The microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates

Abstract

Picoplankton bacteria from a North Sea water sample were cultured under a variety of different conditions (nutrients, temperature, light, agitation, adhesion). Fluorescent in situ hybridization (FISH) analysis of the enrichments showed complex communities which were dominated by gamma-Proteobacteria or beta-Proteobacteria, followed by alpha-Proteobacteria and bacteria from the Cytophaga/Flavobacterium/Bacteroides (CFB) cluster. Among 410 isolates, a high degree of diversity was found, both with respect to colony color and morphology and with respect to genetic diversity. Isolated bacteria were classified into the main taxa by a special PCR approach, termed signature PCR (SIG-PCR). It was based on an oligo primer mixture targeting 16S rDNA which yielded PCR products of taxon-specific lengths. Again, gamma-Proteobacteria dominated (48%), followed by alpha-Proteobacteria (20%). beta-Proteobacteria were rarely isolated (eight strains of 410). The CFB cluster comprised the second largest phylum (14%), and 7.5% of all isolates belonged to the high-GC Gram-positives. Thus, isolated bacteria were representative of enrichment communities with the exception of the beta-Proteobacteria, which were detected in high abundance in certain enrichments by FISH but not isolated, and the high-GC Gram-positives, which were cultivated but not detected by FISH. A genomic fingerprinting technique, randomly amplified polymorphic DNA, showed that among 58 CFB isolates only 18 identical genotypes were found, and among the 84 alpha-Proteobacteria only eight identical genotypes were present. The data show the enormous diversity of cultivated bacteria from picoplankton enrichment cultures of one North Sea water sample, which is only a small fraction of the total picoplankton community.

Phospholipid fatty acid profiles at depositional and non-depositional sites in the North Sea

“…Since the application of molecular biological tools, members of the CFB phylum have been detected in an increasing number of different marine habitats (e.g. DeLong et al 1993, Bowman et al 1997, Llobet-Brossa et al 1998, Rath et al 1998, Eilers et al 2000, Uphoff et al 2001, Weller et al 2000. Although members of the CFB group can adapt to rather low nutrient levels (Höfle 1983) as we observed at the nondepositional sites (Fig.…”

Jannaschia helgolandensis gen. nov., sp. nov., a novel abundant member of the marine Roseobacter clade from the North Sea

“…Approximately 20 % of isolates obtained from a North Sea water sample and from enrichments made from filtered (5 mm) North Sea water using a diverse spectrum of incubation conditions (Uphoff et al, 2001) belonged to the 'Roseobacter-Sulfitobacter-Silicibacter' group on the basis of partial 16S rDNA sequencing. Strains Hel 10 T and Hel 26 were isolated by direct plating of serially diluted sea-water samples on complex media.…”

“…Enrichments made from filtered (5 mm) sea water with a variety of media and incubation conditions yielded 84 members of the a-subclass of the Proteobacteria from a total of 410 strains, as judged by specific 16S rDNA-targeted multiplex PCR (signature PCR) and fluorescent in-situ hybridization analysis (Uphoff et al, 2001). Of these strains, eight were multiple isolates, based on genomic fingerprints (RAPD PCR).…”

Future Antibiotic Agents: Turning to Nature for Inspiration

“…media formulation, light, temperature, agitation) have shown some success (Köpke et al, 2005;Uphoff et al, 2001;Zengler et al, 2002). However, the approach is strictly empirical and the yield is rather unpredictable.…”