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Heribert Cypionka

Publications and source records attributed to Heribert Cypionka.

At least 19 recordsLinked to original sources
PubMed2006

Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea.

The anoxic layers of marine sediments are dominated by sulfate reduction and methanogenesis as the main terminal oxidation processes. The aim of this study was to analyze the vertical succession of microbial populations involved in these processes along the first 4.5 m of a tidal-flat sediment. Therefore, a quantitative PCR approach was applied using primers targeting the domains of Bacteria and Archaea, and key functional genes for sulfate reduction (dsrA) and methanogenesis (mcrA). The sampling site was characterized by an unusual sulfate peak at 250 cm depth resulting in separate sulfate-methane transition zones. Methane and sulfate profiles were diametrically opposed, with a methane maximum in the sulfate-depleted zone showing high numbers of archaea and methanogens. The methane-sulfate interfaces harbored elevated numbers of sulfate reducers, and revealed a slight increase in mcrA and archaeal 16S rRNA genes, suggesting sulfate-dependent anaerobic oxidation of methane. A diversity analysis of both functional genes by PCR-denaturing gradient gel electrophoresis revealed a vertical succession of subpopulations that were governed by geochemical and sedimentologic conditions. Along the upper 200 cm, sulfate-reducing populations appeared quite uniform and were dominated by the Deltaproteobacteria. In the layers beneath, an apparent increase in diversity and a shift to the Firmicutes as the predominant group was observed.

Anaerobiosis↗
PubMed2006

Deep biosphere-related bacteria within the subsurface of tidal flat sediments.

Biogeochemical and microbiological processes in the upper sediment layers of tidal flats were analysed in many investigations, while deeper zones remained largely unexplored. Therefore, denaturant gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments along the depth profile of up to 5.5 m-long sediment cores was performed in comparison with lithological and geochemical parameters. The investigation revealed that different compartments of the sediment columns were characterized by specific microbial communities. These compartments were analysed by sequencing of 113 DGGE bands. The upper layers down to 160-200 cm were dominated by gamma- and delta-Proteobacteria representing more than 60% of the total number of phylotypes. Underneath, a striking shift in community composition was observed, as the Proteobacteria were replaced by Chloroflexi with more than 60% of all sequences. As sulfate was still available as an electron acceptor in these layers, the abundance of Chloroflexi might be promoted by the electron donor or the quality of the carbon source. The dominance of this group, previously known as green non-sulfur bacteria, indicates the presence of a typical deep-biosphere microbial community in relatively young subsurface sediments. Thus, tidal flats might offer a convenient possibility to study and understand certain aspects of the deep biosphere in general.

Bacteria↗
PubMed2006

Widespread distribution and high abundance of Rhizobium radiobacter within Mediterranean subsurface sediments.

Eastern Mediterranean sediments are characterized by the occurrence of distinct, organic-rich layers, called sapropels. These harbour elevated microbial numbers in comparison with adjacent carbon-lean intermediate layers. A recently obtained culture collection from these sediments was composed of 20% of strains closely related to Rhizobium radiobacter, formerly classified as Agrobacterium tumefaciens. To prove and quantify the in situ abundance of R. radiobacter, a highly specific quantitative polymerase chain reaction (PCR) protocol was developed. To convert quantification results into cell numbers, the copy number of rrn operons per genome was determined. Southern hybridization showed that our isolates contained four operons. Finally, quantitative PCR was applied to 45 sediment samples obtained across the eastern Mediterranean. Rhizobium radiobacter was present in 38 of 45 samples indicating an almost ubiquitous distribution. In total, 25-40 000 cells per gram of sediment were detected, corresponding to 0.001-5.1% of the bacterial cells. In general, the relative and absolute abundance of R. radiobacter increased with depth and was higher in sapropels than in intermediate layers. This indicates that R. radiobacter forms an active population in up to 200 000 years old sapropels. The present study shows for the first time that a cultivated subsurface bacterium is highly abundant in this environment.

Agrobacterium tumefaciens↗
PubMed2006

Analysis of aerotactic band formation by Desulfovibrio desulfuricans in a stopped-flow diffusion chamber.

Aerotactic band formation by Desulfovibrio desulfuricans (DSM 9104) was studied in a stopped-flow diffusion chamber. This chamber allowed us to create reproducible, steep oxygen gradients in a flat capillary, time-lapse video recordings and spatio-temporal analysis of band formation. The cells formed two types of bands. Bands of the first type evolved quickly after starting the experiment and were located near the oxic-anoxic interface. Bands of the second type typically appeared several minutes later and a few millimeters inside the initially anoxic volume of the capillary. Band formation depended on metabolism and could be stimulated by lactate addition, and thus appears to be energy taxis. Mathematical modeling of oxygen diffusion and respiration within the chamber revealed that bands formed preferentially at oxygen concentrations close to 4% air saturation. The swimming speed of the cells was determined by digital single-cell tracking and found to be highest (up to 58 mum s(-1)) close to the oxic-anoxic interfaces. Motility patterns were influenced by surfaces, at which cells accumulated. Bioconvection sometimes occurred if very dense bands had formed. The ecological implications of these two phenomena are unknown.

Aerobiosis↗
PubMed2006

Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters.

The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.

Animals↗
PubMed2005

Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients.

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, "Bacteroidetes," "Fusobacteria," Actinobacteria, and "Firmicutes." Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.

Actinobacteria↗
PubMed2004

Quantitative analysis of bacterial communities from Mediterranean sapropels based on cultivation-dependent methods.

Microbial communities of ancient Mediterranean sapropels, buried sediment layers of high organic matter, were analyzed by most probable number (MPN) approaches. Mineral media containing different carbon sources in sub-millimolar concentrations were used. MPN numbers were elevated in sapropels and at the sediment surface, which mirrored total cell count distributions. Highest MPN counts were obtained with a mixture of different monomeric and polymeric substrates, with amino acids or with long-chain fatty acids as sole carbon sources. These values reached up to 2 x 10(7) cm(-3), representing 3.3% of the total cell count. A total of 98 pure cultures were isolated from the highest positive dilutions of the MPN series, representing the most abundant microorganisms culturable by the methods used. The strains were identified by molecular biological methods and could be grouped into 19 different phylotypes. They belonged to the alpha-, beta-, gamma-, and delta-Proteobacteria, to the Actinobacteria and the Firmicutes. However, about half of the number of isolates was closely related to the genera Photobacterium and Agrobacterium. Regarding the high cultivation success, these organisms can be assumed to be typical sapropel bacteria, representing a substantial part of the culturable indigenous microbial community.

Environmental Monitoring↗
PubMed2004

Distributions of microbial activities in deep subseafloor sediments.

Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.

Bacteria↗
PubMed2004

Desulfosporomusa polytropa gen. nov., sp. nov., a novel sulfate-reducing bacterium from sediments of an oligotrophic lake.

Five strains of sulfate-reducing bacteria were isolated from the highest positive dilutions of a most probable number (MPN) series supplemented with lactate and inoculated with sediments from the oligotrophic Lake Stechlin. The isolates were endospore-forming and were motile by means of laterally inserted flagella. They stained Gram-negative and contained b-type cytochromes. CO difference spectra indicated the presence of P582 as a sulfite reductase. Phylogenetic analyses of the 16S rDNA sequences revealed that the isolates were very closely affiliated with the genus Sporomusa. However, sulfate and amorphous Fe(OH)(3), but not sulfite, elemental sulfur, MnO(2), or nitrate were used as terminal electron acceptors. Homoacetogenic growth was found with H(2)/CO(2) gas mixture, formate, methanol, ethanol, and methoxylated aromatic compounds. The strains grew autotrophically with H(2) plus CO(2) in the presence or absence of sulfate. Formate, butyrate, several alcohols, organic acids, carbohydrates, some amino acids, choline, and betaine were also utilized as substrates. The growth yield with lactate and sulfate as substrate was 7.0 g dry mass/mol lactate and thus two times higher than in sulfate-free fermenting cultures. All isolates were able to grow in a temperature range of 4-37 degrees C. Physiologically and by the presence of a Gram-negative cell wall, the new isolates resemble known Desulfosporosinus species. However, phylogenetically they are affiliated with the Gram-negative genus Sporomusa belonging to the Selenomonas subgroup of the Firmicutes. Therefore, the new isolates reveal a new phylogenetic lineage of sulfate-reducing bacteria. A new genus and species, Desulfosporomusa polytropa gen. nov., sp. nov. is proposed.

Bacterial Typing Techniques↗
PubMed2004

Distribution of Nevskia ramosa and other rosette-forming neustonic bacteria.

Samples from 27 natural and artificial aquatic environments were analyzed for the presence of rosette-forming bacteria by a combined cultivation and molecular biological approach. Rosette-forming bacteria developed in 20 enrichment cultures with ammonia-free medium under air. Three morphotypes could be distinguished. The most abundant type I resembled Nevskia ramosa and formed hydrophobic, flat, and dichotomously branching rosettes. Type II rosettes were three-dimensional and were observed in 10 enrichments, often together with those of type I. These rosettes were hydrophilic indicating life in the hyponeuston underneath the air-water interface. Rosettes of a third type consisted of hydrophilic slime stalks that were excreted at the cell poles and were observed in only one sample. Using fluorescence in situ hybridization (FISH) with the Nevskia-specific probes NEV177 and NEV656, the presence of Nevskia ramosa was demonstrated in exactly those samples that showed type I rosettes. In a series of most-probable-number experiments, during a calm and sunny weather period 430,000 Nevskia-like bacteria per mL were found in surface samples, while during rainy weather and within the water body the numbers were lower by several orders of magnitude. Five pure cultures isolated from various enrichments were characterized in detail. The two isolates forming type I rosettes were identified as Nevskia ramosa by 16S rDNA analysis. However, comparison by genomic fingerprinting (ERIC-PCR) revealed differences between the two isolates and previously characterized strains. The 16S rDNA of two isolates forming type II rosettes showed 97.6% similarity to that of Pseudomonas fluorescens. The closest relative of the isolate forming type III rosettes was Sphingomonas parapaucimobilis (96.4% sequence similarity of the 16S rRNA sequence). All isolates grew homogeneously submersed if ammonia was added to the medium. Our results indicate that Nevskia ramosa is a widely distributed epineustonic bacterium, which can specifically be deleted by its flat and hydrophobic rosettes on ammonia-free media.

Biofilms↗
PubMed2004

Isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of Desulfovibrio cavernae sp. nov.

Deep subsurface sandstones in the area of Berlin (Germany) located 600 to 1060 m below the surface were examined for the presence of viable microorganisms. The in situ temperatures at the sampling sites ranged from 37 to 45 degrees C. Investigations focussed on sulfate-reducing bacteria able to grow on methanol and triethylene glycol, which are added as chemicals to facilitate the long-term underground storage of natural gas. Seven strains were isolated from porewater brines in the porous sandstone. Three of them were obtained with methanol (strains H1M, H3M, and B1M), three strains with triethylene glycol (strains H1T, B1T, and B2T) and one strain with a mixture of lactate, acetate and butyrate (strain H1-13). Due to phenotypic properties six isolates could be identified as members of the genus Desulfovibrio, and strain B2T as a Desulfotomaculum. The salt tolerance and temperature range for growth indicated that the isolates originated from the indigenous deep subsurface sandstones. They grew in mineral media reflecting the in situ ionic composition of the different brines, which contained 1.5 to 190 g NaCl x l(-1) and high calcium and magnesium concentrations. The Desulfovibrio strains grew at temperatures between 20 and 50 degrees C, while the Desulfotomaculum strain was thermophilic and grew between 30 and 65 degrees C. The strains utilized a broad spectrum of electron donors and acceptors. They grew with carbon compounds like lactate, pyruvate, formate, n-alcohols (C1-C5), glycerol, ethylene glycol, malate, succinate, and fumarate. Some strains even utilized glucose as electron donor and carbon source. All strains were able to use sulfate, sulfite and nitrate as electron acceptors. Additionally, three Desulfovibrio strains reduced manganese oxide, the Desulfotomaculum strain reduced manganese oxide, iron oxide, and elemental sulfur. The 16S rRNA analysis revealed that the isolates belong to three different species. The strains H1T, H3M and B1M could be identified as Desulfovibrio indonesiensis, and strain B2T as Desulfotomaculum geothermicum. The other Desulfovibrio strains (H1M, H1-13, and B1T) showed identical 16S rDNA sequences and similarities as low as 93% to their closest relative, Desulfovibrio aminophilusT. Therefore, these isolates were assigned to a new species, Desulfovibrio cavernae sp. nov., with strain H1M as the type strain.

Acetates↗
PubMed2003

Aeromicrobium marinum sp. nov., an abundant pelagic bacterium isolated from the German Wadden Sea.

An obligately salt-dependent Gram-positive bacterium, designated strain T2(T), was isolated from surface waters of the German Wadden Sea. The organism exhibited optimum growth at salt concentrations similar to that of sea water. On the basis of phenotypic, chemotaxonomic and phylogenetic differences, it is concluded that strain T2(T) (=DSM 15272(T)=LMG 21768(T)) is the first marine species of the genus Aeromicrobium to be identified, for which the name Aeromicrobium marinum is proposed. It is also the first described marine bacterium within the family Nocardioidaceae. Strain T2(T) is a rod-shaped, aerobic, heterotrophic bacterium containing LL-diaminopimelic acid in the peptidoglycan and MK-9(H(4)) as the major menaquinone. The bacterium is characterized by high proportions of the fatty acids palmitic acid, oleic acid, tuberculostearic acid and hydroxypalmitic acid. DNA-DNA hybridization analysis showed the marine bacterium to display 29.1 % relatedness with Aeromicrobium fastidiosum DSM 10552(T) and 44.4 % relatedness with Aeromicrobium erythreum DSM 8599(T). A. marinum was demonstrated to be an abundant member of the pelagic bacterial community in the German Wadden Sea since it represented about 1 % of the total bacterial population as revealed by dot-blot hybridization and most-probable-number counts.

DNA, Bacterial↗
PubMed2003

Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton.

The effect of signal compounds and of different incubation conditions on the culturability (i.e., the fraction of all cells capable of growth) of natural bacterioplankton from the eutrophic lake Zwischenahner Meer was investigated over a period of 20 months. Numbers of growing cells were determined by the most-probable-number technique in liquid media containing low concentrations (10 micro M) of the signal compounds N-(oxohexanoyl)-DL-homoserine lactone, N-(butyryl)-DL-homoserine lactone, cyclic AMP (cAMP), or ATP. cAMP was the most effective signal compound, leading to significantly increased cultivation efficiencies of up to 10% of the total bacterial counts. Microautoradiography with [2,8-(3)H]cAMP, combined with fluorescence in situ hybridization, demonstrated that cAMP was taken up by 18% of all cells. The bacterial cAMP uptake systems had a very low K(m) value of </=1 nM. Analysis of the cultured bacteria by 16S rRNA gene fingerprinting showed that different bacterial phylotypes were recovered in the presence and in the absence of cAMP. Consequently, the addition of cAMP caused a stimulation of otherwise nonculturable bacteria. Phylogenetically different bacteria were also recovered at different temperatures and oxygen partial pressures. Throughout the study period, mainly members of the beta-subclass of the Proteobacteria were cultivated. In addition, some members of the Actinomycetales were enriched. Quantification by culture-independent fluorescence in situ hybridization demonstrated that beta-Proteobacteria and Actinomycetales also dominated the natural bacterioplankton assemblage. Sequence comparison revealed that two members of the Actinomycetales which reached high numbers in the natural bacterioplankton assemblage could actually be enriched by our cultivation approach.

4-Butyrolactone↗
PubMed2002

Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes.

Late Pleistocene organic-rich sediments (sapropels) from the eastern Mediterranean Sea harbor unknown, metabolically active chemoorganotrophic prokaryotes. As compared to the carbon-lean intermediate layers, sapropels exhibit elevated cell numbers, increased activities of hydrolytic exoenzymes, and increased anaerobic glucose degradation rates, suggesting that microbial carbon substrates originate from sapropel layers up to 217,000 years old. 16S ribosomal RNA gene analyses revealed that as-yet-uncultured green nonsulfur bacteria constitute up to 70% of the total microbial biomass. Crenarchaeota constitute a smaller fraction (on average, 16%). A slow but significant turnover of glucose could be detected. Apparently, sapropels are still altered by the metabolic activity of green nonsulfur bacteria and crenarchaeota.

Alkaline Phosphatase↗
PubMed2002

Desulfobulbus mediterraneus sp. nov., a sulfate-reducing bacterium growing on mono- and disaccharides.

A new sulfate-reducing bacterium, strain 86FS1, was isolated from a deep-sea sediment in the western Mediterranean Sea with sodium lactate as electron and carbon source. Cells were ovoid, gram-negative and motile. Strain 86FS1 contained b- and c-type cytochromes. The organism was able to utilize propionate, pyruvate, lactate, succinate, fumarate, malate, alanine, primary alcohols (C(2)-C(5)), and mono- and disaccharides (glucose, fructose, galactose, ribose, sucrose, cellobiose, lactose) as electron donors for the reduction of sulfate, sulfite or thiosulfate. The major products of carbon metabolism were acetate and CO(2), with exception of n-butanol and n-pentanol, which were oxidized only to the corresponding fatty acids. The growth yield with sulfate and glucose or lactate was 8.3 and 15 g dry mass, respectively, per mol sulfate. The temperature limits for growth were 10 degrees C and 30 degrees C with an optimum at 25 degrees C. Growth was observed at salinities ranging from 10 to 70 g NaCl l(-1). Sulfide concentrations above 4 mmol l(-1) inhibited growth. The fatty acid pattern of strain 86FS1 resembled that of Desulfobulbus propionicus with n-14:0, n-16:1omega7, n-16:1 omega5, n-17:1 omega6 and n-18:1 omega7 as dominant fatty acids. On the basis of its phylogenetic position and its phenotypic properties, strain 86FS1 affiliates with the genus Desulfobulbus and is described as a new species, Desulfobulbus mediterraneus sp. nov.

Deltaproteobacteria↗
PubMed2002

Phospholipid analysis as a tool to study complex microbial communities in marine sediments.

To complement information on microbial communities in marine sediments that can be obtained using microbiological methods, we developed an analytical procedure to trace microbial lipids in environmental samples. We focused on analyzing intact phospholipids as these membrane constituents are known to be biomarkers for viable cells. Analysis of intact phospholipids from a fractionated and preconcentrated sediment extract was achieved using liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS). The combined analysis of phospholipid types and their fatty acid substituents allowed a differentiation between various groups of microorganisms living in the sediment. For comparison three strains of marine sulfate-reducing bacteria (SRB) were analysed for their lipid content.

Bacteria↗
PubMed2002

Bioenergetics of the alkaliphilic sulfate-reducing bacterium Desulfonatronovibrio hydrogenovorans.

Energy metabolism of the alkaliphilic sulfate-reducing bacterium Desulfonatronovibrio hydrogenovorans strain Z-7935 was investigated in continuous culture and in physiological experiments on washed cells. When grown in chemostats with H2 as electron donor, the cells had extrapolated growth yields [Y(max), g dry cell mass (mol electron acceptor)(-1)] of 5.5 with sulfate and 12.8 with thiosulfate. The maintenance energy coefficients were 1.9 and 1.3 mmol (g dry mass)(-1) x h(-1), and the minimum doubling times were 27 and 20 h with sulfate and thiosulfate, respectively. Cell suspensions reduced sulfate, thiosulfate, sulfite, elemental sulfur and molecular oxygen in the presence of H2. In the absence of H2, sulfite, thiosulfate and sulfur were dismutated to sulfide and sulfate. Sulfate and sulfite were only reduced in the presence of sodium ions, whereas sulfur was reduced also in the absence of Na+. Plasmolysis experiments showed that sulfate entered the cells via an electroneutral symport with Na+ ions. The presence of an electrogenic Na+-H+ antiporter was demonstrated in experiments applying monensin (an artificial electroneutral Na+-H+ antiporter) and propylbenzylylcholine mustard.HCl (a specific inhibitor of Na+-H+ antiporters). Sulfate reduction was sensitive to uncouplers (protonophores), whereas sulfite reduction was not affected. Changes in pH upon lysis of washed cells with butanol indicated that the intracellular pH was lower than the optimum pH for growth (pH 9.5). Pulses of NaCl (0.52 M) to cells incubated in the absence of Na+ did not result in ATP formation, whereas HCl pulses (shifting the pH from 9.2 to 7.0) did. Small oxygen pulses, which were reduced within a few seconds, caused a transient alkalinization. The results of preliminary experiments with chemiosmotic inhibitors provided further evidence that the alkalinization was caused by sodium--proton antiport following a primary electron-transport-driven sodium ion translocation. It is concluded that energy conservation in D. hydrogenovorans depends on a proton-translocating ATPase, whereas electron transport appears to be coupled to sodium ion translocation.

Culture Media↗