Changes in soil microbial communities as affected by intensive cattle husbandry

Applied Soil Ecology

Volumn 58, Issue , 2012, Pages 56-65

  Elhottova D ^a   Koubova A ^a,b   Simek M ^a,b   Cajthaml, T ^c   Jirout, J ^a,b   Esperschuetz, J ^d   Schloter, M ^d   Gattinger, A ^d,e  

^a INSTITUTE OF SOIL BIOLOGY   (Czech Republic)

^b UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^c INSTITUTE OF MICROBIOLOGY   (Czech Republic)

^d INSTITUTE OF EPIDEMIOLOGY   (Germany)

^e RESEARCH INSTITUTE OF ORGANIC AGRICULTURE FIBL   (Switzerland)

Author keywords

Anaerobic microbial biomass; Excrements; Organic matter pyrolysis; Outdoor husbandry; Pasture soil; PLFA PLEL

Indexed keywords

ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); BOS;

EID: 84859628378     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2012.03.009     Document Type: Article

References (71)

1. Bauchop T. Rumen anaerobic fungi of cattle and sheep. Appl. Environ. Microbiol. 1979, 38:148-156.
2. Blanco G., Lemus J.A., Grande J. Microbial pollution in wildlife: linking agricultural manuring and bacterial resistance in red-billed choughs. Environ. Res. 2009, 109:405-412.
3. Bland D.E., Logan A.F. The properties of syringyl, guaiacyl and p-hydroxyphenyl artificial lignins. Biochem. J. 1965, 95:515-520.
4. Bol R., Amelung W., Friedrich C., Ostle N. Tracing dung-derived carbon in temperate grassland using C-13 natural abundance measurements. Soil Biol. Biochem. 2000, 32:1337-1343.
5. 2O from pasture soil. Biol. Fertil. Soils 2009, 46:27-36.
6. 2O-reducing ability. Soil Biol. Biochem. 2009, 41:1132-1138.
7. Cools D., Merckx R., Vlassak K., Verhaegen J. Survival of E. coli and Enterococcus spp. derived from pig slurry in soils of different texture. Appl. Soil Ecol. 2001, 17:53-62.
8. čuhel J., Šimek M. Effect of pH on the denitrifying enzyme activity in pasture soils in relation to the intrinsic differences in denitrifier communities. Folia Microbiol. 2011, 56:230-235.
9. 2 emissions and denitrifier community size and activity. Appl. Environ. Microbiol. 2010, 76:1870-1878.
10. de Zorzi P., Barbizzi S., Belli M., Ciceri G., Fajgelj A., Moore D., Sansone U., van der Perk M. Terminology in soil sampling (IUPAC Recommendations 2005). Pure Appl. Chem. 2005, 77:827-841.
11. Dowd S.E., Callaway T.R., Wolcott R.D., Sun Y., McKeehan T., Hagevoort R.G., Edrington T.S. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicons pyrosequencing (bTEFAP). BMC Microbiol. 2008, 8:125. 10.1186/1471-2180-8-125.
12. Federle T.W. Microbial distribution in soil-new techniques. Perspectives in Microbial Ecology 1986, 493-498. Slovene Society for Microbiology, Lublana, Slovenia. F. Megusar, M. Gantar (Eds.).
13. Fontaine S., Mariotti A., Abbadie L. The priming effect of organic matter: a question of microbial competition?. Soil Biol. Biochem. 2003, 35:837-843.
14. Frostegård å., Bååth E. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol. Fertil. Soils 1996, 22:59-65.
15. Gattinger A., Schloter M., Munch J.C. Phospholipid etherlipid and phospholipid fatty acid fingerprints in selected euryarchaeotal monocultures for taxonomic profiling. FEMS Microbiol. Lett. 2002, 213:133-139.
16. Gattinger A., Ruser R., Schloter M., Munch J.C. Microbial community structure varies in different soil zones of a potato field. J. Plant Nutr. Soil Sci. 2002, 165:421-428.
17. Gattinger A., Günthner A., Schloter M., Munch J.C. Characterization of Archaea in soils by polar lipid analysis. Acta Biotechnol. 2003, 23:21-28.
18. Gattinger A., Hoefle M.G., Schloter M., Embacher A., Bohme F., Munch J.C., Labrenz M. Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil. Environ. Microbiol. 2007, 9:612-624.
19. Gebert J., Grongroft A., Schloter M., Gattinger A. Community structure in a methanotroph by phospholipid fatty acid biofilter as revealed analysis. FEMS Microbiol. Lett. 2004, 240:61-68.
20. Grandy A.S., Strickland M.S., Lauber C.L., Bradford M.A., Fierer N. The influence of microbial communities, management, and soil texture on soil organic matter chemistry. Geoderma 2009, 150:278-286.
21. Griffiths B.S., Wheatley R.E., Olesen T., Henriksen K., Ekelund F., Ronn R. Dynamics of nematodes and protozoa following the experimental addition of cattle or pig slurry to soil. Soil Biol. Biochem. 1998, 30:1379-1387.
22. Guckert J.B., Hood M.A., White D.C. Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of Vibrio cholerae: increases in the trans/cis ratio and proportions of cyclopropyl fatty acids. Appl. Environ. Microbiol. 1986, 52:794-801.
23. Hanson R.S., Hanson T.E. Methanotrophic bacteria. Microbiol. Rev. 1996, 60:439-471.
24. Hatakka A. Biodegradation of lignin. Biopolymers, vol. 1, Humic Substances and Coal 2001, 129-180. Wiley-VCH. A. Steinbüchel, M. Hofrichter (Eds.).
25. Hatch D.J., Lovell R.D., Antil R.S., Jarvis S.C. Nitrogen mineralization and microbial activity in permanent pastures amended with nitrogen fertilizer or dung. Biol. Fertil. Soils 2000, 30:288-293.
26. He R., Ruan A., Jiang Ch., Shen D. Responses of oxidation rate and microbial communities to methane in simulated landfill cover soil microcosms. Biores. Technol. 2008, 99:7192-7199.
27. HynŠt J., Brůček P., Šimek M. Nitrous oxide emissions from cattle-impacted pasture soil amended with nitrate and glucose. Biol. Fertil. Soils 2007, 43:853-859.
28. Jackson M.L. Soil Chemical Analysis 1958, Prentice-Hall, Englewood Cliffs, NJ.
29. Jirout J., Tříska J., RůŽičková K., Elhottová D. Disturbing impact of outdoor cattle husbandry on community of arbuscular mycorrhizal fungi in upland pasture soil. Commun. Soil Sci. Plant Anal. 2009, 40:736-745.
30. Jirout J., Šimek M., Elhottová D. Inputs of nitrogen and organic matter govern the composition of fungal communities in soil disturbed by overwintering cattle. Soil Biol. Biochem. 2011, 43:647-656.
31. Jones B.E., Grant W.D., Duckworth A.W., Owenson G.G. Microbial diversity of soda lakes. Extremophiles 1998, 2:191-200.
32. Kaneda T. Iso- and anteiso-fatty acids in bacteria: biosynthesis, function and taxonomic significance. Microbiol. Rev. 1991, 55:288-302.
33. Kendall M.M., Boone D.R. The order Methanosarcinales. Prokaryotes, vol. 3A, Archaea 2006, 244-256. 10.1007/0-387-30743-5_12. M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, E. Stackebrandt (Eds.).
34. Kirk T.K., Farrell R.L. Enzymatic " combustion" : the microbial degradation of lignin. Annu. Rev. Microbiol. 1987, 41:465-505.
35. Knief C., Lipski A., Dunfield P.F. Diversity and activity of methanotrophic bacteria in different upland soils. Appl. Environ. Microbiol. 2003, 69:6703-6714.
36. Koubová A., Goberna M., Šimek M., Chroňáková A., PiŽl V., Insam H., Elhottová D. Effects of the earthworm Eisenia andrei on methanogens in a cattle-impacted soil: a microcosm study. Eur. J. Soil Biol. 2012, 48:32-40.
37. Krashevska V., Maraun M., Ruess L., Scheu S. Carbon and nutrient limitation of soil microorganisms and microbial grazers in a tropical montane rain forest. Oikos 2010, 119:1020-1028.
38. Kroppenstedt R.M. Fatty acid and menaquinone analysis of actinomycetes and related organisms. Chemical Methods in Bacterial Systematics 1985, 173-199. Academic Press, London. M. Goodfellow, D.E. Minnikin (Eds.).
39. Kurz I., OóReilly C.D., Tunney H. Impact of cattle on soil physical properties and nutrient concentrations in overland flow from pasture in Ireland. Agric. Ecosyst. Environ. 2006, 113:378-390.
40. Laczko E., Rudaz A., Aragno M. Diversity of anthropogenically influenced or disturbed soil microbial communities. Functional Versus Structural Approaches 1997, 57-67. Springer-Verlag, Heidelberg. H. Insam, A.M. Rangger (Eds.).
41. Lehtovirta L.E., Prosser J.I., Nicol G.W. Soil pH regulates the abundance and diversity of group 1.1c Crenarchaeota. FEMS Microbiol. Ecol. 2009, 70:367-376.
42. Lovell R.D., Jarvis S.C. Effect of cattle dung on soil microbial biomass C and N in a permanent pasture soil. Soil Biol. Biochem. 1996, 28:291-299.
43. Makula R.A. Phospholipid composition of methane-utilizing bacteria. J. Bacteriol. 1978, 134:771-777.
44. Martínez A.T., Speranza M., Ruiz-Duenas F.J., Ferreira P., Camarero S., Guillen F., Martínez M.J., Gutierrez A., del Rio J.C. Biodegradation of lignocellulosics: microbial chemical, and enzymatic aspects of the fungal attack of lignin. Int. Microbiol. 2005, 8:195-204.
45. Mawdsley J.L., Bardgett R.D., Merry R.J., Pain B.F., Theodorou M.K. Pathogenes in livestock waste, their potential movement through soil and environmental pollution. Appl. Soil Ecol. 1995, 2:1-15.
46. McCarthy A.J. Lignocellulose-degrading actinomycetes. FEMS Microbiol. Lett. 1987, 46:145-163.
47. McGranaghan P., Davies J.C., Griffith G.W., Davies D.R., Theodorou M.K. The survival of anaerobic fungi in cattle faeces. FEMS Microbiol. Ecol. 1999, 29:293-300.
48. Nicol G.W., Webster G., Glover L.A., Prosser J.I. Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil. Environ. Microbiol. 2004, 6:861-867.
49. Nierop K.G.J., van Lagen B., Buurman P. Composition of plant tissues and soil organic matter in the first stages of a vegetation succession. Geoderma 2001, 100:1-24.
50. Orpin C.G. Studies on the rumen flagellate, Neocallimastix frontalis. J. Gen. Microbiol. 1975, 91:249-262.
51. Oyaizu H., Komagata K. Chemotaxonomic and phenotypic characterisation of the strains of species in the Flavobacterium-Cytophaga complex. J. Gen. Appl. Microbiol. 1981, 27:57-107.
52. Peacock A.D., Mullen M.D., Ringelberg D.B., Tyler D.D., Hedrick D.B., Gale P.M., White D.C. Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol. Biochem. 2001, 33:1011-1019.
53. Philippot L., Bru D., Saby N.P., čuhel J., Arrouays D., Šimek M., Hallin S. Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree. Environ. Microbiol. 2009, 11:3096-3104.
54. Radl V., Gattinger A., Chroňáková A., Němcová A., čuhel J., Šimek M., Munch J.C., Schloter M., Elhottová D. Outdoor cattle husbandry influences abundance and activity of methanogenic archaea in an upland pasture soil. ISME J. 2007, 1:443-452.
55. Saiz-Jimenez C. Analytical pyrolysis of humic substances-pitfalls, limitations, and possible solutions. Environ. Sci. Technol. 1994, 28:1773-1780.
56. Schulten H.-R., Schnitzer M. Structural studies on soil humic acids by Curie-point pyrolysis-gas chromatography/mass spectrometry. Soil. Sci. 1992, 153:205-224.
57. Sheppard S.K., McCarthy A.J., Loughnane J.P., Gray N.D., Head I.M., Lloyd D. The impact of sludge amendment on methanogen community structure in an upland soil. Appl. Soil Ecol. 2005, 28:147-162.
58. Šimek M., Brůček P., HynŠt J., Uhlířová E., Petersen S.O. Effects of excretal returns and soil compaction on nitrous oxide emissions from a cattle overwintering area. Agric. Ecosyst. Environ. 2006, 112:186-191.
59. Steffen K.T., Cajthaml T., Šnajdr J., Baldrian P. Differential degradation of oak (Quercus petraea) leaf litter by litter-decomposing basidiomycetes. Res. Microbiol. 2007, 158:447-455.
60. Suzuki K., Goodfellow M., O'Donnell A.G. Cell envelopes and classification. Handbook of New Bacterial Systematics 1993, 195-250. Academic Press Inc., San Diego. M. Goodfellow, A.G. OóDonnell (Eds.).
61. ter Braak C.J.F., Šmilauer P. CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (Version 4.5) 2002, Microcomputer Power, Ithaca, New York, USA.
62. Vancampenhout K., Wouters K., De Vos B., Buurman P., Swennen R., Deckers J. Differences in chemical composition of soil organic matter in natural ecosystems from different climatic regions-a pyrolysis-GC/MS study. Soil Biol. Biochem. 2009, 41:568-579.
63. Virtue P., Nichols P.D., Boon P.I. Simultaneous estimation of microbial phospholipid fatty acids and diether lipids by capillary gas chromatography. J. Microbiol. Methods 1996, 25:177-185.
64. Wassmuth R., Wallbum F., Langholz H-J. Outdoor wintering of suckler cows in low mountain ranges. Livest. Prod. Sci. 1999, 61:193-200.
65. Whalen S.C., Reeburgh W.S., Kizer K.S. Methane consumption by tiaga. Glob. Biogeochem. Cycle 1991, 5:261-273.
66. White D.C. Is there anything else you need to understand about the microbiota that cannot be derived from analysis of nucleic-acids?. Microb. Ecol. 1994, 28:163-166.
67. Zbíral, J., 1995. Analýza půd-I, jednotné pracovní postupy, vydání 1. Státní kontrolní a zkuŠební ústav zemědělský, Odbor agrochemie, půdy a výŽivy rostlin, Brno (in Czech).
68. Zelles L. Phospholipid fatty acid profiles in selected members of soil microbial communities. Chemosphere 1997, 35:275-294.
69. Zelles L. Identification of single cultured micro-organisms based on their whole-community fatty acid profiles, using an extended extraction procedure. Chemosphere 1999, 39:665-682.
70. Zelles L. Fatty acid patterns of phospholipids and lipopolysacharides in the characterization of microbial communities in soil: a review. Biol. Fertil. Soils 1999, 29:111-129.
71. Zelles L., Bai Q.Y. Fractionation of fatty acids derived from soil lipids by soil phase extraction and their quantitative analysis by GC-MS. Soil Biol. Biochem. 1993, 25:130-134.