Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton

Abstract

The diversity of cultured planktonic bacteria was analyzed. Bacterial strains were isolated from a eutrophic lake (Zwischenahner Meer, Niedersachsen, Germany) at three different sampling dates (October 1997, April and May 1998). Phylogenetic diversity was assessed by polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and sequencing of 16S rRNA gene fragments. Enterobacterial repetitive intergenic consensus (ERIC)-PCR revealed a high genomic diversity within the strain collections, which exceeded the diversity of the 16S rRNA gene sequences considerably. The composition of each of the three strain collections was unique since strains isolated at different dates always exhibited different ERIC-PCR fingerprints. Growth tests with 59 different carbon substrates demonstrated that even strains with identical ERIC-PCR fingerprints, isolated on one sampling date, differed in their physiology. The culturable fraction investigated in the present study constituted a relatively small fraction (</=15%) of the whole bacterioplankton assemblage. Nevertheless, the high physiological diversity in this fraction already indicates that a multitude of different ecological niches must exist in the planktonic environment. The majority of strains isolated in April prior to the decay of the phytoplankton bloom were members of the Cytophaga-Flavobacterium group. One month later, not a single strain of this group could be isolated. When a group-specific PCR-DGGE technique was employed, rapid shifts in the diversity of non-cultured Cytophaga-Flavobacteria also became evident. Based on the rapid shifts in the composition of cultivated as well as some non-cultivated bacteria, the ecological niches in the planktonic habitat must undergo rapid temporal changes.

Detection of abundant bacteria in the Weser estuary using culture-dependent and culture-independent approaches

“…1). Such cultivation efficiencies are significantly higher than on solid media and are in line with previous reports applying the same approach without any or with low nutrient addition, or with addition of only signal molecules such as cAMP and acetyl homoserine lactones , Bussmann et al 2001, Jaspers et al 2001, Bruns et al 2002, 2003a. This approach also enabled us to isolate bacteria from dilution steps of 10 -6 to 10 -9…”

“…One promising approach to enrich and isolate members of the bacterioplankton community is the dilution culture technique, involving the addition of nutrients at low concentrations, signal molecules, or no additional nutrients , Bussmann et al 2001, Jaspers et al 2001, Bruns et al 2002, 2003a,b, Rappé et al 2002. It allows for growth of the most abundant bacteria in high dilution steps without the competition of less abundant but possibly faster-growing bacteria.…”

Fate of Heterotrophic Microbes in Pelagic Habitats: Focus on Populations

“…In contrast, traditional microbiological research is mainly centered on the physiological properties of bacterial strains in pure culture (109,127). In between these two levels of analysis there is a conspicuous gap of information.…”

Composition and dynamics of particle-associated and free-living bacterial communities in the Weser estuary, Germany

“…Two of these sequences were most prominent in the particle-associated fraction and not detectable in the free-living bacterial fraction. Most of the sequences affiliating to Actinobacteria fell into 1 narrow cluster which also contained other phylotypes from Crater Lake (Urbach et al 2001), mesotrophic and eutrophic lakes in Germany (Jaspers et al 2001, Zwisler et al 2003, The Netherlands (Zwart et al 1998) and Denmark (Riemann & Winding 2001). These phylotypes represented prominent bands in our DGGE patterns and occurred repeatedly throughout the study period in the freshwater and brackish section.…”