Specific Detection, Isolation, and Characterization of Selected, Previously Uncultured Members of the Freshwater Bacterioplankton Community
Open Access
- 1 October 2005
- journal article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 71 (10), 5908-5919
- https://doi.org/10.1128/aem.71.10.5908-5919.2005
Abstract
High-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. A total of 570 bacterial cultures were obtained by employing the most probable number and MicroDrop techniques. The majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the α -Proteobacteria , β -Proteobacteria , Actinobacteria , Firmicutes , or Flavobacteria-Cytophaga lineage. Correspondingly, the natural bacterioplankton community was analyzed by high-resolution phylogenetic fingerprinting of these five bacterial lineages. 16S rRNA gene fragments were generated for each lineage and subsequently separated by denaturing gradient gel electrophoresis. By the combination of five group-specific PCR protocols, the total number of 16S rRNA gene fingerprints generated from the natural communities was increased sixfold compared to conventional (eubacterial) fingerprinting. Four of the environmental α- Proteobacteria 16S rRNA gene sequences obtained from the natural community were found to be identical to those of bacterial isolates. One of these phylotypes was detected in 14 different cultures and hence represented the most frequently cultured bacterium. Three of these 14 strains were characterized in detail. Their complete 16S rRNA gene sequences showed only 93% similarity to that of Sandaracinobacter sibiricus , the closest relative described so far. The novel phylotype of bacterium is a strict aerobe capable of using numerous organic carbon substrates and contains bacteriochlorophyll a bound to two different photosynthetic light-harvesting complexes. Dot blot hybridization revealed that the strains occur in lakes of different trophic status and constitute up to 2% of the microbial community.Keywords
This publication has 52 references indexed in Scilit:
- Environmental Genome Shotgun Sequencing of the Sargasso SeaScience, 2004
- A novel approach for high throughput cultivation assays and the isolation of planktonic bacteriaFEMS Microbiology Ecology, 2003
- Effect of Signal Compounds and Incubation Conditions on the Culturability of Freshwater BacterioplanktonApplied and Environmental Microbiology, 2003
- Cultivation of the ubiquitous SAR11 marine bacterioplankton cladeNature, 2002
- Unsuspected diversity among marine aerobic anoxygenic phototrophsNature, 2002
- Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplanktonFEMS Microbiology Ecology, 2001
- Contribution of Aerobic Photoheterotrophic Bacteria to the Carbon Cycle in the OceanScience, 2001
- Unusual bacterioplankton community structure in ultra‐oligotrophic Crater LakeLimnology and Oceanography, 2001
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in BacteriologyInternational Journal of Systematic and Evolutionary Microbiology, 1994