Big bacteria

A general framework of persistence strategies for biological systems helps explain domains of life

The nature and cause of the division of organisms in superkingdoms is not fully understood. Assuming that environment shapes physiology, here we construct a novel theoretical framework that helps identify general patterns of organism persistence. This framework is based on Jacob von Uexküll's organism-centric view of the environment and James G. Miller's view of organisms as matter-energy-information processing molecular machines. Three concepts describe an organism's environmental niche: scope, umwelt, and gap. Scope denotes the entirety of environmental events and conditions to which the organism is exposed during its lifetime. Umwelt encompasses an organism's perception of these events. The gap is the organism's blind spot, the scope that is not covered by umwelt. These concepts bring organisms of different complexity to a common ecological denominator. Ecological and physiological data suggest organisms persist using three strategies: flexibility, robustness, and economy. All organisms use umwelt information to flexibly adapt to environmental change. They implement robustness against environmental perturbations within the gap generally through redundancy and reliability of internal constituents. Both flexibility and robustness improve survival. However, they also incur metabolic matter-energy processing costs, which otherwise could have been used for growth and reproduction. Lineages evolve unique tradeoff solutions among strategies in the space of what we call "a persistence triangle." Protein domain architecture and other evidence support the preferential use of flexibility and robustness properties. Archaea and Bacteria gravitate toward the triangle's economy vertex, with Archaea biased toward robustness. Eukarya trade economy for survivability. Protista occupy a saddle manifold separating akaryotes from multicellular organisms. Plants and the more flexible Fungi share an economic stratum, and Metazoa are locked in a positive feedback loop toward flexibility.

DNA replication and genomic architecture of very large bacteria

Large cell size is not restricted to a particular bacterial lifestyle, dispersal method, or cell envelope type. What is conserved among the very large bacteria are the quantity and arrangement of their genomic resources. All large bacteria described to date appear to be highly polyploid. This review focuses on Epulopiscium sp. type B, which maintains tens of thousands of genome copies throughout its life cycle. Only a tiny proportion of mother cell DNA is inherited by intracellular offspring, but surprisingly DNA replication takes place in the terminally differentiated mother cell as offspring grow. Massive polyploidy supports the acquisition of unstable genetic elements normally not seen in essential genes. Further studies of how large bacteria manage their genomic resources will provide insight into how simple cellular modifications can support unusual lifestyles and exceptional cell forms.

Swimming behaviour of the multicellular magnetotactic prokaryote 'Candidatus Magnetoglobus multicellularis' under applied magnetic fields and ultraviolet light

Magnetotactic bacteria move by rotating their flagella and concomitantly are aligned to magnetic fields because they present magnetosomes, which are intracellular organelles composed by membrane-bound magnetic crystals. This results in magnetotaxis, which is swimming along magnetic field lines. Magnetotactic bacteria are morphologically diverse, including cocci, rods, spirilla and multicellular forms known as magnetotactic multicellular prokaryotes (MMPs). 'Candidatus Magnetoglobus multicellularis' is presently the best known MMP. Here we describe the helical trajectories performed by these microorganisms as they swim forward, as well as their response to UV light. We measured the radius of the trajectory, time period and translational velocity (velocity along the helix axis), which enabled the calculation of other trajectory parameters such as pitch, tangential velocity (velocity along the helix path), angular frequency, and theta angle (the angle between the helix path and the helix axis). The data revealed that 'Ca. M. multicellularis' swims along elongated helical trajectories with diameters approaching the diameter of the microorganism. In addition, we observed that 'Ca. M. multicellularis' responds to UV laser pulses by swimming backwards, returning to forward swimming several seconds after the UV laser pulse. UV light from a fluorescence microscope showed a similar effect. Thus, phototaxis is used in addition to magnetotaxis in this microorganism.

Sizing up microbes

The size range of life forms is dictated by basic principles of physics. Large microorganisms, with sizes approaching a millimeter, have compensating features that address the immutable laws of physics. For pathogens, size may impact a range of functions, such as adherence and immune evasion. We review several recent studies on factors impacting, and impacted by, the size of microorganisms.

A Single-cell genome for Thiovulum sp

We determined a significant fraction of the genome sequence of a representative of Thiovulum, the uncultivated genus of colorless sulfur Epsilonproteobacteria, by analyzing the genome sequences of four individual cells collected from phototrophic mats from Elkhorn Slough, California. These cells were isolated utilizing a microfluidic laser-tweezing system, and their genomes were amplified by multiple-displacement amplification prior to sequencing. Thiovulum is a gradient bacterium found at oxic-anoxic marine interfaces and noted for its distinctive morphology and rapid swimming motility. The genomic sequences of the four individual cells were assembled into a composite genome consisting of 221 contigs covering 2.083 Mb including 2,162 genes. This single-cell genome represents a genomic view of the physiological capabilities of isolated Thiovulum cells. Thiovulum is the second-fastest bacterium ever observed, swimming at 615 μm/s, and this genome shows that this rapid swimming motility is a result of a standard flagellar machinery that has been extensively characterized in other bacteria. This suggests that standard flagella are capable of propelling bacterial cells at speeds much faster than typically thought. Analysis of the genome suggests that naturally occurring Thiovulum populations are more diverse than previously recognized and that studies performed in the past probably address a wide range of unrecognized genotypic and phenotypic diversities of Thiovulum. The genome presented in this article provides a basis for future isolation-independent studies of Thiovulum, where single-cell and metagenomic tools can be used to differentiate between different Thiovulum genotypes.

Global distribution of microbial abundance and biomass in subseafloor sediment

The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9⋅10(29) cells [corresponding to 4.1 petagram (Pg) C and ∼0.6% of Earth's total living biomass]. This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate Earth's total number of microbes and total living biomass to be, respectively, 50-78% and 10-45% lower than previous estimates.

Inorganic carbon fixation by chemosynthetic ectosymbionts and nutritional transfers to the hydrothermal vent host-shrimp Rimicaris exoculata

The shrimp Rimicaris exoculata dominates several hydrothermal vent ecosystems of the Mid-Atlantic Ridge and is thought to be a primary consumer harbouring a chemoautotrophic bacterial community in its gill chamber. The aim of the present study was to test current hypotheses concerning the epibiont's chemoautotrophy, and the mutualistic character of this association. In-vivo experiments were carried out in a pressurised aquarium with isotope-labelled inorganic carbon (NaH(13)CO(3) and NaH(14)CO(3)) in the presence of two different electron donors (Na(2)S(2)O(3) and Fe(2+)) and with radiolabelled organic compounds ((14)C-acetate and (3)H-lysine) chosen as potential bacterial substrates and/or metabolic by-products in experiments mimicking transfer of small biomolecules from epibionts to host. The bacterial epibionts were found to assimilate inorganic carbon by chemoautotrophy, but many of them (thick filaments of epsilonproteobacteria) appeared versatile and able to switch between electron donors, including organic compounds (heterotrophic acetate and lysine uptake). At least some of them (thin filamentous gammaproteobacteria) also seem capable of internal energy storage that could supply chemosynthetic metabolism for hours under conditions of electron donor deprivation. As direct nutritional transfer from bacteria to host was detected, the association appears as true mutualism. Import of soluble bacterial products occurs by permeation across the gill chamber integument, rather than via the digestive tract. This first demonstration of such capabilities in a decapod crustacean supports the previously discarded hypothesis of transtegumental absorption of dissolved organic matter or carbon as a common nutritional pathway.

Cell-free protein synthesis from a single copy of DNA in a glass microchamber

To achieve a cell-mimetic reaction environment, we fabricated and tested quartz microchambers for conducting protein synthesis using an in vitro transcription and translation system, the PURE system. By introducing a glass microchamber and blocking the surface of the chamber with amino acids, the concentration of the synthesized marker protein (green fluorescent protein, GFP) was significantly improved compared to that in the poly(dimethylsiloxane) (PDMS) microchamber. The concentration was below the detection limit in the PDMS microchambers, whereas the glass microchambers yielded 700 nM GFP, representing 41% of the bulk reaction. There was no detectable difference when the GFP synthesis was performed in microchambers with sizes ranging from 40 fL to 7 pL, indicating that the present microchamber system can serve as a cell-sized test tube with a variable reaction volume. Finally, we demonstrated that two different proteins, GFP and β-galactosidase, can be expressed from single genes in our experimental setup. Quantized and distinctive signals from proteins synthesized from 0, 1, or 2 copies of genes were obtained. The microchamber presented here can be utilized not only to study the effects of compartment volume on protein synthesis but also for the comprehensive analysis of complex biochemical reactions in cell-mimetic environments.

Study on the microbial safety of an infusion set for contrast-enhanced imaging

OBJECTIVES

Multiple uses of automatic contrast injection systems may impose septic risks on patients. The purpose of this experiment was to verify whether a newly developed replaceable patient-delivery system may allow multiple uses of the system but without such risks.

METHODS

Twelve patient-delivery systems were tested according to a multiple-use approach using an automatic contrast injection system consisting of dual syringes and one filling and injecting set. Two protocols with normal saline only (n = 6) or contrast media plus normal saline (n = 6) loaded in the injection system were performed. Each patient-delivery system was connected through an infusion catheter to the ear vein of a rabbit that was intravenously preinjected with a diffusible radiotracer (99m)Tc-dimercaptopropionyl-human serum albumin. Aliquots were sampled from the filling and injecting set, patient line, and animal blood for radioactive analysis after the replacement of each patient-delivery system.

RESULTS

For the protocol performed using only normal saline, radioactivity was found in the blood circulation of the rabbit (1655903 ± 593221 CPM) and in the patient line (52894 ± 33080 CPM), but, virtually, in none of samples from the filling and injecting set (8 ± 3 CPM), relative to the background (7 ± 3 CPM) (P = 0.726). Similarly, experimental results attained using contrast plus saline show radioactivity in the blood circulation of the rabbit (1119107 ± 183174 CPM) as well as in the patient line (32991 ± 20232 CPM) but in none of samples from the filling and injecting set (6 ± 6 CPM), relative to the background (6 ± 4 CPM) (P = 0.955).

CONCLUSIONS

The tested patient-delivery system proves convenient and safe. It allows multiple uses of the contrast injection system and avoids the risk of cross contamination.

Cell size control in bacteria

Like eukaryotes, bacteria must coordinate division with growth to ensure cells are the appropriate size for a given environmental condition or developmental fate. As single-celled organisms, nutrient availability is one of the strongest influences on bacterial cell size. Classic physiological experiments conducted over four decades ago first demonstrated that cell size is directly correlated with nutrient source and growth rate in the Gram-negative bacterium Salmonella typhimurium. This observation subsequently served as the basis for studies revealing a role for cell size in cell cycle progression in a closely related organism, Escherichia coli. More recently, the development of powerful genetic, molecular, and imaging tools has allowed us to identify and characterize the nutrient-dependent pathway responsible for coordinating cell division and cell size with growth rate in the Gram-positive model organism Bacillus subtilis. Here, we discuss the role of cell size in bacterial growth and development and propose a broadly applicable model for cell size control in this important and highly divergent domain of life.

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

The effects of hypoxia on sediment nitrogen cycling in the Baltic Sea

Primary production in the eutrophic Baltic Sea is limited by nitrogen availability; hence denitrification (natural transformation of nitrate to gaseous N(2)) in the sediments is crucial in mitigating the effects of eutrophication. This study shows that dissimilatory nitrate reduction to ammonium (DNRA) process, where nitrogen is not removed but instead recycled in the system, dominates nitrate reduction in low oxygen conditions (O(2) <110 μM), which have been persistent in the central Gulf of Finland during the past decade. The nitrogen removal rates measured in this study show that nitrogen removal has decreased in the Gulf of Finland compared to rates measured in mid-1990s and the decrease is most likely caused by the increased bottom water hypoxia.

Self-propelled Brownian spinning top: dynamics of a biaxial swimmer at low Reynolds numbers

Recently the Brownian dynamics of self-propelled (active) rodlike particles was explored to model the motion of colloidal microswimmers, catalytically driven nanorods, and bacteria. Here we generalize this description to biaxial particles with arbitrary shape and derive the corresponding Langevin equation for a self-propelled Brownian spinning top. The biaxial swimmer is exposed to a hydrodynamic Stokes friction force at low Reynolds numbers, to fluctuating random forces and torques as well as to an external and an internal (effective) force and torque. The latter quantities control its self-propulsion. Due to biaxiality and hydrodynamic translational-rotational coupling, the Langevin equation can only be solved numerically. In the special case of an orthotropic particle in the absence of external forces and torques, the noise-free (zero-temperature) trajectory is analytically found to be a circular helix. This trajectory is confirmed numerically to be more complex in the general case of an arbitrarily shaped particle under the influence of arbitrary forces and torques involving a transient irregular motion before ending up in a simple periodic motion. By contrast, if the external force vanishes, no transient regime is found, and the particle moves on a superhelical trajectory. For orthotropic particles, the noise-averaged trajectory is a generalized concho-spiral. We furthermore study the reduction of the model to two spatial dimensions and classify the noise-free trajectories completely finding circles, straight lines with and without transients, as well as cycloids and arbitrary periodic trajectories.

Unusual polyphosphate inclusions observed in a marine Beggiatoa strain

Sulfide-oxidizing bacteria of the genus Beggiatoa are known to accumulate phosphate intracellularly as polyphosphate but little is known about the structure and properties of these inclusions. Application of different staining techniques revealed the presence of unusually large polyphosphate inclusions in the marine Beggiatoa strain 35Flor. The inclusions showed a co-occurrence of polyphosphate, calcium and magnesium when analyzed by scanning electron microscopy and energy dispersive X-ray analysis. Similar to polyphosphate-enriched acidocalcisomes of prokaryotes and eukaryotes, the polyphosphate inclusions in Beggiatoa strain 35Flor are enclosed by a lipid layer and store cations. However, they are not notably acidic. 16S rRNA gene sequence-based phylogenetic reconstruction showed an affiliation of Beggiatoa strain 35Flor to a monophyletic branch, comprising other narrow vacuolated and non-vacuolated Beggiatoa species. The polyphosphate inclusions represent a new type of membrane surrounded storage compartment within the genus Beggiatoa, distinct from the mostly nitrate-storing vacuoles known from other marine sulfide-oxidizing bacteria of the family Beggiatoaceae.

Putative fossilized fungi from the lithified volcaniclastic apron of Gran Canaria, Spain

We report the discovery of fossilized filamentous structures in samples of the lithified, volcaniclastic apron of Gran Canaria, which were obtained during Leg 157 of the Ocean Drilling Program (ODP). These filamentous structures are 2-15 μm in diameter and several hundred micrometers in length and are composed of Si, Al, Fe, Ca, Mg, Na, Ti, and C. Chitin was detected in the filamentous structures by staining with wheat germ agglutinin dye conjugated with fluorescein isothiocyanate (WGA-FITC), which suggests that they are fossilized fungal hyphae. The further elucidation of typical filamentous fungal morphological features, such as septa, hyphal bridges, and anastomosis and their respective sizes, support this interpretation. Characteristic structures that we interpreted as fossilized spores were also observed in association with the putative hyphae. The fungal hyphae were found in pyroxene phenocrysts and in siderite pseudomorphs of a basalt breccia. The fungal colonization of the basalt clasts occurred after the brecciation but prior to the final emplacement and lithification of the sediment at ∼16-14 Ma. The siderite appears to have been partially dissolved by the presence of fungal hyphae, and the fungi preferentially colonized Fe-rich carbonates over Fe-poor carbonates (aragonite). Our findings indicate that fungi may be an important geobiological agent in subseafloor environments and an important component of the deep subseafloor biosphere, and that hydrothermal environments associated with volcanism can support a diverse ecosystem, including eukaryotes.

Interplay between energetics and dynamics in bacterial motility

We study how self-propelled organisms administer their energetic resources in order to optimize space exploration. Noting the existence of two very different time scales, we use a quasistatic approximation to analyze the relation between bacterial dynamics and changes in the energy stored by a bacterium. We then find both steady-state and time-dependent solutions for the bacterial speed and stored energy. The model also predicts the volume of the region that a bacterium may visit in a resource-depleted medium.

Energetics and genetics across the prokaryote-eukaryote divide

BACKGROUND

All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont.

RESULTS

The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote.

CONCLUSIONS

The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes.

REVIEWERS

This article was reviewed by: Eugene Koonin, William Martin, Ford Doolittle and Mark van der Giezen. For complete reports see the Reviewers' Comments section.

The bacterial second messenger c-di-GMP: mechanisms of signalling

Cyclic-di-GMP (c-di-GMP) regulates many important bacterial processes. Freely diffusible intracellular c-di-GMP is determined by the action of metabolizing enzymes that allow integration of numerous input signals. c-di-GMP specifically regulates multiple cellular processes by binding to diverse target molecules. This review highlights important questions in research into the mechanisms of c-di-GMP signalling and its role in bacterial physiology.

Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria

We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization.

Vacuolated Beggiatoa-like filaments from different hypersaline environments form a novel genus

In this study, members of a specific group of thin (6-14 µm filament diameter), vacuolated Beggiatoa-like filaments from six different hypersaline microbial mats were morphologically and phylogenetically characterized. Therefore, enrichment cultures were established, filaments were stained with fluorochromes to show intracellular structures and 16S rRNA genes were sequenced. Morphological characteristics of Beggiatoa-like filaments, in particular the presence of intracellular vacuoles, and the distribution of nucleic acids were visualized. In the intracellular vacuole nitrate reached concentrations of up to 650 mM. Fifteen of the retrieved 16S rRNA gene sequences formed a monophyletic cluster and were phylogenetically closely related (≥ 94.4% sequence identity). Sequences of known filamentous sulfide-oxidizing genera Beggiatoa and Thioploca that comprise non-vacuolated and vacuolated filaments from diverse habitats clearly delineated from this cluster. The novel monophyletic cluster was furthermore divided into two sub-clusters: one contained sequences originating from Guerrero Negro (Mexico) microbial mats and the other comprised sequences from five distinct Spanish hypersaline microbial mats from Ibiza, Formentera and Lake Chiprana. Our data suggest that Beggiatoa-like filaments from hypersaline environments displaying a thin filament diameter contain nitrate-storing vacuoles and are phylogenetically separate from known Beggiatoa. Therefore, we propose a novel genus for these organisms, which we suggest to name 'Candidatus Allobeggiatoa'.

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.

Continuous cultivation and thermodynamic aspects of niche definition in the nitrogen cycle

The study of model organisms in pure culture has provided detailed information about the physiology and biochemistry of nitrification and related processes. Metagenomic sequencing of environmental samples is providing information to what extent this understanding also applies to natural microbial communities. Here, we outline a conceptual and experimental strategy that links these two approaches. It consists of the mathematical modeling of nitrification and related processes. The model predictions are subsequently validated experimentally by the study of natural microbial communities in continuous cultures under precisely defined environmental conditions. Combined with calorimetry and metagenomic monitoring this form of "experimental metagenomics" enables the answering of current questions in the ecology of the nitrogen cycle.

Predicting microbial nitrogen pathways from basic principles

Nitrogen compounds are transformed by a complicated network of competing geochemical processes or microbial pathways, each performed by a different ecological guild of microorganisms. Complete experimental unravelling of this network requires a prohibitive experimental effort. Here we present a simple model that predicts relative rates of hypothetical nitrogen pathways, based only on the stoichiometry and energy yield of the performed redox reaction, assuming competition for resources between alternative pathways. Simulating competing pathways in hypothetical freshwater and marine sediment situations, we surprisingly found that much of the variation observed in nature can simply be predicted from these basic principles. Investigating discrepancies between observations and predictions led to two important biochemical factors that may create barriers for the viability of pathways: enzymatic costs for long pathways and high ammonium activation energy. We hypothesize that some discrepancies can be explained by non-equilibrium dynamics. The model predicted a pathway that has not been discovered in nature yet: the dismutation of nitrite to the level of nitrate and dinitrogen gas.

Archaeal populations in hypersaline sediments underlying orange microbial mats in the Napoli mud volcano

Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.

The energetics of genome complexity

All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to evolve greater complexity. Why not? Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis that gave rise to mitochondria restructured the distribution of DNA in relation to bioenergetic membranes, permitting a remarkable 200,000-fold expansion in the number of genes expressed. This vast leap in genomic capacity was strictly dependent on mitochondrial power, and prerequisite to eukaryote complexity: the key innovation en route to multicellular life.

Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain

Sulfur bacteria such as Beggiatoa or Thiomargarita have a particularly high capacity for storage because of their large size. In addition to sulfur and nitrate, these bacteria also store phosphorus in the form of polyphosphate. Thiomargarita namibiensis has been shown to release phosphate from internally stored polyphosphate in pulses creating steep peaks of phosphate in the sediment and thereby inducing the precipitation of phosphorus-rich minerals. Large sulfur bacteria populate sediments at the sites of recent phosphorite formation and are found as fossils in ancient phosphorite deposits. Therefore, it can be assumed that this physiology contributes to the removal of bioavailable phosphorus from the marine system and thus is important for the global phosphorus cycle. We investigated under defined laboratory conditions which parameters stimulate the decomposition of polyphosphate and the release of phosphate in a marine Beggiatoa strain. Initially, we tested phosphate release in response to anoxia and high concentrations of acetate, because acetate is described as the relevant stimulus for phosphate release in activated sludge. To our surprise, the Beggiatoa strain did not release phosphate in response to this treatment. Instead, we could clearly show that increasing sulfide concentrations and anoxia resulted in a decomposition of polyphosphate. This physiological reaction is a yet unknown mode of bacterial polyphosphate usage and provides a new explanation for high phosphate concentrations in sulfidic marine sediments.

The evolution of a capacity to build supra-cellular ropes enabled filamentous cyanobacteria to colonize highly erodible substrates

BACKGROUND

Several motile, filamentous cyanobacteria display the ability to self-assemble into tightly woven or twisted groups of filaments that form macroscopic yarns or ropes, and that are often centimeters long and 50-200 microm in diameter. Traditionally, this trait has been the basis for taxonomic definition of several genera, notably Microcoleus and Hydrocoleum, but the trait has not been associated with any plausible function.

METHOD AND FINDINGS

Through the use of phylogenetic reconstruction, we demonstrate that pedigreed, rope-building cyanobacteria from various habitats do not form a monophyletic group. This is consistent with the hypothesis that rope-building ability was fixed independently in several discrete clades, likely through processes of convergent evolution or lateral transfer. Because rope-building cyanobacteria share the ability to colonize geologically unstable sedimentary substrates, such as subtidal and intertidal marine sediments and non-vegetated soils, it is also likely that this supracellular differentiation capacity imparts a particular fitness advantage in such habitats. The physics of sediment and soil erosion in fact predict that threads in the 50-200 microm size range will attain optimal characteristics to stabilize such substrates on contact.

CONCLUSIONS

Rope building is a supracellular morphological adaptation in filamentous cyanobacteria that allows them to colonize physically unstable sedimentary environments, and to act as successful pioneers in the biostabilization process.

"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.

Three-dimensional morphological and textural complexity of Archean putative microfossils from the Northeastern Pilbara Craton: indications of biogenicity of large (>15 microm) spheroidal and spindle-like structures

We recently reported a diverse assemblage of carbonaceous structures (thread-like, film-like, spheroidal, and spindle-like) from chert in the ca. 3.0 Ga Farrel Quartzite of the Gorge Creek Group in the Pilbara Craton, Western Australia. Results from a rigorous examination of occurrence, composition, morphological complexity, size distributions, and taphonomy provided presumptive evidence for biogenicity. In this study, we present new data of morphological and textural complexity of large (>15 microm) spheroidal and spindle-like structures, using an in-focus, 3-D image reconstruction system, which further raises the scale of credibility that these structures are microfossils. While many of the large spheroids are single-walled, and the wall is irregularly folded, a few specimens are partially blistered, double walled, or have a dimpled wall. The wall-surface texture varies from smooth and homogeneous (hyaline) to patchy, granular or reticulate. Such variation is best explained as resulting from taphonomic processes. Additionally, an inner solitary body, present in some large spheroids, is hollow and partially broken, which indicates a primary origin for this substructure. Spindle-like structures have two types of flange-like appendage; one is attached at the equatorial plane of the body, whereas the other appears to be attached peripherally. In both cases, the appendage tends to have a flat geometry, a tapering thickness, and constancy in shape, proportions, and dimensions. Spindle-wall surfaces are variously textured and heterogeneous. These morphological and textural complexities and heterogeneity refute potential abiogenic formation models for these structures, such as crystals coated with organic matter, fenestrae, and the diagenetic redistribution of carbonaceous matter. When coupled with other data from Raman spectroscopy, NanoSIMS analysis, and palynology, the evidence that these large carbonaceous structures are biogenic appears compelling, though it is still equivocal as to whether they are cells or outer envelopes of colonies of smaller cells.

From the Cover: Osmotrophy in modular Ediacara organisms

The Ediacara biota include macroscopic, morphologically complex soft-bodied organisms that appear globally in the late Ediacaran Period (575-542 Ma). The physiology, feeding strategies, and functional morphology of the modular Ediacara organisms (rangeomorphs and erniettomorphs) remain debated but are critical for understanding their ecology and phylogeny. Their modular construction triggered numerous hypotheses concerning their likely feeding strategies, ranging from micro-to-macrophagus feeding to photoautotrophy to osmotrophy. Macrophagus feeding in rangeomorphs and erniettomorphs is inconsistent with their lack of oral openings, and photoautotrophy in rangeomorphs is contradicted by their habitats below the photic zone. Here, we combine theoretical models and empirical data to evaluate the feasibility of osmotrophy, which requires high surface area to volume (SA/V) ratios, as a primary feeding strategy of rangeomorphs and erniettomorphs. Although exclusively osmotrophic feeding in modern ecosystems is restricted to microscopic bacteria, this study suggests that (i) fractal branching of rangeomorph modules resulted in SA/V ratios comparable to those observed in modern osmotrophic bacteria, and (ii) rangeomorphs, and particularly erniettomorphs, could have achieved osmotrophic SA/V ratios similar to bacteria, provided their bodies included metabolically inert material. Thus, specific morphological adaptations observed in rangeomorphs and erniettomorphs may have represented strategies for overcoming physiological constraints that typically make osmotrophy prohibitive for macroscopic life forms. These results support the viability of osmotrophic feeding in rangeomorphs and erniettomorphs, help explain their taphonomic peculiarities, and point to the possible importance of earliest macroorganisms for cycling dissolved organic carbon that may have been present in abundance during Ediacaran times.

Bacterial formation of phosphatic laminites off Peru

Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10 degrees 01' S and 10 degrees 24' S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS(2)) and sphalerite (ZnS). Low delta(34)S(pyrite) values (average -28.8 per thousand) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction-phosphorite dissolution-extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C(15:0), i/ai-C(17:0) and 10MeC(16:0)) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

The controversial "Cambrian" fossils of the Vindhyan are real but more than a billion years older

The age of the Vindhyan sedimentary basin in central India is controversial, because geochronology indicating early Proterozoic ages clashes with reports of Cambrian fossils. We present here an integrated paleontologic-geochronologic investigation to resolve this conundrum. New sampling of Lower Vindhyan phosphoritic stromatolitic dolomites from the northern flank of the Vindhyans confirms the presence of fossils most closely resembling those found elsewhere in Cambrian deposits: annulated tubes, embryo-like globules with polygonal surface pattern, and filamentous and coccoidal microbial fabrics similar to Girvanella and Renalcis. None of the fossils, however, can be ascribed to uniquely Cambrian or Ediacaran taxa. Indeed, the embryo-like globules are not interpreted as fossils at all but as former gas bubbles trapped in mucus-rich cyanobacterial mats. Direct dating of the same fossiliferous phosphorite yielded a Pb-Pb isochron of 1,650 +/- 89 (2sigma) million years ago, confirming the Paleoproterozoic age of the fossils. New U-Pb geochronology of zircons from tuffaceous mudrocks in the Lower Vindhyan Porcellanite Formation on the southern flank of the Vindhyans give comparable ages. The Vindhyan phosphorites provide a window of 3-dimensionally preserved Paleoproterozoic fossils resembling filamentous and coccoidal cyanobacteria and filamentous eukaryotic algae, as well as problematic forms. Like Neoproterozoic phosphorites a billion years later, the Vindhyan deposits offer important new insights into the nature and diversity of life, and in particular, the early evolution of multicellular eukaryotes.

Particle motion in unsteady two-dimensional peristaltic flow with application to the ureter

Particle motion in an unsteady peristaltic fluid flow is analyzed. The fluid is incompressible and Newtonian in a two-dimensional planar geometry. A perturbation method based on a small ratio of wave height to wavelength is used to obtain a closed-form solution for the fluid velocity field. This analytical solution is used in conjunction with an equation of motion for a small rigid sphere in nonuniform flow taking Stokes drag, virtual mass, Faxén, Basset, and gravity forces into account. Fluid streamlines and velocity profiles are calculated. Theoretical values for pumping rates are compared with available experimental data. An application to ureteral peristaltic flow is considered since fluid flow in the ureter is sometimes accompanied by particles such as stones or bacteriuria. Particle trajectories for parameters that correspond to calcium oxalates for calculosis and Escherichia coli type for bacteria are analyzed. The findings show that retrograde or reflux motion of the particles is possible and bacterial transport can occur in the upper urinary tract when there is a partial occlusion of the wave. Dilute particle mixing is also investigated, and it is found that some of the particles participate in the formation of a recirculating bolus, and some of them are delayed in transit and eventually reach the walls. This can explain the failure of clearing residuals from the upper urinary tract calculi after successful extracorporeal shock wave lithotripsy. The results may also be relevant to the transport of other physiological fluids and industrial applications in which peristaltic pumping is used.

Physiology and behaviour of marine Thioploca

Among prokaryotes, the large vacuolated marine sulphur bacteria are unique in their ability to store, transport and metabolize significant quantities of sulphur, nitrogen, phosphorus and carbon compounds. In this study, unresolved questions of metabolism, storage management and behaviour were addressed in laboratory experiments with Thioploca species collected on the continental shelf off Chile. The Thioploca cells had an aerobic metabolism with a potential oxygen uptake rate of 1760 micromol O2 per dm(3) biovolume per h, equivalent to 4.4 nmol O2 per min per mg protein. When high ambient sulphide concentrations (approximately 200 microM) were present, a sulphide uptake of 6220+/-2230 micromol H2S per dm(3) per h, (mean+/-s.e.m., n=4) was measured. This sulphide uptake rate was six times higher than the oxidation rate of elemental sulphur by oxygen or nitrate, thus indicating a rapid sulphur accumulation by Thioploca. Thioploca reduce nitrate to ammonium and we found that dinitrogen was not produced, neither through denitrification nor through anammox activity. Unexpectedly, polyphosphate storage was not detectable by microautoradiography in physiological assays or by staining and microscopy. Carbon dioxide fixation increased when nitrate and nitrite were externally available and when organic carbon was added to incubations. Sulphide addition did not increase carbon dioxide fixation, indicating that Thioploca use excess of sulphide to rapidly accumulate sulphur rather than to accelerate growth. This is interpreted as an adaptation to infrequent high sulphate reduction rates in the seabed. The physiology and behaviour of Thioploca are summarized and the adaptations to an environment, dominated by infrequent oxygen availability and periods of high sulphide abundance, are discussed.

Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity

The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in the fossil record. The great majority of the increase is accounted for by 2 discrete steps of approximately equal magnitude: the first in the middle of the Paleoproterozoic Era (approximately 1.9 Gya) and the second during the late Neoproterozoic and early Paleozoic eras (0.6-0.45 Gya). Each size step required a major innovation in organismal complexity--first the eukaryotic cell and later eukaryotic multicellularity. These size steps coincide with, or slightly postdate, increases in the concentration of atmospheric oxygen, suggesting latent evolutionary potential was realized soon after environmental limitations were removed.

Mercury stable isotope fractionation during reduction of Hg(II) by different microbial pathways

Mercury (Hg) stable isotope fractionation has recently been developed as a tool in biogeochemistry. In this study, the extent of Hg stable isotope fractionation during reduction of ionic mercury [Hg(II)] by two Hg(II)-resistant strains, Bacillus cereus 5 and the thermophile Anoxybacillus sp. FB9 [which actively detoxify Hg(II) by the mer system] and a Hg(II)-sensitive metal-reducing anaerobe, Shewanella oneidensis MR-1 [which reduces Hg(II) at low concentrations], was investigated. In all cases, barring suppression of fractionation that is likely due to lower Hg(II) bioavailability, the Hg(II) remaining in the reactor became progressively enriched with heavy isotopes with time and underwent mass-dependent Rayleigh fractionation with alpha202/198 values of 1.0016 +/- 0.0004 (1 SD). Based on a multistep framework for the Hg(II) reduction pathways in the three strains, we constrain the processes that could contribute toward fractionation and suggest that for Hg(II)-resistant strains, reduction by mercuric reductase is the primary step causing fractionation. The proposed framework helps explain the variation in the extent of Hg stable isotope fractionation during microbial reduction of Hg(II), furthering the promise of Hg isotope ratios as a tool in determining the role of microbial Hg transformations in the environment.

Effects of inorganic nutrient levels on the biodegradation of benzene, toluene, and xylene (BTX) by Pseudomonas spp. in a laboratory porous media sand aquifer model

The effect of inorganic nutrients (sulfate, phosphate, and ammonium chloride) on the aerobic biodegradation of benzene, toluene, and xylene (BTX) by Pseudomonas spp. was studied in the laboratory using a glass sand tank. The increase of nutrient levels resulted in enhanced bacterial growth and BTX degradation. Sulfate and phosphate serve as key electron acceptors in the microbiological processes degrading BTX. The observed bacterial morphological changes during BTX degradation reveal that the filamentous bacteria were the dominant species at low temperatures about 20 degrees C. The spherical and rod-shaped cells became dominant at higher temperatures ranging from 25 degrees C to 28 degrees C. When the BTX mixture was allowed to be biodegraded for longer incubation periods of 21-42 h at high phosphate concentrations, large amounts of rod-shaped cells were clustered. The morphological adaptation appears to be controlled by the temperature and nutrient levels in the sandy medium where Pseudomonas spp. thrives.