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.     

Age-related migration patterns in Larus fuscus spp.

Migration is a critical period in a bird’s life that can affect the fitness of individuals. Intra-population migratory patterns and the way different sex and/or age classes within a population differ in timing and/or distance of migration are not completely understood. The present study aims to observe inter- and intra-population migratory patterns in the western population of Lesser Black-backed Gulls (Larus fuscus spp.), shedding light on age-related differences of temporal patterns of occurrence in the Portuguese coastal areas during migration and winter. One thousand seven hundred and fifty-four colour ring records were analysed matching a 30-year period of observations on the Portuguese coast between 1975 and 2005. During migration, the graellsii population represents 90% of the migratory flow of L. fuscus through Portugal with the intermedius accounting for 9% and the fuscus population, being vestigial in this period, accounting for 1%. Nevertheless, interesting significant differences were observed between the age classes of the three populations during this period, the graellsii population having a large number of first winters (40% of the migratory contingent of this population) followed by immatures and adults whilst in the intermedius and fuscus populations, the largest age class is the adults. During winter, no inter-population differences were found. When comparing migration and winter periods, intra-population differences were found in the graellsii and fuscus populations regarding distribution and age classes. These results indicate different migratory routes amongst different populations suggesting a leapfrog migration in L. fuscus and also a differential age-related migration pattern that might result from first winters migrating further south in search of a wintering place since adults heavily occupy the closest wintering quarters in their attempt to arrive earlier at their breeding ground.     

Modeling patterns of zooplankton diel vertical migration

Realized predation pressure, defined as the product of predationpressure and light intensity, expresses the mortality pressuredue to visual predation. The part of realized predation pressurewhich is sensed by organisms is here considered to be relatedto food level and temperature. This partly realized predationpressure is referred to as sensed predation pressure. We proposea possible control mechanism of diel vertical migration (DVM):organisms move vertically following the minimum change in sensedpredation pressure. To investigate this assumption, we presenta math ematical model of DVM. We assume that when predatorsare present, the food level is above a minimal level, and temperatureis higher than the tolerance of organisms to growth, prey organismsundertake DVM following the minimum change in sensed predationpressure. We examine how patterns of migration may be affectedby changes in water clarity, predation pressure, food leveland temperature. This work supports the assumption that minimizingchanges in sensed predation pressure can explain the wide variationin the vertical profile of zooplankton.     

Oxygen Responses and Mat Formation by Beggiatoa spp

The behavioral response of single Beggiatoa sp. filaments moving on a gas-permeable membrane was studied by the combined use of microscopy and oxygen microelectrodes during controlled oscillations of oxygen tension. The bacteria reacted to increasing oxygen by reversing the direction of movement. The same step-up phobic response to oxygen was observed when a filament tip or loop glided into a stable microgradient of increasing oxygen. The response was sensitive to a change in oxygen tension of <5% of air saturation min⁻¹. The response time was 20 to 50 s. Frequently, only part of the filament responded, which led to the formation of sharp bends, loops, and coils. This partial response facilitated the positioning of the long filaments within the narrow O₂-H₂S interface. The structure of whole Beggiatoa mats on sediment surfaces varied from loose to dense in relation to shallow or steep oxygen gradients in the 0.3- to 2-mm-thick, unstirred boundary layer. In an illuminated sediment Beggiatoa spp. lived together with photosynthetic organisms and migrated vertically in accordance with light/dark variations. The combined effect of phobic responses to light and oxygen can explain this migration.     

Bacterial community associated with black band disease in corals

Black band disease (BBD) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. While it has been well established that the BBD bacterial mat is dominated by a cyanobacterium, the quantitative composition of the BBD bacterial mat community has not described previously. Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to characterize the infectious bacterial community of the bacterial mat causing BBD. These analyses revealed that the bacterial composition of the BBD mat does not vary between different coral species but does vary when different species of cyanobacteria are dominant within the mat. On the basis of the results of a new method developed to identify organisms detected by T-RFLP analysis, our data show that besides the cyanobacterium, five species of the division Firmicutes, two species of the Cytophaga-Flexibacter-Bacteroides (CFB) group, and one species of delta-proteobacteria are also consistently abundant within the infectious mat. Of these dominant taxa, six were consistently detected in healthy corals. However, four of the six were found in much higher numbers in BBD mats than in healthy corals. One species of the CFB group and one species of Firmicutes were not always associated with the bacterial communities present in healthy corals. Of the eight dominant bacteria identified, two species were previously found in clone libraries obtained from BBD samples; however, these were not previously recognized as important. Furthermore, despite having been described as an important component of the pathogenetic mat, a Beggiatoa species was not detected in any of the samples analyzed. These results will permit the dominant BBD bacteria to be targeted for isolation and culturing experiments aimed at deciphering the disease etiology.     

Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments

Filamentous sulphide-oxidizing Beggiatoa spp. often occur in large numbers in the coastal seabed without forming visible mats on the sediment surface. We studied the diversity, population structure and the nitrate-storing capability of such bacteria in the Danish Limfjorden and the German Wadden Sea. Their distribution was compared to the vertical gradients of O2, NO3- and H2S as measured by microsensors. The main Beggiatoa spp. populations occurred in a 0.5-3 cm thick intermediate zone, below the depth of oxygen and nitrate penetration but above the zone of free sulphide. The Beggiatoa spp. filaments were found to store nitrate, presumably in liquid vacuoles up to a concentration of 370 mM NO3-, similar to the related large marine sulphur bacteria, Thioploca and Thiomargarita. The observations indicate that marine Beggiatoa spp. can live anaerobically and conserve energy by coupling sulphide oxidation with the reduction of nitrate to dinitrogen and/or ammonia. Calculations of the diffusive nitrate flux and the potential sulphide oxidation by Beggiatoa spp. show that the bacteria may play a critical role for the sulphur cycling and the nitrogen balance in these coastal environments. 16S rDNA sequence analysis shows a large diversity of these uncultured, nitrate-storing Beggiatoa spp. Smaller (9-17 micro m wide) and larger (33-40 micro m wide) Beggiatoa spp. represent novel phylogenetic clusters distinct from previously sequenced, large marine Beggiatoa spp. and Thioploca spp. Fluorescence in situ hybridization (FISH) of the natural Beggiatoa spp. populations showed that filament width is a conservative character of each phylogenetic species but a given filament width may represent multiple phylogenetic species in a mixed population.     

Microoxic-Anoxic Niche of Beggiatoa spp.: Microelectrode Survey of Marine and Freshwater Strains

Beggiatoa spp. grow optimally in media containing opposed gradients of oxygen and soluble sulfide, although some strains also require an organic substrate. By using microelectrodes, we characterized oxygen and sulfide gradients during their initial development in uninoculated media and in cultures of marine and freshwater strains. In gradient media, Beggiatoa strains always grew some distance below the air/agar interface as a dense “plate” of constantly gliding filaments with sharply demarcated upper and lower boundaries. Within established plates, the maximum oxygen partial pressure was 0.6 to 6.0% of air saturation and not significantly lower if filaments were fixing nitrogen. Oxygen penetrated only 100 to 300 μm into the plate, and the anoxic fraction increased from less than 10% to approximately 90% during later stages of growth. For lithoautotrophically grown marine strains, the linearity of the oxygen profile above the plate plus its drop to zero therein indicated that oxygen uptake for the entire tube occurred only within the Beggiatoa plate. Consequently, oxygen consumption could be predicted solely from the distance between the air/agar interface and the top of a plate, given the diffusion coefficient for oxygen. By contrast, for freshwater strains grown heterotrophically (with sulfide also in the medium), oxygen profiles were frequently nonlinear because of nonbiological reaction with sulfide which had diffused past the aggregated filaments. For all strains tested, microoxic aggregation also occurred in the absence of sulfide, apparently reflecting a step-up phobic response to oxygen.     

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.     

Porpostoma guamensis n. sp., a philasterine scuticociliate associated with brown-band disease of corals

Brown band disease of coral is caused by a ciliate that consumes the tissue of the corals in the genus Acropora. We describe the ciliate associated with this disease on Guam, based on: general morphology, division stages, and ciliature observed on live and protargol-stained specimens; modification of the oral structures between divisional stages, observed on protargol-stained specimens; and some aspects of behavior in field and laboratory studies. Porpostoma guamensis n. sp. is elongate and has ciliature typical for the genus; live cells are 70-500 × 20-75 μm; the macronucleus is sausage-like, elongate but often bent, positioned centrally along the main cell axis; the oral ciliature follows a basic pattern, being composed of three adoral polykinetidal regions, as described for other species in the genus, although there is variability in the organization, especially in large cells where the three regions are not easily distinguished. Ciliates fed on coral with their oral region adjacent to the tissue, which they engulfed, leaving the coral a bare skeleton. Both zooxanthellae and nematocysts from coral occurred in the ciliates. Zooxanthellae appeared to be ingested alive but deteriorated within 2-3 days. Ciliates formed thin-walled division cysts on the coral and divided up to 3 times. Cysts formed around daughter cells within cysts. We provide some observations on the complex division pattern of the ciliate (i.e. tomont-trophont-cyst) and propose a possible complete pattern that requires further validation.     

Effects of moonlight on the vertical migration patterns of demersal zooplankton

The diel vertical migration patterns of demersal zooplankton, those organisms which habit bottom substrates but periodically emerge to swim freely in the water column, water determined throughout the lunar cycle. Demersal zooplankton were quantitatively sampled on a subtidal sand flat in the Gulf of California every 2 h for 24-h periods at new, full, first, and last-quarter moons, both as they emerged into the water column and as they returned to the benthos. Demersal zooplankton rarely migrated during daylight. Three general patterns of migration were observed. (1) Polychaetes and cumaceans emerged from the benthos at dusk, regardless of the phase of the moon. Polychaetes returned to the benthos throughout the night while cumaceans returned near dawn. (2) Species of amphipods and isopods exhibited significant avoidance of moonlight, delaying emergence until moonset or returning to the benthos at moonrise. (3) Species of copepods, mysids, shrimp, Branchiostoma (cephalochordate), and tanaids emerged into the water column throughout the night. The timing of migration was highly variable and did not correlate with the presence or absence of moonlight. Large zooplankton migrated less frequently into the water column during moonlit periods than small forms, suggesting that nocturnal predation by visually oriented planktivorous fish may be an important selective pressure.Demersal zooplankton emerged into artificially darkened emergence traps in significantly higher numbers during daylight and during full and quarter moons than into undarkened control traps, demonstrating that absence of light is a major cue stimulating migration. Reentry traps resting on the bottom captured higher densities of demersal zooplankton than either emergence traps or reentry traps suspended off the bottom. Thus, many demersal zooplankton remain near the bottom, rarely swimming far into the water column. Some trap avoidance was observed and current methods for collecting demersal zooplankton are evaluated. Since most demersal zooplankton remained in the water column only a short time, dispersal, particularly over short distances, may be a major advantage of migratory behavior. Migration facilitates rapid recolonization of disturbed or defaunated sites, disrupts and mixes bottom sediments, and results in daily variation in the microdistribution, patchiness, and species composition of the benthic fauna.     

The photobehaviour of Daphnia spp. as a model to explain diel vertical migration in zooplankton

Many pelagic animal species in the marine environment and in lakes migrate to deeper water layers before sunrise and return around sunset. The amplitude of these diel vertical migrations (DVM) varies from several hundreds of metres in the oceans to approx. 5–20 m in lakes. DVM can be studied from a proximate and an ultimate point of view. A proximate analysis is intended to reveal the underlying behavioural mechanism and the factors that cause the daily displacements. The ultimate analysis deals with the adaptive significance of DVM and the driving forces that were responsible for the selection of the traits essential to the behavioural mechanism. The freshwater cladoceran Daphnia is the best studied species and results can be used to model migration behaviour in general. Phototaxis in Daphnia spp., which is defined as a light-oriented swimming towards (positive phototaxis) or away (negative phototaxis) from a light source, is considered the most important mechanism basic to DVM. A distinction has been made between primary phototaxis which occurs when light intensity is constant, and secondary phototaxis which is caused by changes in light intensity. Both types of reaction are superimposed on normal swimming. This swimming of Daphnia spp. consists of alternating upwards and downwards displacements over small distances. An internal oscillator seems to be at the base of these alternations. Primary phototaxis is the result of a dominance of either the upwards or the downwards oscillator phase, and the direction depends on internal and external factors: for example, fish-mediated chemicals or kairomones induce a downwards drift. Adverse environmental factors may produce a persistent primary phototaxis. Rare clones of D. magna have been found that show also persistent positive or negative primary phototaxis and interbreeding of the two types produces intermediate progeny: thus a genetic component seems to be involved. Also secondary phototaxis is superimposed on normal swimming: a continuous increase in light intensity amplifies the downwards oscillator phase and decreases the upwards phase. A threshold must be succeeded which depends on the rate and the duration of the relative change in light intensity. The relation between both is given by the stimulus strength versus stimulus duration curve. An absolute threshold or rheobase exists, defined as the minimum rate of change causing a response if continued for an infinitely long time. DVM in a lake takes place during a period of 1-5-2 h when light changes are higher than the rheobase threshold. Accelerations in the rate of relative increase in light intensity strongly enhance downwards swimming in Daphnia spp. and this enhancement increases with increasing fish kairomone and food concentration. This phenomenon may represent a ‘decision-making mechanism’ to realize the adaptive goal of DVM: at high fish predator densities, thus high kairomone concentrations, and sufficiently high food concentrations, DVM is profitable but not so at low concentrations. Body axis orientation in Daphnia spp. is controlled with regard to light-dark boundaries or contrasts. Under water, contrasts are present at the boundaries of the illuminated circular window which results from the maximum angle of refraction at 48–9° with the normal (Snell's window). Contrasts are fixed by the compound eye and appropriate turning of the body axis orients the daphnid in an upwards or an obliquely downwards direction. A predisposition for a positively or negatively phototactic orientation seems to be the result of a disturbed balance of the two oscillators governing normal swimming. Some investigators have tried to study DVM at a laboratory scale during a 24 h cycle. To imitate nature, properties of a natural water column, such as a large temperature gradient, were compressed into a few cm. With appropriate light intensity changes, vertical distributions looking like DVM were obtained. The results can be explained by phototactic reactions and the artificial nature of the compressed environmental factors but do not compare with DVM in the field. A mechanistic model of DVM based on phototaxis is presented. Both, primary and secondary phototaxis is considered an extension of normal swimming. Using the light intensity changes of dawn and the differential enhancement of kairomones and food concentrations, amplitudes of DVM could be simulated comparable to those in a lake. The most important adaptive significance of DVM is avoidance of visual predators such as juvenile fish. However, in the absence of fish kairomones, small-scale DVMs are often present, which were probably evolved for UV-protection, and are realized by not enhanced phototaxis. In addition, the ‘decision-making mechanism’ was probably evolved as based on the enhanced phototactic reaction to accelerations in the rate of relative changes in light intensity and the presence of fish kairomones.     

Polysulfides as Intermediates in the Oxidation of Sulfide to Sulfate by Beggiatoa spp.

Zero-valent sulfur is a key intermediate in the microbial oxidation of sulfide to sulfate. Many sulfide-oxidizing bacteria produce and store large amounts of sulfur intra- or extracellularly. It is still not understood how the stored sulfur is metabolized, as the most stable form of S⁰ under standard biological conditions, orthorhombic α-sulfur, is most likely inaccessible to bacterial enzymes. Here we analyzed the speciation of sulfur in single cells of living sulfide-oxidizing bacteria via Raman spectroscopy. Our results showed that under various ecological and physiological conditions, all three investigated Beggiatoa strains stored sulfur as a combination of cyclooctasulfur (S₈) and inorganic polysulfides (S_n²⁻). Linear sulfur chains were detected during both the oxidation and reduction of stored sulfur, suggesting that S_n²⁻ species represent a universal pool of bioavailable sulfur. Formation of polysulfides due to the cleavage of sulfur rings could occur biologically by thiol-containing enzymes or chemically by the strong nucleophile HS⁻ as Beggiatoa migrates vertically between oxic and sulfidic zones in the environment. Most Beggiatoa spp. thus far studied can oxidize sulfur further to sulfate. Our results suggest that the ratio of produced sulfur and sulfate varies depending on the sulfide flux. Almost all of the sulfide was oxidized directly to sulfate under low-sulfide-flux conditions, whereas only 50% was oxidized to sulfate under high-sulfide-flux conditions leading to S⁰ deposition. With Raman spectroscopy we could show that sulfate accumulated in Beggiatoa filaments, reaching intracellular concentrations of 0.72 to 1.73 M.     

Viral communities associated with healthy and bleaching corals

The coral holobiont is the integrated assemblage of the coral animal, its symbiotic algae, protists, fungi and a diverse consortium of Bacteria and Archaea . Corals are a model system for the study of symbiosis, the breakdown of which can result in disease and mortality. Little is known, however, about viruses that infect corals and their symbionts. Here we present metagenomic analyses of the viral communities associated with healthy and partially bleached specimens of the Caribbean reef-building coral Diploria strigosa . Surprisingly, herpes-like sequences accounted for 4–8% of the total sequences in each metagenome; this abundance of herpes-like sequences is unprecedented in other marine viral metagenomes. Viruses similar to those that infect algae and plants were also present in the coral viral assemblage. Among the phage identified, cyanophages were abundant in both healthy and bleaching corals and vibriophages were also present. Therefore, coral-associated viruses could potentially infect all components of the holobiont – coral, algal and microbial. Thus, we expect viruses to figure prominently in the preservation and breakdown of coral health.     

Distinctive patterns of DNA methylation associated with Parkinson disease

Parkinson disease (PD) is a multifactorial neurodegenerative disorder with high incidence in the elderly, where environmental and genetic factors are involved in etiology. In addition, epigenetic mechanisms, including deregulation of DNA methylation have been recently associated to PD. As accurate diagnosis cannot be achieved pre-mortem, identification of early pathological changes is crucial to enable therapeutic interventions before major neuropathological damage occurs. Here we investigated genome-wide DNA methylation in brain and blood samples from PD patients and observed a distinctive pattern of methylation involving many genes previously associated to PD, therefore supporting the role of epigenetic alterations as a molecular mechanism in neurodegeneration. Importantly, we identified concordant methylation alterations in brain and blood, suggesting that blood might hold promise as a surrogate for brain tissue to detect DNA methylation in PD and as a source for biomarker discovery.     

Culture and identification of Desulfovibrio spp. from corals infected by black band disease on Dominican and Florida Keys reefs

Black band disease (BBD) of corals is characterized as a pathogenic microbial consortium composed of a wide variety of microorganisms. Together, many of these microorganisms contribute to an active sulfur cycle that produces anoxia and high levels of sulfide adjacent to the coral surface, conditions that are lethal to coral tissue. Sulfate-reducing bacteria, as sulfide producers, are an important component of the sulfur cycle and the black band community. Previous molecular survey studies have shown multiple Desulfovibrio species present in BBD but with limited consistency between bacterial species and infections. In this study we compared 16S rRNA gene sequences of sulfate-reducing bacteria selectively cultured from 6 BBD bands on 4 coral species, Diploria clivosa, D. strigosa, D. labyrinthiformes, and Siderastrea siderea, in the Florida Keys and Dominica. The 16S rRNA gene sequences were obtained through direct sequencing of PCR products or by cloning. A BLAST search revealed that 8 out of 10 cultures sequenced were highly homologous to Desulfovibrio sp. strain TBP-1, a strain originally isolated from marine sediment. Although the remaining 2 sequences were less homologous to Desulfovibrio sp. strain TBP-1, they did not match any other sulfate-reducing (or other) species in GenBank.     

Histopathological methods for the investigation of microbial communities associated with disease lesions in reef corals

AIMS: To determine the spatial structure of microbial communities associated with disease lesions of reef corals (Scleractinia). METHODS AND RESULTS: Agarose pre-embedding preserved the structure of the disease lesion and surrounding tissues prior to demineralization of the carbonate exoskeleton and embedding in resin. Fluorescence in situ hybridization (FISH) was used to localize bacteria in the lesions of various diseases. CONCLUSIONS: The techniques successfully preserved the in situ spatial structure of degenerated coral tissues. In one case (white plague disease), significant bacterial populations were found only in fragmented remnants of degenerated coral tissues at the lesion boundary that would not have been detected using conventional histopathological techniques. SIGNIFICANCE AND IMPACT OF THE STUDY: Determining the composition, spatial structure and dynamics of microbial communities within the disease lesions is necessary to understand the process of disease progression. The methods described may be applicable to a wide range of diseases involving necrotic lesion formation and requiring extensive tissue processing, such as skeleton demineralization.     

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.     

Cultivated Beggiatoa spp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria

Within the last 10 years, numerous SSU rRNA sequences have been collected from natural populations of conspicuous, vacuolate, colorless sulfur bacteria, which form a phylogenetically cohesive cluster (large-vacuolate sulfur bacteria clade) in the gamma-Proteobacteria. Currently, this clade is composed of four named or de facto genera: all known Thioploca and Thiomargarita strains, all vacuolate Beggiatoa strains, and several strains of vacuolate, attached filaments, which bear a superficial similarity to Thiothrix. Some of these vacuolate bacteria accumulate nitrate for respiratory purposes. This clade encompasses the largest known prokaryotic cells (Thiomargarita namibiensis) and several strains that are important in the global marine sulfur cycle. Here, we report additional sequences from five pure culture strains of Beggiatoa spp., including the only two cultured marine strains (nonvacuolate), which firmly establish the root of this vacuolate clade. Each of several diverse metabolic motifs, including obligate and facultative chemolithoautotrophy, probable mixotrophy, and seemingly strict organoheterotrophy, is represented in at least one of the nonvacuolate strains that root the vacuolate clade. Because the genus designation Beggiatoa is interspersed throughout the vacuolate clade along with other recognized or de facto genera, the need for taxonomic revision is clear.