The selective value of bacterial shape

Adaptive Responses of Shewanella decolorationis to Toxic Organic Extracellular Electron Acceptor Azo Dyes in Anaerobic Respiration

Bacterial anaerobic respiration using an extracellular electron acceptor plays a predominant role in global biogeochemical cycles. However, the mechanisms of bacterial adaptation to the toxic organic pollutant as the extracellular electron acceptor during anaerobic respiration are not clear, which limits our ability to optimize the strategies for the bioremediation of a contaminated environment. Here, we report the physiological characteristics and the global gene expression of an ecologically successful bacterium, Shewanella decolorationis S12, when using a typical toxic organic pollutant, amaranth, as the extracellular electron acceptor. Our results revealed that filamentous shift (the cells stretched to fiber-like shapes as long as 18 μm) occurred under amaranth stress. Persistent stress led to a higher filamentous cell rate and decolorization ability in subcultural cells compared to parental strains. In addition, the expression of genes involved in cell division, the chemotaxis system, energy conservation, damage repair, and material transport in filamentous cells was significantly stimulated. The detailed roles of some genes with significantly elevated expressions in filamentous cells, such as the outer membrane porin genes ompA and ompW, the cytochrome c genes arpC and arpD, the global regulatory factor gene rpoS, and the methyl-accepting chemotaxis proteins genes SHD_2793 and SHD_0015, were identified by site-directed mutagenesis. Finally, a conceptual model was proposed to help deepen our insights into both the bacterial survival strategy when toxic organics were present and the mechanisms by which these toxic organics were biodegraded as the extracellular electron acceptors.IMPORTANCE Keeping toxic organic pollutants (TOPs) in tolerable levels is a huge challenge for bacteria in extremely unfavorable environments since TOPs could serve as energy substitutes but also as survival stresses when they are beyond some thresholds. This study focused on the underlying adaptive mechanisms of ecologically successful bacterium Shewanella decolorationis S12 when exposed to amaranth, a typical toxic organic pollutant, as the extracellular electron acceptor. Our results suggest that filamentous shift is a flexible and valid way to solve the dilemma between the energy resource and toxic stress. Filamentous cells regulate gene expression to enhance their degradation and detoxification capabilities, resulting in a strong viability. These novel adaptive responses to TOPs are believed to be an evolutionary achievement to succeed in harsh habitats and thus have great potential to be applied to environment engineering or synthetic biology if we could picture every unknown node in this pathway.

Amino Acid-Dependent Alterations in Cell Wall and Cell Morphology of Deinococcus indicus DR1

Deinococcus radiodurans exhibits growth medium-dependent morphological variation in cell shape, but there is no evidence whether this phenomenon is observed in other members of the Deinococcaceae family. In this study, we isolated a red-pigmented, aerobic, Deinococcus indicus strain DR1 from Dadri wetland, India. This D. indicus strain exhibited cell–morphology transition from rod-shaped cells to multi-cell chains in a growth-medium-dependent fashion. In response to addition of 1% casamino acids in the minimal growth medium, rod-shaped cells formed multi-cell chains. Addition of all 20 amino acids to the minimal medium was able to recapitulate the phenotype. Specifically, a combination of L-methionine, L-lysine, L-aspartate, and L-threonine caused morphological alterations. The transition from rod shape to multi-cell chains is due to delay in daughter cell separation after cell division. Minimal medium supplemented with L-ornithine alone was able to cause cell morphology changes. Furthermore, a comparative UPLC analysis of PG fragments isolated from D. indicus cells propagated in different growth media revealed alterations in the PG composition. An increase in the overall cross-linkage of PG was observed in muropeptides from nutrient-rich TSB and NB media versus PYE medium. Overall our study highlights that environmental conditions influence PG composition and cell morphology in D. indicus.

High-throughput time-resolved morphology screening in bacteria reveals phenotypic responses to antibiotics

Image-based high-throughput screening strategies for quantifying morphological phenotypes have proven widely successful. Here we describe a combined experimental and multivariate image analysis approach for systematic large-scale phenotyping of morphological dynamics in bacteria. Using off-the-shelf components and software, we established a workflow for high-throughput time-resolved microscopy. We then screened the single-gene deletion collection of Escherichia coli for antibiotic-induced morphological changes. Using single-cell quantitative descriptors and supervised classification methods, we measured how different cell morphologies developed over time for all strains in response to the β-lactam antibiotic cefsulodin. 191 strains exhibit significant variations under antibiotic treatment. Phenotypic clustering provided insights into processes that alter the antibiotic response. Mutants with stable bulges show delayed lysis, contributing to antibiotic tolerance. Lipopolysaccharides play a crucial role in bulge stability. This study demonstrates how multiparametric phenotyping by high-throughput time-resolved imaging and computer-aided cell classification can be used for comprehensively studying dynamic morphological transitions in bacteria.

Motile curved bacteria are Pareto-optimal

Curved rods are a ubiquitous bacterial phenotype, but the fundamental question of why they are shaped this way remains unanswered. Through in silico experiments, we assessed freely swimming straight- and curved-rod bacteria of a wide diversity of equal-volume shapes parameterized by elongation and curvature, and predicted their performances in tasks likely to strongly influence overall fitness. Performance trade-offs between these tasks lead to a variety of shapes that are Pareto-optimal, including coccoids, all straight rods, and a range of curvatures. Comparison with an extensive morphological survey of motile curved-rod bacteria indicates that the vast majority of species fall within the Pareto-optimal region of morphospace. This result is consistent with evolutionary trade-offs between just three tasks: efficient swimming, chemotaxis, and low cell construction cost. We thus reveal the underlying selective pressures driving morphological diversity in a widespread component of microbial ecosystems.

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome.

Trait-based analysis of the human skin microbiome

BACKGROUND

The past decade of microbiome research has concentrated on cataloging the diversity of taxa in different environments. The next decade is poised to focus on microbial traits and function. Most existing methods for doing this perform pathway analysis using reference databases. This has both benefits and drawbacks. Function can go undetected if reference databases are coarse-grained or incomplete. Likewise, detection of a pathway does not guarantee expression of the associated function. Finally, function cannot be connected to specific microbial constituents, making it difficult to ascertain the types of organisms exhibiting particular traits-something that is important for understanding microbial success in specific environments. A complementary approach to pathway analysis is to use the wealth of microbial trait information collected over years of lab-based, culture experiments.

METHODS

Here, we use journal articles and Bergey's Manual of Systematic Bacteriology to develop a trait-based database for 971 human skin bacterial taxa. We then use this database to examine functional traits that are over/underrepresented among skin taxa. Specifically, we focus on three trait classes-binary, categorical, and quantitative-and compare trait values among skin taxa and microbial taxa more broadly. We compare binary traits using a Chi-square test, categorical traits using randomization trials, and quantitative traits using a nonparametric relative effects test based on global rankings using Tukey contrasts.

RESULTS

We find a number of traits that are over/underrepresented within the human skin microbiome. For example, spore formation, acid phosphatase, alkaline phosphatase, pigment production, catalase, and oxidase are all less common among skin taxa. As well, skin bacteria are less likely to be aerobic, favoring, instead, a facultative strategy. They are also less likely to exhibit gliding motility, less likely to be spirillum or rod-shaped, and less likely to grow in chains. Finally, skin bacteria have more difficulty at high pH, prefer warmer temperatures, and are much less resilient to hypotonic conditions.

CONCLUSIONS

Our analysis shows how an approach that relies on information from culture experiments can both support findings from pathway analysis, and also generate new insights into the structuring principles of microbial communities.

Whole Slide Imaging for High-Throughput Sensing Antibiotic Resistance at Single-Bacterium Level and Its Application to Rapid Antibiotic Susceptibility Testing

Since conventional culture-based antibiotic susceptibility testing (AST) methods are too time-consuming (typically 24–72 h), rapid AST is urgently needed for preventing the increasing emergence and spread of antibiotic resistant infections. Although several phenotypic antibiotic resistance sensing modalities are able to reduce the AST time to a few hours or less, concerning the biological heterogeneity, their accuracy or limit of detection are limited by low throughput. Here, we present a rapid AST method based on whole slide imaging (WSI)-enabled high-throughput sensing antibiotic resistance at single-bacterium level. The time for determining the minimum inhibitory concentration (MIC) was theoretically shortest, which ensures that the growth of each individual cell present in a large population is inhibited. As a demonstration, our technique was able to sense the growth of at least several thousand bacteria at single-cell level. Reliable MIC of Enterobacter cloacae against gentamicin was obtained within 1 h, while the gold standard broth dilution method required at least 16 h for the same result. In addition, the application of our method prevails over other imaging-based AST approaches in allowing rapid and accurate determination of antibiotic susceptibility for phenotypically heterogeneous samples, in which the number of antibiotic resistant cells was negligible compared to that of the susceptible cells. Hence, our method shows great promise for both rapid AST determination and point-of-care testing of complex clinical bacteria isolates.

The Campylobacter jejuni helical to coccoid transition involves changes to peptidoglycan and the ability to elicit an immune response

Campylobacter jejuni is a prevalent enteric pathogen that changes morphology from helical to coccoid under unfavorable conditions. Bacterial peptidoglycan maintains cell shape. As C. jejuni transformed from helical to coccoid, peptidoglycan dipeptides increased and tri- and tetrapeptides decreased. The DL-carboxypeptidase Pgp1 important for C. jejuni helical morphology and putative N-acetylmuramoyl-L-alanyl amidase AmiA were both involved in the coccoid transition. Mutants in pgp1 and amiA showed reduced coccoid formation, with ∆pgp1∆amiA producing minimal coccoids. Both ∆amiA and ∆amiA∆pgp1 lacked flagella and formed unseparated chains of cells consistent with a role for AmiA in cell separation. All strains accumulated peptidoglycan dipeptides over time, but only strains capable of becoming coccoid displayed tripeptide changes. C. jejuni helical shape and corresponding peptidoglycan structure are important for pathogenesis-related attributes. Concomitantly, changing to a coccoid morphology resulted in differences in pathogenic properties; coccoid C. jejuni were non-motile and non-infectious, with minimal adherence and invasion of epithelial cells and an inability to stimulate IL-8. Coccoid peptidoglycan exhibited reduced activation of innate immune receptors Nod1 and Nod2 versus helical peptidoglycan. C. jejuni also transitioned to coccoid within epithelial cells, so the inability of the immune system to detect coccoid C. jejuni may be significant in its pathogenesis.

Vibrio cholerae filamentation promotes chitin surface attachment at the expense of competition in biofilms

The human pathogen Vibrio cholerae, when not inside of a host, grows in cell clusters (biofilms) on pieces of detritus in aquatic environments. Here we discovered that some isolates of V. cholerae can change their shape from small comma-shaped cells to long filaments in seawater. This altered cell shape allows cells to make new types of biofilms, and provides an advantage in quickly colonizing particles in seawater, at the expense of longer-term competitive ability. The filamentous cell-shape strategy is particularly effective at competing in environments with quick turnover of chitin particles. This result showcases how bacterial cell shape can be coupled to environmental success during surface occupation, competition within biofilms, and dispersal to new resource patches.

Collective behavior in spatially structured groups, or biofilms, is the norm among microbes in their natural environments. Though biofilm formation has been studied for decades, tracing the mechanistic and ecological links between individual cell morphologies and the emergent features of cell groups is still in its infancy. Here we use single-cell–resolution confocal microscopy to explore biofilms of the human pathogen Vibrio cholerae in conditions mimicking its marine habitat. Prior reports have noted the occurrence of cellular filamentation in V. cholerae, with variable propensity to filament among both toxigenic and nontoxigenic strains. Using a filamenting strain of V. cholerae O139, we show that cells with this morphotype gain a profound competitive advantage in colonizing and spreading on particles of chitin, the material many marine Vibrio species depend on for growth in seawater. Furthermore, filamentous cells can produce biofilms that are independent of primary secreted components of the V. cholerae biofilm matrix; instead, filamentous biofilm architectural strength appears to derive at least in part from the entangled mesh of cells themselves. The advantage gained by filamentous cells in early chitin colonization and growth is countered in long-term competition experiments with matrix-secreting V. cholerae variants, whose densely packed biofilm structures displace competitors from surfaces. Overall, our results reveal an alternative mode of biofilm architecture that is dependent on filamentous cell morphology and advantageous in environments with rapid chitin particle turnover. This insight provides an environmentally relevant example of how cell morphology can impact bacterial fitness.

Morphological Deconvolution of Beta-Lactam Polyspecificity in E. coli

Beta-lactams comprise one of the earliest classes of antibiotic therapies. These molecules covalently inhibit enzymes from the family of penicillin-binding proteins (PBPs), which are essential in construction of the bacterial cell wall. As a result, beta-lactams cause striking changes to cellular morphology, the nature of which varies by the range of PBPs simultaneously engaged in the cell. The traditional method of exploring beta-lactam polyspecificity is a gel-based binding assay which is low-throughput and typically is run  ex situ in cell extracts. Here, we describe a medium-throughput, image-based assay combined with machine learning methods to automatically profile the activity of beta-lactams in E. coli cells. By testing for morphological change across a panel of strains with perturbations to individual PBP enzymes, our approach automatically and quantifiably relates different beta-lactam antibiotics according to their preferences for individual PBPs in cells. We show the potential of our approach for guiding the design of novel inhibitors toward different PBP-binding profiles by predicting the mechanisms of two recently reported PBP inhibitors.

Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms of the formation of a groundwater microbiome and the subsequent differentiation of Cand. Patescibacteria. In the Hainich Critical Zone Exploratory, Germany, we trace the input of microorganisms from forested soils of preferential recharge areas through fractured aquifers along a 5.4 km hillslope well transect. Cand. Patescibacteria were preferentially mobilized from soils and constituted 66% of species-level OTUs shared between seepage and shallow groundwater. These OTUs, mostly related to Cand. Kaiserbacteraceae, Cand. Nomurabacteraceae, and unclassified UBA9983 at the family level, represented a relative abundance of 71.4% of the Cand. Patescibacteria community at the shallowest groundwater well, and still 44.4% at the end of the transect. Several Cand. Patescibacteria subclass-level groups exhibited preferences for different conditions in the two aquifer assemblages investigated: Cand. Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Cand. Nomurabacteraceae were negatively correlated. Co-occurrence network analysis revealed a central role of Cand. Patescibacteria in the groundwater microbial communities and pointed to potential associations with specific organisms, including abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling. Strong associations among Cand. Patescibacteria themselves further suggested that for many groups within this phylum, distribution was mainly driven by conditions commonly supporting a fermentative life style without direct dependence on specific hosts. We propose that import from soil, and community differentiation driven by hydrochemical conditions, including the availability of organic resources and potential hosts, determine the success of Cand. Patescibacteria in groundwater environments.

Bent Bacteria: A Comparison of Cell Shape Mechanisms in Proteobacteria

Helical cell shape appears throughout the bacterial phylogenetic tree. Recent exciting work characterizing cell shape mutants in a number of curved and helical Proteobacteria is beginning to suggest possible mechanisms and provide tools to assess functional significance. We focus here on Caulobacter crescentus, Vibrio cholerae, Helicobacter pylori, and Campylobacter jejuni, organisms from three classes of Proteobacteria that live in diverse environments, from freshwater and saltwater to distinct compartments within the gastrointestinal tract of humans and birds. Comparisons among these bacteria reveal common themes as well as unique solutions to the task of maintaining cell curvature. While motility appears to be influenced in all these bacteria when cell shape is perturbed, consequences on niche colonization are diverse, suggesting the need to consider additional selective pressures.

Shape and Size Control of Artificial Cells for Bottom-Up Biology

Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is increasingly used for the production of minimal artificial containers such as single-emulsion droplets, double-emulsion droplets, and liposomes. Despite the importance of cell morphology on cellular dynamics, current synthetic-cell studies mainly use spherical containers, and methods to actively shape manipulate these have been lacking. In this paper, we describe a microfluidic platform to deform the shape of artificial cells into a variety of shapes (rods and discs) with adjustable cell-like dimensions below 5 μm, thereby mimicking realistic cell morphologies. To illustrate the potential of our method, we reconstitute three biologically relevant protein systems (FtsZ, microtubules, collagen) inside rod-shaped containers and study the arrangement of the protein networks inside these synthetic containers with physiologically relevant morphologies resembling those found in living cells.

Mechanics and Dynamics of Bacterial Cell Lysis

Membrane lysis, or rupture, is a cell death pathway in bacteria frequently caused by cell wall-targeting antibiotics. Although previous studies have clarified the biochemical mechanisms of antibiotic action, a physical understanding of the processes leading to lysis remains lacking. Here, we analyze the dynamics of membrane bulging and lysis in Escherichia coli, in which the formation of an initial, partially subtended spherical bulge ("bulging") after cell wall digestion occurs on a characteristic timescale of 1 s and the growth of the bulge ("swelling") occurs on a slower characteristic timescale of 100 s. We show that bulging can be energetically favorable due to the relaxation of the entropic and stretching energies of the inner membrane, cell wall, and outer membrane and that the experimentally observed timescales are consistent with model predictions. We then show that swelling is mediated by the enlargement of wall defects, after which cell lysis is consistent with both the inner and outer membranes exceeding characteristic estimates of the yield areal strains of biological membranes. These results contrast biological membrane physics and the physics of thin, rigid shells. They also have implications for cellular morphogenesis and antibiotic discovery across different species of bacteria.

Customizable 3D printed diffusion chambers for studies of bacterial pathogen phenotypes in complex environments

Gaps in our understanding of the natural ecology and survival mechanisms of pathogenic bacteria in complex microenvironments such as soil typically occur due to the difficulty in characterizing biochemical profiles and morphological characteristics as they exist in environmental samples. Conversely, accurate simulation of the abiotic and biotic chemistries of soil habitats within the laboratory is often a significant challenge. Herein, we present the fabrication of customizable and precisely engineered 3D printed diffusion chambers that can be used to incubate bacterial cultures directly in soil matrices within a controlled laboratory experiment, and study the dynamics between bacterial cells and soil components. As part of the design process, different types of 3D printing materials were evaluated for ease of sterilization, structural integrity throughout the experiment, as well as cost/ease of production. To demonstrate potential applications for environmental studies, the diffusion chamber was used to incubate cultures of Bacillus cereus T-strain and Escherichia coli strain O157 directly in soil matrices. We show that the chamber facilitates diffusion of abiotic/biotic components of the soil with target cells without contamination from in situ microbial communities, while allowing for single cell and ensemble level phenotypic analyses of bacteria cultured with and without soil matrices.

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.

Microbial metabolic rates in the Ross Sea: the ABIOCLEAR Project

The Ross Sea is one of the most productive areas of the Southern Ocean and includes several functionally different marine ecosystems. With the aim of identifying signs and patterns of microbial response to current climate change, seawater microbial populations were sampled at different depths, from surface to the bottom, at two Ross Sea mooring areas southeast of Victoria Land in Antarctica. This oceanographic experiment, the XX Italian Antarctic Expedition, 2004-05, was carried out in the framework of the ABIOCLEAR project as part of LTER-Italy. Here, microbial biogeochemical rates of respiration, carbon dioxide production, total community heterotrophic energy production, prokaryotic heterotrophic activity, production (by3H-leucine uptake) and prokaryotic biomass (by image analysis) were determined throughout the water column. As ancillary parameters, chlorophylla, adenosine-triphosphate concentrations, temperature and salinity were measured and reported. Microbial metabolism was highly variable amongst stations and depths. In epi- and mesopelagic zones, respiratory rates varied between 52.4–437.0 and 6.3–271.5 nanol O2l-1h-1; prokaryotic heterotrophic production varied between 0.46–29.5 and 0.3–6.11 nanog C l-1h-1; and prokaryotic biomass varied between 0.8–24.5 and 1.1–9.0 µg C l-1, respectively. The average heterotrophic energy production ranged between 570 and 103 mJ l-1h-1in upper and deeper layers, respectively. In the epipelagic layer, the Prokaryotic Carbon Demand and Prokaryotic Growth Efficiency averaged 9 times higher and 2 times lower, respectively, than in the mesopelagic one. The distribution of plankton metabolism and organic matter degradation was mainly related to the different hydrological and trophic conditions. In comparison with previous research, the Ross Sea results, here, evidenced a relatively impoverished oligotrophic microbial community, throughout the water column.

In situ spectroscopic analysis of Lactobacillus rhamnosus GG flow on an abiotic surface reveals a role for nutrients in biofilm development

In this work, infrared spectroscopy was used to monitor the changes in the biochemical composition of biofilms of the probiotic bacterium Lactobacillus rhamnosus GG (LGG) in three nutritive media (10-fold diluted MRS, AOAC, and mTSB), in situ and under flow conditions. Epifluorescence microscopy was used to observe the shape of LGG cells and their distribution on the surface. Spectroscopic fingerprints recorded as a function of time revealed a medium-dependent content of nucleic acids, phospholipids and polysaccharides in the biofilms. In addition, time-dependent synthesis of lactic acid was observed in MRS/10 and AOAC/10. Polysaccharides were produced to the highest extent in mTSB/10, and the biofilms obtained were the densest in this medium. The rod shape of the cells was preserved in MRS/10, whereas acidic stress induced in AOAC/10 and the nutritional quality of mTSB/10 led to strong morphological changes. These alterations due to the nutritive environment are important to consider in research and use of LGG biofilms.

Imaging cell morphology and physiology using X-rays

Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.

Single molecule super-resolution imaging of bacterial cell pole proteins with high-throughput quantitative analysis pipeline

Bacteria show sophisticated control of their cellular organization, and many bacteria deploy different polar landmark proteins to organize the cell pole. Super-resolution microscopy, such as Photo-Activated Localization Microscopy (PALM), provides the nanoscale localization of molecules and is crucial for better understanding of organization and dynamics in single-molecule. However, analytical tools are not fully available yet, in particular for bacterial cell biology. For example, quantitative and statistical analyses of subcellular localization with multiple cells from multiple fields of view are lacking. Furthermore, brightfield images are not sufficient to get accurate contours of small and low contrast bacterial cells, compared to subpixel presentation of target molecules. Here we describe a novel analytic tool for PALM which integrates precisely drawn cell outlines, of either inner membrane or periplasm, labelled by PALM-compatible fluorescent protein fusions, with molecule data for >10,000 molecules from >100 cells by fitting each cell into an oval arc. In the vibrioid bacterium Vibrio cholerae, the polar anchor HubP constitutes a big polar complex which includes multiple proteins involved in chemotaxis and the flagellum. With this pipeline, HubP is shown to be slightly skewed towards the inner curvature side of the cell, while its interaction partners showed rather loose polar localization.

Rotation and Retention Dynamics of Rod-Shaped Colloids with Surface Charge Heterogeneity in Sphere-in-Cell Porous Media Model

Colloid surface charge heterogeneity was incorporated into a three-dimensional trajectory model, which simulated particle translation and rotation via a force/torque analysis, to study the transport and retention dynamics of rod-shaped colloids over a wide size range in porous media under unfavorable conditions (energy barriers to deposition exist). Our previous study Li , K. ; Ma , H. Deposition Dynamics of Rod-Shaped Colloids during Transport in Porous Media under Favorable Conditions , Langmuir , 2018 , 34 , 9 , 2967 - 2980 , 10.1021/acs.langmuir.7b03983 for rod transport under favorable conditions (lacking energy barriers) demonstrated that particle rotation due to the coupled effect of flow hydrodynamics and Brownian rotation governed rod transport and retention. In this work, we showed that the shape of a colloid affected both transport process and colloid-collector interactions, but shape alone could not make rods to overcome energy barriers of over tens of kT for attachment under unfavorable conditions. The location of colloid surface heterogeneity did not affect transport but predominantly affected colloid-surface interactions by influencing the likelihood of heterogeneity patches facing the collector due to particle rotation. For surface heterogeneity located on the end(s) of a colloid, rods displayed enhanced retention compared with spheres; for surface heterogeneity located on the middle band, rods showed less retention compared with spheres. It was more effective to arrest a traveling rod when surface heterogeneity was located on the end relative to the side, because the tumbling motion greatly increased the likelihood of the end to intercept collector surfaces, and also because a rod would experience less repulsion with an end-on orientation relative to the collector surface compared to a side-on orientation due to the curvature effect. The influences of the particle aspect ratio on retention strongly depended upon the location of colloid surface heterogeneity. Our findings demonstrated that rods had distinct rotation and retention behaviors from spheres under conditions typically encountered in the environment; thus, particle rotation should be considered when studying the transport process of nonspherical colloids or spherical particles with inhomogeneous surface properties.

Genetics and Pathogenicity Factors of Group C and G Streptococci

Of the eight phylogenetic groups comprising the genus Streptococcus , Lancefield group C and G streptococci (GCS and GGS, resp.) occupy four of them, including the Pyogenic, Anginosus, and Mitis groups, and one Unnamed group so far. These organisms thrive as opportunistic commensals in both humans and animals but may also be associated with clinically serious infections, often resembling those due to their closest genetic relatives, the group A streptoccci (GAS). Advances in molecular genetics, taxonomic approaches and phylogenomic studies have led to the establishment of at least 12 species, several of which being subdivided into subspecies. This review summarizes these advances, citing 264 early and recent references. It focuses on the molecular structure and genetic regulation of clinically important proteins associated with the cell wall, cytoplasmic membrane and extracellular environment. The article also addresses the question of how, based on the current knowledge, basic research and translational medicine might proceed to further advance our understanding of these multifaceted organisms. Particular emphasis in this respect is placed on streptokinase as the protein determining the host specificity of infection and the Rsh-mediated stringent response with its potential for supporting bacterial survival under nutritional stress conditions.

Collective oscillation in dense suspension of self-propelled chiral rods

Active particles capable of self-propulsion commonly exhibit rich collective dynamics and have attracted increasing attention due to their applications in biology, robotics, social transport, and biomedicine. However, it remains unclear how the geometric features of active particles affect their collective behaviors. In this paper, we explore the collective dynamics of L-shaped active rods. We show that a dense suspension of self-propelled L-shaped rods exhibits fascinating non-equilibrium oscillatory dynamic clustering. A new oscillation phase can form due to distinct collisions and aggregation mechanisms arising from the L-shaped chirality of elements. A generic diagram of emerging states is provided over a wide range of geometric parameters. Our findings show that the comparative strength between the periodic separation and proximity effect from chirality and the alignment effect from elongated geometry drive the formation and transition of dynamic patterns. This chirality-triggered oscillation phase suggests a new route to understand active matter and paves a way for emerging applications.

Reducing Conditions Favor Magnetosome Production in Magnetospirillum magneticum AMB-1

Magnetotactic bacteria (MTB) are a heterogeneous group of Gram-negative prokaryotes, which all produce special magnetic organelles called magnetosomes. The magnetosome consists of a magnetic nanoparticle, either magnetite (Fe₃O₄) or greigite (Fe₃S₄), embedded in a membrane, which renders the systems colloidaly stable, a desirable property for biotechnological applications. Although these bacteria are able to regulate the formation of magnetosomes through a biologically-controlled mechanism, the environment in general and the physico–chemical conditions surrounding the cells in particular also influence biomineralization. This work thus aims at understanding how such external conditions, in particular the extracellular oxidation reduction potential, influence magnetite formation in the strain Magnetospirillum magneticum AMB-1. Controlled cultivation of the microorganisms was performed at different redox potential in a bioreactor and the formation of magnetosomes was assessed by microscopic and spectroscopic techniques. Our results show that the formation of magnetosomes is inhibited at the highest potential tested (0 mV), whereas biomineralization is facilitated under reduced conditions (-500 mV). This result improves the understanding of the biomineralization process in MTB and provides useful information in sight of a large scale production of magnetosomes for different applications.

Stability of two competing populations in chemostat where one of the population changes its average mass of division in response to changes of its population

This paper considers a novel dynamical behaviour of two microbial populations, competing in a chemostat over a single substrate, that is only possible through the use of population balance equations (PBEs). PBEs are partial integrodifferential equations that represent a distribution of cells according to some internal state, mass in our case. Using these equations, realistic parameter values and the assumption that one population can deploy an emergency mechanism, where it can change the mean mass of division and hence divide faster, we arrive at two different steady states, one oscillatory and one non-oscillatory both of which seem to be stable. A steady state of either form is normally either unstable or only attainable through external control (cycling the dilution rate). In our case no external control is used. Finally, in the oscillatory case we attempt to explain how oscillations appear in the biomass without any explicit dependence on the division rate (the function that oscillates) through the approximation of fractional moments as a combination of integer moments. That allows an implicit dependence of the biomass on the number of cells which in turn is directly dependent on the division rate function.

The optimal size of protocells from simple entropic considerations

Potential constraints on protocell size are developed from simple entropic considerations. To do that, two new different indexes as measures of their structural and dynamic order were developed and applied to an elemental model of the heterotrophic protocell. According to our results, cell size should be a key factor determining the potential of these primitive systems to evolve and consequently to support life. Our analyses also suggest that the size of the optimal vesicles could be constrained to have radii in the interval [Formula: see text], where the two extreme limits [Formula: see text] and [Formula: see text] represent the states of maximum structural order (largest accumulation of substrate inside the vesicle) and the maximum flux of entropy production, respectively. According to the above criteria, the size of the optimum vesicles falls, approximately, in the same spatial range estimated for biological living cells assuming plausible values for the second-order rate constant involved in the catabolic process. Furthermore, the existence of very small vesicles could be seriously affected by the limited efficiency, far from the theoretical limits, with which these catabolic processes may proceed in a prebiotic system.

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection

Background:

Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).

Methods:

Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.

Results:

The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.

Discussion:

Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.

Emergence of evolutionary driving forces in pattern-forming microbial populations

Evolutionary dynamics are controlled by a number of driving forces, such as natural selection, random genetic drift and dispersal. In this perspective article, we aim to emphasize that these forces act at the population level, and that it is a challenge to understand how they emerge from the stochastic and deterministic behaviour of individual cells. Even the most basic steric interactions between neighbouring cells can couple evolutionary outcomes of otherwise unrelated individuals, thereby weakening natural selection and enhancing random genetic drift. Using microbial examples of varying degrees of complexity, we demonstrate how strongly cell-cell interactions influence evolutionary dynamics, especially in pattern-forming systems. As pattern formation itself is subject to evolution, we propose to study the feedback between pattern formation and evolutionary dynamics, which could be key to predicting and potentially steering evolutionary processes. Such an effort requires extending the systems biology approach from the cellular to the population scale.This article is part of the theme issue 'Self-organization in cell biology'.

Changes in Cellular Elasticities and Conformational Properties of Bacterial Surface Biopolymers of Multidrug-Resistant Escherichia coli (MDR-E. coli) Strains in Response to Ampicillin

The roles of the thicknesses and grafting densities of the surface biopolymers of four multi-drug resistant (MDR) Escherichia coli bacterial strains that varied in their biofilm formation in controlling cellular elasticities after exposure to ampicillin were investigated using atomic force microscopy. Exposure to ampicillin was carried out at minimum inhibitory concentrations for different duration times. Our results indicated that the four strains resisted ampicillin through variable mechanisms. Strain A5 did not change its cellular properties upon exposure to ampicillin and as such resisted ampicillin through dormancy. Strain H5 increased its biopolymer brush thickness, adhesion and biofilm formation and kept its roughness, surface area and cell elasticity unchanged upon exposure to ampicillin. As such, this strain likely limits the diffusion of ampicillin by forming strong biofilms. At three hours’ exposure to ampicillin, strains D4 and A9 increased their roughness, surface areas, biofilm formation, and brush thicknesses and decreased their elasticities. Therefore, at short exposure times to ampicillin, these strains resisted ampicillin through forming strong biofilms that impede ampicillin diffusion. At eight hours’ exposure to ampicillin, strains D4 and A9 collapsed their biopolymers, increased their apparent grafting densities and increased their cellular elasticities. Therefore, at long exposure times to ampicillin, cells utilized their higher rigidity to reduce the diffusion of ampicillin into the cells. The findings of this study clearly point to the potential of using the nanoscale characterization of MDR bacterial properties as a means to monitor cell modifications that enhance “phenotypic antibiotic resistance”.

Cardiolipin Alters Rhodobacter sphaeroides Cell Shape by Affecting Peptidoglycan Precursor Biosynthesis

The phospholipid composition of the cell membrane influences the spatial and temporal biochemistry of cells. We studied molecular mechanisms connecting membrane composition to cell morphology in the model bacterium Rhodobacter sphaeroides. The peptidoglycan (PG) layer of the cell wall is a dominant component of cell mechanical properties; consequently, it has been an important antibiotic target. We found that the anionic phospholipid cardiolipin (CL) plays a role in determination of the shape of R. sphaeroides cells by affecting PG precursor biosynthesis. Removing CL in R. sphaeroides alters cell morphology and increases its sensitivity to antibiotics targeting proteins synthesizing PG. These studies provide a connection to spatial biochemical control in mitochondria, which contain an inner membrane with topological features in common with R. sphaeroides.

Cardiolipin (CL) is an anionic phospholipid that plays an important role in regulating protein biochemistry in bacteria and mitochondria. Deleting the CL synthase gene (Δcls) in Rhodobacter sphaeroides depletes CL and decreases cell length by 20%. Using a chemical biology approach, we found that a CL deficiency does not impair the function of the cell wall elongasome in R. sphaeroides; instead, biosynthesis of the peptidoglycan (PG) precursor lipid II is decreased. Treating R. sphaeroides cells with fosfomycin and d-cycloserine inhibits lipid II biosynthesis and creates phenotypes in cell shape, PG composition, and spatial PG assembly that are strikingly similar to those seen with R. sphaeroides Δcls cells, suggesting that CL deficiency alters the elongation of R. sphaeroides cells by reducing lipid II biosynthesis. We found that MurG—a glycosyltransferase that performs the last step of lipid II biosynthesis—interacts with anionic phospholipids in native (i.e., R. sphaeroides) and artificial membranes. Lipid II production decreases 25% in R. sphaeroides Δcls cells compared to wild-type cells, and overexpression of MurG in R. sphaeroides Δcls cells restores their rod shape, indicating that CL deficiency decreases MurG activity and alters cell shape. The R. sphaeroides Δcls mutant is more sensitive than the wild-type strain to antibiotics targeting PG synthesis, including fosfomycin, d-cycloserine, S-(3,4-dichlorobenzyl)isothiourea (A22), mecillinam, and ampicillin, suggesting that CL biosynthesis may be a potential target for combination chemotherapies that block the bacterial cell wall.

Comparative cytology, physiology and transcriptomics of Burkholderia insecticola in symbiosis with the bean bug Riptortus pedestris and in culture

In the symbiosis of the bean bug Riptortus pedestris with Burkholderia insecticola, the bacteria occupy an exclusive niche in the insect midgut and favor insect development and reproduction. In order to understand how the symbiotic bacteria stably colonize the midgut crypts and which services they provide to the host, we compared the cytology, physiology, and transcriptomics of free-living and midgut-colonizing B. insecticola. The analyses revealed that midgut-colonizing bacteria were smaller in size and had lower DNA content, they had increased stress sensitivity, lost motility, and an altered cell surface. Transcriptomics revealed what kinds of nutrients are provided by the bean bug to the Burkholderia symbiont. Transporters and metabolic pathways of diverse sugars such as rhamnose and ribose, and sulfur compounds like sulfate and taurine were upregulated in the midgut-colonizing symbionts. Moreover, pathways enabling the assimilation of insect nitrogen wastes, i.e. allantoin and urea, were also upregulated. The data further suggested that the midgut-colonizing symbionts produced all essential amino acids and B vitamins, some of which are scarce in the soybean food of the host insect. Together, these findings suggest that the Burkholderia symbiont is fed with specific nutrients and also recycles host metabolic wastes in the insect gut, and in return, the bacterial symbiont provides the host with essential nutrients limited in the insect food, contributing to the rapid growth and enhanced reproduction of the bean bug host.

Nanoparticles affect bacterial colonies' optical diffraction patterns

It is increasingly being accepted that bacteria are able to alter their shape/colony pattern in response to adverse environmental conditions. Morphological adaptation of bacteria is known as one of their defence mechanisms against environmental stress/variations. As nanoparticles (NPs) have a unique capacity to induce a wide range of stresses to bacteria, we hypothesized that such NPs can affect the bacterial colony pattern. To test this hypothesis, we incubated a series of superparamagnetic iron oxide nanoparticles (SPIONs) with different physicochemical properties with bacterial colonies and probed the colonies' diffraction patterns by laser. The diffraction patterns of Escherichia coli, Lactobacillus rhamnosus, and Staphylococcus aureus colonies were recorded using a laser. Our results revealed the formation of distinct bacterial diffraction patterns in response to SPIONs with various concentrations and surface chemistries. Our results may pave the way toward the development of new optical approaches for the high-throughput screening of bacterial-NPs/drugs interactions.

A specialized MreB-dependent cell wall biosynthetic complex mediates the formation of stalk-specific peptidoglycan in Caulobacter crescentus

Many bacteria have complex cell shapes, but the mechanisms producing their distinctive morphologies are still poorly understood. Caulobacter crescentus, for instance, exhibits a stalk-like extension that carries an adhesive holdfast mediating surface attachment. This structure forms through zonal peptidoglycan biosynthesis at the old cell pole and elongates extensively under phosphate-limiting conditions. We analyzed the composition of cell body and stalk peptidoglycan and identified significant differences in the nature and proportion of peptide crosslinks, indicating that the stalk represents a distinct subcellular domain with specific mechanical properties. To identify factors that participate in stalk formation, we systematically inactivated and localized predicted components of the cell wall biosynthetic machinery of C. crescentus. Our results show that the biosynthesis of stalk peptidoglycan involves a dedicated peptidoglycan biosynthetic complex that combines specific components of the divisome and elongasome, suggesting that the repurposing of preexisting machinery provides a straightforward means to evolve new morphological traits.

The Effects of β-Lactam Antibiotics on Surface Modifications of Multidrug-Resistant Escherichia coli: A Multiscale Approach

Possible multidrug-resistant (MDR) mechanisms of four resistant strains of Escherichia coli to a model β-lactam, ampicillin, were investigated using contact angle measurements of wettability, crystal violet assays of permeability, biofilm formation, fluorescence imaging, and nanoscale analyses of dimensions, adherence, and roughness. Upon exposure to ampicillin, one of the resistant strains, E. coli A5, changed its phenotype from elliptical to spherical, maintained its roughness and biofilm formation abilities, decreased its length and surface area, maintained its cell wall integrity, increased its hydrophobicity, and decreased its nanoscale adhesion to a model surface of silicon nitride. Such modifications are suggested to allow these cells to conserve energy during metabolic dormancy. In comparison, resistant strains E. coli D4, A9, and H5 elongated their cells, increased their roughness, increased their nanoscale adhesion forces, became more hydrophilic, and increased their biofilm formation upon exposure to ampicillin. These results suggest that these strains resisted ampicillin through biofilm formation that possibly introduces diffusion limitations to antibiotics. Investigations of how MDR bacterial cells modify their surfaces in response to antibiotics can guide research efforts aimed at designing more effective antibiotics and new treatment strategies for MDR bacterial infections.

How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction

Cell shape matters across the kingdoms of life, and cells have the remarkable capacity to define and maintain specific shapes and sizes. But how are the shapes of micron-sized cells determined from the coordinated activities of nanometer-sized proteins? Here, we review general principles that have surfaced through the study of rod-shaped bacterial growth. Imaging approaches have revealed that polymers of the actin homolog MreB play a central role. MreB both senses and changes cell shape, thereby generating a self-organizing feedback system for shape maintenance. At the molecular level, structural and computational studies indicate that MreB filaments exhibit tunable mechanical properties that explain their preference for certain geometries and orientations along the cylindrical cell body. We illustrate the regulatory landscape of rod-shape formation and the connectivity between cell shape, cell growth, and other aspects of cell physiology. These discoveries provide a framework for future investigations into the architecture and construction of microbes.

Chromosome Translocation Inflates Bacillus Forespores and Impacts Cellular Morphology

The means by which the physicochemical properties of different cellular components together determine bacterial cell shape remain poorly understood. Here, we investigate a programmed cell-shape change during Bacillus subtilis sporulation, when a rod-shaped vegetative cell is transformed to an ovoid spore. Asymmetric cell division generates a bigger mother cell and a smaller, hemispherical forespore. The septum traps the forespore chromosome, which is translocated to the forespore by SpoIIIE. Simultaneously, forespore size increases as it is reshaped into an ovoid. Using genetics, timelapse microscopy, cryo-electron tomography, and mathematical modeling, we demonstrate that forespore growth relies on membrane synthesis and SpoIIIE-mediated chromosome translocation, but not on peptidoglycan or protein synthesis. Our data suggest that the hydrated nucleoid swells and inflates the forespore, displacing ribosomes to the cell periphery, stretching septal peptidoglycan, and reshaping the forespore. Our results illustrate how simple biophysical interactions between core cellular components contribute to cellular morphology.

Adaptive locomotion of artificial microswimmers

Bacteria can exploit mechanics to display remarkable plasticity in response to locally changing physical and chemical conditions. Compliant structures play a notable role in their taxis behavior, specifically for navigation inside complex and structured environments. Bioinspired mechanisms with rationally designed architectures capable of large, nonlinear deformation present opportunities for introducing autonomy into engineered small-scale devices. This work analyzes the effect of hydrodynamic forces and rheology of local surroundings on swimming at low Reynolds number, identifies the challenges and benefits of using elastohydrodynamic coupling in locomotion, and further develops a suite of machinery for building untethered microrobots with self-regulated mobility. We demonstrate that coupling the structural and magnetic properties of artificial microswimmers with the dynamic properties of the fluid leads to adaptive locomotion in the absence of on-board sensors.

Morphological responses to nitrogen stress deficiency of a new heterotrophic isolated strain of Ebro Delta microbial mats

Microorganisms living in hypersaline microbial mats frequently form consortia under stressful and changing environmental conditions. In this paper, the heterotrophic strain DE2010 from a microalgae consortium (Scenedesmus sp. DE2009) from Ebro Delta microbial mats has been phenotypically and genotypically characterized and identified. In addition, changes in the morphology and biomass of this bacterium in response to nitrogen deficiency stress have been evaluated by correlative light and electron microscopy (CLEM) combining differential interference contrast (DIC) microscopy and transmission electron microscopy (TEM) and scanning electron microscopy (SEM). These isolated bacteria are chemoorganoheterotrophic, gram-negative, and strictly aerobic bacteria that use a variety of amino acids, organic acids, and carbohydrates as carbon and energy sources, and they grow optimally at 27 °C in a pH range of 5 to 9 and tolerate salinity from 0 to 70‰ NaCl. The DNA-sequencing analysis of the 16S rRNA and nudC and fixH genes and the metabolic characterization highlight that strain DE2010 corresponds to the species Ochrobactrum anthropi. Cells are rod shaped, 1-3 μm in length, and 0.5 μm wide, but under deprived nitrogen conditions, cells are less abundant and become more round, reducing their length and area and, consequently, their biomass. An increase in the number of pleomorphic cells is observed in cultures grown without nitrogen using different optical and electron microscopy techniques. In addition, the amplification of the fixH gene confirms that Ochrobactrum anthropi DE2010 has the capacity to fix nitrogen, overcoming N₂-limiting conditions through a nifH-independent mechanism that is still unidentified.

Stress-induced adaptive morphogenesis in bacteria

Bacteria thrive in virtually all environments. Like all other living organisms, bacteria may encounter various types of stresses, to which cells need to adapt. In this chapter, we describe how cells cope with stressful conditions and how this may lead to dramatic morphological changes. These changes may not only allow harmless cells to withstand environmental insults but can also benefit pathogenic bacteria by enabling them to escape from the immune system and the activity of antibiotics. A better understanding of stress-induced morphogenesis will help us to develop new approaches to combat such harmful pathogens.

Introduction to Genome Biology and Diversity

Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.

Influence of Laboratory Culture Media on in vitro Growth, Adhesion, and Biofilm Formation of Pseudomonas aeruginosa and Staphylococcus aureus

OBJECTIVE

Pseudomonas aeruginosa and Staphylococcus aureus dual-species biofilm infections are notoriously difficult to manage. This study aimed at investigating the influence of four different culture media on the planktonic growth, adhesion, and biofilm formation of P. aeruginosa and S. aureus.

MATERIALS AND METHODS

We monitored four different culture media including Nutrient Broth, Brain Heart Infusion (BHI) broth, Luria-Bertani broth, and RPMI 1640 medium on the planktonic growth, adhesion, and biofilm formation of P. aeruginosa (ATCC 27853) and S. aureus (ATCC 25923) using MTT assay and scanning electron microscopy (SEM).

RESULTS

The most robust growth of the mono- and dual-species cultures was noted in BHI broth. On the contrary, RPMI 1640 medium promoted maximal initial adhesion of both the mono- and dual-species, but BHI broth fostered the maximal biofilm growth. SEM images showed profuse extracellular polysaccharide production in biofilms, particularly in coculture, in BHI medium.

CONCLUSION

Our data demonstrate that BHI broth, relative to the other tested media, is the most conducive for in vitro evaluation of biofilm and planktonic growth kinetics of these two pathogens, both in mono- and coculture.

Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates

Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers’ equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in cellular populations.

Is it better to be left- or right-handed? The answer depends on whether the goal is making a handshake or winning a boxing match. The need for coordination favors the handedness of the majority, but being different could also provide an advantage. The same rules could apply to microbial colonies and cancer tumors. Like humans, cells often have handedness (chirality) that reflects the lack of mirror symmetry in their shapes or movement patterns. We find that cells gain a substantial fitness advantage by either increasing the magnitude of their chirality or switching to the opposite handedness. Selection for specific chirality can overcome differences in growth rate and is mediated by the formation of bulges along the colony edge in regions where cells with different chiralities meet.

DivIVA concentrates mycobacterial cell envelope assembly for initiation and stabilization of polar growth

In many model organisms, diffuse patterning of cell wall peptidoglycan synthesis by the actin homolog MreB enables the bacteria to maintain their characteristic rod shape. In Caulobacter crescentus and Escherichia coli, MreB is also required to sculpt this morphology de novo. Mycobacteria are rod-shaped but expand their cell wall from discrete polar or subpolar zones. In this genus, the tropomyosin-like protein DivIVA is required for the maintenance of cell morphology. DivIVA has also been proposed to direct peptidoglycan synthesis to the tips of the mycobacterial cell. The precise nature of this regulation is unclear, as is its role in creating rod shape from scratch. We find that DivIVA localizes nascent cell wall and covalently associated mycomembrane but is dispensable for the assembly process itself. Mycobacterium smegmatis rendered spherical by peptidoglycan digestion or by DivIVA depletion are able to regain rod shape at the population level in the presence of DivIVA. At the single cell level, there is a close spatiotemporal correlation between DivIVA foci, rod extrusion and concentrated cell wall synthesis. Thus, although the precise mechanistic details differ from other organisms, M. smegmatis also establish and propagate rod shape by cytoskeleton-controlled patterning of peptidoglycan. Our data further support the emerging notion that morphology is a hardwired trait of bacterial cells.

Chemical-Free Recovery of Elemental Selenium from Selenate-Contaminated Water by a System Combining a Biological Reactor, a Bacterium-Nanoparticle Separator, and a Tangential Flow Filter

Biological selenate (SeO₄^2-) reduction to elemental selenium nanoparticles (SeNPs) has been intensively studied but little practiced because of the additional cost associated with separation of SeNPs from water. Recovery of the SeNPs as a valuable resource has been researched to make the approach more competitive. Separation of the intracellular SeNPs from the biomass usually requires the addition of chemicals. In this research, a novel approach that combined a biological reactor, a bacterium-SeNP separator, and a tangential flow ultrafiltration module (TFU) was investigated to biologically reduce selenate and separate the SeNPs, biomass, and water from each other. This approach efficiently removed and recovered selenium while eliminating the use of chemicals for separation. The three units in the approach worked in synergism to achieve the separation and recovery. The TFU module retained the biomass in the system, which increased the biomass retention time and allowed for more biomass decay through which intracellular SeNPs could be released and recovered. SeNP aggregates were separated from bacterial aggregates due to their different interactions with a tilted polyethylene sheet in the bacterium-SeNP separator. SeNP aggregates stayed on the polyethylene sheet while bacterial aggregates settled down to the bottom of the separator.

A Foraging Mandala for Aquatic Microorganisms

Aquatic environments harbor a great diversity of microorganisms, which interact with the same patchy, particulate, or diffuse resources by means of a broad array of physiological and behavioral adaptations, resulting in substantially different life histories and ecological success. To date, efforts to uncover and understand this diversity have not been matched by equivalent efforts to identify unifying frameworks that can provide a degree of generality and thus serve as a stepping stone to scale up microscale dynamics to predict their ecosystem-level consequences. In particular, evaluating the ecological consequences of different resource landscapes and of different microbial adaptations has remained a major challenge in aquatic microbial ecology. Here, inspired by Ramon Margalef’s mandala for phytoplankton, we propose a foraging mandala for microorganisms in aquatic environments, which accounts for both the local environment and individual adaptations. This biophysical framework distills resource acquisition into two fundamental parameters: the search time for a new resource and the growth return obtained from encounter with a resource. We illustrate the foraging mandala by considering a broad range of microbial adaptations and environmental characteristics. The broad applicability of the foraging mandala suggests that it could be a useful framework to compare disparate microbial strategies in aquatic environments and to reduce the vast complexity of microbe-environment interactions into a minimal number of fundamental parameters.

How Important Is Protein Diffusion in Prokaryotes?

That diffusion is important for the proper functioning of cells is without question. The extent to which the diffusion coefficient is important is explored here for prokaryotic cells. We discuss the principles of diffusion focusing on diffusion-limited reactions, summarize the known values for diffusion coefficients in prokaryotes and in in vitro model systems, and explain a number of cases where diffusion coefficients are either limiting for reaction rates or necessary for the existence of phenomena. We suggest a number of areas that need further study including expanding the range of organism growth temperatures, direct measurements of diffusion limitation, expanding the range of cell sizes, diffusion limitation for membrane proteins, and taking into account cellular context when assessing the possibility of diffusion limitation.

Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites

BACKGROUND

The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers. The effects of study-specific biases and statistical power on classification performance and biomarker identification thus remain poorly understood. Furthermore, reliable detection in mixtures of different body sites or with noise from environmental contamination has rarely been investigated thus far. Finally, the impact of ecological associations between microbes on biomarker discovery was usually not considered in previous work.

RESULTS

Here we present the analysis of one of the largest cross-study sequencing datasets of microbial communities from human body sites (15,082 samples from 57 publicly available studies). We show that training a Random Forest Classifier on this aggregated dataset increases prediction performance for body sites by 35% compared to a single-study classifier. Using simulated datasets, we further demonstrate that the source of different microbial contributions in mixtures of different body sites or with soil can be detected starting at 1% of the total microbial community. We apply a biomarker selection method that excludes indirect environmental associations driven by microbe-microbe associations, yielding a parsimonious set of highly predictive taxa including novel biomarkers and excluding many previously reported taxa. We find a considerable fraction of unclassified biomarkers ("microbial dark matter") and observe that negatively associated taxa have a surprisingly high impact on classification performance. We further detect a significant enrichment of rod-shaped, motile, and sporulating taxa for feces biomarkers, consistent with a highly competitive environment.

CONCLUSIONS

Our machine learning model shows strong body site classification performance, both in single-source samples and mixtures, making it promising for tasks requiring high accuracy, such as forensic applications. We report a core set of ecologically informed biomarkers, inferred across a wide range of experimental protocols and conditions, providing the most concise, general, and least biased overview of body site-associated microbes to date.

Who's Your DadA? d-Alanine Levels Regulate Bacterial Stiffness

A central question in mechanobiology is how cellular-scale structures are established and regulated. In bacteria, the cell envelope is essential for mechanical integrity, protecting against environmental stresses and bearing the load from high turgor pressures. Trivedi et al. (mBio 9:e01340-18, 2018, https://doi.org/10.1128/mBio.01340-18) screened a Pseudomonas aeruginosa transposon library and identified genes that influence cell stiffness by measuring cell growth while cells were embedded in an agarose gel. Their findings provide a broad knowledge base for how biochemical pathways regulate cellular mechanical properties in this pathogen. Dozens of genes across diverse functional categories were implicated, suggesting that cellular mechanics is a systems-level emergent property. Furthermore, changes in d-alanine levels in a dadA (d-alanine dehydrogenase) mutant resulted in decreases in the expression of cell wall enzymes, cross-linking density, and cell stiffness. These insights into the biochemical and mechanical roles of dadA highlight the importance of systems-level investigations into the physical properties of cells.

Cell shape-independent FtsZ dynamics in synthetically remodeled bacterial cells

FtsZ is the main regulator of bacterial cell division. It has been implicated in acting as a scaffolding protein for other division proteins, a force generator during constriction, and more recently, as an active regulator of septal cell wall production. FtsZ assembles into a heterogeneous structure coined the Z-ring due to its resemblance to a ring confined by the midcell geometry. Here, to establish a framework for examining geometrical influences on proper Z-ring assembly and dynamics, we sculpted Escherichia coli cells into unnatural shapes using division- and cell wall-specific inhibitors in a micro-fabrication scheme. This approach allowed us to examine FtsZ behavior in engineered Z-squares and Z-hearts. We use stimulated emission depletion (STED) nanoscopy to show that FtsZ clusters in sculpted cells maintain the same dimensions as their wild-type counterparts. Based on our results, we propose that the underlying membrane geometry is not a deciding factor for FtsZ cluster maintenance and dynamics in vivo.

The FtsZ protein assembles into a structure known as ‘Z-ring’ at midcell for bacterial cell division. Here, Söderström et al. show that Z-ring assembly and dynamics in E. coli cells with unnatural shapes, such as squares and hearts, are generally similar to those observed in cells with normal shape.