The use of terminal restriction fragment length polymorphism (T-RFLP) for the characterisation of microbial communities in marine sediments

Geomicrobiology Journal

Volumn 23, Issue 5, 2006, Pages 247-251

  Pereira, M Glória ^a   Latchford, John W ^a   Mudge, Stephen M ^a  

^a BANGOR UNIVERSITY   (United Kingdom)

Author keywords

16S rRNA; Bacteria; Sediments; T RFLP

Indexed keywords

BACTERIUM; MARINE SEDIMENT; MICROBIAL COMMUNITY; PHYLOGENY; POLYMORPHISM;

EURASIA; EUROPE; FARO [PORTUGAL]; PORTUGAL; RIA FORMOSA; SOUTHERN EUROPE;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS);

EID: 33750031069     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490450600760617     Document Type: Conference Paper

References (26)

1. Clement, B and Kehl, L and DeBord, K and Kitts, K. (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities J Microbiol Meth, 31, pp. 135-142. http://www.csa.com/htbin/linkabst.cgi?issn= 0167-7012&vol=31&iss=&firstpage=135
2. Cole, J and Chai, B and Marsh, T and Farris, R and Wang, Q and Kulam, S and Chandra, S and McGarrell, D and Schmidt, T and Garrity, G. (2003) The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy Nucl Acids Res, 1, pp. 442-432. http://dx.doi.org/10.1093%2Fnar%2Fgkg039 http://www.csa.com/htbin/linkabst.cgi?issn=0309-1872&vol=1&iss= &firstpage=442
3. Dollhopf, S and Hashsham, S and Tiedje, J. (2001) Interpreting 16S rRNA T-RFLP data: Application of self-organising maps and principal component analysis to describe community dynamics and convergence Microb Ecol, 42, pp. 495-505. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 12024232&Session=&searchQuery=Microb+Ecol%5BJournal+Name%5D+AND+ 42%5BVolume%5D+AND+495%5BPage+Number%5D+AND+2001%5BPublication+Date%5D+ AND+Dollhopf%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1007%2Fs00248-001-0027-7 http://www.csa.com/htbin/linkabst.cgi?issn=0095-3628&vol=42&iss= &firstpage=495
4. Dunbar, J and Ticknor, L and Kuske, C. (2000) Assessment of microbial diversity in four Southwestern United States soils by 16S rRNA gene terminal restriction fragments analysis Appl Environ Microbiol, 66, pp. 2943-2950. http://www4.infotrieve.com/newmedline/ detail.asp?NameID=10877790&Session=&searchQuery=Appl+Environ+ Microbiol%5BJournal+Name%5D+AND+66%5BVolume%5D+AND+2943%5BPage+Number%5D+ AND+2000%5BPublication+Date%5D+AND+Dunbar%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1128%2FAEM.66.7.2943-2950.2000 http://www.csa.com/htbin/linkabst.cgi?issn= 0099-2240&vol=66&iss=&firstpage=2943
5. Fenchel, T and Finlay, B. (1995) Ecology and evolution in anoxic worlds Microb Ecol, 36, pp. 23-30. http://www.csa.com/htbin/ linkabst.cgi?issn=0095-3628&vol=36&iss=&firstpage=23
6. Franklin, R and Blum, L and McComb, A and Mills, A. (2002) A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments FEMS Microbiol Ecol, 42, pp. 71-80. http://www4.infotrieve.com/newmedline/detail.asp?NameID=12542032& Session=&searchQuery=FEMS+Microbiol+Ecol%5BJournal+Name%5D+AND+ 42%5BVolume%5D+AND+71%5BPage+Number%5D+AND+2002%5BPublication+Date%5D+ AND+Franklin%5BAuthor+Name%5D&count=1 http://dx.doi.org/ 10.1111%2Fj.1574-6941.2002.tb00996.x http://www.csa.com/htbin/ linkabst.cgi?issn=0168-6496&vol=42&iss=&firstpage=71
7. Fuhrman, J and Griffith, J and Schwalbach, M. (2002) Prokaryotic and viral diversity patterns in marine plankton Ecol Res, 17, pp. 183-194. http://dx.doi.org/10.1046%2Fj.1440-1703.2002.00478.x http://www.csa.com/htbin/ linkabst.cgi?issn=1522-4740&vol=17&iss=&firstpage=183
8. Giovannoni, S and Britschgi, T and Moyer, C and Field, K. (1990) Genetic diversity in Sargasso Sea bacterioplankton Nature, 345, pp. 60-63. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 2330053&Session=&searchQuery=Nature%5BJournal+Name%5D+AND+ 345%5BVolume%5D+AND+60%5BPage+Number%5D+AND+1990%5BPublication+Date%5D+ AND+Giovannoni%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1038%2F345060a0 http://www.csa.com/htbin/linkabst.cgi?issn=0028-0887&vol= 345&iss=&firstpage=60
9. Gordon, D and Giovannoni, S. (1996) Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific Oceans Appl Environ Microbiol, 62, pp. 1171-1177. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 8919778&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+62%5BVolume%5D+AND+1171%5BPage+Number%5D+AND+ 1996%5BPublication+Date%5D+AND+Gordon%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=62&iss= &firstpage=1171
10. Guschin, D and Maobarry, B and Prodnikov, D and Stahl, D and Rittmann, B and Mirzabekov, A. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology Appl Environ Microbiol, 63, pp. 2397-2402. http://www4.infotrieve.com/ newmedline/detail.asp?NameID=9172361&Session=&searchQuery=Appl+ Environ+Microbiol%5BJournal+Name%5D+AND+63%5BVolume%5D+AND+2397%5BPage+ Number%5D+AND+1997%5BPublication+Date%5D+AND+Guschin%5BAuthor+ Name%5D&count=1 http://www.csa.com/htbin/ linkabst.cgi?issn=0099-2240&vol=63&iss=&firstpage=2397
11. Hugenholtz, P and Goebel, B and Pace, N. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity J Bacteriol, 180, pp. 4765-4774. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 9733676&Session=&searchQuery=J+Bacteriol%5BJournal+Name%5D+AND+ 180%5BVolume%5D+AND+4765%5BPage+Number%5D+AND+1998%5BPublication+Date%5D+ AND+Hugenholtz%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/ linkabst.cgi?issn=0368-3494&vol=180&iss=&firstpage=4765
12. Kaplan, C and Kitts, C. (2003) Variation between observed and true Terminal Restriction Fragment length is dependent on true TRF length and purine content J Microbiol Meth, 54, pp. 121-125. http://dx.doi.org/10.1016%2FS0167-7012%2803%2900003-4 http://www.csa.com/htbin/linkabst.cgi?issn=0167-7012&vol=54&iss= &firstpage=121
13. Kent, A and Smith, D and Benson, B and Triplett, E. (2003) Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities Appl Environ Microbiol, 69, pp. 6768-6776. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 14602639&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+69%5BVolume%5D+AND+6768%5BPage+Number%5D+AND+ 2003%5BPublication+Date%5D+AND+Kent%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1128%2FAEM.69.11.6768-6776.2003 http://www.csa.com/ htbin/linkabst.cgi?issn=0099-2240&vol=69&iss=&firstpage=6768
14. Liu, W-T and Marsh, T and Cheng, H and Forney, L. (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA Appl Environ Microbiol, 63, pp. 4516-4522. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 9361437&Session=&searchQuery=Appl+Environ+Microbiol%5BJournal+ Name%5D+AND+63%5BVolume%5D+AND+4516%5BPage+Number%5D+AND+ 1997%5BPublication+Date%5D+AND+Liu%5BAuthor+Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=63&iss= &firstpage=4516
15. Luna, G and Dell'Anno, A and Giuliano, L and Danovaro, R. (2004) Bacterial diversity in deep Mediterranean sediments: Relationship with the active bacterial fraction and substrate availability Environmental Microbiology., 6, pp. 745-753. http://www4.infotrieve.com/ newmedline/detail.asp?NameID=15186353&Session=&searchQuery= Environmental+Microbiology%2E%5BJournal+Name%5D+AND+6%5BVolume%5D+AND+ 745%5BPage+Number%5D+AND+2004%5BPublication+Date%5D+AND+Luna%5BAuthor+ Name%5D&count=1 http://dx.doi.org/10.1111%2Fj.1462-2920.2004.00611.x http://www.csa.com/htbin/ linkabst.cgi?issn=1462-2912&vol=6&iss=&firstpage=745
16. Marsh, T and Saxman, P and Cole, J and Tiedje, J. (2000) Terminal restriction fragment length polymorphism analysis program, a web based research tool for microbial community analysis Appl Environ Microbiol, 66, pp. 3616-3620. http://www4.infotrieve.com/newmedline/ detail.asp?NameID=10919828&Session=&searchQuery=Appl+Environ+ Microbiol%5BJournal+Name%5D+AND+66%5BVolume%5D+AND+3616%5BPage+Number%5D+ AND+2000%5BPublication+Date%5D+AND+Marsh%5BAuthor+Name%5D&count=1 http://dx.doi.org/10.1128%2FAEM.66.8.3616-3620.2000 http://www.csa.com/htbin/linkabst.cgi?issn=0099-2240&vol=66&iss= &firstpage=3616
17. Moeseneder, M and Arrieta, J and Muyze, G and Winter, C and Herndl, G. (1999) Optimization of Terminal-Restriction Length Polymorphism (T-RFLP) analysis for complex marine bacterioplankton communities and comparison with Denaturing Gradient Gel Electrophoresis (DGGE) Appl Environ Microbiol, 65, pp. 3518-3525. http://www4.infotrieve.com/ newmedline/detail.asp?NameID=10427043&Session=&searchQuery=Appl+ Environ+Microbiol%5BJournal+Name%5D+AND+65%5BVolume%5D+AND+3518%5BPage+ Number%5D+AND+1999%5BPublication+Date%5D+AND+Moeseneder%5BAuthor+ Name%5D&count=1 http://www.csa.com/htbin/linkabst.cgi?issn= 0099-2240&vol=65&iss=&firstpage=3518
18. Moeseneder, M and Winter, C and Arrieta, J and Herndl, G. (2001) Terminal-restriction length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes J Microbiol Meth, 44, pp. 159-172. http://dx.doi.org/ 10.1016%2FS0167-7012%2800%2900247-5 http://www.csa.com/htbin/linkabst.cgi?issn= 0167-7012&vol=44&iss=&firstpage=159
19. Pace, N. (1997) A molecular view of microbial diversity and the biosphere Science, 276, pp. 734-740. http://www4.infotrieve.com/newmedline/detail.asp?NameID= 9115194&Session=&searchQuery=Science%5BJournal+Name%5D+AND+ 276%5BVolume%5D+AND+734%5BPage+Number%5D+AND+1997%5BPublication+Date%5D+ AND+Pace%5BAuthor+Name%5D&count=1 http://dx.doi.org/ 10.1126%2Fscience.276.5313.734 http://www.csa.com/htbin/ linkabst.cgi?issn=0294-0337&vol=276&iss=&firstpage=734
20. Pace, N and Stahl, D and Lane, D and Olsen, G. (1986) The analysis of natural microbial populations by ribosomal RNA sequences Adv Microb Ecol, 9, pp. 1-55. http://www.csa.com/htbin/ linkabst.cgi?issn=0147-4863&vol=9&iss=&firstpage=1
21. Pinhassi, J and Winding, A and Binnerup, S and Zweifel, U and Riemann, B and Hagsodie;m, Å. (2003) Spatial variability in bacterioplankton community composition at the Skagerrak-Kattegat Front Mar Ecol Prog Ser, 255, pp. 1-13. http://www.csa.com/htbin/linkabst.cgi?issn= 0171-8630&vol=255&iss=&firstpage=1
22. Stepanauskas, R and Moran, M and Bergamaschi, B and Hollibaugh, J. (2003) Covariance of bacterioplankton composition and environmental variables in a temperate delta system Aquatic Microb Ecol, 31, pp. 85-98. http://www.csa.com/htbin/linkabst.cgi?issn= 0948-3055&vol=31&iss=&firstpage=85
23. Tiedje, J and Asuming-Brempong, S and Nüslei, K and Marsh, T and Flynn, S. (1999) Opening the black box of soil microbial diversity Appl Soil Ecol, 13, pp. 109-122. http://dx.doi.org/ 10.1016%2FS0929-1393%2899%2900026-8 http://www.csa.com/htbin/linkabst.cgi?issn= 0929-1393&vol=13&iss=&firstpage=109
24. Torsvik, V and Sorheim, R and Goksoyr, J. (1996) Total bacterial diversity in soil and sediment communities - a review J Ind Microbiol, 17, pp. 170-178. http://dx.doi.org/10.1007%2FBF01574690 http://www.csa.com/htbin/ linkabst.cgi?issn=0169-4146&vol=17&iss=&firstpage=170
25. Urakawa, H and Yoshida, T and Nishimura, M and Ohwada, K. (2001) Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling Mar Ecol Prog Ser, 220, pp. 47-57. http://www.csa.com/htbin/linkabst.cgi?issn=0171-8630&vol=220&iss= &firstpage=47
26. Zwisler, W and Selje, N and Simon, M. (2003) Seasonal patterns of the bacterioplankton community composition in a large mesotrophic lake Aquatic Microb Ecol, 31, pp. 211-225. http://www.csa.com/ htbin/linkabst.cgi?issn=0948-3055&vol=31&iss=&firstpage=211