Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils

Applied and Environmental Microbiology

Volumn 78, Issue 20, 2012, Pages 7398-7406

  Naether, Astrid ^a,b   Foesel, Bärbel U ^c,d   Naegele, Verena ^c,e   Wüst, Pia K ^d   Weinert, Jan ^f   Bonkowski, Michael ^f   Alt, Fabian ^g   Oelmann, Yvonne ^g   Polle, Andrea ^h   Lohaus, Gertrud ^h,q   Gockel, Sonja ⁱ   Hemp, Andreas ^j   Kalko, Elisabeth K V ^k   Linsenmair, Karl Eduard ^l   Pfeiffer, Simone ^m   Renner, Swen ^k   Schöning, Ingo ⁿ   Weisser, Wolfgang W ⁱ   Wells, Konstans ^j   Fischer, Markus ^m,o   Overmann, Jörg ^c,d,p   Friedrich, Michael W ^a,b   more..

^a UNIVERSITY OF BREMEN   (Germany)

^b MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^c Mikrobiologie   (Germany)

^d LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^e Pullacher Platz 7   (Germany)

^f UNIVERSITY OF COLOGNE   (Germany)

^g Geoecology   (Germany)

^h UNIVERSITY OF GÖTTINGEN   (Germany)

ⁱ TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^j Biosphärenreservat Schorfheide Chorin ^*  (Germany)

^k UNIVERSITY OF ULM   (Germany)

^l UNIVERSITY OF WÜRZBURG   (Germany)

^m UNIVERSITY OF POTSDAM   (Germany)

ⁿ MAX PLANCK INSTITUTE FOR BIOGEOCHEMISTRY   (Germany)

^o UNIVERSITY OF BERN   (Switzerland)

^p TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^q UNIVERSITY OF WUPPERTAL   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; C/N RATIO; CLONE SEQUENCES; COMMUNITY COMPOSITION; DENATURING GRADIENT GEL ELECTROPHORESES (DGGE); ENVIRONMENTAL FACTORS; ENVIRONMENTAL PARAMETER; FOREST SOILS; GRASSLAND SOILS; NITROGEN CONTENT; PLANT DIVERSITY; POTENTIAL EFFECTS; SOIL PROPERTY; SOIL RESPIRATION; SOIL TEMPERATURE; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS; TERMINAL RESTRICTION FRAGMENTS; TOTAL NITROGEN; VASCULAR PLANT DIVERSITY;

AMMONIUM COMPOUNDS; CLONING; ELECTROPHORESIS; GENES; PHOSPHORUS; RNA; SOIL MOISTURE;

FORESTRY;

BACTERIAL DNA; CARBON; NITROGEN; PHOSPHORUS; RIBOSOME DNA; RNA 16S;

BACTERIUM; COMMUNITY COMPOSITION; ELECTROKINESIS; ENVIRONMENTAL FACTOR; FOREST SOIL; GRASSLAND; MICROBIAL COMMUNITY; POLYMORPHISM; SOIL MICROORGANISM;

ACIDOBACTERIA; ARTICLE; BIOTA; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA FINGERPRINTING; DNA SEQUENCE; GENETICS; GERMANY; ISOLATION AND PURIFICATION; METAGENOME; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PH; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL; TEMPERATURE; TREE;

ACIDOBACTERIA; BIOTA; CARBON; CLUSTER ANALYSIS; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA FINGERPRINTING; DNA, BACTERIAL; DNA, RIBOSOMAL; GERMANY; HYDROGEN-ION CONCENTRATION; METAGENOME; MOLECULAR SEQUENCE DATA; NITROGEN; PHOSPHORUS; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; TEMPERATURE; TREES;

AMMONIUM COMPOUNDS; CLONES; ELECTROPHORESIS; FORESTRY; GENES; MOISTURE; NUCLEIC ACIDS; PHOSPHORUS; SOIL;

GERMANY;

ACIDOBACTERIA; TRACHEOPHYTA;

EID: 84868347617     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01325-12     Document Type: Article

References (65)

1. Abdo Z, et al. 2006. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ. Microbiol. 8:929 -938.
2. Alt F, Oelmann Y, Herold N, Schrumpf M, Wilcke W. 2011. Phosphorus partitioning in grassland and forest soils of Germany as related to land-use type, management intensity, and land use-related pH. J. Plant Nutr. Soil Sci. 174:195-209.
3. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72:5734 -5741.
4. Barns SM, Cain EC, Sommerville L, Kuske CR. 2007. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol. 73:3113-3116.
5. Barns SM, Takala SL, Kuske CR. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65:1731-1737.
6. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol. 57:289 -300.
7. Blüthgen N, et al. 2012. An index of land-use intensity in grasslands that integrates the quantity of mowing, grazing and fertilization. Basic Appl. Ecol. 13:207-220.
8. Bonkowski M. 2004. Protozoa and plant growth: the microbial loop in soil revisited. New Phytol. 162:617- 631.
9. Bonkowski M, Griffiths B, Scrimgeour C. 2000. Substrate heterogeneity and microfauna in soil organic 'hotspots' as determinants of nitrogen capture and growth of ryegrass. Appl. Soil Ecol. 14:37-53.
10. Buckley DH, Schmidt TM. 2001. The structure of microbial communities in soil and the lasting impact of cultivation. Microb. Ecol. 42:11-21.
11. Carrascal LM, Galvan I, Gordo O. 2009. Partial least squares regression as an alternative to current regression methods used in ecology. Oikos 118:681- 690.
12. Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW. 2010. Soil microbial community responses to multiple experimental climate change drivers. Appl. Environ. Microbiol. 76:999 -1007.
13. Chan OC, et al. 2008. Vegetation cover of forest, shrub and pasture strongly influences soil bacterial community structure as revealed by 16S rRNA gene T-RFLP analysis. FEMS Microbiol. Ecol. 64:449-458.
14. Culman SW, Bukowski R, Gauch HG, Cadillo-Quiroz H, Buckley DH. 2009. T-REX: software for the processing and analysis of T-RFLP data. BMC Bioinformatics 10:171. doi:10.1186/1471-2105-10-171.
15. Dedysh SN, Pankratov TA, Belova SE, Kulichevskaya IS, Liesack W. 2006. Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. Appl. Environ. Microbiol. 72:2110 -2117.
16. Egert M, Friedrich MW. 2003. Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl. Environ. Microbiol. 69:2555-2562.
17. Eichorst SA, Breznak JA, Schmidt TM. 2007. Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl. Environ. Microbiol. 73:2708 -2717.
18. Fierer N, Bradford MA, Jackson RB. 2007. Toward an ecological classification of soil bacteria. Ecology 88:1354 -1364.
19. 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.
20. Fischer M, et al. 2010. Implementing large-scale and long-term functional biodiversity research: the biodiversity exploratories. Basic Appl. Ecol. 11:473- 485.
21. Griffiths RI, et al. 2011. The bacterial biogeography of British soils. Environ. Microbiol. 13:1642-1654.
22. Gruter D, Schmid B, Brandl H. 2006. Influence of plant diversity and elevated atmospheric carbon dioxide levels on belowground bacterial diversity. BMC Microbiol. 6:68. doi:10.1186/1471-2180-6-68.
23. Hammer O, Harper DAT, Ryan PD. 2001. PAST: paleontological statistics software package for education and data analysis. Palaeontol. Electron. 4:1-9.
24. Hedley MJ, Stewart JWB, Chauhan BS. 1982. Changes in inorganic and organic soil-phosphorus fractions induced by cultivation practices and by laboratory incubations. Soil Sci. Soc. Am. J. 46:970 -976.
25. Henckel T, Friedrich M, Conrad R. 1999. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl. Environ. Microbiol. 65:1980 -1990.
26. Huber T, Faulkner G, Hugenholtz P. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317-2319.
27. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366- 376.
28. Janssen PH. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72:1719- 1728.
29. Jones RT, et al. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3:442- 453.
30. Kielak A, Pijl AS, van Veen JA, Kowalchuk GA. 2008. Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field. FEMS Microbiol. Ecol. 63:372-382.
31. Kielak A, Pijl AS, van Veen JA, Kowalchuk GA. 2009. Phylogenetic diversity of Acidobacteria in a former agricultural soil. ISME J. 3:378 -382.
32. Kleinsteuber S, Muller FD, Chatzinotas A, Wendt-Potthoff K, Harms H. 2008. Diversity and in situ quantification of Acidobacteria subdivision 1 in an acidic mining lake. FEMS Microbiol. Ecol. 63:107-117.
33. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA. 2002. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek 81:509 -520.
34. Kuo S. 1996. Phosphorus, p 869-920. In Sparks DL, et al (ed), Methods of soil analysis-part 3. Chemical methods. Soil Science Society of America, Madison, WI.
35. Kuske CR, Barns SM, Busch JD. 1997. Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63:3614 -3621.
36. Lane DJ. 1991. 16S/23S rRNA sequencing, p 115-175. In Stackebrandt E, GoodfellowM(ed), Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, NY.
37. Lauber CL, Strickland MS, Bradford MA, Fierer N. 2008. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40:2407-2415.
38. Lee SH, Cho JC. 2011. Group-specific PCR primers for the phylum Acidobacteria designed based on the comparative analysis of 16S rRNA gene sequences. J. Microbiol. Methods 86:195-203.
39. Ludwig W, et al. 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol. Lett. 153:181-190.
40. Ludwig W, et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
41. Lueders T, Friedrich M. 2000. Archaeal population dynamics during sequential reduction processes in rice field soil. Appl. Environ. Microbiol. 66:2732-2742.
42. Luyssaert S, Hessenmoller D, von Lupke N, Kaiser S, Schulze ED. 2011. Quantifying land use and disturbance intensity in forestry, based on the self-thinning relationship. Ecol. Appl. 21:3272-3284.
43. Mannisto MK, Tiirola M, Haggblom MM. 2007. Bacterial communities in Arctic fjelds of Finnish Lapland are stable but highly pH-dependent. FEMS Microbiol. Ecol. 59:452- 465.
44. Meisinger DB, et al. 2007. In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA). Environ. Microbiol. 9:1523-1534.
45. Murphy J, Riley JP. 1962. A modified single solution method for determination of phosphate in natural waters. Anal. Chim. Acta 27:31-36.
46. Muyzer G, Teske A, Wirsen C, Jannasch H. 1995. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
47. Nacke H, et al. 2011. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6(2):e17000. doi:10.1371/journal.pone.0017000.
48. Pruesse E, et al. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188 -7196.
49. Quaiser A, et al. 2008. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ. Microbiol. 10:2704 -2717.
50. Ramette A. 2007. Multivariate analyses in microbial ecology. FEMS Microbiol. Ecol. 62:142-160.
51. Rasche F, et al. 2011. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. ISME J. 5:389-402.
52. R Development Core Team. 2011. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
53. Ricke P, Kolb S, Braker G. 2005. Application of a newly developed ARB software-integrated tool for in silico terminal restriction fragment length polymorphism analysis reveals the dominance of a novel pmoA cluster in a forest soil. Appl. Environ. Microbiol. 71:1671-1673.
54. Schloss PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
55. Singleton DR, Furlong MA, Rathbun SL, Whitman WB. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:4374-4376.
56. Smith CJ, et al. 2005. T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiol. Ecol. 54:375-380.
57. Sun HY, Deng SP, Raun WR. 2004. Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl. Environ. Microbiol. 70:5868 -5874.
58. ter Braak CJF, Smilauer P. 2011. CANOCO reference manual and Cano-Draw for Windows user's guide: software for canonical community ordination (version 4.5). Microcomputer Power, Ithaca, NY.
59. Ward NL, et al. 2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl. Environ. Microbiol. 75:2046 -2056.
60. Webb CO, Ackerly DD, Kembel SW. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24:2098 -2100.
61. Will C, et al. 2010. Horizon-specific bacterial community composition of German grassland soils as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl. Environ. Microbiol. 76:6751- 6759.
62. Wold H. 1966. Estimation of principal components and related models by iterative least squares, p 391-420. In Krishnaiah PR (ed), Multivariate analysis. Academic Press, New York, NY.
63. Zak DR, Holmes WE, White DC, Peacock AD, Tilman D. 2003. Plant diversity, soil microbial communities, and ecosystem function: are there any links? Ecology 84:2042-2050.
64. Zimmermann J, Gonzalez JM, Saiz-Jimenez C, Ludwig W. 2005. Detection and phylogenetic relationships of highly diverse uncultured acidobacterial communities in Altamira cave using 23S rRNA sequence analyses. Geomicrobiol. J. 22:379 -388.
65. Zul D, Denzel S, Kotz A, Overmann J. 2007. Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity. Appl. Environ. Microbiol. 73:6916-6929.