Rapid identification of marine bioluminescent bacteria by amplified 16S ribosomal RNA gene restriction analysis.
To rapidly identify natural isolates of marine bioluminescent bacteria, we developed amplified ribosomal DNA restriction analysis (ARDRA) methods. ARDRA, which is based on the restriction patterns of 16S rRNA gene digested with five enzymes (EcoRI, DdeI, HhaI, HinfI, RsaI), clearly distinguished the 14 species of marine bioluminescent bacteria currently known, which belong to the genera Vibrio, Photobacterium, and Shewanella. When we applied ARDRA to 129 natural isolates from two cruises in Sagami Bay, Japan, 127 were grouped into six ARDRA types with distinctive restriction patterns; these isolates represented the bioluminescent species, P. angustum, P. leiognathi, P. phosphoreum, S. woodyi, V. fischeri, and V. harveyi. The other two isolates showing unexpected ARDRA patterns turned out to have 16S rRNA gene sequences similar to P. leiognathi and P. phosphoreum. Nevertheless, ARDRA provides a simple and fairly robust means for rapid identification of the natural isolates of marine bioluminescent bacteria, and is therefore useful in studying their diversity.
Kita-Tsukamoto
Kumiko
K
Ocean Research Institute, The University of Tokyo, Minamidai, Tokyo, Japan. tukamoto@ori.u-tokyo.ac.jp
Wada
Minoru
M
Yao
Katomi
K
Kamiya
Akiko
A
Yoshizawa
Susumu
S
Uchiyama
Nami
N
Kogure
Kazuhiro
K
D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D018407:Bacterial Physiological Phenomena; D033342:Copepoda / Q000382:microbiology; D016172:DNA Fingerprinting / Q000379:methods*; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004269:DNA, Bacterial / Q000032:analysis / Q000378:metabolism; D004275:DNA, Ribosomal / Q000032:analysis / Q000378:metabolism; D004587:Electrophoresis, Agar Gel; D020459:Genes, rRNA; D019015:Geologic Sediments / Q000382:microbiology*; D007564:Japan; D049449:Luminescence; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D010776:Photobacterium / Q000145:classification / Q000302:isolation & purification; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012623:Seawater / Q000382:microbiology*; D020592:Shewanella / Q000145:classification / Q000302:isolation & purification; D014733:Vibrio / Q000145:classification / Q000302:isolation & purification
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D004262:DNA Restriction Enzymes