Horizontal and vertical complexity of attached and free‐living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints

Abstract

The community structure of attached and free-living bacteria in the Aegean Sea (eastern Mediterranean Sea) was analyzed with use of terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting. Since the Aegean Sea is characterized by rather small temperature fluctuations between surface and deep-water layers, it represents an ideal study site to determine the variations in the community structure of bacteria with depth, since environmental factors other than temperature are likely to determine depth zonation of bacteria. The analysis of 132 T-RFLP electropherograms indicated pronounced differences among the attached and free-living bacterial communities defined as operational taxonomic units (OTUs). Distinct vertical differences of attached and free-living OTUs were found between mesopelagic waters (Ͼ200 m depth) and the upper mixed water column (ϳ10-200 m). Attached and free-living OTUs differed considerably throughout the water column, with only ϳ35% for the South Aegean and ϳ24% for the North Aegean of all OTUs in both free-living and attached OTUs. Approximately 50% of attached and free-living OTUs were present throughout the water column. Fingerprinting analysis using 16S rRNA indicated that only ϳ14% of the attached and ϳ33% of the free-living OTUs were identical to the 16S rDNA fingerprints. The distribution of free-living versus attached bacteria as obtained in this study suggests that even in the absence of temperature as a major selective factor, a distinct deep-water bacterial community exists (particularly in the free-living mode). The deep-water free-living bacterial community appears to be as compositionally complex as the surface water free-living bacterial community.

Disentangling the spatial patterns in community composition of prokaryotic and eukaryotic lake plankton

“…Peaks that were located closer than 2 bp from each other were binned. We used the limit of 2 bp for all fragment sizes (Moeseneder et al 2001). …”

Analysis of bacterial core communities in the central Baltic by comparative RNA–DNA-based fingerprinting provides links to structure–function relationships

“…The decrease in richness in the anoxic part of the Baltic might be due to the limited groups of bacteria that could thrive without oxygen and use the available mix of electron donors and acceptors. Various vertical major communities along the water column have been observed in many aquatic ecosystems, ranging from open oceans to small lakes (Moeseneder et al, 2001;Dominik and Hö fle, 2002;Treusch et al, 2009). In comparison with large ocean basins, the vertical extent of the central Baltic is more than an order of magnitude less.…”

“…The discrepancy between RNA-and DNA-based studies of surface bacterioplankton has been observed in marine and freshwater ecosystems (Moeseneder et al, 2001;Troussellier et al, 2002;Lami et al, 2009;Treusch et al, 2009;Logue and Lindströ m, 2010). Most studies explained this phenomenon by hypothesis 2, that is, some of the present bacteria are not as active as others due to the high dynamics of surface water in terms of the diurnal light cycle.…”

Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-series Study site

“…While less specific than direct cell counts or quantitative PCR estimates, T-RFLP analyses have been used to identify differences between prokaryotic communities in response to various environmental factors. For example, Moeseneder et al (2001) used T-RFLP to compare attached and free-living bacterial communities of the eastern Mediterranean Sea, while González and coworkers (2000) used this method to fingerprint bacterioplankton communities associated with an eddy-induced oceanic algal bloom in the North Atlantic Ocean. Here we use NMS, T-RFLP, rDNA cloning, and phylogenetic analyses to identify and characterize bacterioplankton community shifts from monthly surface and 200-m samples collected at the BATS site between 1992 and 2002.…”