The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China

ISME Journal

Volumn 7, Issue 7, 2013, Pages 1299-1309

  Wu, Bing ^a,b   Tian, Jianqing ^a   Bai, Chunming ^c   Xiang, Meichun ^a   Sun, Jingzu ^a   Liu, Xingzhong ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

biogeography; contemporary disturbance; culture dependent method; fungal community; historical contingencies; PCR DGGE

Indexed keywords

BIOGEOGRAPHY; COMMUNITY STRUCTURE; ENVIRONMENTAL FACTOR; FUNGUS; LACUSTRINE DEPOSIT; NITROGEN; POLYMERASE CHAIN REACTION; POTASSIUM; REGRESSION ANALYSIS; WETLAND;

ARTICLE; BIODIVERSITY; CHEMISTRY; CHINA; CLASSIFICATION; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOSYSTEM; FUNGUS; GENETICS; MICROBIOLOGY; MULTIVARIATE ANALYSIS; PHYSIOLOGY; POLYMERASE CHAIN REACTION; RIVER; SEDIMENT; WETLAND;

BIODIVERSITY; CHINA; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; FUNGI; GEOLOGIC SEDIMENTS; MULTIVARIATE ANALYSIS; POLYMERASE CHAIN REACTION; RIVERS; WETLANDS;

CHINA; QINGHAI-XIZANG PLATEAU; YANGTZE BASIN;

ASPERGILLUS; FUNGI; FUSARIUM; OTUS; PENICILLIUM; TALAROMYCES; TRICHODERMA;

EID: 84880924556     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.29     Document Type: Article

References (63)

1. Bates ST, Nash TH, Garcia-Pichel F. (2012). Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States. Mycologia 104: 353-361
2. Beijerinck M. (1913). De Infusies en de Ontdekking der Backterien, Jaarboek van de Koninklijke Akademie v. Wetenschappen, Muller: Amsterdam, Netherlands
3. Brown JKM, Hovmoller MS. (2002). Epidemiology-aerial dispersal of pathogens on the global and continental scales and its impact on plant disease. Science 297: 537-541
4. Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S et al. (2009). 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184: 449-456
5. Bärlocher F, Stewart M, Ryder DS. (2011). Analyzing aquatic fungal communities in Australia: Impacts of sample incubation and geographic distance of streams. Czech Mycol 63: 113-132
6. Cordier T, Robin C, Capdevielle X, Desprez-Loustau M-L, Vacher C. (2012). Spatial variability of phyllosphere fungal assemblages: Genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecol 5: 509-520
7. DéAth G. (2002). Multivariate regression trees: A new technique for modeling species-environment relationships. Ecology 83: 1105-1117
8. Declerck SAJ, Coronel JS, Legendre P, Brendonck L. (2011). Scale dependency of processes structuring metacommunities of cladocerans in temporary pools of High-Andes wetlands. Ecography 34: 296-305
9. Doaré-Lebrun E, El Arbi A, Charlet M, Guérin L, Pernelle JJ, Ogier JC et al. (2006). Analysis of fungal diversity of grapes by application of temporal temperature gradient gel electrophoresis-potentialities and limits of the method. J Appl Microbiol 101: 1340-1350
10. K. H. Domsch, W. Gams, and T. H. Anderson, Compendium of Soil Fungi (Academic Press, New York, NY, 2007)
11. Fenchel T, Finlay JB. (2005). Bacteria and island biogeography. Science 309: 1997-1999
12. Fierer N, Jackson RB. (2006). The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631
13. Fierer N, Morse JL, Berthrong ST, Bernhardt ES, Jackson RB. (2007). Environmental controls on the landscape-scale biogeography of stream bacterial communities. Ecology 88: 2162-2173
14. Finlay BJ. (2002). Global dispersal of free-living microbial eukaryote species. Science 296: 1061-1063
15. Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL et al. (2008). A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci USA 105: 7774-7778
16. Fuhrman JA. (2009). Microbial community structure and its functional implications. Nature 459: 193-199
17. Ge Y, He JZ, Zhu YG, Zhang JB, Xu Z, Zhang LM et al (2008). Differences in soil bacterial diversity: Driven by contemporary disturbances or historical contingencies? ISME J 2: 254-264
18. Green JL, Holmes AJ, Westoby M, Oliver I, Briscoe D, Dangerfield M et al. (2004). Spatial scaling of microbial eukaryote diversity. Nature 432: 747-750
19. E. G. Gregorich and M. R. Carter, Soil Sampling and Methods of Analysis (CRC Press, Boca Raton, FL, 2008)
20. Harvey JW, Fuller CC. (1998). Effect of enhanced manganese oxidation in the hyporheic zone on basin-scale geochemical mass balance. Water Resour Res 34: 623-636
21. Hewson I, Fuhrman JA. (2004). Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70: 3425-3433
22. Hewson I, Jacobson-Meyers ME, Fuhrman JA. (2007). Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands. Environ Microbiol 9: 923-933
23. Horner-Devine MC, Lage M, Hughes JB, Bohannan BJM. (2004). A taxa-area relationship for bacteria. Nature 432: 750-753
24. Huang XL, Lei FM, Qiao GX. (2008). Areas of endemism and patterns of diversity for aphids of the Qinghai-Tibetan Plateau and the Himalayas. J Biogeogr 35: 230-240
25. Jin JH, Liao WB, Wang BS, Peng SL. (2003). Global change in Cenozoic and evolution of flora in China (in Chinese). Guihaia 23: 217-225
26. Kang MY, Zhu Y. (2007). Discussion and analysis on the geo-ecological boundary in Qinling Range (in Chinese). Acta Ecol Sin 27: 2774-2784
27. Kivlin SN, Hawkes CV, Treseder KK. (2011). Global diversity and distribution of arbuscular mycorrhizal fungi. Soil Biol Biochem 43: 2294-2303
28. Li CG, Yin HF, Yu QW. (2000). Evolution of drainage systems and its developing trend in connection with tectonic uplift of Eastern Kunlun Mt. Chinese Sci Bull 45: 1904-1908
29. Mantel N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220
30. P. Marschner, (2007). Soil microbial community structure and function assessed by FAME, PLFA and DGGE-advantages and limitations. In: Varma A, Oelmüller R (eds) Advanced Techniques in Soil Microbiology. Springer: USA, pp 181-200
31. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL et al. (2006). Microbial biogeography: Putting microorganisms on the map. Nat Rev Microbiol 4: 102-112
32. Marzorati M, Wittebolle L, Boon N, Daffonchio D, Verstraete W. (2008). How to get more out of molecular fingerprints: Practical tools for microbial ecology. Environ Microbiol 10: 1571-1581
33. Mertens B, Boon N, Verstraete W. (2005). Stereospecific effect of hexachlorocyclohexane on activity and structure of soil methanotrophic communities. Environ Microbiol 7: 660-669
34. Mohamed DJ, Martiny JBH. (2011). Patterns of fungal diversity and composition along a salinity gradient. ISME J 5: 379-388
35. Monroy F, van der Putten WH, Yergeau E, Mortimer SR, Duyts H, Bezemer TM. (2012). Community patterns of soil bacteria and nematodes in relation to geographic distance. Soil Biol Biochem 45: 1-7
36. D. W. Nelson and L. E. Sommers, (1982). Dry combustion method using medium temperature resistance furnace. In: Page AL (ed) Methods of Soil Analysis. Part 2: Chemical and Microbial Properties, 2nd edn. Soil Science Society of American and American Society: Madison, WI, USA, pp 539-579
37. M. Neteler, Introduction to GRASS GIS Software (University of Hannover, Hannover, Germany, 1998)
38. O'Malley MA. (2007). The nineteenth century roots of 'everything is everywheré. Nat Rev Microbiol 5: 647-651
39. Pagaling E, Wang H, Venables M, Wallace A, Grant WD, Cowan DA et al. (2009). Microbial biogeography of six salt lakes in Inner Mongolia China and a salt lake in Argentina. Appl Environ Microbiol 75: 5750-5760
40. Pommier T, Canback B, Riemann L, Bostrom KH, Simu K, Lundberg P et al. (2007). Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16: 867-880
41. Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP et al. (2007). Essay-the role of ecological theory in microbial ecology. Nat Rev Microbiol 5: 384-392
42. Qi D, Guo S, Zhao X, Yang J, Tang W. (2007). Genetic diversity and historical population structure of Schizopygopsis pylzovi (Teleostei: Cyprinidae) in the Qinghai-Tibetan Plateau. Freshwater Biol 52: 1090-1104
43. Ramette A, Tiedje JM. (2007). Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci USA 104: 2761-2766
44. Reche I, Pulido-Villena E, Morales-Baquero R, Casamayor EO. (2005). Does ecosystem size determine aquatic bacterial richness? Ecology 86: 1715-1722
45. Schauer R, Bienhold C, Ramette A, Harder J. (2010). Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J 4: 159-170
46. Schiaffino MR, Unrein F, Gasol JM, Massana R, BalaguÉ V, Izaguirre I (2011). Bacterial community structure in a latitudinal gradient of lakes: The roles of spatial versus environmental factors. Freshwater Biol 56: 1973-1991
47. K. A. Seifert, G. Morgan-Jones, W. Gams, and B. Kendrick, The Genera of Hyphomycetes (Centraalbureau voor Schimmelcultures, Utrecht, Netherlands, 2011)
48. Sekiguchi H,Watanabe M, Nakahara T, Xu B, Uchiyama H. (2002). Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Appl Environ Microbiol 68: 5142-5150
49. Y. F. Shi, J. J. Li, and B. Y. Li, Uplift and Environmental Change of Qinghai-Xizang (Tibetan) Plateau in the Late Cenozoic (Guangdong Science and Technology Press, Guangzhou, China 1998) (in Chinese)
50. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR et al. (2006). Microbial diversity in the deep sea and the underexplored 'rare biospheré. Proc Natl Acad Sci USA 103: 12115-12120
51. Sun BD, Liu XZ. (2008). Occurrence and diversity of insect-associated fungi in natural soils in China. Appl Soil Ecol 39: 100-108
52. Sutcliffe JV, Parks YP. (1989). Comparative water balances of selected African wetlands. Hydrol Sci J 34: 49-62
53. Tamura K, Dudley J, Nei M, Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24: 1596-1599
54. Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTALW: 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
55. Thormann MN. (2006). Diversity and function of fungi in peatlands: A carbon cycling perspective. Can J Soil Sci 86: 281-293
56. van der Gast CJ, Gosling P, Tiwari B, Bending GD. (2011). Spatial scaling of arbuscular mycorrhizal fungal diversity is affected by farming practice. Environ Microbiol 13: 241-249
57. Wang L, Abbott RJ, Zheng W, Chen P, Wang Y, Liu J. (2009). History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Mol Ecol 18: 709-721
58. T. J. White, T. Bruns, S. Lee, and J. Taylor, (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA (ed) PCR Protocols: A Guide to Methods and Applications. Academic Press: New York, NY, USA, pp 315-322
59. Williams SE, Marsh H, Winter J. (2002). Spatial scale, species diversity, and habitat structure: Small mammals in australian tropical rain forest. Ecology 83: 1317-1329
60. Xue F, Wang Y, Xu S, Zhang F, Wen B, Wu XS et al. (2008). A spatial analysis of genetic structure of human populations in China reveals distinct difference between maternal and paternal lineages. Eur J Hum Genet 16: 705-717
61. Zachow C, Berg C, Mueller H, Meincke R, Komon-Zelazowska M, Druzhinina IS et al. (2009). Fungal diversity in the rhizosphere of endemic plant species of Tenerife (Canary Islands): Relationship to vegetation zones and environmental factors. ISME J 3: 79-92
62. Zhang XZ, Zhang ZY. (1979). A preliminary discussion on the northern boundary of subtropical zone in China: Based on the distribution of broad-leaf woody evergreens on the Qingling Mountain (in Chinese). Acta Geograph Sin 34: 342-352
63. Zhang YJ, Zhang S, Liu XZ, Wen HA, Wang M. (2010). A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains. Lett Appl Microbiol 51: 114-118