Land Use Intensity Controls Actinobacterial Community Structure

Microbial Ecology

Volumn 61, Issue 2, 2011, Pages 286-302

  Hill, Patrick ^a,d   Krištůfek, Václav ^b   Dijkhuizen, Lubbert ^c   Boddy, Christopher ^d   Kroetsch, David ^e   van Elsas, Jan Dirk ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b INSTITUTE OF SOIL BIOLOGY   (Czech Republic)

^c UNIVERSITY OF GRONINGEN   (Netherlands)

^d UNIVERSITY OF OTTAWA   (Canada)

^e OTTAWA RESEARCH AND DEVELOPMENT CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PRIMER DNA; RNA 16S;

ACTINOBACTERIA; AGRICULTURE; ARTICLE; BIOTA; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; MONTE CARLO METHOD; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL;

ACTINOBACTERIA; AGRICULTURE; BIOTA; CLUSTER ANALYSIS; DNA PRIMERS; DNA, BACTERIAL; MONTE CARLO METHOD; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); ANIMALIA; BACTERIA (MICROORGANISMS);

EID: 79951513317     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-010-9752-0     Document Type: Article

References (45)

1. Bent SJ, Pierson JD, Forney LJ (2007) Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl Environ Microbiol 73: 2399-2401.
2. Blackwood C, Marsh T, Kim S-H, Paul EA (2003) Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 69: 926-932.
3. Bossio DA, Girvan MS, Verchot L, Bullimore J, Borelli T, Albrecht A, Scow KM, Ball AS, Pretty JN, Osborn AM (2005) Soil microbial community response to land use change in an agricultural landscape of Western Kenya. Microb Ecol 49: 50-62.
4. Buckley DH, Schmidt TM (2001) Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil. FEMS Microbiol Ecol 35: 105-112.
5. Burke RA, Molina M, Cox JE, Osher LJ, Piccolo MC (2003) Stable carbon isotope ratio and composition of microbial fatty acids in tropical soils. J Environ Qual 32: 198-206.
6. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33: 294-296.
7. Ellis RJ, Morgan P, Weightman AJ, Fry JC (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69: 3223-3230.
8. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626-631.
9. Fierer N, Carney KM, Horner-Devine MC, Megonigal JP (2009) The biogeography of ammonia-oxidizing bacterial communities in soil. Microb Ecol 58: 435-445.
10. Gelsomino A, Keijzer-Wolters AC, Cacco G, van Elsas JD (1999) Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gel electrophoresis. J Microbiol Methods 38: 1-15.
11. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69: 1800-1809.
12. Gomez-Alvarez V, King G, Nuesslein K (2007) Comparative bacterial diversity in recent Hawaiian volcanic deposits of different ages. FEMS Microbiol Ecol 60: 60-73.
13. Graff A, Conrad R (2005) Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees. FEMS Microbiol Ecol 53: 401-415.
14. Gurtner C, Piñar G, Lubitz W, Swings J, Rölleke S (2000) Comparative analyses of the bacterial diversity on two different biodeteriorated wall paintings by DGGE and 16S rDNA sequence analysis. Int Biodeterior Biodegrad 46: 229-239.
15. Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63: 3233-3241.
16. Hill P, Krištůfek V, Martinez AF, Gallego G (2005) The characterization of wormcasts through of amplified ribosomal DNA (ARDRA) and 16S ribosomal sequencing. In: Tajovský K, Schalghamerský J, Pižl V (eds) Proceedings of the 7th Central European Workshop on Soil Zoology, 14-15 April 2003. Institute of Soil Biology ASCR, České Budějovice, pp 25-29.
17. Holmes AJ, Bowyer J, Holley MP, O'Donoghue M, Montgomery M, Gillings MR (2000) Diverse, yet-to-be-cultured members of the Rubrobacter subdivision of the Actinobacteria are widespread in Australian arid soils. FEMS Microbiol Ecol 33: 111-120.
18. Hong SH, Bunge J, Leslin C, Jeon S, Epstein SS (2009) Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J 12: 1365-1373.
19. İnceoǧlu Ö, Hoogwout EF, Hill P, van Elsas JD (2010) Effect of DNA extraction method on the apparent microbial diversity of soil. Appl Environ Microbiol 76: 3378-3382.
20. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72: 1719-1728.
21. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analysis. ISME J 3: 442-453.
22. Kanokratana P, Chanapan S, Pootanakit K, Eurwilaichitr L (2004) Diversity and abundance of bacteria and archaea in the Bor Khlueng Hot Spring in Thailand. J Basic Microbiol 44: 430-444.
23. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5: 150-163.
24. LaMontagne MG, Schimel JP, Holden PA (2003) Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes. Microb Ecol 46: 216-227.
25. 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.
26. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
27. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
28. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795-799.
29. Marfenina OE, Ivanova AE, Kislova EE, Sacharov (2008) The mycological properties of medieval culture layers as a form of soil 'biological memory' about urbanization. J Soils Sediments 8: 340-348.
30. Monciardini P, Sosio M, Cavaletti L, Chiocchini C, Donadio S (2002) New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol Ecol 43: 419-429.
31. Nercessian O, Noyes E, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L (2005) Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake. Appl Environ Microbiol 71: 6885-6899.
32. Neufeld JD, Mohn WW (2005) Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. Appl Environ Microbiol 71: 5710-5718.
33. Nováková A, Elhottová D, Krištůfek V, Lukešová A, Hill P, Kováč L, Mochk A, Lùptáčik P (2005) Feeding sources of invertebrates in Ardovská and Domica cave systems. In: Tajovský K, Schalghamerský J, Pižl V (eds) Proceedings of the 7th Central European Workshop on Soil Zoology, 14-15 April 2003. Institute of Soil Biology ASCR, České Budějovice, pp 107-112.
34. Reed DW, FujitaY DME, Blackwelder DB, Sheridan P, Uchida T, Colwell FS (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a Forearc Basin. Appl Environ Microbiol 68: 3759-3770.
35. Rodrigues DF, da Jesus EC, Ayala-del-Rio HL, Pellizari VH, Gilichinsky D, Sepulveda-Torres L, Tiedje JT (2009) Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium. ISME J 3: 658-665.
36. Rölleke S, Gurtner C, Drewello D, Lubitz W, Weissmann R (2000) Analysis of bacterial communities on historical glass by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. J Microbiol Methods 36: 107-114.
37. Schabereiter-Gurtner C, Piñar G, Vybiral D, Lubitz W, Rölleke S (2001) Rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings. Arch Microbiol 176: 347-354.
38. Selenska-Pobell S, Kampf G, Flemming K, Radevaand G, Satchanska G (2001) Bacterial diversity in soil samples from two uranium waste piles as determined by rep-APD, RISA and 16S rDNA retrieval. Antonie Leeuwenhoek 79: 149-161.
39. Sangwan P, Chen X, Hugenholtz P, Janssen PH (2004) Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov. of the phylum Verrucomicrobia. Appl Environ Microbiol 70: 5875-5881.
40. Sangwan P, Kovacs S, Davis KER, Sait M, Janssen PH (2005) Detection and cultivation of soil Verrucomicrobia. Appl Environ Microbiol 71: 8402-8410.
41. Waldrop MP, Balser TC, Firestone MK (2000) Linking microbial community composition to function in a tropical soil. Soil Biol Biochem 32: 1837-1846.
42. Wawrik B, Kutliev D, Abdivasievna UA, Kukor JJ, Zylstra GJ, Kerkhof L (2007) Biogeography of actinomycete communities and type II polyketide synthase genes in soil collected in New Jersey and Central Asia. Appl Environ Microbiol 73: 2982-2989.
43. Ulrich A, Becker R (2006) Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiol Ecol 56: 430-443.
44. Zhou J, Beicheng X, Huang H, Treves DS, Hauser LJ, Mural RJ, Palumbo A, Tiedje JM (2003) Bacterial phylogenetic diversity and a novel candidate division of two humid region sandy surface soils. Soil Biol Biochem 3: 915-924.
45. Zhou J, Bruns M (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322.