Identification of Culturable Oligotrophic Bacteria within Naturally Occurring Bacterioplankton Communities of the Ligurian Sea by 16S rRNA Sequencing and Probing |
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Authors: | L Giuliano M De Domenico E De Domenico MG Höfle MM Yakimov |
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Institution: | (1) Dipartimento di Biologia Animale ed Ecologia Marina, Universitá di Messina, Salita Sperone, 31, 98166 Messina, Italy, IT;(2) GBF National Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany, DE;(3) CSRAFA Sicilian Centre for Atmospheric Research and Applied Physics, Universite' di Messina, Salite Sperone, 31, 98166, Messina, Italy, IT |
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Abstract: | Abstract
Typical marine bacteria (i.e., obligately oligotrophic) that were numerically dominant members of naturally occurring marine
communities were identified by cloning and sequencing the amplified 16S rRNA genes obtained from dilution cultures of the
original samples. The data reported here refer to two different habitats of a marine pelagic environment (28 miles offshore,
in the northwestern Mediterranean Sea). The samples were taken from the water column at two representative layers, i.e., the
30-m depth, corresponding to the chlorophyll maximum layer, and the 1800-m depth, representative of a deep, oligotrophic environment.
Three major lineages were found in the 16S rDNA clone libraries prepared from the two samples, two of which could be assigned
to the Vibrio and the Rhodobacter groups. The third lineage was a distant relative of the genus Flavobacterium, but it was not closely related to any marine isolate. Six oligonucleotide probes, either complementary to the conserved sequence
domains or selectively hybridizing to the clone sequences, were designed for use as hybridization group-specific and strain-specific
probes. A single-mismatch discrimination between certain probes and nontarget sequences was demonstrated by detecting the
probes' specificity at different hybridization and washing conditions. The screening of the clone libraries with the obtained
probes revealed that neither the 30-m sample higher dilution nor the 1800-m one were pure cultures. While some representatives
of the Vibrio group were found in both the surface and the deep sample, the members of the Flavobacterium and Rhodobacter lineages were detected only in the deep and the euphotic layers, respectively. We suggest an approach for analyzing autochthonous
marine bacteria able to grow in unamended seawater.
Received: 19 May 1998; Accepted: 29 October 1998 |
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