A cyanobacterium capable of swimming motility

Water column stratification governs picophytoplankton community structure in the oligotrophic eastern Indian ocean

Under the background of global warming, the area extent of the oligotrophic tropical oceans has growing due to increased water-column stratification over the past decades. Picophytoplankton is usually the most dominant phytoplankton group in oligotrophic tropical oceans and substantially contribute to carbon biomass and primary production three. Understanding how vertical stratification governs the community structure of picophytoplankton communities in oligotrophic tropical oceans is important for comprehensively understanding the plankton ecology and biogeochemical cycle in these areas. In this study, the distribution of the picophytoplankton communities in the eastern Indian Ocean (EIO) was investigated during a period of thermal stratification in the spring of 2021. Prochlorococcus contributed most (54.9%) to picophytoplankton carbon biomass, followed by picoeukaryotes (38.5%) and Synechococcus (6.6%). Vertically, the three picophytoplankton groups showed quite different distribution pattern: the abundance of Synechococcus was highest in the surface layer, while Prochlorococcus and picoeukaryotes were usually located between 50 m and 100 m. The relationship between the abundance of picophytoplankton and environmental factors was analyzed, and the results revealed that picophytoplankton distribution was strongly correlated with the degree of vertical stratification of the water column. The density of Synechococcus was higher in strongly stratified waters, while Prochlorococcus was more abundant in regions of weaker stratification. This is mainly attributed to variation of physicochemical parameters such as nutrient structures and temperature resulted from water column stratification. Understanding the distribution patterns of these organisms and their relationship with stratification in the oligotrophic EIO is essential for comprehensive understanding on oligotrophic tropical ecosystem with increasing stratification in future.

Recent advances in experimental design and data analysis to characterize prokaryotic motility

Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying run distances and speeds, turn angles and behavior by surfaces or cell-cell interactions) remains a challenging task. A qualitative and quantitative understanding of bacterial motility is needed to bridge the gap between experimentation, omics analysis, and bacterial motility theory. In this review, we discuss the strengths and limitations of how phase contrast microscopy, fluorescence microscopy, and digital holographic microscopy have been used to quantify bacterial motility. Approaches to automated software analysis, including cell recognition, tracking, and track analysis, are also discussed with a view to providing a guide for experimenters to setting up the appropriate imaging and analysis system for their needs.

Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak

The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3–V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 104 cells ml–1. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.

Bacterial motility: machinery and mechanisms

Bacteria have developed a large array of motility mechanisms to exploit available resources and environments. These mechanisms can be broadly classified into swimming in aqueous media and movement over solid surfaces. Swimming motility involves either the rotation of rigid helical filaments through the external medium or gyration of the cell body in response to the rotation of internal filaments. On surfaces, bacteria swarm collectively in a thin layer of fluid powered by the rotation of rigid helical filaments, they twitch by assembling and disassembling type IV pili, they glide by driving adhesins along tracks fixed to the cell surface and, finally, non-motile cells slide over surfaces in response to outward forces due to colony growth. Recent technological advances, especially in cryo-electron microscopy, have greatly improved our knowledge of the molecular machinery that powers the various forms of bacterial motility. In this Review, we describe the current understanding of the physical and molecular mechanisms that allow bacteria to move around.

Pili allow dominant marine cyanobacteria to avoid sinking and evade predation

How oligotrophic marine cyanobacteria position themselves in the water column is currently unknown. The current paradigm is that these organisms avoid sinking due to their reduced size and passive drift within currents. Here, we show that one in four picocyanobacteria encode a type IV pilus which allows these organisms to increase drag and remain suspended at optimal positions in the water column, as well as evade predation by grazers. The evolution of this sophisticated floatation mechanism in these purely planktonic streamlined microorganisms has important implications for our current understanding of microbial distribution in the oceans and predator-prey interactions which ultimately will need incorporating into future models of marine carbon flux dynamics.

A Trace Amount of Surfactants Enables Diffusiophoretic Swimming of Bacteria

From birth to health, surfactants play an essential role in our lives. Due to the importance, their environmental impacts are well understood. One of the aspects that has been extensively studied is their impact on bacteria, particularly on their motility. Here, we uncover an alternate chemotactic strategy triggered by surfactants-diffusiophoresis. We show that even a trace amount of ionic surfactants, down to a single ppm level, can promote the bacterial diffusiophoresis by boosting the surface charge of the cells. Because diffusiophoresis is driven by the surface-solute interactions, surfactant-enhanced diffusiophoresis is observed regardless of the types of bacteria. Whether Gram-positive or -negative, flagellated or nonflagellated, the surfactants enable fast migration of freely suspended bacteria, suggesting a ubiquitous locomotion mechanism that has been largely overlooked. We also demonstrate the implication of surfactant-enhanced bacterial diffusiophoresis on the rapid formation of biofilms in flow networks, suggesting environmental and biomedical implications.

Tree of motility - A proposed history of motility systems in the tree of life

Motility often plays a decisive role in the survival of species. Five systems of motility have been studied in depth: those propelled by bacterial flagella, eukaryotic actin polymerization and the eukaryotic motor proteins myosin, kinesin and dynein. However, many organisms exhibit surprisingly diverse motilities, and advances in genomics, molecular biology and imaging have showed that those motilities have inherently independent mechanisms. This makes defining the breadth of motility nontrivial, because novel motilities may be driven by unknown mechanisms. Here, we classify the known motilities based on the unique classes of movement‐producing protein architectures. Based on this criterion, the current total of independent motility systems stands at 18 types. In this perspective, we discuss these modes of motility relative to the latest phylogenetic Tree of Life and propose a history of motility. During the ~4 billion years since the emergence of life, motility arose in Bacteria with flagella and pili, and in Archaea with archaella. Newer modes of motility became possible in Eukarya with changes to the cell envelope. Presence or absence of a peptidoglycan layer, the acquisition of robust membrane dynamics, the enlargement of cells and environmental opportunities likely provided the context for the (co)evolution of novel types of motility.

Vertical migration by bulk phytoplankton sustains biodiversity and nutrient input to the surface ocean

Phytoplankton subsumes the great variety of unicellular photoautotrophs that perform roughly half of Earth's primary production. They achieve this despite their challenging oceanic habitat, with opposing vertical gradients of nutrients (which often limit their growth near the surface) and light (which becomes limiting with increasing depth). Most phytoplankton species are commonly assumed to be incapable of moving actively between the zones of light and nutrient availability, which are separated vertically by from 30-120 m. Here we propose that a considerable fraction of phytoplankton vertically traverse these gradients over time scales from hours to weeks, employing variations of a common migration strategy to acquire multiple resources. We present a mechanistic Lagrangian model resolving phytoplankton growth linked to optimal migration behaviour and demonstrate unprecedented agreement of its calculated vertical CHL-a distributions with 773 profiles observed at five prominent marine time-series stations. Our simulations reveal that vertically cycling phytoplankton can pump up enough nutrient to sustain as much as half of oceanic Net Primary Production (NPP). Active locomotion is therefore a plausible mechanism enabling relatively high NPP in the oligotrophic surface ocean. Our simulations also predict similar fitness for a variety of very different migration strategies, which helps to explain the puzzling diversity of phytoplankton observed in the ocean.

Marine picoplankton size distribution and optical property contrasts throughout the Atlantic Ocean revealed using flow cytometry

Depth-resolved flow cytometric observations have been used to determine the size distribution and refractive index (RI) of picoplankton throughout the Atlantic Ocean. Prochlorococcus frequently showed double size distribution peaks centered on ${0.75 \pm 0.25}$0.75±0.25 and ${1.75 \pm 0.25}\,\,{\rm \unicode{x00B5}{\rm m}}$1.75±0.25µm; the smallest peak diameters were ${\le}{0.65}\,\,{\rm \unicode{x00B5}{\rm m}}$≤0.65µm in the equatorial upwelling with larger cells (${\sim}{0.95}\,\,{\rm \unicode{x00B5}{\rm m}}$∼0.95µm) in the surface layers of the tropical gyres. Synechococcus was strongly monodispersed: the smallest (${\sim}{1.5}\,\,{\rm \unicode{x00B5}{\rm m}}$∼1.5µm) and largest cells (${\sim}{2.25{-}2.50}\,\,{\rm \unicode{x00B5}{\rm m}}$∼2.25-2.50µm) were encountered in the lowest and highest abundance regions, respectively. Typical RI for Prochlorococcus was found to be ${\sim}{1.06}$∼1.06, whereas for Synechococcus surface RI varied between 1.04-1.08 at high and low abundances, respectively.

Enhanced ion tolerance of electrokinetic locomotion in polyelectrolyte-coated microswimmer

Over the last decade, researchers have endeavored to mimic the naturally motile microorganisms and develop artificial nano/microswimmers, which propel themselves in aqueous media. However, most of these nano/microswimmers are propelled by the self-electrophoretic mechanism, which has one critical incompetency: the inability to operate in a high concentration electrolyte solution, such as the most important body fluid, blood. This ionic quenching behavior is well backed by the classical Helmholtz-Smoluchowski theory and seems to be an insurmountable challenge which has shadowed the otherwise promising biomedical applications for artificial nano/microswimmers. Here, we propose that the active nano/microswimmer's self-electrophoresis is fundamentally different from the passive nanoparticle electrophoresis. By significantly increasing the Dukhin number with polyelectrolyte coating and geometry optimization, a favorable deviation from the Helmholtz-Smoluchowski behavior can be realized, and ion tolerance is enhanced by over 100 times for a visible light-powered self-electrophoretic microswimmer.

Gene Expression Measurement Module (GEMM) for space application: Design and validation

In order to facilitate studies on the impact of the space environment on biological systems, we have developed a prototype of GEMM (Gene Expression Measurement Module) - an automated, miniaturized, integrated fluidic system for in-situ measurements of gene expression in microbial samples. The GEMM instrument is capable of (1) lysing bacterial cell walls, (2) extracting and purifying RNA released from cells, (3) hybridizing the RNA to probes attached to a microarray and (4) providing electrochemical readout, all in a microfluidics cartridge. To function on small, uncrewed spacecraft, the conventional, laboratory protocols for both sample preparation and hybridization required significant modifications. Biological validation of the instrument was carried out on Synechococcus elongatus, a photosynthetic cyanobacterium known for its metabolic diversity and resilience to adverse conditions. It was demonstrated that GEMM yielded reliable, reproducible gene expression profiles. GEMM is the only high throughput instrument that can be deployed in near future on space platforms other than the ISS to advance biological research in space. It can also prove useful for numerous terrestrial applications in the field.

Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation

Identifying shifts in microbial metabolism across redox gradients will improve efforts to model marine oxygen minimum zone (OMZ) ecosystems. Here, we show that aerobic morphology and metabolism increase cell size, sulfur storage capacity, and carbon fixation rates in “Ca. Thioglobus autotrophicus,” a chemosynthetic bacterium from the SUP05 clade that crosses oxic-anoxic boundaries.

Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic bacteria survive across oxygen and sulfur gradients and how their mode of survival impacts the environment. Here, we use growth experiments, proteomics, and cryo-electron tomography to show that a SUP05 isolate, “Candidatus Thioglobus autotrophicus,” is amorphous in shape and several times larger and stores considerably more intracellular sulfur when it respires oxygen. We also show that these cells can use diverse sources of reduced organic and inorganic sulfur at submicromolar concentrations. Enhanced cell size, carbon content, and metabolic activity of the aerobic phenotype are likely facilitated by a stabilizing surface-layer (S-layer) and an uncharacterized form of FtsZ-less cell division that supports morphological plasticity. The additional sulfur storage provides an energy source that allows cells to continue metabolic activity when exogenous sulfur sources are not available. This metabolic flexibility leads to the production of more organic carbon in the ocean than is estimated based solely on their anaerobic phenotype.

The Small Regulatory Antisense RNA PilR Affects Pilus Formation and Cell Motility by Negatively Regulating pilA11 in Synechocystis sp. PCC 6803

Pili are found on the surface of many bacteria and play important roles in cell motility, pathogenesis, biofilm formation, and sensing and reacting to environmental changes. Cell motility in the model cyanobacterium Synechocystis sp. PCC 6803 relies on expression of the putative pilA9-pilA10-pilA11-slr2018 operon. In this study, we identified the antisense RNA PilR encoded in the noncoding strand of the prepilin-encoding gene pilA11. Analysis of overexpressor [PilR(+)] and suppressor [PilR(-)] mutant strains revealed that PilR is a direct negative regulator of PilA11 protein. Although overexpression of PilR did not affect cell growth, it greatly reduced levels of pilA11 mRNA and protein and decreased both the thickness and number of pili, resulting in limited cell motility and small, distinct colonies. Suppression of PilR had the opposite effect. A hypothetical model on the regulation of pilA9-pilA10-pilA11-slr2018 operon expression by PilR was proposed. These results add a layer of complexity to the mechanisms controlling pilA11 gene expression and cell motility, and provide novel insights into how sRNA and the intergenic region secondary structures can work together to discoordinatly regulate target gene in an operon in cyanobacterium.

Type 4 pili are dispensable for biofilm development in the cyanobacterium Synechococcus elongatus

The hair-like cell appendages denoted as type IV pili are crucial for biofilm formation in diverse eubacteria. The protein complex responsible for type IV pilus assembly is homologous with the type II protein secretion complex. In the cyanobacterium Synechococcus elongatus PCC 7942, the gene Synpcc7942_2071 encodes an ATPase homologue of type II/type IV systems. Here, we report that inactivation of Synpcc7942_2071 strongly affected the suite of proteins present in the extracellular milieu (exo-proteome) and eliminated pili observable by electron microscopy. These results support a role for this gene product in protein secretion as well as in pili formation. As we previously reported, inactivation of Synpcc7942_2071 enables biofilm formation and suppresses the planktonic growth of S. elongatus. Thus, pili are dispensable for biofilm development in this cyanobacterium, in contrast to their biofilm-promoting function in type IV pili-producing heterotrophic bacteria. Nevertheless, pili removal is not required for biofilm formation as evident by a piliated mutant of S. elongatus that develops biofilms. We show that adhesion and timing of biofilm development differ between the piliated and non-piliated strains. The study demonstrates key differences in the process of biofilm formation between cyanobacteria and well-studied type IV pili-producing heterotrophic bacteria.

Diversity of Synechococcus at the Martha's Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry

The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world's oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance.

Can the self-propulsion of anisotropic microswimmers be described by using forces and torques?

The self-propulsion of artificial and biological microswimmers (or active colloidal particles) has often been modelled by using a force and a torque entering into the overdamped equations for the Brownian motion of passive particles. This seemingly contradicts the fact that a swimmer is force-free and torque-free, i.e. that the net force and torque on the particle vanish. Using different models for mechanical and diffusiophoretic self-propulsion, we demonstrate here that the equations of motion of microswimmers can be mapped onto those of passive particles with the shape-dependent grand resistance matrix and formally external effective forces and torques. This is consistent with experimental findings on the circular motion of artificial asymmetric microswimmers driven by self-diffusiophoresis. The concept of effective self-propulsion forces and torques significantly facilitates the understanding of the swimming paths, e.g. for a microswimmer under gravity. However, this concept has its limitations when the self-propulsion mechanism of a swimmer is disturbed either by another particle in its close vicinity or by interactions with obstacles, such as a wall.

Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro

EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds after addition of magnesium. Purified EF-Tu enhanced the amount of MreB filaments, as seen by sedimentation assays, the speed of filament formation and the length of MreB filaments in vitro. EF-Tu had the strongest impact on MreB filaments in a 1:1 ratio, and EF-Tu co-sedimented with MreB filaments, revealing a stoichiometric interaction between both proteins. This was supported by cross-linking assays where 1:1 species were well detectable. When expressed in E. coli cells, B. subtilis MreB formed filaments and induced the formation of co-localizing B. subtilis EF-Tu structures, indicating that MreB can direct the positioning of EF-Tu structures in a heterologous cell system. Fluorescence recovery after photobleaching analysis showed that MreB filaments have a higher turnover in B. subtilis cells than in E. coli cells, indicating different filament kinetics in homologous or heterologous cell systems. The data show that MreB can direct the localization of EF-Tu in vivo, which in turn positively affects the formation and dynamics of MreB filaments. Thus, EF-Tu is a modulator of the activity of a bacterial actin-like protein.

The putative eukaryote-like O-GlcNAc transferase of the cyanobacterium Synechococcus elongatus PCC 7942 hydrolyzes UDP-GlcNAc and is involved in multiple cellular processes

The posttranslational addition of a single O-linked β-N-acetylglucosamine (O-GlcNAc) to serine or threonine residues regulates numerous metazoan cellular processes. The enzyme responsible for this modification, O-GlcNAc transferase (OGT), is conserved among a wide variety of organisms and is critical for the viability of many eukaryotes. Although OGTs with domain structures similar to those of eukaryotic OGTs are predicted for many bacterial species, the cellular roles of these OGTs are unknown. We have identified a putative OGT in the cyanobacterium Synechococcus elongatus PCC 7942 that shows active-site homology and similar domain structure to eukaryotic OGTs. An OGT deletion mutant was created and found to exhibit several phenotypes. Without agitation, mutant cells aggregate and settle out of the medium. The mutant cells have higher free inorganic phosphate levels, wider thylakoid lumen, and differential accumulation of electron-dense inclusion bodies. These phenotypes are rescued by reintroduction of the wild-type OGT but are not fully rescued by OGTs with single amino acid substitutions corresponding to mutations that reduce eukaryotic OGT activity. S. elongatus OGT purified from Escherichia coli hydrolyzed the sugar donor, UDP-GlcNAc, while the mutant OGTs that did not fully rescue the deletion mutant phenotypes had reduced or no activity. These results suggest that bacterial eukaryote-like OGTs, like their eukaryotic counterparts, influence multiple processes.

Denitrifying alphaproteobacteria from the Arabian Sea that express nosZ, the gene encoding nitrous oxide reductase, in oxic and suboxic waters

Marine ecosystems are significant sources of the powerful greenhouse gas nitrous oxide (N2O). A by-product of nitrification and an intermediate in the denitrification pathway, N2O is formed primarily in oxygen-deficient waters and sediments. We describe the isolation of a group of alphaproteobacteria from the suboxic waters of the Arabian Sea that are phylogenetically affiliated with Labrenzia spp. and other denitrifiers. Quantitative PCR assays revealed that these organisms were very broadly distributed in this semienclosed ocean basin. Their biogeographical range extended from the productive, upwelling region off the Omani shelf to the clear, oligotrophic waters that are found much further south and also included the mesotrophic waters overlying the oxygen minimum zone (OMZ) in the northeastern sector of the Arabian Sea. These organisms actively expressed NosZ (N2O reductase, the terminal step in the denitrification pathway) within the OMZ, an established region of pelagic denitrification. They were found in greatest numbers outside the OMZ, however, and nosZ mRNAs were also readily detected near the base of the upper mixed layer in nutrient-poor, oxic regions. Our findings provide firm molecular evidence of a potential sink for N2O within well-ventilated, oceanic surface waters in this biogeochemically important region. We show that the Labrenzia-like denitrifiers and their close relatives are habitual colonizers of the pseudobenthic environment provided by Trichodesmium spp. We develop the conjecture that the O2-depleted microzones that occur within the colonies of these filamentous, diazotrophic cyanobacteria might provide unexpected niches for the reduction of nitrogen oxides in tropical and subtropical surface waters.

Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean

Marine Synechococcus is a globally significant genus of cyanobacteria that is comprised of multiple genetic lineages or clades. These clades are thought to represent ecologically distinct units, or ecotypes. Because multiple clades often co-occur together in the oceans, Synechococcus are ideal microbes to explore how closely related bacterial taxa within the same functional guild of organisms co-exist and partition marine habitats. Here we sequenced multiple gene loci from cultured strains to confirm the congruency of clade classifications between the 16S-23S rDNA internally transcribed spacer (ITS), 16S rDNA, narB, ntcA, and rpoC1 loci commonly used in Synechococcus diversity studies. We designed quantitative PCR (qPCR) assays that target the ITS for 10 Synechococcus clades, including four clades, XV, XVI, CRD1, and CRD2, not covered by previous assays employing other loci. Our new qPCR assays are very sensitive and specific, detecting down to tens of cells per ml. Application of these qPCR assays to field samples from the northwest Atlantic showed clear shifts in Synechococcus community composition across a coastal to open-ocean transect. Consistent with previous studies, clades I and IV dominated cold, coastal Synechococcus communities. Clades II and X were abundant at the two warmer, off-shore stations, and at all stations multiple Synechococcus clades co-occurred. qPCR assays developed here provide valuable tools to further explore the dynamics of microbial community structure and the mechanisms of co-existence.

Biophysical Dynamics in Disorderly Environments

Three areas where time-independent disorder plays a key role in biological dynamics far from equilibrium are reviewed. We first discuss the anomalous localization dynamics that arises when a single species spreads in space and time via diffusion and fluid advection in the presence of frozen heterogeneities in the growth rate. Next we treat the unzipping of double-stranded DNA as a function of force and temperature, a challenge that must be surmounted every time a cell divides. Heterogeneity in the DNA sequence dominates the physics of single-molecule force-extension curves for a broad range of forces upon approaching a sharp unzipping transition. The dynamics of the unzipping fork exhibits anomalous drift and diffusion in a similar range above this transition, with energy barriers that scale as the square root of the genome size. Finally, we describe how activated peptidoglycan strand extension sites, called dislocations in materials science, can mediate the growth of bacterial cell walls. Enzymatically driven circumferential motions of a few dozen of these defects are sufficient to describe the exponential elongation rates observed in experiments on Escherichia coli in a nutrient-rich environment. However, long-range elastic forces transmitted by the peptidoglycan meshwork cause the moving dislocations to interact not only with each other, but also with a disorderly array of frozen, inactivated strand ends.

On the mysterious propulsion of Synechococcus

We propose a model for the self-propulsion of the marine bacterium Synechococcus utilizing a continuous looped helical track analogous to that found in Myxobacteria [1]. In our model cargo-carrying protein motors, driven by proton-motive force, move along a continuous looped helical track. The movement of the cargo creates surface distortions in the form of small amplitude traveling ridges along the S-layer above the helical track. The resulting fluid motion adjacent to the helical ribbon provides the propulsive thrust. A variation on the helical rotor model of [1] allows the motors to be anchored to the peptidoglycan layer, where they drive rotation of the track creating traveling helical waves along the S-layer. We derive expressions relating the swimming speed to the amplitude, wavelength, and velocity of the surface waves induced by the helical rotor, and show that they fall in reasonable ranges to explain the velocity and rotation rate of swimming Synechococcus.

Thin phytoplankton layers: characteristics, mechanisms, and consequences

For over four decades, aggregations of phytoplankton known as thin layers have been observed to harbor large amounts of photosynthetic cells within narrow horizontal bands. Field observations have revealed complex linkages among thin phytoplankton layers, the physical environment, cell behavior, and higher trophic levels. Several mechanisms have been proposed to explain layer formation and persistence, in the face of the homogenizing effect of turbulent dispersion. The challenge ahead is to connect mechanistic hypotheses with field observations to gain better insight on the phenomena that shape layer dynamics. Only through a mechanistic understanding of the relevant biological and physical processes can we begin to predict the effect of thin layers on the ecology of phytoplankton and higher organisms.

Differential distributions of synechococcus subgroups across the california current system

Synechococcus is an abundant marine cyanobacterial genus composed of different populations that vary physiologically. Synechococcus narB gene sequences (encoding for nitrate reductase in cyanobacteria) obtained previously from isolates and the environment (e.g., North Pacific Gyre Station ALOHA, Hawaii or Monterey Bay, CA, USA) were used to develop quantitative PCR (qPCR) assays. These qPCR assays were used to quantify populations from specific narB phylogenetic clades across the California Current System (CCS), a region composed of dynamic zones between a coastal-upwelling zone and the oligotrophic Pacific Ocean. Targeted populations (narB subgroups) had different biogeographic patterns across the CCS, which appear to be driven by environmental conditions. Subgroups C_C1, D_C1, and D_C2 were abundant in coastal-upwelling to coastal-transition zone waters with relatively high to intermediate ammonium, nitrate, and chl. a concentrations. Subgroups A_C1 and F_C1 were most abundant in coastal-transition zone waters with intermediate nutrient concentrations. E_O1 and G_O1 were most abundant at different depths of oligotrophic open-ocean waters (either in the upper mixed layer or just below). E_O1, A_C1, and F_C1 distributions differed from other narB subgroups and likely possess unique ecologies enabling them to be most abundant in waters between coastal and open-ocean waters. Different CCS zones possessed distinct Synechococcus communities. Core California current water possessed low numbers of narB subgroups relative to counted Synechococcus cells, and coastal-transition waters contained high abundances of Synechococcus cells and total number of narB subgroups. The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system.

Variability in protist grazing and growth on different marine Synechococcus isolates

Grazing mortality of the marine phytoplankton Synechococcus is dominated by planktonic protists, yet rates of consumption and factors regulating grazer-Synechococcus interactions are poorly understood. One aspect of predator-prey interactions for which little is known are the mechanisms by which Synechococcus avoids or resists predation and, in turn, how this relates to the ability of Synechococcus to support growth of protist grazer populations. Grazing experiments conducted with the raptorial dinoflagellate Oxyrrhis marina and phylogenetically diverse Synechococcus isolates (strains WH8102, CC9605, CC9311, and CC9902) revealed marked differences in grazing rates-specifically that WH8102 was grazed at significantly lower rates than all other isolates. Additional experiments using the heterotrophic nanoflagellate Goniomonas pacifica and the filter-feeding tintinnid ciliate Eutintinnis sp. revealed that this pattern in grazing susceptibility among the isolates transcended feeding guilds and grazer taxon. Synechococcus cell size, elemental ratios, and motility were not able to explain differences in grazing rates, indicating that other features play a primary role in grazing resistance. Growth of heterotrophic protists was poorly coupled to prey ingestion and was influenced by the strain of Synechococcus being consumed. Although Synechococcus was generally a poor-quality food source, it tended to support higher growth and survival of G. pacifica and O. marina relative to Eutintinnis sp., indicating that suitability of Synechococcus varies among grazer taxa and may be a more suitable food source for the smaller protist grazers. This work has developed tractable model systems for further studies of grazer-Synechococcus interactions in marine microbial food webs.

Locomotion by tangential deformation in a polymeric fluid

In several biologically relevant situations, cell locomotion occurs in polymeric fluids with Weissenberg number larger than 1. Here we present results of three-dimensional numerical simulations for the steady locomotion of a self-propelled body in a model polymeric (Giesekus) fluid at low Reynolds number. Locomotion is driven by steady tangential deformation at the surface of the body (the so-called squirming motion). In the case of a spherical squirmer, we show that the swimming velocity is systematically less than that in a Newtonian fluid, with a minimum occurring for Weissenberg numbers of order 1. The rate of work done by the swimmer always goes up compared to that occurring in the Newtonian solvent alone but is always lower than the power necessary to swim in a Newtonian fluid with the same viscosity. The swimming efficiency, defined as the ratio between the rate of work necessary to pull the body at the swimming speed in the same fluid and the rate of work done by swimming, is found to always be increased in a polymeric fluid. Further analysis reveals that polymeric stresses break the Newtonian front-back symmetry in the flow profile around the body. In particular, a strong negative elastic wake is present behind the swimmer, which correlates with strong polymer stretching, and its intensity increases with Weissenberg number and viscosity contrasts. The velocity induced by the squirmer is found to decay in space faster than in a Newtonian flow, with a strong dependence on the polymer relaxation time and viscosity. Our computational results are also extended to prolate spheroidal swimmers and smaller polymer stretching are obtained for slender shapes compared to bluff swimmers. The swimmer with an aspect ratio of two is found to be the most hydrodynamically efficient.

Hydrodynamics of helical-shaped bacterial motility

To reveal the underlying hydrodynamic mechanism for the directed propulsion of the bacterium Spiroplasma, we formulate a coarse-grained elastic polymer model with domains of alternating helicities along the contour. Using hydrodynamic simulations and analytic arguments, we show that the propagation of helical domain walls leads to the directed propulsion of the cell body opposite to the domain-wall traveling direction. Several key features of Spiroplasma motility are reproduced by our model. We in particular show that the helical pitch angle observed for Spiroplasma meliferum, psi=35 degrees , is optimized for maximal swimming speed and energy-conversion efficiency. Our analytic theory based on the slender-body hydrodynamic approximation agrees very well with our numerical data demonstrating how the chirality switch propagating along the helical cell body is converted to a translational thrust for the cell body itself. We in detail consider thermal effects on the propulsion efficiency in the form of orientational fluctuations and conformational fluctuations of the helix shape. The body length dependence of the cell motility is studied numerically and compared to our approximate analytic theory. For fixed pitch angle psi=35 degrees , the swimming speed is maximized at a ratio of cell-body length to domain length of about 2-3, which are typical values for real cells. We also propose simple analytic arguments for an enhancement of the swimming velocity with increasing solution viscosity by taking into account the effects of transient confinement of a helical cell body in a polymeric meshwork. Comparison with a generalized theory for the swimming speed of flagellated bacteria in polymeric meshworks shows that the presence of a finite-sized bacterial head gives rise to a maximal swimming speed at a finite solution viscosity, whereas in the absence of a head the swimming speed monotonically increases with increasing viscosity.

Ecological genomics of marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45 degrees N to 40 degrees S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

The surprisingly diverse ways that prokaryotes move

Prokaryotic cells move through liquids or over moist surfaces by swimming, swarming, gliding, twitching or floating. An impressive diversity of motility mechanisms has evolved in prokaryotes. Movement can involve surface appendages, such as flagella that spin, pili that pull and Mycoplasma 'legs' that walk. Internal structures, such as the cytoskeleton and gas vesicles, are involved in some types of motility, whereas the mechanisms of some other types of movement remain mysterious. Regardless of the type of motility machinery that is employed, most motile microorganisms use complex sensory systems to control their movements in response to stimuli, which allows them to migrate to optimal environments.

Bacterial motility: handedness and symmetry

Many bacteria swim by rotating thin helical filaments that extend into the external medium, as with common bacteria, or run beneath the outer membrane, as with spirochetes. Each filament is driven at its base by a motor that turns alternately clockwise and counterclockwise. The motor-filament complex is called a flagellum. Other kinds of bacteria glide, but their organelles of locomotion are not known. Since bacteria are microscopic and live in an aqueous environment, they swim at low Reynolds' number; cyclic motion works (e.g. rotation of a helix) but reciprocal motion does not (e.g. stroking of a singly hinged oar). By measuring concentrations of certain chemicals as they move through their environment, making temporal comparisons and modulating the direction of flagellar rotation, bacteria accumulate in regions that they find more favourable. Studies of bacterial chemotaxis are highly advanced, particularly for the peritrichously flagellated species Escherichia coli. A great deal is known about chemoreception, receptor-flagellar coupling and adaptation. Recently it has been found that E. coli can aggregate in response to signals generated by the cells themselves. Complex patterns form with remarkable symmetries.

Nanoscale visualization of a fibrillar array in the cell wall of filamentous cyanobacteria and its implications for gliding motility

Many filamentous cyanobacteria are motile by gliding, which requires attachment to a surface. There are two main theories to explain the mechanism of gliding. According to the first, the filament is pushed forward by small waves that pass along the cell surface. In the second, gliding is powered by the extrusion of slime through pores surrounding each cell septum. We have previously shown that the cell walls of several motile cyanobacteria possess an array of parallel fibrils between the peptidoglycan and the outer membrane and have speculated that the function of this array may be to generate surface waves to power gliding. Here, we report on a study of the cell surface topography of two morphologically different filamentous cyanobacteria, using field emission gun scanning electron microscopy (FEGSEM) and atomic force microscopy (AFM). FEGSEM and AFM images of Oscillatoria sp. strain A2 confirmed the presence of an array of fibrils, visible as parallel corrugations on the cell surface. These corrugations were also visualized by AFM scanning of fully hydrated filaments under liquid; this has not been achieved before for filamentous bacteria. FEGSEM images of Nostoc punctiforme revealed a highly convoluted, not parallel, fibrillar array. We conclude that an array of parallel fibrils, beneath the outer membrane of Oscillatoria, may function in the generation of thrust in gliding motility. The array of convoluted fibrils in N. punctiforme may have an alternative function, perhaps connected with the increase in outer membrane surface area resulting from the presence of the fibrils.

SwmB, a 1.12-megadalton protein that is required for nonflagellar swimming motility in Synechococcus

SwmB is required for swimming motility in Synechococcus sp. strain WH8102. This highly repetitive 1.12-MDa polypeptide is associated with the cell surface, where it is arranged in a punctate manner. Inactivation of swmB does not affect the localization of SwmA, an S-layer protein also required for swimming.

Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies

Marine microbial communities often contain multiple closely related phylogenetic clades, but in many cases, it is still unclear what physiological traits differentiate these putative ecotypes. The numerically abundant marine cyanobacterium Synechococcus can be divided into at least 14 clades. In order to better understand ecotype differentiation in this genus, we assessed the diversity of a Synechococcus community from a well-mixed water column in the Sargasso Sea during March 2002, a time of year when this genus typically reaches its annual peak in abundance. Diversity was estimated from water sampled at three depths (approximately 5, 70, and 170 m) using both culture isolation and construction of cyanobacterial 16S-23S rRNA internal transcribed sequence clone libraries. Clonal isolates were obtained by enrichment with ammonium, nitrite, or nitrate as the sole N source, followed by pour plating. Each method sampled the in situ diversity differently. The combined methods revealed a total of seven Synechococcus phylotypes including two new putative ecotypes, labeled XV and XVI. Although most other isolates grow on nitrate, clade XV exhibited a reduced efficiency in nitrate utilization, and both clade XV and XVI are capable of chromatic adaptation, demonstrating that this trait is more widely distributed among Synechococcus strains than previously known. Thus, as in its sister genus Prochlorococcus, light and nitrogen utilization are important factors in ecotype differentiation in the marine Synechococcus lineage.

Chemical Locomotion

Research into the autonomous motion of artificial nano- and microscale objects provides basic principles to explore possible applications, such as self-assembly of superstructures, roving sensors, and drug delivery. Although the systems described have unique propulsion mechanisms, motility in each case is made possible by the conversion of locally available chemical energy into mechanical energy. The use of catalysts onboard can afford nondissipative systems that are capable of directed motion. Key to the design of nano- and micromotors is the asymmetric placement of the catalyst: its placement in an environment containing a suitable substrate translates into non-uniform consumption of the substrate and distribution of reaction products, which results in the motility of the object. These same principles are exploited in nature to effect autonomous motion.

An application of statistics to comparative metagenomics

Background

Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments.

Results

Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified.

Conclusion

The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.

Spiroplasma swim by a processive change in body helicity

Microscopic organisms must rely on very different strategies than their macroscopic counterparts to swim through liquid. To date, the best understood method for prokaryotic swimming employs the rotation of flagella. Here, we show that Spiroplasma, tiny helical bacteria that infect plants and insects, use a very different approach. By measuring cell kinematics during free swimming, we find that propulsion is generated by the propagation of kink pairs down the length of the cell body. A processive change in the helicity of the body creates these waves and enables directional movement.

Motility of Catalytic Nanoparticles through Self-Generated Forces

Small-scale synthetic motors capable of generating their own motive forces by exploiting the chemical free energy of their environment represent an important step in developing practical nanomachines. Catalytic particles are capable of generating concentration and other gradients that can be used to self-propel small objects. However, the autonomous movement of catalytic nanoparticles by self-generated forces is a relatively unexplored area in colloid and interfacial chemistry. This paper explores the potential of catalytically self-generated forces for propulsion of small objects through fluids.

Transposon mutagenesis in a marine synechococcus strain: isolation of swimming motility mutants

Certain marine unicellular cyanobacteria of the genus Synechococcus exhibit a unique type of swimming motility characterized by the absence of flagella or any other obvious organelles of motility. While the abundant cell surface-associated 130-kDa glycoprotein SwmA is known to be required for the generation of thrust, identification of other components of the motility apparatus has, until recently, been unsuccessful. Here we report on the development of a transposon mutagenesis system for use with marine Synechococcus sp. strain WH8102, a model organism for which the genome has been sequenced. Utilizing this mutagenesis technique, we have isolated 17 independent mutants impaired in swimming motility. These 17 transposon insertions are located in nine open reading frames, which cluster in three separate regions of the genome. Included within these clusters are several multicomponent transport systems as well as a number of glycosyltransferases.

Inactivation of swmA results in the loss of an outer cell layer in a swimming synechococcus strain

The mechanism of nonflagellar swimming of marine unicellular cyanobacteria remains poorly understood. SwmA is an abundant cell surface-associated 130-kDa glycoprotein that is required for the generation of thrust in Synechococcus sp. strain WH8102. Ultrastructural comparisons of wild-type cells to a mutant strain in which the gene encoding SwmA has been insertionally inactivated reveal that the mutant lacks a layer external to the outer membrane. Cryofixation and freeze-substitution are required for the preservation of this external layer. Freeze fracturing and etching reveal that this additional layer is an S-layer. How the S-layer might function in motility remains elusive; however, this work describes an ultrastructural component required for this unique type of swimming. In addition, the work presented here describes the envelope structure of a model swimming cyanobacterium.

Light matters: phototaxis and signal transduction in unicellular cyanobacteria

Many photosynthetic microorganisms have evolved the ability to sense light quality and/or quantity and can steer themselves into optimal conditions within the environment. Phototaxis and gliding motility in unicellular cyanobacteria require type IV pili, which are multifunctional cell surface appendages. Screens for cells exhibiting aberrant motility uncovered several non-motile mutants as well as some that had lost positive phototaxis (consequently, they were negatively phototactic). Several negatively phototactic mutants mapped to the tax1 locus, which contains five chemotaxis-like genes. This locus includes a gene that encodes a putative photoreceptor (TaxD1) for positive phototaxis. A second chemotaxis-like cluster (tax3 locus) appears to be involved in pilus biogenesis. The biosynthesis and regulation of type IV pilus-based motility as well as the communication between the pilus motor and photosensory molecules appear to be complex and tightly regulated. Furthermore, the discovery that cyclic AMP and novel gene products are necessary for phototaxis/motility suggests that there might be additional levels of communication and signal processing.

The junctional pore complex and the propulsion of bacterial cells

Gliding motility is defined as translocation in the direction of the long axis of the bacterium while in contact with a surface. This definition leaves unspecified any mechanism and, indeed, it appears that there is more than one physiological system underlying the same type of motion. Currently, two distinct mechanisms have been discovered in myxobacteria. One requires the extension, attachment, and retraction of type IV pili to pull the cell forwards. Recent experimental evidence suggests that a second mechanism for gliding motility involves the extrusion of slime from an organelle called the 'junctional pore complex'. This review discusses the role of slime extrusion and the junctional pore complex in the gliding motility of both cyanobacteria and myxobacteria.

Physiological diversity and niche adaptation in marine Synechococcus

During the twenty years or so since the discovery of tiny photosynthetic cells of the genus Synechococcus in marine oceanic systems, a tremendous expansion of interest has been seen in the literature pertaining to these organisms. The fact that they are ubiquitous and abundant in major oceanic regimes underlies their ecological importance as significant contributors to marine C fixation. Recent advances in the physiology and biochemistry of these organisms are presented here, focusing on strains of the MC-A and MC-B clusters; it is stressed that the data contained herein should be put into the context of the ecological niche occupied by particular genotypes in situ. This system is ripe for joining the often separate disciplines of molecular ecology and microbial physiology and provides a great opportunity to tease out the underlying processes that both mediate organism evolution and also the environmental factors that dictate this.