Pattern formation by bacteria-driven flow

Some marine bacterial species form mucosal layers, called veils, on sulfidic marine sediment. The bacteria attached to this veil actively swim and exert force on the surrounding fluid. The bacteria can break free of the veil and swim, chemotacting back to the veil. Over time the veil forms holes arranged in a hexagonal pattern. Motivated by this system, we present a simplified model to describe pattern formation induced by force-generating bodies embedded in a layer surrounded by fluid. When the bacteria break free of the layer, they are advected by the flow and diffuse. Competition between the fluid flow generated by the embedded bacteria and diffusion of the swimmers leads to a novel instability that drives bacterial aggregation. Analytic and numeric analysis of this system correctly defines the length scale and developmental timescale for the biological system. Similar flow dynamics may also play a role in other biological systems such as encrusting bryozoan colonies.     

Colorless Sulfur Bacteria, Beggiatoa spp. and Thiovulum spp., in O(2) and H(2)S Microgradients

The interactions between colorless sulfur bacteria and the chemical microgradients at the oxygen-sulfide interface were studied in Beggiatoa mats from marine sediments and in Thiovulum veils developing above the sediments. The gradients of O(2), H(2)S, and pH were measured by microelectrodes at depth increments of 50 mum. An unstirred boundary layer in the water surrounding the mats and veils prevented microturbulent or convective mixing of O(2) and H(2)S. The two substrates reached the bacteria only by molecular diffusion through the boundary layer. The bacteria lived as microaerophiles or anaerobes even under stirred, oxic water. Oxygen and sulfide zones overlapped by 50 mum in the bacterial layers. Both compounds had concentrations in the range of 0 to 10 mumol liter and residence times of 0.1 to 0.6 s in the overlapping zone. The sulfide oxidation was purely biological. Diffusion calculations showed that formation of mats on solid substrates or of veils in the water represented optimal strategies for the bacteria to achieve a stable microenvironment, a high substrate supply, and an efficient competition with chemical sulfide oxidation. The continuous gliding movement of Beggiatoa cells in mats or the flickering motion of Thiovulum cells in veils were important for the availability of both O(2) and H(2)S for the individual bacteria.     

Colorless Sulfur Bacteria, Beggiatoa spp. and Thiovulum spp., in O2 and H2S Microgradients

The interactions between colorless sulfur bacteria and the chemical microgradients at the oxygen-sulfide interface were studied in Beggiatoa mats from marine sediments and in Thiovulum veils developing above the sediments. The gradients of O₂, H₂S, and pH were measured by microelectrodes at depth increments of 50 μm. An unstirred boundary layer in the water surrounding the mats and veils prevented microturbulent or convective mixing of O₂ and H₂S. The two substrates reached the bacteria only by molecular diffusion through the boundary layer. The bacteria lived as microaerophiles or anaerobes even under stirred, oxic water. Oxygen and sulfide zones overlapped by 50 μm in the bacterial layers. Both compounds had concentrations in the range of 0 to 10 μmol liter⁻¹ and residence times of 0.1 to 0.6 s in the overlapping zone. The sulfide oxidation was purely biological. Diffusion calculations showed that formation of mats on solid substrates or of veils in the water represented optimal strategies for the bacteria to achieve a stable microenvironment, a high substrate supply, and an efficient competition with chemical sulfide oxidation. The continuous gliding movement of Beggiatoa cells in mats or the flickering motion of Thiovulum cells in veils were important for the availability of both O₂ and H₂S for the individual bacteria.     

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.     

Motility patterns of filamentous sulfur bacteria, Beggiatoa spp

The large sulfur bacteria, Beggiatoa spp., live on the oxidation of sulfide with oxygen or nitrate, but avoid high concentrations of both sulfide and oxygen. As gliding filaments, they rely on reversals in the gliding direction to find their preferred environment, the oxygen-sulfide interface. We observed the chemotactic patterns of single filaments in a transparent agar medium and scored their reversals and the glided distances between reversals. Filaments within the preferred microenvironment glided distances shorter than their own length between reversals that anchored them in their position as a microbial mat. Filaments in the oxic region above the mat or in the sulfidic, anoxic region below the mat glided distances longer than the filament length between reversals. This reversal behavior resulted in a diffusion-like spreading of the filaments. A numerical model of such gliding filaments was constructed based on our observations. The model was applied to virtual filaments in the oxygen- and sulfide-free zone of the sediment, which is a main habitat of Beggiatoa in the natural environment. The model predicts a long residence time of the virtual filament in the suboxic zone and explains why Beggiatoa accumulate high nitrate concentrations in internal vacuoles as an alternative electron acceptor to oxygen.     

Survival of sulfate-reducing bacteria after oxygen stress, and growth in sulfate-free oxygen-sulfide gradients

Abstract The survival after oxygen stress was studied with eight species of sulfate-reducing bacteria. In the absence of sulfide all species tolerated 6 min of aeration without loss of viability. Even after 3 h of aeration the viability of four species ( Desulfovibrio vulgaris, D. desulfuricans, D. salexigens and Desulfobacter postgatei ) was not impaired. Four other species were sensitive to 3 h of aeration: the surviving fractions of Desulfotomaculum ruminis, D. nigrificans and Desulfococcus multivorans were about 1%, that of Desulfotomaculum orientis about 0.01%. Formation of spores resulted in oxygen resistance of D. orientis . Reducing agents did not protect the vegetative cells of this strain against oxygen toxicity. In contrast, sulfhydryl group-containing agents increased the oxygen sensitivity considerably.
Growth of sulfate- and sulfur-reducing bacteria in oxygen-sulfide gradients in agar tubes was studied. In the gradients these strictly anaerobic bacteria revealed oxygen-dependent growth in sulfate- and sulfur-free medium. Three sulfate-reducing bacteria that could not use thiosulfate or sulfur as electron acceptor failed to grow in oxygen-sulfide gradients. Obviously, not directly molecular oxygen, but oxidation products of sulfide, such as thiosulfate or sulfur, were used as electron acceptors and were continuously regenerated in a cycling process from sulfide by autoxidation. The conceivable ecological significance of a short sulfur cycle driven by autoxidation of sulfide is discussed.     

Mathematical simulation of the interactions among cyanobacteria, purple sulfur bacteria and chemotrophic sulfur bacteria in microbial mat communities

Abstract: A deterministic one-dimensional reaction diffusion model was constructed to simulate benthic stratification patterns and population dynamics of cyanobacteria, purple and colorless sulfur bacteria as found in marine microbial mats. The model involves the major biogeochemical processes of the sulfur cycle and includes growth metabolism and their kinetic parameters as described from laboratory experimentation. Hence, the metabolic production and consumption processes are coupled to population growth. The model is used to calculate benthic oxygen, sulfide and light profiles and to infer spatial relationships and interactions among the different populations. Furthermore, the model is used to explore the effect of different abiotic and biotic environmental parameters on the community structure. A strikingly clear pattern emerged of the interaction between purple and colorless sulfur bacteria: either colorless sulfur bacteria dominate or a coexistence is found of colorless and purple sulfur bacteria. The model predicts that purple sulfur bacteria only proliferate when the studied environmental parameters surpass well-defined threshold levels. However, once the appropriate conditions do occur, the purple sulfur bacteria are extremely successful as their biomass outweighs that of colorless sulfur bacteria by a factor of up to 17. The typical stratification pattern predicted closely resembles the often described bilayer communities which comprise a layer of purple sulfur bacteria below a cyanobacterial top-layer; colorless sulfur bacteria are predicted to sandwich in between both layers. The profiles of oxygen and sulfide shift on a diel basis similarly as observed in real systems.     

Phylogeny of Rozites, Cuphocybe and Rapacea inferred from ITS and LSU rDNA sequences

Phylogenetic relationships of Rozites, Cuphocybe, and Rapacea were assessed using molecular phylogenetic approaches. These three genera are placed in Cortinariaceae and have been regarded as closely related to Cortinarius. Rozites includes more than 20 species, which are characterized by having both a membranaceous partial veil in the form of a persistent annulus and a membranaceous universal veil. Cuphocye (4 species) lacks an annulus or cortina, but has pigmented veil fibrils or scales. The monotypic genus Rapacea accommodates a distinct taxon with pale, nearly smooth and thick-walled basidiospores. We analyzed 56 sequences of the internal transcribed spacer region (ITS1, ITS2, and the intervening 5.8S rRNA gene) for nine species of Rozites, three species of Cuphocybe, 28 species of Cortinarius, Rapacea mariae and Protoglossum luteum. Two species of Hebeloma were used as outgroup. Large subunit (LSU) rDNA sequences from selected taxa were also analyzed. The results clearly demonstrate that Rozites species are nested within the clade/Cortinarius, and that Rozites is polyphyletic, suggesting that membranaceous veils have evolved several times in the genus Cortinarius. Also Rapacea and Cuphocybe are nested within Cortinarius, making the latter genus paraphyletic. Based on phylogenetic studies, Rozites, Cuphocybe and Rapacea are artificial genera and do not reflect natural relationships.     

Two-Dimensional Patterns in Bacterial Veils Arise from Self-generated,Three-Dimensional Fluid Flows

The behavior of collections of oceanic bacteria is controlled by metabolic (chemotaxis) and physical (fluid motion) processes. Some sulfur-oxidizing bacteria, such as Thiovulum majus, unite these two processes via a material interface produced by the bacteria and upon which the bacteria are transiently attached. This interface, termed a bacterial veil, is formed by exo-polymeric substances (EPS) produced by the bacteria. By adhering to the veil while continuing to rotate their flagella, the bacteria are able to exert force on the fluid surroundings. This behavior induces a fluid flow that, in turn, causes the bacteria to aggregate leading to the formation of a physical pattern in the veil. These striking patterns are very similar in flavor to the classic convection instability observed when a shallow fluid is heated from below. However, the physics are very different since the flow around the veil is mediated by the bacteria and affects the bacterial densities.     

“Veils” Against Predators: Modified Web Structure of a Host Spider Induced by an Ichneumonid Parasitoid, Brachyzapus nikkoensis (Uchida) (Hymenoptera)

When the larva of Brachyzapus nikkoensis, a koinobiont ectoparasitoid of Agelena limbata forming a funnel web, is a penultimate instar, “veils” of very fine and dense threads covering the spider and parasitoid larva were observed in the tunnel of funnel web. As the veils are not formed until the parasitoid became penultimate instar and the parasitoid larvae are on active hosts at this stage, the veils are considered to be formed by the spider under the manipulation of the parasitoid larva. Removal of the veil indicated that penultimate larvae and pupae were more likely to fail to emerge in manipulated webs compared to the controls. The modified web seems resistant against predators and scavengers such as ants. This is the first record of web modification demonstrating its resistance to predators.     

Opposing the veil in the name of liberalism: popular attitudes to liberalism and Muslim veiling in the Netherlands

Is popular antagonism towards Muslim veils in Europe rooted in an exclusionary ‘enlightenment liberalism’? By examining different conceptions of liberalism and readings of veiling in a Dutch survey from 2014, we present the first study that investigates this question empirically. We thus bring together two hitherto largely unconnected literatures. The first is the work on immigration and ethnicity, which has shown the centrality of enlightenment liberalism in anti-Muslim media and policy discourses. The second is the literature on anti-Muslim attitudes in public opinion, which explains support for veil bans as the result of perceiving veils as threatening the respondent's own, supposedly liberal, values – but has failed to distinguish between different conceptions of liberalism and thus reached inconclusive results. This, we show, can be remedied by distinguishing between ‘enlightenment liberals’, who hold negative attitudes, and ‘reformation liberals’, who hold positive attitudes towards Muslim veils.     

Video-supported Analysis of Beggiatoa Filament Growth, Breakage, and Movement

A marine Beggiatoa sp. was cultured in semi-solid agar with opposing oxygen-sulfide gradients. Growth pattern, breakage of filaments for multiplication, and movement directions of Beggiatoa filaments in the transparent agar were investigated by time-lapse video recording. The initial doubling time of cells was 15.7 +/- 1.3 h (mean +/- SD) at room temperature. Filaments grew up to an average length of 1.7 +/- 0.2 mm, but filaments of up to approximately 6 mm were also present. First breakages of filaments occurred approximately 19 h after inoculation, and time-lapse movies illustrated that a parent filament could break into several daughter filaments within a few hours. In >20% of the cases, filament breakage occurred at the tip of a former loop. As filament breakage is accomplished by the presence of sacrificial cells, loop formation and the presence of sacrificial cells must coincide. We hypothesize that sacrificial cells enhance the chance of loop formation by interrupting the communication between two parts of one filament. With communication interrupted, these two parts of one filament can randomly move toward each other forming the tip of a loop at the sacrificial cell.     

Arp2/3 complex-dependent actin networks constrain myosin II function in driving retrograde actin flow

The Arp2/3 complex nucleates actin filaments to generate networks at the leading edge of motile cells. Nonmuscle myosin II produces contractile forces involved in driving actin network translocation. We inhibited the Arp2/3 complex and/or myosin II with small molecules to investigate their respective functions in neuronal growth cone actin dynamics. Inhibition of the Arp2/3 complex with CK666 reduced barbed end actin assembly site density at the leading edge, disrupted actin veils, and resulted in veil retraction. Strikingly, retrograde actin flow rates increased with Arp2/3 complex inhibition; however, when myosin II activity was blocked, Arp2/3 complex inhibition now resulted in slowing of retrograde actin flow and veils no longer retracted. Retrograde flow rate increases induced by Arp2/3 complex inhibition were independent of Rho kinase activity. These results provide evidence that, although the Arp2/3 complex and myosin II are spatially segregated, actin networks assembled by the Arp2/3 complex can restrict myosin II-dependent contractility with consequent effects on growth cone motility.     

Nanometer-scale visualization and structural analysis of the inorganic/organic hybrid structure of Gallionella ferruginea twisted stalks

The so-called Fe/Mn-oxidizing bacteria have long been recognized for their potential to form extracellular iron hydroxide or manganese oxide structures in aquatic environments. Bacterial species belonging to the genus Gallionella, one type of such bacteria, oxidize iron and produce uniquely twisted extracellular stalks consisting of iron oxide-encrusted inorganic/organic fibers. This paper describes the ultrastructure of Gallionella cells and stalks and the visualized structural and spatial localization of constitutive elements within the stalks. Electron microscopy with energy-dispersive X-ray microanalysis showed the export site of the stalk fibers from the cell and the uniform distribution of iron, silicon, and phosphorous in the stalks. Electron energy-loss spectroscopy revealed that the stalk fibers had a central carbon core of bacterial exopolymers and that aquatic iron interacted with oxygen at the surface of the carbon core, resulting in deposition of iron oxides at the surface. This new knowledge of the structural and spatial associations of iron with oxygen and carbon provides deeper insights into the unique inorganic/organic hybrid structure of the stalks.     

A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria

The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.     

Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column.

The vertical distribution of major and intermediate electron acceptors and donors was measured in a shallow stratified fjord. Peaks of zero valence sulfur, Mn(IV), and Fe(III) were observed in the chemocline separating oxic surface waters from sulfidic and anoxic bottom waters. The vertical fluxes of electron acceptors and donors (principally O2 and H2S) balanced within 5%; however, the zones of oxygen reduction and sulfide oxidation were clearly separated. The pathway of electron transfer between O2 and H2S was not apparent from the distribution of sulfur, nitrogen, or metal compounds investigated. The chemical zonation was related to bacterial populations as detected by ethidium bromide (EtBr) staining and by in situ hybridization with fluorescent oligonucleotide probes of increasing specificity. About half of all EtBr-stained cells were detectable with a general oligonucleotide probe for all eubacteria when digital image analysis algorithms were used to improve sensitivity. Both EtBr staining and hybridization indicated a surprisingly uniform distribution of bacteria throughout the water column. However, the average cell size and staining intensity as well as the abundance of different morphotypes changed markedly within the chemocline. The constant overall cell counts thus concealed pronounced population shifts within the water column. Cells stained with a delta 385 probe (presumably sulfate-reducing bacteria) were detected at the chemocline at about 5 x 10(4) cells per ml, and this concentration increased to 2 x 10(5) cells per ml beneath the chemocline. A long slim rod-shaped bacterium was found in large numbers in the oxic part of the chemocline, whereas large ellipsoid cells dominated at greater depth. Application of selective probes for known genera of sulfate-reducing bacteria gave only low cell counts, and thus it was not possible to identify the dominant morphotypes of the sulfate-reducing community.     

Unusual swimming behavior of a magnetotactic bacterium

Magnetotactic bacteria of strain Mar 1–83, when swimming in an applied magnetic field, did not move as a homogeneous cell suspension, but aggregated in distinct wave-like structures. The waves remained stable during forward movement. The number of cells per wave ranged from a few cells in permanent lateral contact to hundreds of bacteria moving visibly within a wave. Wave formation required a horizontal and vertical magnetic component. Electron microscopy indicated at least 3 distinct parallel chains of magnetosomes inside the bacterium. The cellular magnetic dipole moment was determined. Cell-to-cell magnetic interaction could be ruled out as the sole mechanism that induced wave formation and kept waves stable. Other mechanisms are discussed.     

Pattern Formation in Dictyostelium discoideum: Temporal and Spatial Distribution of Prespore Vacuoles

Cell differentiation, cell determination and pattern formation in the pseudoplasmodium of Dictyostelium discoideum , was investigated using the prespore specific vacuole (PV) as a morphological marker. Concomitantly, measurements of cell movement within the pseudoplasmodium were made by tracing radioactively labelled cells. The main results indicate that 1) prespore cells appear first during late aggregation and occur randomly throughout the pseudoplasmodium with the exception of the very tip which stays free of prespore cells throughout development; 2) after late aggregation the number of prespore cells increases over a period of several hours; 3) each prespore cell takes on a progressively more prespore-like character as judged by the increase in number of PVs it contains; 4) establishment of the distribution pattern of prespore and prestalk cells takes place within the first 2 h, mainly by a sorting out mechanism; 5) presumptive spore areas are likely to contain a small proportion of cells lacking PVs (prestalk-cells?) while presumptive stalk cell areas are homogeneous throughout; 6) maintenance of the pattern during migration may be facilitated by a circulation at low level of prestalk cells between prestalk and prespore areas; and 7) during the development of this organism the events of cell determination, cell differentiation and pattern formation overlap substantially in time.     

Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids

Within the upper 400 m at western, central and eastern stations in the world's largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alpha-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 microM including layers where previously anammox bacteria were described. Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared with the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 microM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared with the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.     

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."