Functional Profiling and Distribution of the Forest Soil Bacterial Communities Along the Soil Mycorrhizosphere Continuum

Microbial Ecology

Volumn 66, Issue 2, 2013, Pages 404-415

  Uroz, S ^a,e   Courty, P E ^a,b   Pierrat, J C ^c   Peter, M ^d   Buee M ^a   Turpault, M P ^e   Garbaye, J ^a   Frey Klett, P ^a  

^a UNIVERSITÉ DE LORRAINE   (France)

^b UNIVERSITY OF BASEL   (Switzerland)

^c CEMAGREF   (France)

^d SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

^e Centre INRA de Nancy   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; FUNGUS; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; MYCORRHIZA; PHYLOGENY; RHIZOSPHERE; SOIL;

BACTERIA; BIODIVERSITY; FUNGI; MOLECULAR SEQUENCE DATA; MYCORRHIZAE; PHYLOGENY; RHIZOSPHERE; SOIL; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); BURKHOLDERIA; COLLIMONAS; DYELLA; FUNGI; MESORHIZOBIUM; PSEUDOMONAS; RHIZOBIUM; SCLERODERMA CITRINUM; SPHINGOMONAS;

EID: 84880047986     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-013-0199-y     Document Type: Article

References (52)

1. Agerer R (2001) Exploration types of ectomycorrhizae: a proposal to classify ectomycorrhizal mycelial systems according to their patterns of différentiation and putative ecological importance. Mycorrhiza 11: 107-114.
2. Alarcon-Gutierrez E, Floch C, Augur C, Le Petit J, Ziarelli F, Criquet S (2009) Spatial variations of chemical composition, microbial functional diversity, and enzyme activities in a Mediterranean litter (Quercus ilex L.) profile. Pedobiologia 52: 387-399.
3. Ausec L, Zarkrzewski M, Goesmann A, Schlüter A, Mandic-Mulec I (2011) Bioinformatic analysis reveals high diversity of bacterial laccase-like enzymes. PLoS One 6: e25724.
4. Baldrian P (2006) Fungal laccases-occurrence and properties. FEMS Microbiol Rev 30: 215-242.
5. Baldrian P, Stursova M (2011) Enzymes in forest soils. Soil Biol Biochem 22: 61-73.
6. Béguin P (1990) Mol Biol Cellul Degrad Annu Rev Microbiol 44: 219-248.
7. Bell CW, Acosta-Martinez V, McIntyre NE, Cox S, Tissue DT, Zak JC (2009) Linking microbial community structure and function to seasonal differences in soil moisture and temperature in a Chihuahuan desert grassland. Microb Ecol 58: 827-842.
8. Biely P, Puls J, Schneider H (1985) Acetyl xylan esterases in fungal cellulolytic systems. FEBS Lett 186: 80-84.
9. Brooks DD, Chan R, Starks ER, Grayston SJ, Jones MD (2011) Ectomycorrhizal hyphae structure components of the soil bacterial community for decreased phosphatase production. FEMS Microbiol Ecol 76: 245-255.
10. Buée M, Maurice JP, Zeller B, Andrianarisoa S, Ranger J, Courtecuisse R, Marçais B, Le Tacon F (2011) Influence of tree species on richness and diversity of epigeous fungal communities in a French temperate forest stand. Fungal Ecol 4: 22-31.
11. Bugg TDH, Ahmad M, Hardiman EM, Singh R (2011) The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol 22: 394-400.
12. Calvaruso C, Turpault MP, Leclerc E, Frey-Klett P (2007) Impact of ectomycorrhizosphere on the functional diversity of soil bacterial and fungal communities from a forest stand in relation to nutrient mobilization processes. Microb Ecol 54: 567-577.
13. Calvaruso C, Turpault M-P, Leclerc E, Ranger J, Garbaye J, Uroz S, Frey-Klett P (2010) Forest trees influence distribution of the mineral weathering bacterial communities from the Scleroderma citrinum mycorrhizosphere. Appl Environ Microbiol 76: 4780-4787.
14. Courty PE, Pritsch K, Schloter M, Hartmann A, Garbaye J (2005) Activity profiling of ectomycorrhiza communities in two forest soils using multiple enzymatic tests. New Phytol 167: 309-319.
15. Courty PE, Pouysegur R, Buée M, Garbaye J (2006) Laccase and phosphatase activities of the dominant ectomycorrhizal types in a lowland oak forest. Soil Biol Biochem 38: 1219-1222.
16. Courty PE, Hoegger PJ, Kilaru S, Kohler A, Buée M, Garbaye J, Martin F, Kües U (2009) Phylogenetic analysis, genomic organization, and expression analysis of multi-copper oxidases in the ectomycorrhizal basidiomycète Laccaria bicolor. New Phytol 182: 736-750.
17. Courty PE, Buée M, Diedhiou AG, Frey-Klett P, Le Tacon F, Rineau F, Turpault MP, Uroz S, Garbaye J (2010) The role of ectomycorrhizal communities in forest ecosystem processes: new perspectives and emerging concepts. Soil Biol Biochem 42: 679-698.
18. Courty PE, Labbe J, Kohler A, Marçais B, Bastien C, Churin JL, Garbaye J, Le Tacon F (2011) Effect of poplar genotypes on mycorrhizal infection and secreted enzyme activities in mycorrhizal and non-mycorrhizal roots. J Exp Bot 62: 249-260.
19. Criquet S, Tagger S, Vogt G, Iacazio G, LePetit J (1999) Laccase activity of forest litter. Soil Biol Biochem 31: 1239-1244.
20. de Boer W, Leveau JH, Kowalchuk GA, Klein Gunnewiek PJ, Abeln EC, Figge MJ, Sjollema K, Janse JD, van Veen JA (2004) Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae. Int J Syst Evol Microbiol 54: 857-864.
21. Frey-Klett P, Garbaye J, Tarkka M (2007) Tansley review: the mycorrhiza helper bacteria revisited. New Phytol 176: 22-36.
22. Gramms G, Günther T, Fritsche W (1998) Spot tests on oxidative enzymes in ectomycorrhizal, wood- and litter decaying fungi. Mycol Res 102: 67-72.
23. Gügi B, Orange N, Hellio F, Burini JF, Guillou C, Leriche F, Guespin-Michel JF (1991) Effect of growth temperature on several exported enzyme activities in the psychrotropic bacterium Pseudomonas fluorescens. J Bacteriol 173: 3814-3820.
24. Hoppe HG (1983) Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates. Mar Ecol Prog Ser 11: 299-308.
25. Hsu SC, Lockwood JL (1975) Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 29: 422-426.
26. Kellner H, Luis P, Zimdars B, Kiesel B, Buscot F (2008) Diversity of laccase-like multicopper oxidase genes in forest and grassland Cambisol soil samples. Soil Biol Biochem 40: 638-648.
27. Kirk TK, Farrell RL (1987) Enzymatic " combustion": The microbial degradation of lignin. Annu Rev Microbiol 41: 465-505.
28. Koide RT, Sharda JN, Herr JR, Malcolm GM (2008) Ectomycorrhizal fungi and the biotrophy-saprotrophy continuum. New Phytol 178: 230-233.
29. Lambers H, Mougel C, Jaillard B, Hinsinger P (2009) Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective. Plant Soil 321: 83-115.
30. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115-176.
31. Lehman RM, O'Connell SP (2002) Comparison of extracellular enzyme activities and community composition of attached and free-living bacteria in porous medium columns. Appl Environ Microbiol 68: 1569-1575.
32. Leveau JHJ, Uroz S, de Boer W (2009) The bacterial genus Collimonas: mycophagy, weathering, and other adaptive solutions to life in oligotrophic environments. Environ Microbiol 12: 281-292.
33. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66: 506-577.
34. Niku-Paavola ML, Raaska L, Itävaara M (1990) Detection of white-rot fungi by a non-toxic stain. Mycol Res 94: 27-31.
35. Peng X, Masai E, Kitayama H, Harada K, Katayama Y, Fukuda M (2002) Characterization of the 5-carboxyvanillate decarboxilase gene and its role in lignin related biphenyl catabolism in Sphingomonas paucimobilis SYK-6. Appl Environ Microbiol 68: 4407-4415.
36. Poole EJ, Bending GD, Whipps JM, Read DJ (2001) Bacteria associated with Pinus sylvestris-Lactarius rufus ectomycorrhizas and their effects on mycorrhiza formation in vitro. New Phytol 151: 553-766.
37. Pritsch K, Esperschuetz J, Haeler F, Raidl S, Winkler B, Schloter M (2009) Structure and activities of ectomycorrhizal and microbial communities in the rhizosphere of Fagus sylvatica under ozone and pathogen stress in a lysimeter study. Plant Soil 323: 97-109.
38. Rambelli A (1973) The rhizosphere of mycorrhizae. In: Marks GC, Kozlowski TT (eds) Ectomycorrhizae, their ecology and physiology. Academic, New York, pp 299-349.
39. Rodriguez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17: 319-339.
40. Sinsabaugh RL (2005) Fungal enzymes at the community scale. In: Dighton J, Oudermans P, White J (eds) The fungal community, 3rd edn. CRC, New York, pp 237-247.
41. Smith SE, Read DJ (2008) Mycorrhizal symbiosis, 3rd edn. Academic, London.
42. Stursova M, Zifcakova L, Leigh B, Burgess R, Baldrian P (2012) Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol. doi: 10. 1111/j. 1574-6941. 2012. 01343. x.
43. Sun YP, Unestam T, Lucas SD, Johanson KJ, Kenne L, Finlay RD (1999) Exudation-reabsorption in mycorrhizal fungi, the dynamic interface for interaction with soil and other microorganisms. Mycorrhiza 9: 137-144.
44. Ter Braak CJF, Smilauer P (2002) CANOCO reference manual and CanoDraw for Windows user's guide: software for Canonical Community Ordination (version 4. 5). Microcomputer Power, Ithaca.
45. Thompson JD, Higgins DJ, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
46. Timonen S, Jorgensen KS, Haahtela K, Sen R (1998) Bacterial community structure at defined locations of Pinus sylvestris-Suillus bovinus and Pinus sylvestris-Paxillus involutus mycorrhizospheres in dry pine forest humus and nursery peat. Can J Microbiol 44: 499-513.
47. Uroz S, Calvaruso C, Turpault MP, Pierrat JC, Mustin C, Frey-Klett P (2007) Effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil. Appl Environ Microbiol 73: 3019-3027.
48. Uroz S, Calvaruso C, Turpault MP, Frey-Klett P (2009) Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 17: 378-387.
49. Uroz S, Oger P, Lepleux C, Collignon C, Frey-Klett P, Turpault MP (2011) Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems. Res Microbiol 162: 820-831.
50. Uroz S, Oger PM, Morin E, Frey-Klett P (2012) Distinct ectomycorrhizospheres share similar bacterial communities composition as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 78: 3020-3024.
51. Waldrop MP, Balser TC, Firestone MK (2000) Linking microbial community composition to function in a tropical soil. Soil Biol Biochem 32: 1837-1846.
52. Zifcakova L, Dobiasova P, Kolarova Z, Koukol O, Baldrian P (2011) Enzyme activities of fungi associated with Picea abies needles. Fungal Ecol 4: 427-436.