Biogenic Mn oxide minerals coating in a subsurface granite environment

Chemical Geology

Volumn 322-323, Issue , 2012, Pages 181-191

  Miller, A Z ^a   Dionisio A ^a   Sequeira Braga, M A ^b   Hernandez Marine M ^c   Afonso, M J ^d,i   Muralha, V S F ^e   Herrera, L K ^f   Raabe, J ^g   Fernandez Cortes, A ^h   Cuezva, S ^h   Hermosin, B ^f   Sanchez Moral, S ^h   Chamine H ^d   Saiz Jimenez, C ^f  

^a INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^b UNIVERSITY OF MINHO   (Portugal)

^c UNIVERSITY OF BARCELONA   (Spain)

^d INSTITUTO SUPERIOR DE ENGENHARIA DO PORTO   (Portugal)

^e UNIVERSIDADE NOVA DE LISBOA   (Portugal)

^f INSTITUTO DE RECURSOS NATURALES Y AGROBIOLOGÍA DE SEVILLA   (Spain)

^g PAUL SCHERRER INSTITUTE   (Switzerland)

^h MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

ⁱ Centro GeoBioTec UA   (Portugal)

Author keywords

Biominerals; Birnessite; Black coatings; Granite; Subsurface environment; Todorokite

Indexed keywords

BACTERIAL COMMUNITY; BIOMINERALS; BIRNESSITE; EXTRA-CELLULAR POLYMERIC SUBSTANCES; EXTRACELLULAR; FTIR; LOW DEGREE; MN OXIDES; NANO-DIMENSIONS; PORTUGAL; SPRING WATER; SUBSURFACE ENVIRONMENT; TEM-EDS; TODOROKITES; XRD;

BIOACTIVITY; BLACK COATINGS; GROUNDWATER; MANGANESE; MANGANESE OXIDE; OXIDE MINERALS;

GRANITE;

BEDROCK; BIOGENIC MINERAL; BIOMINERALIZATION; BIRNESSITE; CRYSTALLINITY; GRANITE; MANGANESE OXIDE; TODOROKITE; TRACE ELEMENT;

PORTO [PORTUGAL]; PORTUGAL;

BACTERIA (MICROORGANISMS);

EID: 84864485901     PISSN: 00092541     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemgeo.2012.07.005     Document Type: Article

References (79)

1. Afonso M.J., Marques J.M., Guimarães L., Costa I., Teixeira J., Seabra C., Rocha F., Guilhermino L., Chaminé H.I. Urban hydrogeological mapping of the Porto area (NW Portugal): a geoenvironmental perspective. IAH Special Publications 2007, 10:389-404. Taylor & Francis CRC Press, London.
2. Afonso M.J., Chaminé H.I., Marques J.M., Carreira P.M., Guimarães L., Guilhermino L., Gomes A., Fonseca P.E., Pires A., Rocha F. Environmental issues in urban groundwater systems: a multidisciplinary study of the Paranhos and Salgueiros spring waters, Porto (NW Portugal). Environmental Earth Science 2010, 61:379-392.
3. Almeida A. Geology and the urban landscape: the granite of Oporto. Journal of the European Federation of Geologists 2006, 21:4-8.
4. Banerjee R., Iyer S.D. Biogenic influence on the growth of ferromanganese micronodules in the Central Indian Basin. Marine Geology 1991, 97:413-421.
5. Bargar J.R., Tebo B.M., Bergmann U., Webb S.M., Glatzel P., Chiu V.Q., Villalobos M. Biotic and abiotic products of Mn(II) oxidation by spores of the marine Bacillus sp. strain SG-1. American Mineralogist 2005, 90:143-154.
6. Bargar J.R., Fuller C.C., Marcus M.A., Brearley A.J., De la Rosa M.P., Webb S.M., Caldwell W.A. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ. Geochimica et Cosmochimica Acta 2009, 73:889-910.
7. Barton H.A., Northup D.E. Geomicrobiology in cave environments: past, current and future perspectives. Journal of Cave and Karst Studies 2007, 69:163-178.
8. Bäuerlein E. Biomineralization: From Biology to Biotechnology and Medical Application 2000, Wiley-VHC Verlag GmbH & Co. KgaA, Weinheim, Germany.
9. Bäuerlein E. Biomineralization: Progress in biology, molecular biology and application 2004, Wiley-VHC Verlag GmbH & Co. KgaA, Weinheim, Germany.
10. Begonha A. Meteorização do granito e deterioração da pedra em monumentos e edifícios da cidade do Porto 1997, PhD Thesis, Univ. Minho, Braga, 393 pp.
11. Begonha A., Sequeira Braga M.A. Weathering of the Oporto granite: geotechnical and physical properties. Catena 2002, 49:57-76.
12. Bilinski H., Giovanoli R., Usui A., Hanzel D. Characterization of Mn oxides in cemented streambed crusts from Pinal Creek, Arizona, USA, and in hot-spring deposits from Yuno-Taki Falls, Hokkaido, Japan. American Mineralogist 2002, 87:580-591.
13. Brindley G.W., Brown G. Crystal structures of clay minerals and their identification. Monograph 1980, 5. Mineralogical Society, London.
14. 2+ oxidation in Pseudomonas putida GB-1. Applied and Environmental Microbiology 1999, 65:1762-1768.
15. Chalmin E., Vignaud C., Salomon H., Farges F., Susini J., Menu M. Minerals discovered in paleolithic black pigments by transmission electron microscopy and micro-X-ray absorption near-edge structure. Applied Physics A: Materials Science and Processing 2006, 83:213-218.
16. Chaminé H.I., Afonso M.J., Robalo P.M., Rodrigues P., Cortez C., Monteiro Santos F.A., Plancha J.P., Fonseca P.E., Gomes A., Devy-Vareta N.F., Marques J.M., Lopes M.E., Fontes G., Pires A., Rocha F. Urban speleology applied to groundwater and geo-engineering studies: underground topographic surveying of the ancient Arca D'Água galleries catchworks (Porto, NW Portugal). International Journal of Speleology 2010, 39:1-14.
17. Chan C.S., De Stasio G., Welch S.A., Girasole M., Frazer B.H., Nesterova M.V., Fakra S., Banfield J.F. Microbial polysaccharides template assembly of nanocrystal fibers. Science 2004, 303:1656-1658.
18. Coentro S., Mimoso J.M., Lima A.M., Silva A.S., Pais A.N., Muralha V.S.F. Multi-analytical identification of pigments and pigment mixtures used in 17th century Portuguese azulejos. Journal of the European Ceramic Society 2012, 32:37-48.
19. Dick G.J., Tebo B.M. Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume. Environmental Microbiology 2010, 12:1334-1347.
20. Dick G.J., Clement B.G., Webb S.M., Fodrie F.J., Bargar J.R., Tebo B.M. Enzymatic microbial Mn(II) oxidation and Mn biooxide production in the Guaymas Basin deep-sea hydrothermal plume. Geochimica et Cosmochimica Acta 2009, 73:6517-6530.
21. Dorn R.I. Rock coatings. Developments in Earth Surface Processes 1998, 6. Elsevier, The Netherlands.
22. Fein J.B. Quantifying the effects of bacteria on adsorption reactions in water-rock systems. Chemical Geology 2000, 169:265-280.
23. Fein J.B. Thermodynamic modeling of metal adsorption onto bacterial cell walls: current challenges. Advances in Agronomy 2006, 90:179-202.
24. Fein J.B., Scott S., Rivera N. The effect of Fe on Si adsorption by Bacillus subtilis cell walls: insights into non-metabolic bacterial precipitation of silicate minerals. Chemical Geology 2002, 182:265-273.
25. Feng X.H., Zhu M., Ginder-Vogel M., Ni C., Parikh S.J., Sparks D.L. Formation of nano-crystalline todorokite from biogenic Mn oxides. Geochimica et Cosmochimica Acta 2010, 74:3232-3245.
26. Fontes, A., 1908. Contribuição para a hygiene do Porto: analyse sanitaria do seu abastecimento em água potável. I. Estudo dos mananciais de Paranhos e Salgueiros [Contributions to the hygiene of the Porto city: sanitary analysis for the potable water supply. I. Study of the Paranhos and Salgueiros springs]. PhD thesis, Escola Médico-Cirúrgica do Porto, Portugal, 190p.
27. Fortin D., Langley S. Formation and occurrence of biogenic iron-rich minerals. Earth-Science Reviews 2005, 72:1-19.
28. Francis C.A., Tebo B.M. Enzymatic manganese (II) oxidation by metabolically dormant spores of diverse Bacillus species. Applied and Environmental Microbiology 2002, 68:874-880.
29. Frankel R.B., Bazylinski D.A. Biologically induced mineralization by bacteria. Reviews in Mineralogy and Geochemistry 2003, 54:95-114.
30. Frierdich A.J., Hasenmueller E.A., Catalano J.G. Composition and structure of nanocrystalline Fe and Mn oxide cave deposits: implications for trace element mobility in karst systems. Chemical Geology 2011, 284:82-96.
31. Gázquez F., Calaforra J.M., Forti P. Black Mn-Fe crusts as markers of abrupt palaeoenvironmental changes in El Soplao Cave (Cantabria, Spain). International Journal of Speleology 2011, 40:163-169.
32. Ghiorse W.C., Hirsch P. An ultrastructural study of iron and manganese deposition associated with extracellular polymers of Pedomicrobium-like budding bacteria. Archives of Microbiology 1979, 123:213-226.
33. Grangeon S., Lanson B., Miyata N., Tani Y., Manceau A. Structure of nanocrystalline phyllomanganates produced by freshwater fungi. American Mineralogist 2010, 95:1608-1611.
34. Haas J.R., Dichristina T.J., Wade R. Thermodynamics of U(VI) sorption onto Shewanella putrefaciens. Chemical Geology 2001, 180:33-54.
35. Hitchcock A.P. aXis2000: analysis of X-ray images and spectra http://unicorn.mcmaster.ca/aXis2000.html.
36. Hitchcock A.P., Dynes J.J., Lawrence J.R., Obst M., Swerhone G.D., Korber D.R., Leppard G.G. Soft X-ray Spectromicroscopy of nickel sorption in a natural river biofilm. Geobiology 2009, 7:432-453.
37. Jones B. Cave pearls - The integrated product of abiogenic and biogenic processes. Journal of Sedimentary Research 2009, 79:689-710.
38. Julien C.M., Massot M., Baddour-Hadjean R., Franger S., Bach S., Pereira-Ramos J.P. Raman spectra of birnessite manganese dioxides. Solid State Ionics 2003, 159:345-356.
39. Julien C.M., Massot M., Poinsignon C. Lattice vibrations of manganese oxides Part I. Periodic structures. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2004, 60:689-700.
40. Lack J.G., Chaudhuri S.K., Kelly S.D., Kemmer K.M., O'Connor S.M., Coates J.D. Immobilization of radionuclides and heavy metals through anaerobic bio-oxidation of Fe(II). Applied and Environmental Microbiology 2002, 68:2704-2710.
41. Learman D.R., Voelker B.M., Vazquez-Rodriguez A.I., Hansel C.M. Formation of manganese oxides by bacterially generated superoxide. Nature Geoscience 2011, 4:95-98.
42. Mann S. Biomineralization: principles and concepts in bioinorganic materials chemistry 2001, Oxford University Press, New York.
43. Melim L.A., Northup D.E., Spilde M.N., Jones B., Boston P.J., Bixby R.J. Reticulated filaments in cave pool speleothems: microbe or mineral?. Journal of Cave and Karst Studies 2008, 70:135-141.
44. Miller, A.Z., Hernández-Mariné, M., Jurado, V., Dionísio, A., Barquinha, P., Fortunato, E., Afonso, M.J., Chaminé, H.I., Saiz-Jimenez, C., in press. Enigmatic reticulated filaments in subsurface granite. Environmental Microbiology Reports.
45. Miyata N., Tani Y., Maruo K., Tsuno H., Sakata M., Iwahori K. Manganese(IV) oxide production by Acremonium sp. strain KR21-2 and extracellular Mn(II) oxidase activity. Applied and Environmental Microbiology 2006, 72:6467-6473.
46. 2 and Mn(II) species in aqueous solutions. Geochimica et Cosmochimica Acta 2005, 69:35-48.
47. Northup D.E., Dahm C.N., Melim L.A., Spilde M.N., Crossey L.J., Lavoie K.H., Mallory L.M., Boston P.J., Cunningham K.I., Barns S.M. Evidence for geomicrobiological interactions in Guadalupe caves. Journal of Cave and Karst Studies 2000, 62:80-90.
48. Northup D.E., Barns S.M., Yu L.E., Spilde M.N., Schelble R.T., Dano K.E., Crossey L.J., Connolly C.A., Boston P.J., Natvig D.O., Dahm C.N. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environmental Microbiology 2003, 5:1071-1086.
49. Oaki Y., Imai H. One-pot synthesis of manganese oxide nanosheets in aqueous solution: chelation-mediated parallel control of reaction and morphology. Angewandte Chemie International Edition 2007, 46:4951-4955.
50. Onac B.P., Pedersen R.B., Tysseland M. Presence of rare-earth elements in black ferromanganese coatings from Vântului Cave. Journal of Cave and Karst Studies 1997, 59:128-131.
51. Palmer A.N. Cave Geology 2007, Cave Books, Dayton.
52. Potter R.M., Rossman G.R. The tetravalent manganese oxides: identification, hydration, and structural relationships by infrared spectroscopy. American Mineralogist 1979, 64:1199-1218.
53. Raabe J., Tzvetkov G., Flechsig U., Boge M., Jaggi A., Sarafimov B., Vernooij M.G.C., Huthwelker T., Ade H., Kilcoyne D., Tyliszczak T., Fink R.H., Quitmann C. Pollux: a new facility for soft X-ray spectromicroscopy at the Swiss light source. The Review of Scientific Instruments 2008, 79:113704. 10.1063/1.3021472.
54. Ridge J.P., Lin M., Larsen E.I., Fegan M., McEwan A.G., Sly L.I. A multicopper oxidase is essential for manganese oxidation and laccase-like activity in Pedomicrobium sp. ACM 3067. Environmental Microbiology 2007, 9:944-953.
55. Rosson R.A., Nealson K.H. Manganese binding and oxidation by spores of a marine bacillus. Journal of Bacteriology 1982, 174:575-585.
56. Sanchez-Moral S., Fernandez-Cortes A., Cuezva S., Cañaveras J.C., Correcher V., Miller A.Z., Dionisio A., Marques J.M., Saiz-Jimenez C., Afonso M.J., Chaminé H.I., Furio M., Garcia-Guinea J. Uranyl-evansites from Porto (Northwest Portugal) and Galicia (Northwest Spain): Structure and assignment of spectra catholuminescence and Raman bands. Spectroscopy Letters 2011, 44:511-515.
57. Santelli C.M., Pfister D., Lazarus D., Sun L., Burgos W.D., Hansel C.M. Promotion of Mn(II) oxidation and remediation of coal mine drainage in passive treatment systems by diverse fungal and bacterial communities. Applied and Environmental Microbiology 2010, 76:4871-4875.
58. Santelli C.M., Webb S.M., Dohnalkova A.C., Hansel C.M. Diversity of Mn oxides produced by Mn(II)-oxidizing fungi. Geochimica et Cosmochimica Acta 2011, 75:2762-2776.
59. Saratovsky I., Wightman P.G., Pasten P.A., Gaillard J.F., Poeppelmeier K.R. Manganese oxides: parallels between abiotic and biotic structures. Journal of the American Chemical Society 2006, 128:11188-11198.
60. Saratovsky I., Gurr S., Hayward M. The structure of manganese oxide formed by the fungus Acremonium sp. Strain KR21-2. Geochimica et Cosmochimica Acta 2009, 73:3291-3300.
61. Skinner H.C.W., Jahren A.H. Biomineralization. Treatise on Geochemistry 2003, 8:117-184.
62. 2 by extracellular polysaccharides of Pedomicrobium manganicum. Applied and Environmental Microbiology 1990, 56:2791-2794.
63. Spilde M.N., Northup D.E., Boston P.J., Schelble R.T., Dano K.E., Crossey L.J., Dahm C.N. Geomicrobiology of cave ferromanganese deposits: a field and laboratory investigation. Geomicrobiology Journal 2005, 22:99-116.
64. Tan H., Zhang G., Heaney P.J., Webb S.M., Burgos W.D. Characterization of manganese oxide precipitates from Appalachian coal mine drainage treatment systems. Applied Geochemistry 2010, 25:389-399.
65. Tazaki K. Clays, microorganisms, and biomineralization. Handbook of clay science 2006, 477-497. Elsevier, Amsterdam. F. Bergaya, B.K.G. Theng, G. Lagaly (Eds.).
66. Tebo B.M., Ghiorse W.C., van Waasbergen L.G., Siering P.L., Caspi R. Bacterially mediated mineral formation: Insights into manganese (II) oxidation from molecular genetic and biochemical studies. Reviews in Mineralogy 1997, 35:225-266.
67. Tebo B.M., Bargar J.R., Clement B.G., Dick D.J., Murray K.J., Parker D., Verity R., Webb S.M. Biogenic manganese oxides: properties and mechanisms of formation. Annual Review of Earth and Planetary Sciences 2004, 32:287-328.
68. Tebo B.M., Johnson H.A., McCarthy J.K., Templeton A.S. Geomicrobiology of manganese(II) oxidation. Trends in Microbiology 2005, 13:421-428.
69. Toner B., Fakra S., Villalobos M., Warwick T., Sposito G. Spatially resolved characterization of biogenic manganese oxide production within a bacterial biofilm. Applied and Environmental Microbiology 2005, 71:1300-1310.
70. Toner B., Manceau A., Webb S.M., Sposito G. Zinc sorption to biogenic hexagonal-birnessite particles within a hydrated bacterial biofilm. Geochimica et Cosmochimica Acta 2006, 70:27-43.
71. Vidal Romaní J.R., Vaqueiro M.R. Types of granite cavities and associated speleothems: genesis and evolution. Nature Conservation 2005, 63:41-46.
72. Villalobos M., Toner B., Bargar J., Sposito G. Characterization of the manganese oxide produced by Pseudomonas putida strain MnB1. Geochimica et Cosmochimica Acta 2003, 67:2649-2662.
73. Villalobos M., Bargar J., Sposito G. Trace metal retention on biogenic manganese oxide nanoparticles. Elements 2005, 1:223-226.
74. Wang W., Shao Z., Liu Y., Wang G. Removal of multi-heavy metals using biogenic manganese oxides generated by a deep-sea sedimentary bacterium - Brachybacterium sp. strain Mn32. Microbiology 2009, 155:1989-1996.
75. Webb S.M., Dick G.J., Bargar J.R., Tebo B.M., Fridovich I. Evidence for the presence of Mn(III) intermediates in the bacterial oxidation of Mn(II). Proceedings of the National Academy of Sciences of the United States of America 2005, 102:5558-5563.
76. Webb S.M., Tebo B.M., Bargar J.R. Structural characterization of biogenic Mn oxides produced in seawater by the marine Bacillus sp. strain SG-1. American Mineralogist 2005, 90:1342-1357.
77. Weiner S., Dove P.M. An overview of biomineralization processes and the problem of the vital effect. Reviews in Mineralogy and Geochemistry 2003, 54:1-29.
78. White W.B., Vito C., Scheetz B.E. The mineralogy and trace chemistry of black manganese oxide deposits from caves. Journal of Cave and Karst Studies 2009, 71:136-143.
79. Wu S.C., Luo Y.M., Cheung K.C., Wong M.H. Influence of bacteria on Pb and Zn speciation, mobility and bioavailability in soil: a laboratory study. Environmental Pollution 2006, 144:765-773.