Survival strategies of bacteria in the natural environment.

Fluorescence in situ hybridization (FISH) in combination with polynucleotide probes revealed that the two major groups of planktonic Archaea (Crenarchaeota and Euryarchaeota) exhibit a different distribution pattern in the water column of the Pacific subtropical gyre and in the Antarctic Circumpolar Current system. While Euryarchaeota were found to be more dominant in nearsurface waters, Crenarchaeota were relatively more abundant in the mesopelagic and bathypelagic waters. We determined the abundance of archaea in the mesopelagic and bathypelagic North Atlantic along a south-north transect of more than 4,000 km. Using an improved catalyzed reporter deposition-FISH (CARD-FISH) method and specific oligonucleotide probes, we found that archaea were consistently more abundant than bacteria below a 100-m depth. Combining microautoradiography with CARD-FISH revealed a high fraction of metabolically active cells in the deep ocean. Even at a 3,000-m depth, about 16% of the bacteria were taking up leucine. The percentage of Euryarchaeota and Crenarchaeaota taking up leucine did not follow a specific trend, with depths ranging from 6 to 35% and 3 to 18%, respectively. The fraction of Crenarchaeota taking up inorganic carbon increased with depth, while Euryarchaeota taking up inorganic carbon decreased from 200 m to 3,000 m in depth. The ability of archaea to take up inorganic carbon was used as a proxy to estimate archaeal cell production and to compare this archaeal production with total prokaryotic production measured via leucine incorporation. We estimate that archaeal production in the mesopelagic and bathypelagic North Atlantic contributes between 13 to 27% to the total prokaryotic production in the oxygen minimum layer and 41 to 84% in the Labrador Sea Water, declining to 10 to 20% in the North Atlantic Deep Water. Thus, planktonic archaea are actively growing in the dark ocean although at lower growth rates than bacteria and might play a significant role in the oceanic carbon cycle.

/pdf/contribution-of-archaea-to-total-prokaryotic-production-in-53ly3oj20p.pdf

Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean

The sulfate-reducing bacterial populations of a stratified marine water column, Mariager Fjord, Denmark, were investigated by molecular and culture-dependent approaches in parallel. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA and DNA encoding rRNA (rDNA) isolated from the water column indicated specific bacterial populations in different water column layers and revealed a highly differentiated pattern of rRNA- and rDNA-derived PCR amplificates, probably reflecting active and resting bacterial populations. Hybridization of DGGE patterns with rRNA probes indicated the increased presence and activity (by at least 1 order of magnitude) of sulfate-reducing bacteria within and below the chemocline. Parallel to this molecular approach, an approach involving most-probable-number (MPN) counts was used, and it found a similar distribution of cultivable sulfate-reducing bacteria in the water column of Mariager Fjord, Approximately 25 cells and 250 cells per ml above and below the chemocline, respectively, were found. Desulfovibrio- and Desulfobulbus-related strains occurred in the oxic zone. DGGE bands from MPN cultures were sequenced and compared with those obtained from nucleic acids extracted from water column samples. The MPN isolates were phylogenetically affiliated with sulfate-reducing delta subdivision proteobacteria (members of the genera Desulfovibrio, Desulfobulbus, and Desulfobacter), whereas the molecular isolates constituted an independent lineage of the delta subdivision proteobacteria. DGGE of PCR-amplified nucleic acids with general eubacterial PCR primers conceptually revealed the general bacterial population, whereas the use of culture media allowed cultivable sulfate-reducing bacteria to be selected. A parallel study of Mariager Fjord biogeochemistry, bacterial activity, and bacterial counts complementing this investigation has been presented elsewhere (N.B. Ramsing, H. Fossing, T. G. Ferdelman, F. Andersen, and B. Thamdrup, Appl. Environ.

/pdf/distribution-of-sulfate-reducing-bacteria-in-a-stratified-1stxit1gjb.pdf

Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments.

The bacterioplankton community of confined seawater at 25 degrees C changed significantly within 16 h of collection. Confinement increased CFU, total cell number (by epifluorescence microscopy), and average cell volume of bacterioplankton and increased the turnover rate of amino acids in seawater sampled at Frying Pan Shoals, N.C. The bacterioplankton community was characterized by two components: differential doubling times during confinement shifted dominance from bacteria which were nonculturable to bacteria which were culturable on a complex nutrient medium. Culturable cells (especially those of the genera Pseudomonas, Alcaligenes, and Acinetobacter) increased from 0.08% of the total cell number in the seawater immediately after collection to 13% at 16 h and 41% at 32 h of confinement. Differential filtration before confinement indicated that particles passing through a 3.9-microns-, but retained by a 0.2-micron-, pore-size Nuclepore filter may be a major source of primary amines to the confined population. The 3.0-microns filtration increased growth rate and ultimate numbers of culturable cells through the removal of bacterial predators or the release of primary amines from cells damaged during filtration or both.

Response of marine bacterioplankton to differential filtration and confinement.

The distribution of phytoplankton primary production into four size fractions (>10 μm, 10-3 μm, 3-0.2 μm and <0.2 μm), the utilization of algal exudates by bacteria and the bacterial production were studied in a eutrophication gradient in the northern Baltic proper. The polluted area exhibits substantially increased nutrient, especially nitrogen, levels while only minor differences occur in salinity and temperature regimes. Total primary production was 160 g C · m-2 · yr-1 at the control station and about 275 g C · m-2 · yr-1 at the eutrophicated stations. The estimated total exudate release was 16% of the totally fixed 14CO2 in the control area and 12% in the eutrophicated area (including the estimated bacterial uptake of exudates). The difference in14CO2 uptake rates between incubation of previously filtered water (<3, <2, <1 μm) and unfiltered water was used to estimate bacterial uptake of phytoplankton exudates which were found to contribute about half of the estimated bacterial carbon requirement in both areas. Bacterial production was estimated by the frequency of dividing cells (FDC) method as being 38 g C · m-2 · yr-1 at the control station and 50 g C · m-2 · yr-1 at the eutrophicated stations. To estimate the mean in situ bacterial cell volume a correlation between FDC and cell volume was used. The increased annual primary production in the eutrophicated area was due mainly to higher production during spring and autumn, largely by phytoplankton cells (mainly diatoms) retained by a 10 μm filter. Primary production duringsummer was similarin the two areas, as was the distribution on different size fractions. This could possibly explain the similar bacterial production in the trophic layers at all stations since the bulk of bacterial production occurs during summer. It was demonstrated that selective filtration does not quantitatively separate photoautotrophs and bacteria. A substantial fraction of the primary production occurs in the size fraction <3 μm. The primary production encountered in the 3-0.2 μm fraction was due to abundant picoplankton (0.5 to 8 · 107 ind · l-1), easily passing a 3 μm filter. The picoplankton was estimated to constitute up to 25% of the total phytoplankton biomass in the control area and up to 10% in the eutrophicated area.

H.-G. Hoppe

Papers

Relations between active bacteria and heterotrophic potential in the sea