Detection and Direct Count of Specific Bacteria in Natural Seawater Using 16S rRNA Oligonucleotide Probe.

Partial sequences of the 16S rRNA molecules of nine strains belonging to four Azospirillum species were used to design species-specific oligonucleotide probes. Azospirillum strains sequences were analyzed and three homologous fragments containing 16 nucleotides were determined. These three probes were found to be characteristic of A. lipoferum (Al), A. irakense (Ai), and A. brasilense/amazonense species (Aba) and of few nontarget organisms. The specificity of these three probes was tested both against sequences in the GenBank data base and in numerous colony hybridization experiments. As a few non-target organisms hyridized with the different Azospirillum probes, the use of these probes in bulk soil hybridization is not permitted. However, their use together with specific isolation techniques is validated.Key words: Azospirillum, bacterial isolation, hybridization, oligonucleotide probe, sequence analysis, 16S rRNA.

Download Full-text

Design and Performance of a 16S rRNA-Targeted Oligonucleotide Probe for Detection of Members of the Genus Bdellovibrio by Fluorescence In Situ Hybridization

Applied and Environmental Microbiology ◽

10.1128/aem.02754-07 ◽

2008 ◽

Vol 74 (3) ◽

pp. 921-921

Author(s):

Khaled K. Mahmoud ◽

Damian McNeely ◽

Chelsea Elwood ◽

Susan F. Koval

Keyword(s):

In Situ Hybridization ◽

16S Rrna ◽

Fluorescence In Situ Hybridization ◽

Oligonucleotide Probe ◽

And Performance

Download Full-text

Distribution of viable marine bacteria in neritic seawater around Japan

Canadian Journal of Microbiology ◽

10.1139/m80-052 ◽

1980 ◽

Vol 26 (3) ◽

pp. 318-323 ◽

Cited By ~ 42

Author(s):

Kazuhiro Kogure ◽

Ushio Simidu ◽

Nobuo Taga

Keyword(s):

Organic Matter ◽

Viable Count ◽

Tokyo Bay ◽

Natural Seawater ◽

Sagami Bay ◽

Direct Count ◽

Free Living ◽

The Kuroshio ◽

Kuroshio Region ◽

Living Bacteria

The direct viable count (DVC) method of determining the number of living bacteria in natural seawater was applied to samples collected from areas around Japan ranging from polluted to oligotrophic. In summer, the DVC comprised 1.5–39.8% (mean, 11.2%) of the total direct count (TDC) in Tokyo Bay, which was highly eutrophic. In offshore areas (Sagami Bay and the Kuroshio region), the percentages ranged from 0.7 to 7.9 (mean, 2.8%). In winter, slightly higher percentages were observed in Sagami Bay. The majority of DVC cells were free-living. The distribution of bacteria correlated closely with particulate or dissolved organic matter.

Download Full-text

Development and application of 16S rRNA-targeted oligonucleotide probe for detection of the phosphate-accumulating bacterium microlunatus phosphovorus in an enhanced biological phosphorus removal process

Water Science & Technology ◽

10.2166/wst.1998.0700 ◽

1998 ◽

Vol 37 (4-5) ◽

pp. 481-484 ◽

Cited By ~ 7

Author(s):

Mamoru Kawaharasaki ◽

Takahiro Kanagawa ◽

Hideo Tanaka ◽

Kazunori Nakamura

Keyword(s):

16S Rrna ◽

Activated Sludge ◽

Phosphorus Removal ◽

Oligonucleotide Probe ◽

Enhanced Biological Phosphorus Removal ◽

Biological Phosphorus Removal ◽

Phylogenetic Groups ◽

Removal Process ◽

Biological Phosphorus ◽

Total Bacteria

A 16S rRNA-targeted oligonucletide probe (MP2) specific for the phosphate-accumulating bacterium (PAB) M. phosphovorus was designed and applied to a sludge from an enhanced biological phosphorus removal (EBPR) process. Probes specific for defined phylogenetic groups and the polyphosphate staining dye, DAPI (4′, 6-diamidino-2-phenylindol dihydrochloride) were also used to analyze the activated sludge community. M. phosphovorus was about 3% of the total bacteria in the EBPR sludge used. Proteobacteria belonging to the beta subclass were the most abundant. Many coccoid bacteria similar to M. phosphovorus were stained with DAPI. The percentage of PABs detected by DAPI stain was about 9% of the total bacteria.

Download Full-text

Section 3 update: Use of Cloned Artificial Targets for FISH (catFISH) for the optimization of oligonucleotide probe hybridization conditions with 16S rRNA clones for in situ quantification of uncultivated prokaryotic cells

Molecular Microbial Ecology Manual ◽

10.1007/978-1-4020-2177-0_312 ◽

2008 ◽

pp. 2629-2644

Author(s):

Cleber C. Ouverney ◽

Gary C. Armitage ◽

David A. Relman

Keyword(s):

16S Rrna ◽

Oligonucleotide Probe ◽

Probe Hybridization

Download Full-text

Devosia subaequoris sp. nov., isolated from beach sediment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65185-0 ◽

2007 ◽

Vol 57 (10) ◽

pp. 2212-2215 ◽

Cited By ~ 31

Author(s):

Soon Dong Lee

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Marine Bacterium ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

Natural Seawater ◽

Phenotypic Data ◽

Beach Sediment ◽

Type Strains

A novel marine bacterium was isolated from a sediment sample from Hwasun Beach in Jeju, Republic of Korea. The cells were found to be Gram-negative, aerobic, oxidase-positive, catalase-positive, motile rods. The organism required natural seawater or artificial sea salts for growth. The temperature and pH ranges for growth were 20–42 °C and pH 5.1–12.1, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the order Rhizobiales and formed a robust cluster with members of the genus Devosia. Its phylogenetic neighbours were the type strains of Devosia riboflavina (96.8 % 16S rRNA gene sequence similarity), Devosia neptuniae (96.7 %), Devosia soli (96.5 %) and Devosia limi (96.2 %), ‘Devosia terrae’ DCY11 (96.2 %) and ‘Candidatus Devosia euplotis’ (96.2 %). The predominant ubiquinone was Q-10, the major fatty acids were C18 : 1, C18 : 0 and C16 : 0 and the G+C content of the DNA was 59.1 mol%. On the basis of phenotypic data and the results of phylogenetic analyses, strain HST3-14T represents a novel species of the genus Devosia, for which the name Devosia subaequoris sp. nov. is proposed. The type strain is strain HST3-14T (=KCTC 12772T =JCM 14206T).

Download Full-text