Effect of restriction endonucleases on assessment of biodiversity of cultivable polar marine planktonic bacteria by amplified ribosomal DNA restriction analysis.
To choose a suitable restriction endonuclease for quick assessment of bacterial diversity in polar environments by ARDRA, we investigated the effect of restriction enzymes on ARDRA patterns of cultivable marine planktonic bacteria isolated from polar region. Thirty-three isolates were analyzed by ARDRA using five enzymes (HinfI, HaeIII, AluI, and the mix AfaI/MspI), respectively, resulting in different groups, each group corresponding to a particular genotype. A comparison of the ARDRA patterns was carried out, and phylogenetic position of all thirty-three bacteria was obtained by 16S rDNA sequencing. Consistent with phylogenetic analysis, ARDRA pattern comparison revealed that AluI, being sensitive and reliable enough to generate species-specific patterns, was a suitable restriction enzyme used for evaluating bacterial diversity, suggesting a combination of ARDRA with AluI and 16S rDNA sequencing can provide a simple, fast and reliable means for bacterial identification and diversity assessment in polar environments.
Zeng
Yinxin
Y
Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai, 200136, People's Republic of China. yxzeng@yahoo.com
Liu
Wenqi
W
Li
Huirong
H
Yu
Yong
Y
Chen
Bo
B
D000864:Antarctic Regions; D001110:Arctic Regions; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D044822:Biodiversity; D003081:Cold Climate; D004262:DNA Restriction Enzymes / Q000378:metabolism*; D004269:DNA, Bacterial / Q000378:metabolism*; D004275:DNA, Ribosomal / Q000378:metabolism*; D019003:Deoxyribonuclease HpaII / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D005838:Genotype; D010802:Phylogeny; D010933:Plankton / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D015203:Reproducibility of Results; D015183:Restriction Mapping; D021521:Ribotyping / Q000379:methods*; D012623:Seawater / Q000382:microbiology; D014871:Water Microbiology
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D004262:DNA Restriction Enzymes; D019003:Deoxyribonuclease HpaII; C024669:endodeoxyribonuclease AluI; D015252:Deoxyribonucleases, Type II Site-Specific; C032229:GANTC-specific type II deoxyribonucleases; C024403:GGCC-specific type II deoxyribonucleases; C040158:GTAC-specific type II deoxyribonucleases