Variable effects of labile carbon on the carbon use of different microbial groups in black slate degradation

Geochimica et Cosmochimica Acta

Volumn 75, Issue 10, 2011, Pages 2557-2570

  Seifert, Anne Gret ^a   Trumbore, Susan ^a,b   Xu, Xiaomei ^b   Zhang, Dachung ^b   Kothe, Erika ^c   Gleixner, Gerd ^a  

^a MAX PLANCK INSTITUTE FOR BIOGEOCHEMISTRY   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOGEOCHEMICAL CYCLE; CARBON; DEGRADATION; FATTY ACID; FUNGUS; MASS BALANCE; MICROBIAL COMMUNITY; MICROORGANISM; PHOSPHOLIPID; SLATE; WEATHERING;

FUNGI; NEGIBACTERIA; POSIBACTERIA; SCHIZOPHYLLUM; SCHIZOPHYLLUM COMMUNE;

EID: 79955094170     PISSN: 00167037     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gca.2011.02.037     Document Type: Article

References (74)

1. Abadulla E., Robra K.H., Gubitz G.M., Silva L.M., Cavaco-Paulo A. Enzymatic decolorization of textile dyeing effluents. Text. Res. J. 2000, 70:409-414.
2. Abraham W.R., Hesse C., Pelz O. Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage. Appl. Environ. Microbiol. 1998, 64(11):4202-4209.
3. Abraham W.R., Hesse C. Isotope fractionations in the biosynthesis of cell components by different fungi: a basis for environmental carbon flux studies. FEMS Microbiol. Ecol. 2003, 46(1):121-128.
4. Andersson B.E., Welinder L., Olsson P.A., Olsson S., Henrysson T. Growth of inoculated white-rot fungi and their interactions with the bacterial community in soil contaminated with polycyclic aromatic hydrocarbons, as measured by phospholipid fatty acids. Bioresour. Technol. 2000, 73:29-36.
5. Bååth E. Thymidine and leucine incorporation in soil bacteria with different cell-size. Microb. Ecol. 1994, 27(3):267-278.
6. Bååth E., Anderson T.H. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol. Biochem. 2003, 35(7):955-963.
7. Ball A.S., Betts W.B., McCarthy A.J. Degradation of lignin-related compounds by actinomycetes. Appl. Environ. Microbiol. 1989, 55(6):1642-1644.
8. Bayman P., Radkar G.V. Transformation and tolerance of TNT (2, 4, 6-trinitrotoluene) by fungi. Int. Biodeterior. Biodegrad. 1997, 39:45-53.
9. Berner R.A. Models for carbon and sulfur cycles and atmospheric oxygen - application to paleozoic geologic history. Am. J. Sci. 1987, 287:177-196.
10. Berner R.A. Biogeochemical cycles of carbon and sulfur and their effect on atmospheric oxygen over phanerozoic time. Global Planet. Change 1989, 75(1-2):97-122.
11. Berrocal M.M., Rodriguez J., Ball A.S., PerezLeblic M.I., Arias M.E. Solubilisation and mineralisation of [C-14]lignocellulose from wheat straw by Streptomyces cyaneus CECT 3335 during growth in solid-state fermentation. Appl. Microbiol. Biotechnol. 1997, 48(3):379-384.
12. Bligh E.G., Dyer W.J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 1959, 37(8):911-917.
13. Bossio D.A., Scow K.M. Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization patterns. Microb. Ecol. 1998, 35(3):265-278.
14. Bouchez J., Beyssac O., Galy V., Gaillardet J., France-Lanord C., Maurice L., Moreira-Turcq P. Oxidation of petrogenic organic carbon in the Amazon floodplain as a source of atmospheric CO2. Geology 2010, 38:255-258.
15. Burke R.A., Molina M., Cox J.E., Osher L.J., Piccolo M.C. Stable carbon isotope ratio and composition of microbial fatty acids in tropical soils. J. Environ. Qual. 2003, 32(1):198-206.
16. Buswell J.A., Odier E. Lignin biodegradation. Crit. Rev. Biotechnol. 1987, 6:1-60.
17. Catcheside D.E.A., Mallett K.J. Solubilization of australian lignites by fungi and other microorganisms. Energy Fuels 1991, 5(11):141-145.
18. Chang S.B., Berner R.A. Humic substance formation via the oxidative weathering of coal. Environ. Sci. Technol. 1998, 32:2883-2886.
19. Chang S.B., Berner R.A. Coal weathering and the geochemical carbon cycle. Geochim. Cosmochim. Acta 1999, 63:3301-3310.
20. Colwell F.S., Onstott T.C., Delwiche M.E., Chandler D., Fredrickson J.K., Yao Q.J., McKinley J.P., Boone D.R., Griffiths R., Phelps T.J., Ringelberg D., White D.C., LaFreniere L., Balkwill D., Lehman R.M., Konisky J., Long P.E. Microorganisms from deep, high temperature sandstones: constraints on microbial colonization. FEMS Microbiol. Rev. 1997, 20(3-4):425-435.
21. Coplen T.B., Brand W.A., Gehre M., Groning M., Meijer H.A.J., Toman B., Verkouteren R.M. After two decades a second anchor for the VPDB delta C-13 scale. Rapid Commun. Mass Spectrom. 2006, 20:3165-3166.
22. De Nobili M., Contin M., Mondini C., Brookes P.C. Soil microbial biomass is triggered into activity by trace amounts of substrate. Soil Biol. Biochem. 2001, 33(9):1163-1170.
23. Fierer N., Schimel J.P., Holden P.A. Variations in microbial community composition through two soil depth profiles. Soil Biol. Biochem. 2003, 35:167-176.
24. Fischer C., Schmidt C., Bauer A., Gaupp R., Heide K. Mineralogical and geochemical alteration of low-grade metamorphic black slates due to oxidative weathering. Chem. Erde 2009, 69:127-142.
25. Frostegård A., Bååth E. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol. Fert. Soils 1996, 22(1-2):59-65.
26. Frostegård A., Bååth E., Tunlid A. Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty-acid analysis. Soil Biol. Biochem. 1993, 25(6):723-730.
27. Frostegård A., Tunlid A., Bååth E. Phospholipid fatty-acid composition, biomass, and activity of microbial communities from 2 soil types experimentally exposed to different heavy-metals. Appl. Environ. Microbiol. 1993, 59(11):3605-3617.
28. Gleixner G., Poirier N., Bol R., Balesdent J. Molecular dynamics of organic matter in a cultivated soil. Org. Geochem. 2002, 33:357-366.
29. Godden B., Ball A.S., Helvenstein P., McCarthy A.J., Penninckx M.J. Towards elucidation of the lignin degradation pathway in actinomycetes. J. Gen. Microbiol. 1992, 138:2441-2448.
30. Habekost M., Eisenhauer N., Scheu S., Steinbeiss S., Weigelt A., Gleixner G. Seasonal changes in the soil microbial community in a grassland plant diversity gradient four years after establishment. Soil Biol. Biochem. 2008, 40(10):2588-2595.
31. Hamer U., Marschner B. Priming effects of sugars, amino acids, organic acids and catechol on the mineralization of lignin and peat. J. Plant Nutr. Soil Sci. 2002, 165(3):261-268.
32. Hamer U., Marschner B., Brodowski S., Amelung W. Interactive priming of black carbon and glucose mineralisation. Org. Geochem. 2004, 35:823-830.
33. Hofrichter M., Bublitz F., Fritsche W. Fungal attack on coal II. Solubilization of low-rank coal by filamentous fungi. Fuel Process. Technol. 1997, 52(1-3):55-64.
34. Hofrichter M., Bublitz F., Fritsche W. Fungal attack on coal: I. Modification of hard coal by fungi. Fuel Process. Technol. 1997, 52(1-3):43-53.
35. Hofrichter M., Ziegenhagen D., Sorge S., Ullrich R., Bublitz F., Fritsche W. Degradation of lignite (low-rank coal) by ligninolytic basidiomycetes and their manganese peroxidase system. Appl. Microbiol. Biotechnol. 1999, 52(1):78-84.
36. in der Wiesche C., Martens R., Zadrazil F. Two-step degradation of pyrene by white-rot fungi and soil microorganisms. Appl. Microbiol. Biotechnol. 1996, 46:653-659.
37. Jaffe L.A., Peucker-Ehrenbrink B., Petsch S.T. Mobility of rhenium, platinum group elements and organic carbon during black slate weathering. Earth Planet Sci. Lett. 2002, 198(3-4):339-353.
38. Klamer M., Bååth E. Estimation of conversion factors for fungal biomass determination in compost using ergosterol and PLFA 18:2 omega 6,9. Soil Biol. Biochem. 2004, 36(1):57-65.
39. Kramer C., Gleixner G. Soil organic matter in soil depth profiles: distinct carbon preferences of microbial groups during carbon transformation. Soil Biol. Biochem. 2008, 40:425-433.
40. Kramer C., Gleixner G. Variable use of plant- and soil-derived carbon by microorganisms in agricultural soils. Soil Biol. Biochem. 2006, 38(11):3267-3278.
41. Kramer C., Trumbore S., Froberg M., Dozal L.M.C., Zhang D.C., Xu X.M., Santos G.M., Hanson P.J. Recent (< 4 year old) leaf litter is not a major source of microbial carbon in a temperate forest mineral soil. Soil Biol. Biochem. 2010, 42:1028-1037.
42. Kunert V. (1999) Die Frankenwalder Querzone - Entwicklung einer thermischen Anomalie im Saxothuringikum, Ph.D. Thesis, University of Giessen.
43. Kuzyakov Y., Bol R. Sources and mechanisms of priming effect induced in two grassland soils amended with slurry and sugar. Soil Biol. Biochem. 2006, 38(4):747-758.
44. Kuzyakov Y., Friedel J.K., Stahr K. Review of mechanisms and quantification of priming effects. Soil Biol. Biochem. 2000, 32:1485-1498.
45. Kuzyakov Y., Subbotina I., Chen H.Q., Bogomolova I., Xu X.L. Black carbon decomposition and incorporation into soil microbial biomass estimated by C-14 labeling. Soil Biol. Biochem. 2009, 41:210-219.
46. Lechevalier H., Lechevalier M.P. Chemotaxonomic use of lipids an overview. Microbial Lipids 1988, Vol. 1 Xviii+963p:869-902. Academic Press, London, England, UK; San Diego, California, USA; Illus.
47. Leckie S.E., Prescott C.E., Grayston S.J., Neufeld J.D., Mohn W.W. Characterization of humus microbial communities in adjacent forest types that differ in nitrogen availability. Microb. Ecol. 2004, 48:29-40.
48. Martens R., Zadrazil F. Screening of white-rot fungi for their ability to mineralize polycyclic aromatic hydrocarbons in soil. Folia Microbiol. 1998, 43:97-103.
49. Matsubara M., Lynch J.M., De Leij F. A simple screening procedure for selecting fungi with potential for use in the bioremediation of contaminated land. Enzyme Microb. Technol. 2006, 39:1365-1372.
50. Morgan P., Lee S.A., Lewis S.T., Sheppard A.N., Watkinson R.J. Growth and biodegradation by white-rot fungi inoculated into soil. Soil Biol. Biochem. 1993, 25:279-287.
51. Perestelo F., Rodriguez A., Perez R., Carnicero A., de la Fuente G., Falcon M.A. Isolation of a bacterium capable of limited degradation of industrial and labelled, natural and synthetic lignins. World J. Microbiol. Biotechnol. 1996, 12:111-112.
52. Petsch S.T., Berner R.A. Coupling the geochemical cycles of C, P, Fe, and S: the effect on atmospheric O-2 and the isotopic records of carbon and sulfur. Am. J. Sci. 1998, 298:246-262.
53. Petsch S.T., Smernik R.J., Eglinton T.I., Oades J.M. A solid state 13C-NMR study of kerogen degradation during black slate weathering. Geochim. Cosmochim. Acta 2001, 65(12):1867-1882.
54. Petsch S.T., Eglinton T.I., Edwards K.J. C-14-dead living biomass: evidence for microbial assimilation of ancient organic carbon during share weathering. Science 2001, 292(5519):1127-1131.
55. Petsch S.T., Edwards K.J., Eglinton T.I. Abundance, distribution and delta C-13 analysis of microbial phospholipid-derived fatty acids in a black slate weathering profile. Org. Geochem. 2003, 34(6):731-743.
56. Pombo S.A., Pelz O., Schroth M.H., Zeyer J. Field-scale C-13-labeling of phospholipid fatty acids (PLFA) and dissolved inorganic carbon: tracing acetate assimilation and mineralization in a petroleum hydrocarbon-contaminated aquifer. FEMS Microbiol. Ecol. 2002, 41(3):259-267.
57. Radtke C., Cook W.S., Anderson A. Factors affecting antagonism of the growth of Phanerochaete chrysosporium by bacteria isolated from soils. Appl. Microbiol. Biotechnol. 1994, 41:274-280.
58. Rethemeyer J., Kramer C., Gleixner G., Wiesenberg G.L.B., Schwark L., Andersen N., Nadeau M.J., Grootes P.M. Complexity of soil organic matter: AMS C-14 analysis of soil lipid fractions and individual compounds. Radiocarbon 2004, 46:465-473.
59. Rethemeyer J., Kramer C., Gleixner G., John B., Yamashita T., Flessa H., Andersen N., Nadeau M.J., Grootes P.M. Transformation of organic matter in agricultural soils: radiocarbon concentration versus soil depth. Geoderma 2005, 128(1-2):94-105.
60. Ringelberg D.B., Sutton S., White D.C. Biomass, bioactivity and biodiversity: microbial ecology of the deep subsurface. analysis of ester-linked phospholipid fatty acids. FEMS Microbiol. Rev. 1997, 20(3-4):371-377.
61. Rubino M., Lubritt C., D'Onofrio A., Terrasi F., Kramer C., Gleixner G., Cotrufo M.F. Isotopic evidences for microbiologically mediated and direct C input to soil compounds from three different leaf litters during their decomposition. Environ. Chem. Lett. 2009, 7:85-95.
62. Santos G.M., Moore R.B., Southon J.R., Griffin S., Hinger E., Zhang D. AMS C-14 sample preparation at the KCCAMS/UCI facility: status report and performance of small samples. Radiocarbon 2007, 49(2):255-269.
63. Santos G.M., Southon J.R., Griffin S., Beaupre S.R., Druffel E.R.M. Ultra small-mass AMS C-14 sample preparation and analyses at KCCAMS/UCI Facility. Nucl. Instrum. Meth. B 2007, 259(1):293-302.
64. Slater G.F., Nelson R.K., Kile B.M., Reddy C.M. Intrinsic bacterial biodegradation of petroleum contamination demonstrated in situ using natural abundance, molecular-level C-14 analysis. Org. Geochem. 2006, 37(9):981-989.
65. Southon J.R., Santos G.M. Ion source development at KCCAMS, University of California, Irvine. Radiocarbon 2004, 46(1):33-39.
66. Steinhof A., Adamiec G., Gleixner G., van Klinken G.J., Wagner T. The new C-14 analysis laboratory in Jena, Germany. Radiocarbon 2004, 46(1):51-58.
67. Tunlid A., White D.C. Biochemical analysis of biomass community structure nutritional status and metabolic activity of microbial communities in soil. Soil Biochemistry 1992, 229-262. Marcel Dekker, New York, (Chapter 7). G. Stotzky, J.-M. Bollag (Eds.).
68. Volkman J.K., Alexander R., Kagi R.I., Rowland S.J., Sheppard P.N. Biodegradation of aromatic hydrocarbons in crude oils from the Barrow Sub-basin of Western Australia. Org. Geochem. 1984, 6:619-632.
69. Vicuna R. Bacterial degradation of lignin. Enzyme Microb. Technol. 1988, 10:646-655.
70. Wengel M., Kothe E., Schmidt C.M., Heide K., Gleixner G. Degradation of organic matter from black slates and charcoal by the wood-rotting fungus Schizophyllum commune and release of DOC and heavy metals in the aqueous phase. Sci. Total Environ. 2006, 367(1):383-393.
71. White D.C., Davis W.M., Nickels J.S., King J.D., Bobbie R.J. Determination of the sedimentary microbial biomass by extractable lipid phosphate. Oecologia 1979, 40(1):51-62.
72. Zelles L. Phospholipid fatty acid profiles in selected members of soil microbial communities. Chemosphere 1997, 35:275-294.
73. Zelles L. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fert. Soils 1999, 29:111-129.
74. Zimmermann W. Degradation of lignin by bacteria. J. Biotechnol. 1990, 13:119-130.