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Use of 16S ribosomal RNA probes for the detection of marine bacteria
Department of Microbiology, Umeå University. (Forskningsmiljön Man and Biosphere Health (MABH))ORCID iD: 0000-0002-8059-0156
1994 (English)Doctoral thesis, comprehensive summary (Other academic)
Place, publisher, year, edition, pages
Umåe: Univ. , 1994. , 35 p.
National Category
Microbiology
Identifiers
URN: urn:nbn:se:hkr:diva-10356ISBN: 91-7174-888-1 (print)OAI: oai:DiVA.org:hkr-10356DiVA: diva2:614089
Available from: 2013-04-03 Created: 2013-04-03 Last updated: 2014-06-24Bibliographically approved
List of papers
1. Identification of Vibrio anguillarum in fish by using partial 16S rRNA sequences and a specific 16S rRNA oligonucleotide probe
Open this publication in new window or tab >>Identification of Vibrio anguillarum in fish by using partial 16S rRNA sequences and a specific 16S rRNA oligonucleotide probe
1989 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 55, no 8, 1907-1910 p.Article in journal (Refereed) Published
Abstract [en]

16S rRNA from seven different Vibrio anguillarum strains was partially sequenced and compared. From this sequence information we could design a 25-base-long oligonucleotide and use it as a specific probe for identification of V. anguillarum. This was determined by RNA-DNA colony hybridization and slot-blot hybridization. Strong, specific hybridization to the probe was observed for all V. anguillarum strains tested. Furthermore, no cross-hybridization could be seen against five other bacterial species. The detection limit was 5 x 10(3) bacteria per ml. It was even possible to detect V. anguillarum, by slot-blot hybridization, directly in a homogenized kidney from a fish that had died of vibriosis. The partial sequence information revealed small but significant differences between strains of the same species. These sequence differences are sufficiently significant to allow serotyping on the RNA level. Comparing strains of different serotypes revealed a 10-base and an 11-base difference in V. anguillarum serotypes O8 and O9, respectively, in a 122-base partial sequence.

National Category
Microbiology
Identifiers
urn:nbn:se:hkr:diva-10325 (URN)A1989AH86600009 ()2782871 (PubMedID)
Available from: 2013-03-19 Created: 2013-03-19 Last updated: 2014-06-24Bibliographically approved
2. Blooms of sequence-specific culturable bacteria in the sea
Open this publication in new window or tab >>Blooms of sequence-specific culturable bacteria in the sea
Show others...
1993 (English)In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 102, no 3-4, 161-166 p.Article in journal (Refereed) Published
Abstract [en]

Using specific deoxyoligonucleotide probes we have discovered seasonally strong (up to ∼ 100%) dominance of bacteria hybridizing to a single probe, in near shore waters off Scripps pier (32°53′N; 117°15′W). The probes were designed from partially sequenced 16S rRNA (V3 domain) of isolated marine bacteria. The results indicate that this approach may be used for studies of bacterial populations in the marine environment. We have shown that a number of genotypes that at times are dominant in the natural assemblages are culturable (and not, ‘viable-but-unculturable’). Additionally, our data suggests that the discrepancy between viable counts and direct counts in sea water samples can be explained by low plating efficiency.

Keyword
Marine bacterium, Bloom, DNA probe, Identification, Colony forming
National Category
Microbiology
Identifiers
urn:nbn:se:hkr:diva-10344 (URN)10.1111/j.1574-6968.1993.tb05806.x (DOI)A1993KY71600003 ()
Available from: 2013-03-27 Created: 2013-03-27 Last updated: 2014-06-24Bibliographically approved
3. Specificity of 16S rDNA determinative probes for the detection of heterotrophic bacteria in seawater
Open this publication in new window or tab >>Specificity of 16S rDNA determinative probes for the detection of heterotrophic bacteria in seawater
(English)Manuscript (preprint) (Other academic)
National Category
Microbiology
Identifiers
urn:nbn:se:hkr:diva-10355 (URN)
Available from: 2013-04-03 Created: 2013-04-03 Last updated: 2014-06-24Bibliographically approved
4. Release of bacterial DNA by marine nanoflagellates, an intermediate step in phosphorus regeneration
Open this publication in new window or tab >>Release of bacterial DNA by marine nanoflagellates, an intermediate step in phosphorus regeneration
1992 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 58, no 11, 3744-3750 p.Article in journal (Refereed) Published
Abstract [en]

The concentrations of dissolved DNA and nanoflagellates were found to covary during a study of diel dynamics of the microbial food web in the Adriatic Sea. This observation was further investigated in a continuous seawater culture when nanoflagellates were fed bacteria grown in filtered seawater. Analysis of dissolved organic phosphorus and dissolved DNA showed a sixfold increase of dissolved DNA in the presence of the nanoflagellates (Ochromonas sp.). The amount of DNA released suggested that the majority of the consumed bacterial DNA was ejected. Phagotrophic nanoflagellates thus represent an important source of origin for dissolved DNA. The rate of breakdown of dissolved DNA and release of inorganic phosphorus in the pelagic ecosystem is suggested to be dependent on the ambient phosphate pool. In the P-limited northern Adriatic Sea, rapid degradation of the labelled DNA could be demonstrated, whereas the N-limited southern California bight water showed a much lower rate. Phosphorus originating from dissolved DNA was shown to be transferred mainly to organisms in the <3-μm-size fractions. On the basis of the C/P ratios, we suggest that a significant fraction of the phosphorus demand by the autotrophs may be sustained by the released DNA during stratified conditions. Thus, the nucleic acid-rich bacterial biomass grazed by protozoa plays an important role in the biogeochemical cycling of phosphorus in the marine environment.

National Category
Microbiology
Identifiers
urn:nbn:se:hkr:diva-10328 (URN)099-2240/92/113744-07 (DOI)A1992JW47300042 ()16348813 (PubMedID)
Available from: 2013-03-19 Created: 2013-03-19 Last updated: 2014-06-24Bibliographically approved

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