Is biofilm formation intrinsic to the origin of life?

An astrobiological perspective on microbial biofilms: their importance for habitability and production of detectable and lasting biosignatures

The search for life elsewhere in the universe has remained one of the main goals of astrobiological exploration. In this quest, extreme environments on Earth have served as analogs to study the potential habitability of Mars and icy moons, which include but are not limited to hydrothermal vent systems, acid lakes, deserts, and polar ice, among others. Within the various forms that life manifests, biofilms constitute one of the most widespread phenotypes and are ubiquitous in extreme environments. Biofilms are structured communities of microorganisms enclosed in a matrix of extracellular polymeric substances (EPS) that protect against unfavorable and dynamic conditions. These concentrated structures and their associated chemistry may serve as unique and persistent signatures of life processes that may aid in their detection. Here we propose biofilms as a model system to understand the habitability of extraterrestrial systems and as sources of recognizable and persistent biosignatures for life detection. By testing these ideas in extreme analog environments on Earth, this approach could be used to guide and focus future exploration of samples encompassing the geologic record of early Earth as well as other planets and moons of our solar system.

Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion

Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a "biofilm-in-capillary" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.

Rapid Stiffness Mapping in Soft Biologic Tissues With Micrometer Resolution Using Optical Multifrequency Time-Harmonic Elastography

Rapid mapping of the mechanical properties of soft biological tissues from light microscopy to macroscopic imaging can transform fundamental biophysical research by providing clinical biomarkers to complement in vivo elastography. This work introduces superfast optical multifrequency time-harmonic elastography (OMTHE) to remotely encode surface and subsurface shear wave fields for generating maps of tissue stiffness with unprecedented detail resolution. OMTHE rigorously exploits the space-time propagation characteristics of multifrequency time-harmonic waves to address current limitations of biomechanical imaging and elastography. Key solutions are presented for stimulation, wave decoding, and stiffness reconstruction of shear waves at multiple harmonic frequencies, all tuned to provide consistent stiffness values across resolutions from microns to millimeters. OMTHE's versatility is demonstrated by simulations, phantoms, Bacillus subtilis biofilms, zebrafish embryos and adult zebrafish, reflecting the diversity of biological systems from a mechanics perspective. By zooming in on stiffness details from coarse to finer scales, OMTHE has the potential to advance mechanobiology and offers a way to perform biomechanics-based tissue histology that consistently matches in vivo time-harmonic elastography in patients.

Hidden Places for Foodborne Bacterial Pathogens and Novel Approaches to Control Biofilms in the Meat Industry

Biofilms are of great concern for the meat industry because, despite the implementation of control plans, they remain important hotspots of contamination by foodborne pathogens, highlighting the need to better understand the ecology of these microecosystems. The objective of this paper was to critically survey the recent scientific literature on microbial biofilms of importance for meat safety and quality, also pointing out the most promising methods to combat them. For this, the databases PubMed, Scopus, Science Direct, Web of Science, and Google Scholar were surveyed in a 10-year time frame (but preferably papers less than 5 years old) using selected keywords relevant for the microbiology of meats, especially considering bacteria that are tolerant to cleaning and sanitization processes. The literature findings showed that massive DNA sequencing has deeply impacted the knowledge on the species that co-habit biofilms with important foodborne pathogens (Listeria monocytogenes, Salmonella, pathogenic Escherichia coli, and Staphylococcus aureus). It is likely that recalcitrant commensal and/or spoilage microbiota somehow protect the more fastidious organisms from harsh conditions, in addition to harboring antimicrobial resistance genes. Among the members of background microbiota, Pseudomonas, Acinetobacter, and Enterobacteriales have been commonly found on food contact and non-food contact surfaces in meat processing plants, in addition to less common genera, such as Psychrobacter, Enhydrobacter, Brevundimonas, and Rothia, among others. It has been hypothesized that these rare taxa may represent a primary layer in microbial biofilms, offering better conditions for the adhesion of otherwise poor biofilm formers, especially considering their tolerance to cold conditions and sanitizers. Taking into consideration these findings, it is not only important to target the foodborne pathogens per se in cleaning and disinfection plans but the use of multiple hurdles is also recommended to dismantle the recalcitrant structures of biofilms. In this sense, the last part of this manuscript presents an updated overview of the antibiofilm methods available, with an emphasis on eco-friendly approaches.

Conformational change as a mechanism for toxin activation in bacterial toxin-antitoxin systems

Toxin/antitoxin (TA) systems are present in nearly every prokaryotic genome and play the important physiological roles of phage inhibition by reducing metabolism (this includes persistence for the extreme case of complete cessation of metabolism), genetic element stabilization, and biofilm formation. TA systems have also been incorporated into other cell systems, such as CRISPR-Cas and phage quorum sensing. For the simplest and best-studied case, proteinaceous toxins and antitoxins (i.e., type II), toxin activity is masked by direct binding of the antitoxin. A long-standing, unresolved question in the TA field is how toxins are activated when bound to antitoxins at nanomolar affinity. The current paradigm envisions preferential degradation of the antitoxin by a protease, but this is highly unlikely in that a protease cannot discriminate between bound toxin and bound antitoxin because both are highly structured. Strikingly, recent results from several studies show one likely mechanism for toxin activation is conformational changes in the TA complex that result in the release or activation of the toxin as a result of a protein trigger, such as that from phages, and as a result of thermally-driven refolding dynamics.

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes

Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.

Polyhexamethylene biguanide promotes adaptive cross-resistance to gentamicin in Escherichia coli biofilms

Antimicrobial resistance is a critical public health issue that requires a thorough understanding of the factors that influence the selection and spread of antibiotic-resistant bacteria. Biocides, which are widely used in cleaning and disinfection procedures in a variety of settings, may contribute to this resistance by inducing similar defense mechanisms in bacteria against both biocides and antibiotics. However, the strategies used by bacteria to adapt and develop cross-resistance remain poorly understood, particularly within biofilms -a widespread bacterial habitat that significantly influences bacterial tolerance and adaptive strategies. Using a combination of adaptive laboratory evolution experiments, genomic and RT-qPCR analyses, and biofilm structural characterization using confocal microscopy, we investigated in this study how Escherichia coli biofilms adapted after 28 days of exposure to three biocidal active substances and the effects on cross-resistance to antibiotics. Interestingly, polyhexamethylene biguanide (PHMB) exposure led to an increase of gentamicin resistance (GenR) phenotypes in biofilms formed by most of the seven E. coli strains tested. Nevertheless, most variants that emerged under biocidal conditions did not retain the GenR phenotype after removal of antimicrobial stress, suggesting a transient adaptation (adaptive resistance). The whole genome sequencing of variants with stable GenR phenotypes revealed recurrent mutations in genes associated with cellular respiration, including cytochrome oxidase (cydA, cyoC) and ATP synthase (atpG). RT-qPCR analysis revealed an induction of gene expression associated with biofilm matrix production (especially curli synthesis), stress responses, active and passive transport and cell respiration during PHMB exposure, providing insight into potential physiological responses associated with adaptive crossresistance. In addition, confocal laser scanning microscopy (CLSM) observations demonstrated a global effect of PHMB on biofilm architectures and compositions formed by most E. coli strains, with the appearance of dense cellular clusters after a 24h-exposure. In conclusion, our results showed that the PHMB exposure stimulated the emergence of an adaptive cross-resistance to gentamicin in biofilms, likely induced through the activation of physiological responses and biofilm structural modulations altering gradients and microenvironmental conditions in the biological edifice.

Cyclic di-GMP signaling-Where did you come from and where will you go?

Microbes including bacteria are required to respond to their often continuously changing ecological niches in order to survive. While many signaling molecules are produced as seemingly circumstantial byproducts of common biochemical reactions, there are a few second messenger signaling systems such as the ubiquitous cyclic di-GMP second messenger system that arise through the synthesis of dedicated multidomain enzymes triggered by multiple diverse external and internal signals. Being one of the most numerous and widespread signaling system in bacteria, cyclic di-GMP signaling contributes to adjust physiological and metabolic responses in all available ecological niches. Those niches range from deep-sea and hydrothermal springs to the intracellular environment in human immune cells such as macrophages. This outmost adaptability is possible by the modularity of the cyclic di-GMP turnover proteins which enables coupling of enzymatic activity to the diversity of sensory domains and the flexibility in cyclic di-GMP binding sites. Nevertheless, commonly regulated fundamental microbial behavior include biofilm formation, motility, and acute and chronic virulence. The dedicated domains carrying out the enzymatic activity indicate an early evolutionary origin and diversification of "bona fide" second messengers such as cyclic di-GMP which is estimated to have been present in the last universal common ancestor of archaea and bacteria and maintained in the bacterial kingdom until today. This perspective article addresses aspects of our current view on the cyclic di-GMP signaling system and points to knowledge gaps that still await answers.

Evolution of cyclic di-GMP signalling on a short and long term time scale

Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.

A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism

The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.