Impact of phanerochaete chrysosporium on the functional diversity of bacterial communities associated with decaying wood

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Hervé, Vincent ^a,b   Ketter, Elodie ^a,b   Pierrat, Jean Claude ^c   Gelhaye, Eric ^a,b   Frey Klett, Pascale ^a,b  

^a UNIVERSITÉ DE LORRAINE   (France)

^b UNIVERSITÉ DE LORRAINE   (France)

^c LERFoB   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CONTROLLED STUDY; DECAYING WOOD; DECOMPOSITION; FOREST; FUNGUS GROWTH; HIGH THROUGHPUT SEQUENCING; MICROBIAL COMMUNITY; MICROCOSM; NONHUMAN; PHANEROCHAETE; PYROSEQUENCING; SPECIES DIVERSITY; WOOD; BACTERIUM; BEECH; BIODIVERSITY; BIOREMEDIATION; CLASSIFICATION; ECOSYSTEM; GENETICS; METABOLISM; MICROBIAL CONSORTIUM; MICROBIOLOGY; ORGANISMAL INTERACTION; PHYLOGENY; PHYSIOLOGY;

BACTERIA; BIODEGRADATION, ENVIRONMENTAL; BIODIVERSITY; ECOSYSTEM; FAGUS; FORESTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROBIAL CONSORTIA; MICROBIAL INTERACTIONS; PHANEROCHAETE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; WOOD;

EID: 84959036917     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0147100     Document Type: Article

References (60)

1. Cornwell WK, Cornelissen JHC, Allison SD, Bauhus J, Eggleton P, Preston CM, et al. Plant traits and wood fates across the globe: Rotted, burned, or consumed? Glob Chang Biol. 2009; 15: 2431-2449.
2. Baldrian P. Enzymes of Saprotrophic Basidiomycetes. In: Boddy L, Frankland JC, van West P, editors. Ecology of Saprotrophic Basidiomycetes. Academic P. Oxford, UK; 2008. pp. 19-41.
3. Leonowicz A, Matuszewska A, Luterek J, Ziegenhagen D, Wojtas-Wasilewska M, Cho NS, et al. Biodegradation of lignin by white rot fungi. Fungal Genet Biol. 1999; 27: 175-85. PMID: 10441443
4. Blanchette RA. Delignification by wood-decay fungi. Annu Rev Phytopathol. 1991; 29: 381-403.
5. Fukasawa Y. The geographical gradient of pine log decomposition in Japan. For Ecol Manage. 2015; 349: 29-35.
6. Schilling JS, Ayres A, Kaffenberger JT, Powers JS. Initial white rot type dominance of wood decomposition and its functional consequences in a regenerating tropical dry forest. Soil Biol Biochem. 2015; 88: 58-68.
7. Rajala T, Peltoniemi M, Pennanen T, Mäkipää R. Fungal community dynamics in relation to substrate quality of decaying Norway spruce (Picea abies [L.] Karst.) logs in boreal forests. FEMS Microbiol Ecol. 2012; 81: 494-505. doi: 10.1111/j.1574-6941.2012.01376.x PMID: 22458543
8. Schilling JS, Kaffenberger JT, Liew FJ, Song Z. Signature Wood Modifications Reveal Decomposer Community History. PLoS One. 2015; 10: E0120679. doi: 10.1371/journal.pone.0120679 PMID: 25811364
9. Clausen CA. Bacterial associations with decaying wood: A review. Int Biodeterior Biodegradation. 1996; 37: 101-107.
10. Hoppe B, Krger K, Kahl T, Arnstadt T, Buscot F, Bauhus J, et al. A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies. Sci Rep. 2015; 5: 9456. doi: 10.1038/srep09456 PMID: 25851097
11. Berlemont R, Martiny AC. Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol. 2013; 79: 1545-54. doi: 10.1128/AEM.03305-12 PMID: 23263967
12. Watts J, McDonald R, Daniel R, Schreier H. Examination of a Culturable Microbial Population from the Gastrointestinal Tract of the Wood-Eating Loricariid Catfish Panaque nigrolineatus. Diversity. 2013; 5: 641-656.
13. Lee CS, Jung Y-T, Park S, Oh T-K, Yoon J-H. Lysinibacillus xylanilyticus sp. nov., a xylan-degrading bacterium isolated from forest humus. Int J Syst Evol Microbiol. 2010; 60: 281-6. doi: 10.1099/ijs.0. 013367-0 PMID: 19651743
14. Woo HL, Hazen TC, Simmons BA, DeAngelis KM. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils. Syst Appl Microbiol. 2014; 37: 60-7. doi: 10.1016/j.syapm.2013. 10.001 PMID: 24238986
15. Bugg TDH, Ahmad M, Hardiman EM, Singh R. The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol. 2011; 22: 394-400. doi: 10.1016/j.copbio.2010.10.009 PMID: 21071202
16. Brown ME, Chang MC. Exploring bacterial lignin degradation. Curr Opin Chem Biol. 2014; 19C: 1-7.
17. Vetrovský T, Steffen KT, Baldrian P. Potential of cometabolic transformation of polysaccharides and lignin in lignocellulose by soil Actinobacteria. PLoS One. 2014; 9: E89108. doi: 10.1371/journal.pone. 0089108 PMID: 24551229
18. Frey-Klett P, Burlinson P, Deveau A, Barret M, Tarkka M, Sarniguet A. Bacterial-fungal interactions: Hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiol Mol Biol Rev. 2011; 75: 583-609. doi: 10.1128/MMBR.00020-11 PMID: 22126995
19. Pion M, Spangenberg JE, Simon A, Bindschedler S, Flury C, Chatelain A, et al. Bacterial farming by the fungus Morchella crassipes. Proc R Soc B Biol Sci. 2013; 280: 20132242.
20. de Boer W, Folman LB, Summerbell RC, Boddy L. Living in a fungal world: Impact of fungi on soil bacterial niche development. FEMS Microbiol Rev. 2005; 29: 795-811. PMID: 16102603
21. Valásková V, de Boer W, Gunnewiek PJAK, Pospísek M, Baldrian P. Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood. ISME J. 2009; 3: 1218-21. doi: 10.1038/ismej.2009.64 PMID: 19516282
22. Warmink JA, Nazir R, van Elsas JD. Universal and species-specific bacterial "fungiphiles" in the mycospheres of different basidiomycetous fungi. Environ Microbiol. 2009; 11: 300-312. doi: 10.1111/j.1462-2920.2008.01767.x PMID: 19196267
23. Tornberg K, Baath E, Olsson S. Fungal growth and effects of different wood decomposing fungi on the indigenous bacterial community of polluted and unpolluted soils. Biol Fertil Soils. 2003; 37: 190-197.
24. Folman LB, Klein Gunnewiek PJ, Boddy L, De Boer W. Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil. FEMS Micriobiology Ecol. 2008; 63: 181-191.
25. Hervé V, Le Roux X, Uroz S, Gelhaye E, Frey-Klett P. Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay. Environ Microbiol. 2014; 16: 2238-2252. doi: 10.1111/1462-2920.12347 PMID: 24286477
26. Frey-Klett P, Chavatte M, Clausse M-L, Courrier S, Le Roux C, Raaijmakers J, et al. Ectomycorrhizal symbiosis affects functional diversity of rhizosphere fluorescent pseudomonads. New Phytol. 2005; 165: 317-28. PMID: 15720643
27. Antony-Babu S, Deveau A, Van Nostrand JD, Zhou J, Le Tacon F, Robin C, et al. Black truffle-associated bacterial communities during the development and maturation of T uber melanosporum ascocarps and putative functional roles. Environ Microbiol. 2014; 16: 2831-2847. doi: 10.1111/1462-2920.12294 PMID: 24118660
28. Hoppe B, Kahl T, Karasch P, Wubet T, Bauhus J, Buscot F, et al. Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi. PLoS One. 2014; 9: E88141. doi: 10.1371/journal.pone.0088141 PMID: 24505405
29. Uroz S, Frey-Klett P. Linking diversity to function: Highlight on the mineral weathering bacteria. Cent Eur J Biol. 2011; 6: 817-820.
30. Lequy E, Calvaruso C, Conil S, Turpault M-P. Atmospheric particulate deposition in temperate deciduous forest ecosystems: Interactions with the canopy and nutrient inputs in two beech stands of Northeastern France. Sci Total Environ. 2014; 487: 206-15. doi: 10.1016/j.scitotenv.2014.04.028 PMID: 24784745
31. Lindahl V, Bakken LR. Evaluation of methods for extraction of bacteria from soil. FEMS Microbiol Ecol. 1995; 16: 135-142.
32. Frey P, Frey-Klett P, Garbaye J, Berge O, Heulin T. Metabolic and Genotypic Fingerprinting of Fluorescent Pseudomonads Associated with the Douglas Fir-Laccaria bicolor Mycorrhizosphere. Appl Environ Microbiol. 1997; 63: 1852-60. PMID: 16535600
33. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989; 17: 7843-53. PMID: 2798131
34. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics. 1991. pp. 115-175.
35. Kim O-S, Cho Y-JY-J, Lee K, Yoon S-HS-H, Kim M, Na H, et al. Introducing EzTaxon-e: A prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012; 62: 716-721. doi: 10.1099/ijs.0.038075-0 PMID: 22140171
36. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. ClustalWand Clustal X version 2.0. Bioinformatics. 2007; 23: 2947-2948. PMID: 17846036
37. Stamatakis A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006; 22: 2688-2690. PMID: 16928733
38. Lozupone C, Hamady M, Knight R. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics. 2006; 7: 371. PMID: 16893466
39. Ulrich A, Klimke G, Wirth S. Diversity and activity of cellulose-decomposing bacteria, isolated from a sandy and a loamy soil after long-term manure application. Microb Ecol. 2008; 55: 512-22. PMID: 17665240
40. Alexander DB, Zuberer DA. Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biol Fertil Soils. 1991; 12: 39-45.
41. Murray AC, Woodward S. Temporal changes in functional diversity of culturable bacteria populations in Sitka spruce stumps. For Pathol. 2007; 37: 217-235.
42. Teather RM, Wood PJ. Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol. 1982; 43: 777-80. PMID: 7081984
43. Garland JL, Mills AL. Classification and Characterization of Heterotrophic Microbial Communities on the Basis of Patterns of Community-Level Sole-Carbon-Source. Appl Environ Microbiol. 1991; 57: 2351-2359. PMID: 16348543
44. Zak J, Willig M, Moorhead D, Wildman H. Functional diversity of microbial communities: A quantitative approach. Soil Biol Biochem. 1994; 26: 1101-1108.
45. R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria; 2015.
46. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: Opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75: 7537-7541. doi: 10.1128/AEM.01541-09 PMID: 19801464
47. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One. 2011; 6: E27310. doi: 10.1371/journal.pone.0027310 PMID: 22194782
48. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007; 35: 7188-7196. PMID: 17947321
49. Zhang H-B, Yang M-X, Tu R. Unexpectedly high bacterial diversity in decaying wood of a conifer as revealed by a molecular method. Int Biodeterior Biodegradation. 2008; 62: 471-474.
50. Blomqvist J, Leong S-LL, Sandgren M, Lestander T, Passoth V. Temperature-dependent changes in the microbial storage flora of birch and spruce sawdust. Biotechnol Appl Biochem. 2014; 61: 58-64. doi: 10.1002/bab.1153 PMID: 24527731
51. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73: 5261-5267. PMID: 17586664
52. Vaninsberghe D, Hartmann M, Stewart GR, Mohn WW. Isolation of a Substantial Proportion of Forest Soil Bacterial Communities Detected via Pyrotag Sequencing. Appl Environ Microbiol. 2013; 79: 2096-8. doi: 10.1128/AEM.03112-12 PMID: 23315727
53. Radtke C, Cook W, Anderson A. Factors affecting antagonism of the growth of Phanerochaete chrysosporium by bacteria isolated from soils. Appl Microbiol Biotechnol. 1994; 41: 274-280.
54. Leveau JHJ, Uroz S, De Boer W. The bacterial genus Collimonas: Mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments. Environ Microbiol. 2010; 12: 281-292. doi: 10.1111/j.1462-2920.2009.02010.x PMID: 19638176
55. Stopnisek N, Bodenhausen N, Frey B, Fierer N, Eberl L, Weisskopf L. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations. Environ Microbiol. 2014; 16: 1503-1512. doi: 10.1111/1462-2920.12211 PMID: 23945027
56. Fekete FA, Chandhoke V, Jellison J. Iron-Binding Compounds Produced by Wood-Decaying Basidiomycetes. Appl Envir Microbiol. 1989; 55: 2720-2722.
57. Goodell B, Jellison J, Liu J, Daniel G, Paszczynski A, Fekete F, et al. Low molecular weight chelators and phenolic compounds isolated from wood decay fungi and their role in the fungal biodegradation of wood. J Biotechnol. 1997; 53: 133-162.
58. Weißhaupt P, Naumann A, Pritzkow W, Noll M. Nitrogen uptake of Hypholoma fasciculare and coexisting bacteria. Mycol Prog. 2012; 12: 283-290.
59. Lynd LR, Weimer PJ, Van Zyl WH, Pretorius IS. Microbial Cellulose Utilization: Fundamentals and Biotechnology. Microbiol Mol Biol Rev. 2002; 66: 506-577. PMID: 12209002
60. Sun H, Terhonen E, Kasanen R, Asiegbu FO. Diversity and Community Structure of Primary Wood-Inhabiting Bacteria in Boreal Forest. Geomicrobiol J. 2014; 31: 315-324.