Complex pattern formation of marine gradient bacteria explained by a simple computer model.

We report on the formation of conspicuous patterns by the sulfide-oxidizing bacterium Thiovulum majus and a recently described vibrioid bacterium. These microaerophilic bacteria form mucus veils on top of sulfidic marine sediment exhibiting regular spaced bacterial patterns (honeycombs, interwoven bands, or inverse honeycombs). A simple qualitative computer model, based on chemotaxis towards oxygen and the ability of the bacteria to induce water advection when attached, can explain the formation of the observed patterns. Our study shows that complex bacterial patterns in nature can be explained in terms of chemotaxis and resource optimisation without involvement of cell-cell signalling or social behavior amongst bacteria.

Spatial distribution of gymnamoebae (Rhizopoda, Lobosea) in brackish-water sediments at the scale of centimeters and millimeters.

In order to study micro-spatial distribution of amoebae, an intact slice of sandy sediment from the brackish-water Nivå Bay (Baltic Sea, The Sound), 40 x 24 mm in size and 2 mm in thickness was gently sectioned into cubes, 2 x 2 x 2 mm in size. Each cube was inoculated into enrichment media to reveal the biodiversity of amoebae. Seventeen species of amoebae were recovered. The 2-D map of amoebae species distribution in the slice, consisting of 240 2 x 2 mm cells was drawn and analyzed. Results show heterogeneous distribution of amoebae at the scale of centimeters and millimeters and confirm the idea of the presence of microhabitats, selectively occupied by amoebae species. Three types of distribution patterns were found: random, aggregated and equally spaced. Microelectrode studies indicated that amoebae distribution was not related to the dissolved oxygen content in the sediment. The studied slice of sediment contained several pronounced "hotspots" of amoebae biodiversity, where up to four species co-occur in the same area. Seven species of amoebae numbered 1-4 specimens in the studied slice (i.e. there was 0.5-2 cell ml(-1)). Analysis of the amoebae distribution map shows the high probability of undersampling rare amoebae species during faunistic studies.

Vertical distribution of gymnamoebae (rhizopoda, lobosea) in the top layer of brackish-water sediments.

The paper reports on the distribution of amoebae in a vertical slice of sandy sediment from the brackish-water Nivå Bay (Baltic Sea, The Sound). The 24 x 20 mm slice 2 mm in thickness was gently cut from the top of sediment to a depth of 20 mm using coverslips, and further sectioned into 2 x 2 x 2 mm cubes. Each cube was inoculated into enrichment media to reveal the biodiversity of amoebae. The map of amoebae species distribution in the slice was drawn and analyzed. The results show patchy distributions of many amoebae species. Amoebae tend to form a band of maximum diversity within the depth interval 2-16 mm. Two mini-cores of sediment located close to the butt-ends of the slice were collected using cut 1 ml syringes. They were sliced and inoculated to reveal the biodiversity of amoebae at different depths. The distribution patterns of amoebae in the mini-cores were similar to the ones obtained in the slice, and show evident patchiness of some species. It seems that abundant species mostly form irregular patches 1-2 cm across, whereas many species are rare and appear in few number of specimens or in patches smaller than 2 mm.

Combined imaging of bacteria and oxygen in biofilms.

Transparent sensors for microscopic O(2) imaging were developed by spin coating an ultrathin (<1- to 2-microm) layer of a luminescent O(2) indicator onto coverslips. The sensors showed (i) an ideal Stern-Volmer quenching behavior of the luminescence lifetime towards O(2) levels, (ii) homogeneous measuring characteristics over the sensor surface, and (iii) a linear decline of luminescence lifetime with increasing temperature. When a batch of such coverslip sensors has been characterized, their use is thus essentially calibration free at a known temperature. The sensors are easy to use in flow chambers and other growth devices used in microbiology. We present the first application for combined imaging of O(2) and bacteria in a biofilm flow chamber mounted on a microscope equipped with a spinning-disk confocal unit and a luminescence lifetime camera system.

Survey of motile microaerophilic bacterial morphotypes in the oxygen gradient above a marine sulfidic sediment.

Enrichment cultures for free-swimming microaerophilic bacteria were prepared from marine sulfidic sediment samples (Nivå Bay, Denmark). We observed nine different morphotypes; three of these morphotypes represented already-described species, i.e., Thiovulum majus, "Candidatus Ovobacter propellens," and an as-yet-unnamed large vibrioid bacterium. In addition, we observed several morphotypes of spirilla and one vibrioid morphotype. A common feature of all investigated bacteria was that they aggregated chemotactically at the oxic-anoxic interface, whereas preferred oxygen concentration were in the range of 1 to 10 muM. The motile behavior and flagellar dynamics are analyzed in detail with an emphasis on spirilla.

Identification of "Candidatus Thioturbo danicus," a microaerophilic bacterium that builds conspicuous veils on sulfidic sediments.

Molecular analysis of bacteria enriched under in situ-like conditions and mechanically isolated by micromanipulation showed that a hitherto-uncultivated microaerophilic bacterium thriving in oxygen-sulfide counter-gradients (R. Thar and M. Kühl, Appl. Environ. Microbiol. 68:6310-6320, 2000) is affiliated with the epsilon-subdivision of the Proteobacteria. The affiliation was confirmed by the use of whole-cell hybridization with newly designed specific oligonucleotide probes. The bacterium belongs to a new genus and received the provisional name "Candidatus Thioturbo danicus."

Conspicuous veils formed by vibrioid bacteria on sulfidic marine sediment.

We describe the morphology and behavior of a hitherto unknown bacterial species that forms conspicuous veils (typical dimensions, 30 by 30 mm) on sulfidic marine sediment. The new bacteria were enriched on complex sulfidic medium within a benthic gradient chamber in oxygen-sulfide countergradients, but the bacteria have so far not been isolated in pure culture, and a detailed characterization of their metabolism is still lacking. The bacteria are colorless, gram-negative, and vibrioid-shaped (1.3- to 2.5- by 4- to 10- micro m) cells that multiply by binary division and contain several spherical inclusions of poly-beta-hydroxybutyric acid. The cells have bipolar polytrichous flagella and exhibit a unique swimming pattern, rotating and translating along their short axis. Free-swimming cells showed aerotaxis and aggregated at ca. 2 micro M oxygen within opposing oxygen-sulfide gradients, where they were able to attach via a mucous stalk, forming a cohesive whitish veil at the oxic-anoxic interface. Bacteria attached to the veil kept rotating and adapted their stalk lengths dynamically to changing oxygen concentrations. The joint action of rotating bacteria on the veil induced a homogeneous water flow from the oxic water region toward the veil, whereby the oxygen uptake rate could be enhanced up to six times, as shown by model calculations. The veils showed a pronounced succession pattern. New veils were generated de novo within 24 h and had a homogeneous whitish translucent appearance. Bacterial competitors or eukaryotic predators were apparently kept away by the low oxygen concentration prevailing at the veil surface. Frequently, within 2 days the veil developed a honeycomb pattern of regularly spaced holes. After 4 days, most veils were colonized by grazing ciliates, leading to the fast disappearance of the new bacteria. Several-week-old veils finally developed into microbial mats consisting of green, purple, and colorless sulfur bacteria.

Bacteria are not too small for spatial sensing of chemical gradients: an experimental evidence.

By analyzing the chemotactic behavior of a recently described marine bacterial species, we provide experimental evidence that bacteria are not too small for sensing chemical gradients spatially. The bipolar flagellated vibrioid bacteria (typical size 2 x 6 microm) exhibit a unique motility pattern as they translate along as well as rotate around their short axis, i.e., the pathways of the cell poles describe a double helix. The natural habitat of the bacteria is characterized by steep oxygen gradients where they accumulate in a band at their preferred oxygen concentration of approximately 2 microM. Single cells leaving the band toward the oxic region typically return to the band within 16 s following a U-shaped track. A detailed analysis of the tracks reveals that the cells must be able to sense the oxygen gradient perpendicular to their swimming direction. Thus, they can detect oxygen gradients along a distance of approximately 5 microm corresponding to the extension of their long axis. The observed behavior can be explained by the presence of two independent sensor regions at either cell pole that modulate the rotation speed of the polar flagellar bundles, i.e., the flagellar bundle at the cell pole exposed to higher oxygen concentration is rotating faster than the other bundle. A mathematical model based on these assumptions reproduces the observed swimming behavior of the bacteria.

Propagation of electromagnetic radiation in mitochondria?

Mitochondria are the main source of ultra-weak chemiluminescence generated by reactive oxygen species, which are continuously formed during the mitochondrial oxidative metabolism. Vertebrate cells show typically filamentous mitochondria associated with the microtubules of the cytoskeleton, forming together a continuous network (mitochondrial reticulum). The refractive index of both mitochondria and microtubules is higher than the surrounding cytoplasm, which results that the mitochondrial reticulum can act as an optical waveguide, i.e. electromagnetic radiation can propagate within the network. A detailed analysis of the inner structure of mitochondria shows, that they can be optically modelled as a multi-layer system with alternating indices of refraction. The parameters of this multi-layer system are dependent on the physiologic state of the mitochondria. The effect of the multi-layer system on electromagnetic radiation propagating along the mitochondrial reticulum is analysed by the transfer-matrix method. If induced light emission could take place in mitochondria, the multi-layer system could lead to lasing action like it has been realized in technical distributed feedback laser. Based on former reports about the influence of external illumination on the physiology of mitochondria it is speculated whether there exists some kind of long-range interaction between individual mitochondria mediated by electromagnetic radiation.

"Candidatus Ovobacter propellens": a large conspicuous prokaryote with an unusual motility behaviour.

A new type of bacterium "Candidatus Ovobacter propellens" is described. It is a large ovoid species with a number of unusual features including special intracellular membrane systems and a huge flagellar tuft consisting of about 400 flagella. "Ovobacter" lives in oxygen gradients in the surface layer of sulphidic marine sediments at an O(2)-tension of about 0.5% atmospheric saturation. It swims continuously and very fast (up to 1 mm s(-1)). Its mode of swimming and its chemosensory behaviour towards O(2) are described in detail.

Growth and chemosensory behavior of sulfate-reducing bacteria in oxygen-sulfide gradients.

Growth and chemotactic behavior in oxic-anoxic gradients were studied with two freshwater and four marine strains of sulfate-reducing bacteria related to the genera Desulfovibrio, Desulfomicrobium or Desulfobulbus. Cells were grown in oxygen-sulfide counter-gradients within tubes filled with agar-solidified medium. The immobilized cells grew mainly in the anoxic zone, revealing a peak below the oxic-anoxic interface. All tested strains survived exposure to air for 8 h and all were capable of oxygen reduction with lactate. Most strains also oxidized sulfide with oxygen. Desulfovibrio desulfuricans responded chemotactically to lactate, nitrate, sulfate and thiosulfate, and even sulfide functioned as an attractant. In oxic-anoxic gradients the bacteria moved away from high oxygen concentrations and formed bands at the outer edge of the oxic zone at low oxygen concentration (<5% O2 saturation). They were able to actively change the extension and slope of the gradients by oxygen reduction with lactate or even sulfide as electron donor. Generally, the chemotactic behavior was in agreement with a defense strategy that re-establishes anoxic conditions, thus promoting anaerobic growth and, in a natural community, fermentative production of the preferred electron donors of the sulfate-reducing bacteria.

Microbially mediated sulphide production in a thermal, acidic algal mat community in Yellowstone National Park.

Our objective in this study was to characterize prokaryotic sulphide production within the oxygenic, predominantly eukaryotic algal mat in an acidic stream, Nymph Creek, in Yellowstone National Park (YNP). We used microsensors to examine fluctuations in H2S and O2 concentrations over time through the vertical aspect of the approximately 3 mm mat in a 46-48 degrees C region of the creek. We also used analyses of PCR-amplified 16S rRNA gene sequences obtained from denaturing gradient gels, and PCR-amplified sequences of a functional gene associated with microbial sulphate respiration (dsrA) to characterize the bacterial community in the same region of the mat. During midday, photosynthesis rates were high within the first 500 micro m interval of the mat and high oxygen concentrations (600% air saturation) penetrated deeply (>1800 micro m) into the mat. During early evening and night, oxygen concentrations within the first 1100 micro m of the mat decreased over time from 60% air saturation (a.s) to 12% a.s. A precipitous decline in oxygen concentration occurred at a depth of 1100 micro m in all night measurements and anoxic conditions were present below 1200 micro m. Within this anoxic region, sulphide concentrations increased from nearly 0 micro M at 1200 micro m depth to 100 micro M at 2400 micro m depth. Enrichment cultures inoculated with Nymph Creek mat organisms also produced H2S. Sequence analyses of 16S rRNA and dsrA genes indicated the presence of at least five bacterial genera including species involved in dissimilative sulphate or sulphur reduction.