. Isolation and characterization of novel ironoxidizing bacteria that grow at circumneutral pH. Appl Environ Microbiol, 63: 4784–4792Google Scholar
  13. Emerson D, Weiss J V. 2004. Bacterial iron oxidation in circumneutral freshwater habitats: Findings from the field and the laboratory. Geomicrobiol J, 21: 405–414CrossRefGoogle Scholar
  14. Emerson D, Weiss J V, Megonigal J P. 1999. Iron-oxidizing bacteria are associated with ferric hydroxide precipitates (Fe-plaque) on the roots of wetland plants. Appl Environ Microbiol, 65: 2758–2761Google Scholar
  15. Ge T, Wu X, Chen X, Yuan H, Zou Z, Li B, Zhou P, Liu S, Tong C, Brookes P, Wu J. 2013. Microbial phototrophic fixation of atmospheric CO2 in China subtropical upland and paddy soils. Geochim Cosmochim Acta, 113: 70–78CrossRefGoogle Scholar
  16. Geelhoed J S, Sorokin D Y, Epping E, Tourova T P, Banciu H L, Muyzer G, Stams A J M, van Loosdrecht M C M. 2009. Microbial sulfide oxidation in the oxic-anoxic transition zone of freshwater sediment: Involvement of lithoautotrophic Magnetospirillum strain J10. FEMS Microbiol Ecol, 70: 54–65CrossRefGoogle Scholar
  17. Ishii S, Joikai K, Otsuka S, Senoo K, Okabe S. 2016 Denitrification and nitrate-dependent Fe(II) oxidation in various Pseudogulbenkiania strains. Microbes Environ, 31: 293–298CrossRefGoogle Scholar
  18. Joshi N A, Fass J N. 2011. Sickle: A sliding-window, adaptive, qualitybased trimming tool for FastQ files (Version 1.33). Citeulike: 13260426Google Scholar
  19. Kappler A, Newman D K. 2004. Formation of Fe(III)-minerals by Fe(II)- oxidizing photoautotrophic bacteria. Geochim Cosmochim Acta, 68: 1217–1226CrossRefGoogle Scholar
  20. Kunapuli U, Lueders T, Meckenstock R U. 2007. The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation. ISME J, 1: 643–653CrossRefGoogle Scholar
  21. Laufer K, Nordhoff M, Røy H, Schmidt C, Behrens S, Jørgensen B B, Kappler A. 2015. Coexistence of microaerophilic, nitrate-reducing, and phototrophic Fe(II) oxidizers and Fe(III) reducers in coastal marine sediment. Appl Environ Microbiol, 82: 1433–1447CrossRefGoogle Scholar
  22. Li F, Wang X, Li Y, Liu C, Zeng F, Zhang L, Hao M, Ruan H. 2008. Enhancement of the reductive transformation of pentachlorophenol by polycarboxylic acids at the iron oxide-water interface. J Colloid Interface Sci, 321: 332–341CrossRefGoogle Scholar
  23. Li J, Li Y L. 2014. Simulation of the impacts of diagenesis or low-grade metamorphism on neutrophilic microaerobic Fe(II)-oxidizing biofilm. Sci China Earth Sci, 57: 1021–1029CrossRefGoogle Scholar
  24. Li X, Zhang W, Liu T, Chen L, Chen P, Li F. 2016. Changes in the composition and diversity of microbial communities during anaerobic nitrate reduction and Fe(II) oxidation at circumneutral pH in paddy soil. Soil Biol Biochem, 94: 70–79CrossRefGoogle Scholar
  25. Lin C, Larsen E I, Nothdurft L D, Smith J J. 2012. Neutrophilic, microaerophilic Fe(II)-oxidizing bacteria are ubiquitous in aquatic habitats of a subtropical Australian coastal catchment (ubiquitous FeOB in catchment aquatic habitats). Geomicrobiol J, 29: 76–87CrossRefGoogle Scholar
  26. Liu C S, Wei Z Q, Li F B, Dong J. 2016. The Fe atom exchange mechanism in Fe(II)-induced recrystallization of hematite: Stable Fe isotope tracing study (in Chinese). Sci China Earth Sci, 46: 1542–1553Google Scholar
  27. Long X E, Yao H, Wang J, Huang Y, Singh B K, Zhu Y G. 2015. Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils. Environ Sci Technol, 49: 7152–7160CrossRefGoogle Scholar
  28. Lu R K. 2000. Methods for Chemical Analysis of Soil Agriculture. Beijing: China Agricultural Science and Technology PressGoogle Scholar
  29. Lyons T W, Reinhard C T. 2009. Early Earth: Oxygen for heavy-metal fans. Nature, 461: 179–181CrossRefGoogle Scholar
  30. Melton E D, Swanner E D, Behrens S, Schmidt C, Kappler A. 2014. The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle. Nat Rev Microbiol, 12: 797–808CrossRefGoogle Scholar
  31. Miot J, Benzerara K, Morin G, Kappler A, Bernard S, Obst M, Férard C, Skouri-Panet F, Guigner J M, Posth N, Galvez M, Brown Jr. G E, Guyot F. 2009. Iron biomineralization by anaerobic neutrophilic iron-oxidizing bacteria. Geochim Cosmochim Acta, 73: 696–711CrossRefGoogle Scholar
  32. Muehe E M, Scheer L, Daus B, Kappler A. 2013. Fate of arsenic during microbial reduction of biogenic versus abiogenic As-Fe(III)-mineral coprecipitates. Environ Sci Technol, 47: 8297–8307Google Scholar
  33. Murage E W, Voroney P R. 2007. Modification of the original chloroform fumigation extraction technique to allow measurement of δ13C of soil microbial biomass carbon. Soil Biol Biochem, 39: 1724–1729CrossRefGoogle Scholar
  34. Neubauer S C, Emerson D, Megonigal J P. 2002. Life at the energetic edge: Kinetics of circumneutral iron oxidation by lithotrophic iron-oxidizing bacteria isolated from the wetland-plant rhizosphere. Appl Environ Microbiol, 68: 3988–3995CrossRefGoogle Scholar
  35. Ortiz M, Legatzki A, Neilson J W, Fryslie B, Nelson W M, Wing R A, Soderlund C A, Pryor B M, Maier R M. 2014. Making a living while starving in the dark: Metagenomic insights into the energy dynamics of a carbonate cave. ISME J, 8: 478–491CrossRefGoogle Scholar
  36. Pantke C, Obst M, Benzerara K, Morin G, Ona-Nguema G, Dippon U, Kappler A. 2012. Green Rust Formation during Fe(II) Oxidation by the Nitrate-Reducing Acidovorax sp. Strain BoFeN1. Environ Sci Technol, 46: 1439–1446CrossRefGoogle Scholar
  37. Price M N, Dehal P S, Arkin A P. 2009. FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol, 26: 1641–1650CrossRefGoogle Scholar
  38. Qiao J T, Li X M, Hu M, Li F B, Young L Y, Sun W M, Huang W, Cui J H. 2018. Transcriptional activity of arsenic-reducing bacteria and genes regulated by lactate and biochar during arsenic transformation in flooded paddy soil. Environ Sci Technol, 52: 61–70CrossRefGoogle Scholar
  39. Raiswell R, Canfield D E. 2011. The iron biogeochemical cycle past and present. Geochem Persp, 1: 1–220CrossRefGoogle Scholar
  40. Rameshkumar N, Lang E, Tanaka N. 2016. Description of Vogesella oryzae sp. nov., isolated from the rhizosphere of saline tolerant pokkali rice. Syst Appl Microbiol, 39: 20–24Google Scholar
  41. Ratering S, Schnell S. 2001. Nitrate-dependent iron(II) oxidation in paddy soil. Environ Microbiol, 3: 100–109CrossRefGoogle Scholar
  42. Sahin N, Portillo M C, Kato Y, Schumann P. 2009. Description of Oxalicibacterium horti sp. nov. and Oxalicibacterium faecigallinarum sp. nov., new aerobic, yellow-pigmented, oxalotrophic bacteria. FEMS Microbiol Lett, 296: 198–202Google Scholar
  43. Sobolev D, Roden E. 2004. Characterization of a neutrophilic, chemolithoautotrophic Fe(II)-oxidizing ß-proteobacterium from freshwater wetland sediments. Geomicrobiol J, 21: 1–10CrossRefGoogle Scholar
  44. Spring S. 2006. The Genera Leptothrix and Sphaerotilus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K H, Stackebrandt E, eds. The Prokaryotes. New York: Springer. 758–777Google Scholar
  45. Straub K L, Benz M, Schink B, Widdel F. 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl Environ Microbiol, 62: 1458–1460Google Scholar
  46. Tao L, Zhang W, Li H, Li F B, Yu W M, Chen M J. 2012. Effect of pH and weathering indices on the reductive transformation of 2-nitrophenol in south China. Soil Sci Soc Am J, 76: 1579–1591CrossRefGoogle Scholar
  47. Trouwborst R E, Johnston A, Koch G, Luther Ii i G W, Pierson B K. 2007. Biogeochemistry of Fe(II) oxidation in a photosynthetic microbial mat: Implications for Precambrian Fe(II) oxidation. Geochim Cosmochim Acta, 71: 4629–4643CrossRefGoogle Scholar
  48. Wang J, Muyzer G, Bodelier P L E, Laanbroek H J. 2009. Diversity of iron oxidizers in wetland soils revealed by novel 16S rRNA primers targeting Gallionella-related bacteria. ISME J, 3: 715–725CrossRefGoogle Scholar
  49. Wang Q, Garrity G M, Tiedje J M, Cole J R. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol, 73: 5261–5267CrossRefGoogle Scholar
  50. Weber K A, Achenbach L A, Coates J D. 2006. Microorganisms pumping iron: Anaerobic microbial iron oxidation and reduction. Nat Rev Microbiol, 4: 752–764CrossRefGoogle Scholar
  51. Weiss J V, Rentz J A, Plaia T, Neubauer S C, Merrill-Floyd M, Lilburn T, Bradburne C, Megonigal J P, Emerson D. 2007. Characterization of neutrophilic Fe(II)-oxidizing bacteria isolated from the rhizosphere of wetland plants and description of Ferritrophicum radicicola gen. nov. sp. nov., and Sideroxydans paludicola sp. nov. Geomicrobiol J, 24: 559–570Google Scholar
  52. Weon H Y, Kim B Y, Lee C M, Hong S B, Jeon Y A, Koo B S, Kwon S W. 2009. Solitalea koreensis gen. nov., sp. nov. and the reclassification of [Flexibacter] canadensis as Solitalea canadensis comb. nov. Int J Syst Evol Microbiol, 59: 1969–1975CrossRefGoogle Scholar
  53. Werner R A, Brand W A. 2001. Referencing strategies and techniques in stable isotope ratio analysis. Rapid Commun Mass Spectrom, 15: 501–519CrossRefGoogle Scholar
  54. Wrighton K C, Thomas B C, Sharon I, Miller C S, Castelle C J, Ver-Berkmoes N C, Wilkins M J, Hettich R L, Lipton M S, Williams K H, Long P E, Banfield J F. 2012. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science, 337: 1661–1665CrossRefGoogle Scholar
  55. Wu J, Joergensen R G, Pommerening B, Chaussod R, Brookes P C. 1990. Measurement of soil microbial biomass C by fumigation-extraction— An automated procedure. Soil Biol Biochem, 22: 1167–1169CrossRefGoogle Scholar
  56. Xu Y, He Y, Feng X, Liang L, Xu J, Brookes P C, Wu J. 2014. Enhanced abiotic and biotic contributions to dechlorination of pentachlorophenol during Fe(III) reduction by an iron-reducing bacterium Clostridium beijerinckii Z. Sci Total Environ, 473–474: 215–223CrossRefGoogle Scholar
  57. Zhao L, Dong H, Kukkadapu R, Agrawal A, Liu D, Zhang J, Edelmann R E. 2013. Biological oxidation of Fe(II) in reduced nontronite coupled with nitrate reduction by Pseudogulbenkiania sp. Strain 2002. Geochim Cosmochim Acta, 119: 231–247CrossRefGoogle Scholar
  58. Zumsteg A, Schmutz S, Frey B. 2013. Identification of biomass utilizing bacteria in a carbon-depleted glacier forefield soil by the use of 13C DNA stable isotope probing. Environ Microbiol Rep, 5: 424–437CrossRefGoogle Scholar

Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Xiaomin Li
    • 1
    • 2
  • Shan Mou
    • 2
    • 3
  • Yating Chen
    • 2
    • 4
  • Tongxu Liu
    • 2
  • Jun Dong
    • 2
  • Fangbai Li
    • 2
    Email author
  1. 1.SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical ChemistrySouth China Normal UniversityGuangzhouChina
  2. 2.Guangdong Key Laboratory of Integrated Agri-Environment Pollution Control and ManagementGuangdong Institute of Eco-Environmental Science & TechnologyGuangzhouChina
  3. 3.School of Micro-Electronics and Solid-State ElectronicsUniversity of Electronic Science and Technology of ChinaChengduChina
  4. 4.Institute for Disaster Management and ReconstructionSichuan University-Hong Kong Polytechnic UniversityChengduChina

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