CARD-FISH analysis of prokaryotic community composition and abundance along small-scale vegetation gradients in a dry arctic tundra ecosystem

Soil Biology and Biochemistry

Volumn 64, Issue , 2013, Pages 147-154

  Ushio, Masayuki ^a   Makoto, Kobayashi ^b,c   Klaminder, Jonatan ^b   Nakano, Shin Ichi ^a  

^a KYOTO UNIVERSITY   (Japan)

^b UMEÅ UNIVERSITY   (Sweden)

^c YOKOHAMA NATIONAL UNIVERSITY   (Japan)

Author keywords

Archaea; Bacteria; CARD FISH; Soil microbial community; Tundra ecosystem; Vegetation gradients

Indexed keywords

ARCHAEA; CARD-FISH; COMMUNITY COMPOSITION; FLUORESCENT IN SITU HYBRIDIZATION; MULTI VARIATE ANALYSIS; SMALL-SCALE VEGETATION; SOIL MICROBIAL COMMUNITY; TERRESTRIAL ECOSYSTEMS;

BACTERIA; CARBON; ECOSYSTEMS; FISH; LANDFORMS; SOILS;

VEGETATION;

ABUNDANCE; CELL ORGANELLE; COMMUNITY COMPOSITION; PLANT COMMUNITY; PROKARYOTE; SOIL CARBON; SOIL MICROORGANISM; SOIL MOISTURE; TUNDRA; VEGETATION COVER; VEGETATION STRUCTURE;

SWEDEN;

ACIDOBACTERIA; ALPHAPROTEOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84878431009     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2013.05.002     Document Type: Article

References (52)

1. Allison V.J., Condron L.M., Peltzer D.A., Richardson S.J., Turner B.L. Changes in enzyme activities and soil microbial community composition along carbon and nutrient gradients at the Franz Josef chronosequence, New Zealand. Soil Biology and Biochemistry 2007, 39:1770-1781.
2. Amann R., Fuchs B.M. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nature Reviews Microbiology 2008, 6:339-348.
3. Amann R.I., Krumholz L., Stahl D.A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. Journal of Bacteriology 1990, 172:762-770.
4. Bååth E., Anderson T.H. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biology and Biochemistry 2003, 35:955-963.
5. Balser T.C., Firestone M.K. Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 2005, 73:395-415.
6. Bates S.T., Berg-Lyons D., Caporaso J.G., Walters W.A., Knight R., Fierer N. Examining the global distribution of dominant archaeal populations in soil. ISME Journal 2011, 5:908-917.
7. Becher M., Olid C., Klaminder J. Buried soil organic inclusions in non-sorted circles fields in northern Sweden: age and paleoclimatic context. Journal of Geophysical Research: Biogeosciences 2013, 10.1002/jgrg.20016.
8. Bell T.H., Yergeau E., Maynard C., Juck D., Whyte L.G., Greer C.W. Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance. ISME Journal 2013, 10.1038/ismej.2013.1031.
9. Chu H., Fierer N., Lauber C.L., Caporaso J.G., Knight R., Grogan P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environmental Microbiology 2010, 12:2998-3006.
10. Eickhorst T., Tippkötter R. Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH). Soil Biology and Biochemistry 2008, 40:1883-1891.
11. Fierer N., Jackson R.B. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:626-631.
12. Fierer N., Jackson J.A., Vilgalys R., Jackson R.B. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied and Environmental Microbiology 2005, 71:4117-4120.
13. Fierer N., Strickland M.S., Liptzin D., Bradford M.A., Cleveland C.C. Global patterns in belowground communities. Ecology Letters 2009, 12:1238-1249.
14. French H.M. The Periglacial Environment 2007, 458. John Wiley and Sons Ltd., Chichester, UK.
15. Giovannoni S.J., Britschgi T.B., Moyer C.L., Field K.G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 1990, 345:60-63.
16. Ishii K., Mußmann M., MacGregor B.J., Amann R. An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments. FEMS Microbiology Ecology 2004, 50:203-212.
17. Josefsson M. The Geoecology of Subalpine Heaths in the Abisko Valley, Northern Sweden; a Study of Periglacial Conditions 1990, 187. Dep. Physical Geography, Uppsala University, Uppsala.
18. Klaminder J., Giesler R., Makoto K. Physical mixing between humus and mineral matter found in cryoturbated soils increases short-term heterotrophic respiration rates. Soil Biology and Biochemistry 2013, 57:922-924.
19. Kobabe S., Wagner D., Pfeiffer E.M. Characterisation of microbial community composition of a Siberian tundra soil by fluorescence in situ hybridisation. FEMS Microbiology Ecology 2004, 50:13-23.
20. Kuffner M., Hai B., Rattei T., Melodelima C., Schloter M., Zechmeister-Boltenstern S., Jandl R., Schindlbacher A., Sessitsch A. Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiology Ecology 2012, 82:551-562.
21. Lauber C.L., Hamady M., Knight R., Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 2009, 75:5111-5120.
22. Makoto K., Klaminder J. The influence of non-sorted circles on species diversity of vascular plants, bryophytes and lichens in Sub-Arctic Tundra. Polar Biology 2012, 35:1659-1667.
23. Mangan S.A., Schnitzer S.A., Herre E.A., MacK K.M.L., Valencia M.C., Sanchez E.I., Bever J.D. Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest. Nature 2010, 466:752-755.
24. Martiny J.B.H., Eisen J.A., Penn K., Allison S.D., Horner-Devine M.C. Drivers of bacterial ß-diversity depend on spatial scale. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:7850-7854.
25. Miki T., Ushio M., Fukui S., Kondoh M. Functional diversity of microbial decomposers facilitates plant coexistence in a model of plant-microbe-soil feedback. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:14251-14256.
26. Muyzer G., De Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 1993, 59:695-700.
27. Okazaki Y., Hodoki Y., Nakano S.I. Seasonal dominance of CL500-11 bacterioplankton (phylum Chloroflexi) in the oxygenated hypolimnion of Lake Biwa, Japan. FEMS Microbiology Ecology 2013, 83:82-92.
28. Oksanen J., Kindt R., Legendre P., O'Hara B., Simpson G.L., Solymos P., Stevens M.H.H., Wagner H. vegan: Community Ecology Package 2008.
29. Pernthaler A., Pernthaler J., Amann R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Applied and Environmental Microbiology 2002, 68:3094-3101.
30. Pinheiro J., Bates D., DebRoy S., Sarkar D., R Development Core Team nlme: Linear and Nonlinear Mixed Effects of Models 2009.
31. Porter K.G., Feig Y.S. The use of DAPI for identifying and counting aquatic microflora. Limnology and Oceanography 1980, 25:943-948.
32. Prosser J.I. Ecosystem processes and interactions in a morass of diversity. FEMS Microbiology Ecology 2012, 81:507-519.
33. R Development Core Team R: A Language and Environment for Statistical Computing 2012, R Foundation for Statistical Computing, Vienna, Austria.
34. Rousk J., Brookes P.C., Bååth E. The microbial PLFA composition as affected by pH in an arable soil. Soil Biology and Biochemistry 2010, 42:516-520.
35. Schmidt M.W.I., Torn M.S., Abiven S., Dittmar T., Guggenberger G., Janssens I.A., Kleber M., Kogel-Knabner I., Lehmann J., Manning D.A.C., Nannipieri P., Rasse D.P., Weiner S., Trumbore S.E. Persistence of soil organic matter as an ecosystem property. Nature 2011, 478:49-56.
36. Sinsabaugh R.L., Hill B.H., Follstad Shah J.J. Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment. Nature 2009, 462:795-798.
37. Sklyar O., Pau G., Smith M., Huber W. EBImage: Image Processing Toolbox for R 2012.
38. Sogin M.L., Morrison H.G., Huber J.A., Welch D.M., Huse S.M., Neal P.R., Arrieta J.M., Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America 2006, 103:12115-12120.
39. Strickland M.S., Lauber C., Fierer N., Bradford M.A. Testing the functional significance of microbial community composition. Ecology 2009, 90:441-451.
40. Takasu H., Kunihiro T., Nakano S.-I. Estimation of carbon biomass and community structure of planktonic bacteria in Lake Biwa using respiratory quinone analysis. Limnology 2013, 10.1007/s10201-013-0402-3.
41. Tilman D., Knops J., Wedin D., Reich P., Ritchie M., Siemann E. The influence of functional diversity and composition on ecosystem processes. Science 1997, 277:1300-1302.
42. Ushio M., Kitayama K., Balser T.C. Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest. Soil Biology & Biochemistry 2010, 42:1588-1595.
43. Vance E.D., Chapin F.S. Substrate limitations to microbial activity in taiga forest floors. Soil Biology and Biochemistry 2001, 33:173-188.
44. Vitousek P. Ecosystem science and human-environment interactions in the Hawaiian archipelago. Journal of Ecology 2006, 94:510-521.
45. Walker D.A., Epstein H.E., Romanovsky V.E., Ping C.L., Michaelson G.J., Daanen R.P., Shur Y., Peterson R.A., Krantz W.B., Raynolds M.K., Gould W.A., Gonzalez G., Nicolsky D.J., Vonlanthen C.M., Kade A.N., Kuss P., Kelley A.M., Munger C.A., Tarnocai C.T., Matveyeva N.V., Daniëls F.J.A. Arctic patterned-ground ecosystems: a synthesis of field studies and models along a North American Arctic transect. Journal of Geophysical Research G: Biogeosciences 2008, 113. 10.1029/2007JG000504.
46. Wardle D.A., Walker L.R., Bardgett R.D. Ecosystem properties and forest decline in contrasting long-term chronosequences. Science 2004, 305:509-513.
47. Wardle D.A., Zackrisson O., Hörnberg G., Gallet C. The influence of island area on ecosystem properties. Science 1997, 277:1296-1299.
48. Wardle D.A., Bardgett R.D., Klironomos J.N., Setala H., van der Putten W.H., Wall D.H. Ecological linkages between aboveground and belowground biota. Science 2004, 304:1629-1633.
49. Washburn A.L. Geocryology: A Survey of Periglacial Processes and Environments 1980, 406. Edward Arnold, London.
50. Welc M., Bünemann E.K., Fließbach A., Frossard E., Jansa J. Soil bacterial and fungal communities along a soil chronosequence assessed by fatty acid profiling. Soil Biology and Biochemistry 2012, 49:184-192.
51. Wendeberg A. Fluorescene in situ hybridization for the identification of environmental microbes. Cold Spring Harbor Protocols 2010, 5. 10.1101/pdb.prot5366.
52. Wood S.N. Stable and efficient multiple smoothing parameter estimation for generalized additive models. Journal of the American Statistical Association 2004, 99:673-686.