Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

Journal of Environmental Sciences

Volumn 20, Issue 2, 2008, Pages 224-230

  ZHAO, Xingqing ^a   YANG, Liuyan ^a   YU, Zhenyang ^a   PENG, Naiying ^a   XIAO, Lin ^a   YIN, Daqiang ^a   QIN, Boqiang ^b  

^a NANJING UNIVERSITY   (China)

^b NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

Author keywords

16S rRNA; denaturing gradient gel electrophoresis (DGGE); Lake Taihu; microbial diversity; sediment; vertical distribution

Indexed keywords

CHARACTERIZATION; ELECTROPHORESIS; MICROORGANISMS; NITROGEN; ORGANIC COMPOUNDS; PH; PHOSPHORUS; SEDIMENTS;

CULTURE-INDEPENDENT METHOD; DENATURING GRADIENT GEL ELECTROPHORESIS; MICROBIAL DIVERSITY; PRINCIPLE COORDINATES ANALYSIS; REDOX POTENTIAL;

LAKE POLLUTION;

BACTERIAL RNA; FRESH WATER; NITROGEN; OXYGEN; PHOSPHORUS; RNA 16S;

CHARACTERIZATION; ELECTROPHORESIS; LAKE POLLUTION; MICROORGANISMS; NITROGEN; ORGANIC COMPOUNDS; PH; PHOSPHORUS; SEDIMENTS;

ELECTROKINESIS; LACUSTRINE DEPOSIT; MICROBIAL COMMUNITY; NITROGEN; ORGANIC MATTER; PH; PHOSPHORUS; PHYSICOCHEMICAL PROPERTY; REDOX POTENTIAL; RNA; SEDIMENT CHEMISTRY; SEDIMENT CORE; VERTICAL DISTRIBUTION;

ARTICLE; BACTERIUM; CHINA; CLASSIFICATION; ELECTROPHORESIS; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PH; PHYLOGENY; POLYMERASE CHAIN REACTION; SEDIMENT;

BACTERIA; BASE SEQUENCE; CHINA; ELECTROPHORESIS; FRESH WATER; GEOLOGIC SEDIMENTS; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; NITROGEN; OXYGEN; PHOSPHORUS; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; WATER MICROBIOLOGY;

ASIA; CHINA; EURASIA; FAR EAST; TAIHU LAKE;

ACINETOBACTER; ACINETOBACTER SP.; BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); BREVIBACILLUS; EXIGUOBACTERIUM; GAMMAPROTEOBACTERIA; PROTEOBACTERIA; UNIDENTIFIED BACTERIUM;

EID: 38949142333     PISSN: 10010742     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1001-0742(08)60035-2     Document Type: Article

References (30)

1. Amann R., Ludwig W., and Schleifer K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59 (1995) 143-169
2. Andreoni V., Cavalca L., Rao M., Nocerino G., Bernascorri S., Dell'Amico M., Colombo M., and Gianfreda L. Bacteria communities and enzyme activities of PAHs polluted soils. Chemosphere 57 (2004) 401-412
3. Atlas R. Diversity of microbial communities. Adv Microb Ecol 1 (1984) 1-47
4. Bakermans C., and Madsen E. Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tar-waste-contaminated aquifer waters. Microb Ecol 44 (2002) 95-106
5. Boon N., Marie C., Top E., and Verstraete W. Comparison of the spatial homogeneity of physicochemical parameters and bacterial 16S rRNA genes in sediment samples from a dumping site for dredging sludge. Appl Microbiol Biotech-nol 53 (2000) 742-747
6. Bosshard P., Stettler R., and Bachofen R. Seasonal and spatial community dynamics in the meromictic Lake Cadagno. Arch Microbiol 174 (2000) 168-174
7. Casamayor E., Schafer H., Baneras L., Pedrós-Alió C., and Muyzer G. Identification and spatiotemporal difference between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Appl Environ Microbiol 66 (2000) 499-508
8. Eichner C., Erb R., Timmis K., and Wagner-Döbler I. Thermal gradient gel electrophoresis analysis of bioprotec-tion from pollutant shocks in the activated sludge microbial community. Appl Environ Microbiol 65 (1999) 102-109
9. Erik J., Gabriel Z., Micranda P., Herman J., Jeannine E., and Hendrikus J. Changes in bacterial and ewukaryotic community structure after mass lysis of filamentous cyanobacteria associated with virus. Appl Environ Microbiol 65 (1999) 795-801
10. Felske A., and Akkermans A. Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils. Microb Ecol 36 (1998) 31-36
11. Ferris M., Muyzer G., and Ward D. Denaturing gradient gel electrophoresis profiles of 16S rRNA defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 62 (1996) 340-346
12. Hollibaugh J., Wong P., Bano N., Pak S., Prager E., and Orrego C. Stratification of microbial assemblage in Mono Lake, California, and response to amixing event. Hydrobiologia 466 (2001) 45-60
13. Humayoun S., Bano N., and Hollibaugh J. Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Appl Environ Microbiol 69 (2003) 1030-1042
14. Koizumi Y., Takii S., and Fukui M. Depth-related change in archaeal community structure in a freshwater lake sediment as determined with denaturing gradient gel electrophoresis of amplified 16S rRNA genes and reversely transcribed rRNA fragments. FEMS Microbiol Ecol 48 (2004) 285-292
15. Lai X., Zeng X., Fang S., Huang Y., Cao L., and Zhou S. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial community composition in deep-sea sediments of the South China Sea. J Microbiol Biotechnol 22 (2006) 1337-1345
16. Li S., Xiao X., Yin X., and Wang F. Bacterial community along a historic lake sediment core of Ardley Island, west Antarctica. Extremophiles 10 (2006) 461-467
17. Luo H., Qi H., and Zhang H. Diversity surveys of soil bacterial community by cultivation-based methods and molecular fingerprinting techniques. J Environ Sci 16 4 (2004) 581-584
18. Macnaughton S., Stephen J., Venosa A., Davis G., Chang Y., and White D. Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microbiol 65 (1999) 3566-3574
19. Miskin I., Farrimond P., and Head I. Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR. Microbiology 145 (1999) 1977-1987
20. Muyzer G., Waal E., and Uitterlinden A. Profiling of complex microbial populations using denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl Environ Microbiol 59 (1993) 695-700
21. Øvreås L., Forney L., Daae F., and Torsvik V. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63 (1997) 3367-3373
22. Pringaut O., de W., and Caumette P. A benthic gradient chamber for culturing phototrophic sulfur bacteria on reconstituted sediments. FEMS Microbiol Ecol 20 (1996) 237-250
23. Ravenschlag K., Sahm K., Knoblauch C., Jørgensen B., and Amann R. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl Environ Microbiol 66 (2000) 3592-3602
24. Sahm K., MacGregor B., Jørgensen B., and Stahl D. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ Microbiol 1 (1999) 65-74
25. Schauer M., Massana R., and Pedrós-Alió C. Spatial differences in bacterioplankton composition along the Catalan coast (NW Mediterranean) assessed by molecular fingerprinting. FEMS Microbiol Ecol 33 (2000) 51-59
26. Sheppard S., and Lloyd D. Direct mass spectrometric measur-ment of gases in soil monoliths. J Microbiol Methods 50 (2002) 175-188
27. Teske A., Wawer C., Muyer G., and Ramsing N. Distribution of sulfate-reducing bacteria in stratified fjord (Mariager Fjord, Denmark) as evauated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl Environ Microbiol 62 (1996) 1405-1415
28. Urakawa H., Yoshida T., Nishimura M., and Ohwada K. Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling. Environ Microbiol 2 (2000) 542-554
29. Wilms R., Köpke B., Sass H., Chang T., Cypionka H., and Engelen B. Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8 4 (2006) 709-719
30. Zhou J., Mary B., and James M. DNA recovery from soils of diverse composition. Appl Environ Microbiol 62 (1996) 316-322