Non-surface Attached Bacterial Aggregates: A Ubiquitous Third Lifestyle

Beneficial applications of biofilms

Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.

Multitasking functions of bacterial extracellular DNA in biofilms

Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.

Nontuberculous Mycobacteria, Mucociliary Clearance, and Bronchiectasis

Nontuberculous mycobacteria (NTM) are environmental and ubiquitous, but only a few species are associated with disease, often presented as nodular/bronchiectatic or cavitary pulmonary forms. Bronchiectasis, airways dilatations characterized by chronic productive cough, is the main presentation of NTM pulmonary disease. The current Cole's vicious circle model for bronchiectasis proposes that it progresses from a damaging insult, such as pneumonia, that affects the respiratory epithelium and compromises mucociliary clearance mechanisms, allowing microorganisms to colonize the airways. An important bronchiectasis risk factor is primary ciliary dyskinesia, but other ciliopathies, such as those associated with connective tissue diseases, also seem to facilitate bronchiectasis, as may occur in Lady Windermere syndrome, caused by M. avium infection. Inhaled NTM may become part of the lung microbiome. If the dose is too large, they may grow excessively as a biofilm and lead to disease. The incidence of NTM pulmonary disease has increased in the last two decades, which may have influenced the parallel increase in bronchiectasis incidence. We propose that ciliary dyskinesia is the main promoter of bronchiectasis, and that the bacteria most frequently involved are NTM. Restoration of ciliary function and impairment of mycobacterial biofilm formation may provide effective therapeutic alternatives to antibiotics.

Understanding the intricacies of microbial biofilm formation and its endurance in chronic infections: a key to advancing biofilm-targeted therapeutic strategies

Bacterial biofilms can adhere to various surfaces in the environment with human beings being no exception. Enclosed in a self-secreted matrix which contains extracellular polymeric substances, biofilms are intricate communities of bacteria that play a significant role across various sectors and raise concerns for public health, medicine and industries. These complex structures allow free-floating planktonic cells to adopt multicellular mode of growth which leads to persistent infections. This is of great concern as biofilms can withstand external attacks which include antibiotics and immune responses. A more comprehensive and innovative approach to therapy is needed in view of the increasing issue of bacterial resistance brought on by the overuse of conventional antimicrobial medications. Thus, to oppose the challenges posed by biofilm-related infections, innovative therapeutic strategies are being explored which include targeting extracellular polymeric substances, quorum sensing, and persister cells. Biofilm-responsive nanoparticles show promising results by improving drug delivery and reducing the side effects. This review comprehensively examines the factors influencing biofilm formation, host immune defence mechanisms, infections caused by biofilms, diagnostic approaches, and biofilm-targeted therapies.

Bacteria Living in Biofilms in Fluids: Could Chemical Antibiofilm Pretreatment of Culture Represent a Paradigm Shift in Diagnostics?

Biofilms are multicellular aggregates of bacteria immersed in an extracellular matrix that forms on various surfaces, including biological tissues and artificial surfaces. However, more and more reports point out the fact that even biological fluids and semifluid, such as synovial liquid, blood, urine, or mucus and feces, harbor "non-attached" biofilm aggregates of bacteria, which represent a significant phenomenon with critical clinical implications that remain to be fully investigated. In particular, biofilm aggregates in biological fluid samples have been shown to play a relevant role in bacterial count and in the overall accuracy of microbiological diagnosis. In line with these observations, the introduction in the clinical setting of fluid sample pretreatment with an antibiofilm chemical compound called dithiothreitol (DTT), which is able to dislodge microorganisms from their intercellular matrix without killing them, would effectively improve the microbiological yield and increase the sensitivity of cultural examination, compared to the current microbiological techniques. While other ongoing research continues to unveil the complexity of biofilm formation in biological fluids and its impact on infection pathogenesis and diagnosis, we here hypothesize that the routine use of a chemical antibiofilm pretreatment of fluid and semi-solid samples may lead to a paradigm shift in the microbiological approach to the diagnosis of biofilm-related infections and should be further investigated and eventually implemented in the clinical setting.

How to study biofilms: technological advancements in clinical biofilm research

Biofilm formation is an important survival strategy commonly used by bacteria and fungi, which are embedded in a protective extracellular matrix of organic polymers. They are ubiquitous in nature, including humans and other animals, and they can be surface- and non-surface-associated, making them capable of growing in and on many different parts of the body. Biofilms are also complex, forming polymicrobial communities that are difficult to eradicate due to their unique growth dynamics, and clinical infections associated with biofilms are a huge burden in the healthcare setting, as they are often difficult to diagnose and to treat. Our understanding of biofilm formation and development is a fast-paced and important research focus. This review aims to describe the advancements in clinical biofilm research, including both in vitro and in vivo biofilm models, imaging techniques and techniques to analyse the biological functions of the biofilm.

Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure

An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qβ (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.

The non-attached biofilm aggregate

Biofilms have conventionally been perceived as dense bacterial masses on surfaces, following the five-step model of development. Initial biofilm research focused on surface-attached formations, but detached aggregates have received increasing attention in the past decade due to their pivotal role in chronic infections. Understanding their nature sparked fervent discussions in biofilm conferences and scientific literature. This review consolidates current insights on non-attached aggregates, offering examples of their occurrence in nature and diseases. We discuss their formation and dispersion mechanisms, resilience to antibiotics and immune-responses, drawing parallels to surface-attached biofilms. Moreover, we outline available in vitro models for studying non-attached aggregates.

Microbial Biofilms: Applications, Clinical Consequences, and Alternative Therapies

Biofilms are complex communities of microorganisms that grow on surfaces and are embedded in a matrix of extracellular polymeric substances. These are prevalent in various natural and man-made environments, ranging from industrial settings to medical devices, where they can have both positive and negative impacts. This review explores the diverse applications of microbial biofilms, their clinical consequences, and alternative therapies targeting these resilient structures. We have discussed beneficial applications of microbial biofilms, including their role in wastewater treatment, bioremediation, food industries, agriculture, and biotechnology. Additionally, we have highlighted the mechanisms of biofilm formation and clinical consequences of biofilms in the context of human health. We have also focused on the association of biofilms with antibiotic resistance, chronic infections, and medical device-related infections. To overcome these challenges, alternative therapeutic strategies are explored. The review examines the potential of various antimicrobial agents, such as antimicrobial peptides, quorum-sensing inhibitors, phytoextracts, and nanoparticles, in targeting biofilms. Furthermore, we highlight the future directions for research in this area and the potential of phytotherapy for the prevention and treatment of biofilm-related infections in clinical settings.

Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures

Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. These aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or secreted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth, and Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicellular aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and biological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.

Effects of Algal Extracellular Polysaccharides on the Formation of Filamentous Manganese Oxide Particles in the Near-Bottom Layer of Lake Biwa

Filamentous manganese (Mn) oxide particles, which occur in the suboxic zone of stratified waterbodies, are important drivers of diverse elemental cycles. These particles are considered to be bacteriogenic; despite the importance of biogeochemical implications, however, the environmental factor responsible for their formation has not been identified. The aim of this study was to demonstrate the involvement of algal extracellular polysaccharides in Mn oxide particle formation. Based on this study of laboratory cultures of a model Mn(II)-oxidizing bacterium, the supply of algal extracellular mucilage was shown to stimulate Mn(II) oxidation and thus the production of filamentous Mn oxide particles. This observation was consistent with the results obtained for naturally occurring particles collected from a near-bottom layer (depth of approximately 90 m) in the northern basin of Lake Biwa, Japan, that is, most Mn particles resembling δ-MnO₂ were associated with an extracellular mucilage-like gelatinous matrix, which contained dead algal cells and was lectin-stainable. In the lake water column, polysaccharides produced by algal photosynthesis sank to the bottom layer. The analysis of the quality of water samples, which have been collected from the study site for 18 years, reveals that the annual average total phytoplankton biovolume in the surface layer correlates with the density of filamentous Mn particles in the near-bottom layer. Among different phytoplankton species, green algae appeared to be the key species. The results of this study suggest that algal extracellular polysaccharides serve as an important inducer for the formation of filamentous Mn oxide particles in the near-bottom layer of the northern basin of Lake Biwa.

A systematic review of the use of bacteriophages for in vitro biofilm control

Bacteriophages (phages) are very promising biological agents for the prevention and control of bacterial biofilms. However, little is known about the parameters that can influence the efficacy of phages on biofilms. This systematic review provides a summary and analysis of the published data about the use of phages to control pre-formed biofilms in vitro, suggesting recommendations for future experiments in this area. A total of 68 articles, containing data on 605 experiments addressing the efficacy of phages to control biofilms in vitro were included, after a search conducted in Web of Science, Embase, and Medline (PubMed). The data collected from each experiment included information about biofilm growth conditions, phage characteristics, treatment conditions and biofilm reduction. In most cases, biofilms were formed in the surface of microtiter plates (82.5%); the median time for biofilm formation was 24 h, as is the median treatment duration. Quantification of biofilm biomass (52.6%), viable cells (25.5%) and metabolic activity (17.9%) were the most common biofilm assessment methods. Correlation analysis revealed that some phage parameters can influence the treatment outcome: higher phage concentrations were strongly associated with improved biofilm control, leading to higher levels of biofilm reduction, and phages with higher burst sizes and shorter latent periods seem to be the best candidates to control biofilms in vitro. However, the great variability of the methodologies used prompts the need for the development of standardized in vitro methodologies to characterize phage/biofilm interactions and to assess the efficacy of phages to control biofilms.

Tools of the Trade: Image Analysis Programs for Confocal Laser-Scanning Microscopy Studies of Biofilms and Considerations for Their Use by Experimental Researchers

Confocal laser-scanning microscopy (CLSM) is the bedrock of the microscopic visualization of biofilms. Previous applications of CLSM in biofilm studies have largely focused on observations of bacterial or fungal elements of biofilms, often seen as aggregates or mats of cells. However, the field of biofilm research is moving beyond qualitative observations alone, toward the quantitative analysis of the structural and functional features of biofilms, across clinical, environmental, and laboratory conditions. In recent times, several image analysis programs have been developed to extract and quantify biofilm properties from confocal micrographs. These tools not only vary in their scope and relevance to the specific biofilm features under study but also with respect to the user interface, compatibility with operating systems, and raw image requirements. Understanding these considerations is important when selecting tools for quantitative biofilm analysis, including at the initial experimental stages of image acquisition. In this review, we provide an overview of image analysis programs for confocal micrographs of biofilms, with a focus on tool selection and image acquisition parameters that are relevant for experimental researchers to ensure reliability and compatibility with downstream image processing.

Klebsiella aerogenes Adhesion Behaviour during Biofilm Formation on Monazite

The adsorption behaviour of micro-organisms during the initial attachment stage of biofilm formation affects subsequent stages. The available area for attachment and the chemophysical properties of a surface affect microbial attachment performance. This study focused on the initial attachment behaviour of Klebsiella aerogenes on monazite by measuring the ratio of planktonic against sessile subpopulations (P:S ratio), and the potential role of extracellular DNA (eDNA). eDNA production, effects of physicochemical properties of the surface, particle size, total available area for attachment, and the initial inoculation size on the attachment behaviour were tested. K. aerogenes attached to monazite immediately after exposure to the ore; however, the P:S ratio significantly (p = 0.05) changed in response to the particle size, available area, and inoculation size. Attachment occurred preferentially on larger-sized (~50 µm) particles, and either decreasing the inoculation size or increasing the available area further promoted attachment. Nevertheless, a portion of the inoculated cells always remained in a planktonic state. K. aerogenes produced lower eDNA in response to the changed surface chemical properties when monazite was replaced by xenotime. Using pure eDNA to cover the monazite surface significantly (p ≤ 0.05) hindered bacterial attachment due to the repulsive interaction between the eDNA layer and bacteria.

C-Type Natriuretic Peptide Acts as a Microorganism-Activated Regulator of the Skin Commensals Staphylococcus epidermidis and Cutibacterium acnes in Dual-Species Biofilms

The effect of C-type natriuretic peptide in a concentration closer to the normal level in human blood plasma was studied on the mono-species and dual-species biofilms of the skin commensal bacteria Cutibacterium acnes HL043PA2 and Staphylococcus epidermidis ATCC14990. Despite the marginal effect of the hormone on cutibacteria in mono-species biofilms, the presence of staphylococci in the community resulted in a global shift of the CNP effect, which appeared to increase the competitive properties of C. acnes, its proliferation and the metabolic activity of the community. S. epidermidis was mostly inhibited in the presence of CNP. Both bacteria had a significant impact on the gene expression levels revealed by RNA-seq. CNP did not affect the gene expression levels in mono-species cutibacterial biofilms; however, in the presence of staphylococci, five genes were differentially expressed in the presence of the hormone, including two ribosomal proteins and metal ABC transporter permease. In staphylococci, the Na-translocating system protein MpsB NADH-quinone oxidoreductase subunit L was downregulated in the dual-species biofilms in the presence of CNP, while in mono-species biofilms, two proteins of unknown function were downregulated. Hypothetically, at least one of the CNP mechanisms of action is via the competition for zinc, at least on cutibacteria.

Impact of direct physical association and motility on fitness of a synthetic interkingdom microbial community

Mutualistic exchange of metabolites can play an important role in microbial communities. Under natural environmental conditions, such exchange may be compromised by the dispersal of metabolites and by the presence of non-cooperating microorganisms. Spatial proximity between members during sessile growth on solid surfaces has been shown to promote stabilization of cross-feeding communities against these challenges. Nonetheless, many natural cross-feeding communities are not sessile but rather pelagic and exist in turbulent aquatic environments, where partner proximity is often achieved via direct cell-cell adhesion, and cooperation occurs between physically associated cells. Partner association in aquatic environments could be further enhanced by motility of individual planktonic microorganisms. In this work, we establish a model bipartite cross-feeding community between bacteria and yeast auxotrophs to investigate the impact of direct adhesion between prokaryotic and eukaryotic partners and of bacterial motility in a stirred mutualistic co-culture. We demonstrate that adhesion can provide fitness benefit to the bacterial partner, likely by enabling local metabolite exchange within co-aggregates, and that it counteracts invasion of the community by a non-cooperating cheater strain. In a turbulent environment and at low cell densities, fitness of the bacterial partner and its competitiveness against a non-cooperating strain are further increased by motility that likely facilitates partner encounters and adhesion. These results suggest that, despite their potential fitness costs, direct adhesion between partners and its enhancement by motility may play key roles as stabilization factors for metabolic communities in turbulent aquatic environments.

Challenges and opportunities in the development of novel antimicrobial therapeutics for cystic fibrosis

Chronic respiratory infection is the primary driver of mortality in individuals with cystic fibrosis (CF). Existing drug screening models utilised in preclinical antimicrobial development are unable to mimic the complex CF respiratory environment. Consequently, antimicrobials showing promising activity in preclinical models often fail to translate through to clinical efficacy in people with CF. Model systems used in CF anti-infective drug discovery and development range from antimicrobial susceptibility testing in nutrient broth, through to 2D and 3D in vitro tissue culture systems and in vivo models. No single model fully recapitulates every key aspect of the CF lung. To improve the outcomes of people with CF (PwCF) it is necessary to develop a set of preclinical models that collectively recapitulate the CF respiratory environment to a high degree of accuracy. Models must be validated for their ability to mimic aspects of the CF lung and associated lung infection, through evaluation of biomarkers that can also be assessed following treatment in the clinic. This will give preclinical models greater predictive power for identification of antimicrobials with clinical efficacy. The landscape of CF is changing, with the advent of modulator therapies that correct the function of the CFTR protein, while antivirulence drugs and phage therapy are emerging alternative treatments to chronic infection. This review discusses the challenges faced in current antimicrobial development pipelines, including the advantages and disadvantages of current preclinical models and the impact of emerging treatments.

Adding a new dimension: Multi-level structure and organization of mixed-species Pseudomonas aeruginosa and Staphylococcus aureus biofilms in a 4-D wound microenvironment

Biofilms in wounds typically consist of aggregates of bacteria, most often Pseudomonas aeruginosa and Staphylococcus aureus, in close association with each other and the host microenvironment. Given this, the interplay across host and microbial elements, including the biochemical and nutrient profile of the microenvironment, likely influences the structure and organization of wound biofilms. While clinical studies, in vivo and ex vivo model systems have provided insights into the distribution of P. aeruginosa and S. aureus in wounds, they are limited in their ability to provide a detailed characterization of biofilm structure and organization across the host-microbial interface. On the other hand, biomimetic in vitro systems, such as host cell surfaces and simulant media conditions, albeit reductionist, have been shown to support the co-existence of P. aeruginosa and S. aureus biofilms, with species-dependent localization patterns and interspecies interactions. Therefore, composite in vitro models that bring together key features of the wound microenvironment could provide unprecedented insights into the structure and organization of mixed-species biofilms. We have built a four-dimensional (4-D) wound microenvironment consisting of a 3-D host cell scaffold of co-cultured human epidermal keratinocytes and dermal fibroblasts, and an in vitro wound milieu (IVWM); the IVWM provides the fourth dimension that represents the biochemical and nutrient profile of the wound infection state. We leveraged this 4-D wound microenvironment, in comparison with biofilms in IVWM alone and standard laboratory media, to probe the structure of mixed-species P. aeruginosa and S. aureus biofilms across multiple levels of organization such as aggregate dimensions and biomass thickness, species co-localization and spatial organization within the biomass, overall biomass composition and interspecies interactions. In doing so, the 4-D wound microenvironment platform provides multi-level insights into the structure of mixed-species biofilms, which we incorporate into the current understanding of P. aeruginosa and S. aureus organization in the wound bed.

One Health-One Biofilm

Bacterial biofilms are structured clusters of bacterial cells enclosed in a self-produced polymer matrix that are attached to a biotic or abiotic surface. This structure protects bacteria from hostile environmental conditions. There are also accumulating reports about bacterial aggregates associated but not directly adherent to surfaces. Interestingly, these bacterial aggregates exhibit many of the same phenotypes as surface-attached biofilms. Surface-attached biofilms as well as non-attached aggregates are ubiquitous and found in a wide variety of natural and clinical settings. This strongly suggests that biofilm/aggregate formation is important at some steps in the bacterial lifecycle. Biofilm/aggregate formation might therefore be important for some bacterial species for persistence within their host or their environment, while for other bacterial species it might be more important for persistence in the environment between infection of different individuals or even between infection of different hosts (humans or animals). This is strikingly similar to the One Health concept which recognizes that the health and well-being of humans, animals and the environment are intricately linked. We would like to propose that within this One Health concept, the One Biofilm concept also exists, where biofilm/aggregate formation in humans, animals and the environment are also intricately linked. Biofilm/aggregates could represent the unifying factor underneath the One Health concept. The One Biofilm concept would support that biofilm/aggregate formation might be important for persistence during infection but might as well be even more important for persistence in the environment and for transmission between different individuals/different hosts.

The c-di-GMP Phosphodiesterase PipA (PA0285) Regulates Autoaggregation and Pf4 Bacteriophage Production in Pseudomonas aeruginosa PAO1

In Pseudomonas aeruginosa PAO1, 41 genes encode proteins predicted to be involved in the production or degradation of c-di-GMP, a ubiquitous secondary messenger that regulates a variety of physiological behaviors closely related to biofilm and aggregate formation. Despite extensive effort, the entire picture of this important signaling network is still unclear, with one-third of these proteins remaining uncharacterized. Here, we show that the deletion of pipA, which produces a protein containing two PAS domains upstream of a GGDEF-EAL tandem, significantly increased the intracellular c-di-GMP level and promoted the formation of aggregates both on surfaces and in planktonic cultures. However, this regulatory effect was not contributed by either of the two classic pathways modulating biofilm formation, exopolysaccharide (EPS) overproduction or motility inhibition. Transcriptome sequencing (RNA-Seq) data revealed that the expression levels of 361 genes were significantly altered in a ΔpipA mutant strain compared to the wild type (WT), indicating the critical role of PipA in PAO1. The most remarkably downregulated genes were located on the Pf4 bacteriophage gene cluster, which corresponded to a 2-log reduction in the Pf4 phage production in the ΔpipA mutant. The sizes of aggregates in ΔpipA cultures were affected by exogenously added Pf4 phage in a concentration-dependent manner, suggesting the quantity of phage plays a part in regulating the formation of aggregates. Further analysis demonstrated that PipA is highly conserved across 83 P. aeruginosa strains. Our work therefore for the first time showed that a c-di-GMP phosphodiesterase can regulate bacteriophage production and provided new insights into the relationship between bacteriophage and bacterial aggregation. IMPORTANCE The c-di-GMP signaling pathways in P. aeruginosa are highly organized and well coordinated, with different diguanylate cyclases and phosphodiesterases playing distinct roles in a complex network. Understanding the function of each enzyme and the underlying regulatory mechanisms not only is crucial for revealing how bacteria decide the transition between motile and sessile lifestyles, but also greatly facilitates the development of new antibiofilm strategies. This work identified bacteriophage production as a novel phenotypic output controlled transcriptionally by a phosphodiesterase, PipA. Further analysis suggested that the quantity of phage may be important in regulating autoaggregation, as either a lack of phage or overproduction was associated with higher levels of aggregation. Our study therefore extended the scope of c-di-GMP-controlled phenotypes and discovered a potential signaling circuit that can be target for biofilm treatment.

Cellular Modifications of Rhodococci Exposed to Separate and Combined Effects of Pharmaceutical Pollutants

Actinomycetes of the genus Rhodococcus (class Actinomycetia) are dominant dwellers of biotopes with anthropogenic load. They serve as a natural system of primary response to xenobiotics in open ecosystems, initiate defensive responses in the presence of pollutants, and are regarded as ideal agents capable of transforming and degrading pharmaceuticals. Here, the ability of selected Rhodococcus strains to co-metabolize nonsteroidal anti-inflammatory drugs (ibuprofen, meloxicam, and naproxen) and information on the protective mechanisms of rhodococci against toxic effects of pharmaceuticals, individually or in a mixture, have been demonstrated. For the first time, R. ruber IEGM 439 provided complete decomposition of 100 mg/L meloxicam after seven days. It was shown that versatile cellular modifications occurring at the early development stages of nonspecific reactions of Rhodococcus spp. in response to separate and combined effects of the tested pharmaceuticals included changes in electrokinetic characteristics and catalase activity; transition from unicellular to multicellular life forms accompanied by pronounced morphological abnormalities; changes in the average size of vegetative cells and surface area-to-volume ratio; and the formation of linked cell assemblages. The obtained data are considered as adaptation mechanisms in rhodococci, and consequently their increased resistance to separate and combined effects of ibuprofen, meloxicam, and naproxen.

Protein-conjugated microbubbles for the selective targeting of S. aureus biofilms

Staphylococcus aureus (S. aureus) is an important human pathogen and a common cause of bloodstream infection. The ability of S. aureus to form biofilms, particularly on medical devices, makes treatment difficult, as does its tendency to spread within the body and cause secondary foci of infection. Prolonged courses of intravenous antimicrobial treatment are usually required for serious S. aureus infections. This work investigates the in vitro attachment of microbubbles to S. aureus biofilms via a novel Affimer protein, AClfA1, which targets the clumping factor A (ClfA) virulence factor – a cell-wall anchored protein associated with surface attachment. Microbubbles (MBs) are micron-sized gas-filled bubbles encapsulated by a lipid, polymer, or protein monolayer or other surfactant-based material. Affimers are small (∼12 kDa) heat-stable binding proteins developed as replacements for antibodies. The binding kinetics of AClfA1 against S. aureus ClfA showed strong binding affinity (K_D = 62 ± 3 nM). AClfA1 was then shown to bind S. aureus biofilms under flow conditions both as a free ligand and when bound to microparticles (polymer beads or microbubbles). Microbubbles functionalized with AClfA1 demonstrated an 8-fold increase in binding compared to microbubbles functionalized with an identical Affimer scaffold but lacking the recognition groups. Bound MBs were able to withstand flow rates of 250 μL/min. Finally, ultrasound was applied to burst the biofilm bound MBs to determine whether this would lead to biofilm biomass loss or cell death. Application of a 2.25 MHz ultrasound profile (with a peak negative pressure of 0.8 MPa and consisting of a 22-cycle sine wave, at a pulse repetition rate of 10 kHz) for 2 s to a biofilm decorated with targeted MBs, led to a 25% increase in biomass loss and a concomitant 8% increase in dead cell count. The results of this work show that Affimers can be developed to target S. aureus biofilms and that such Affimers can be attached to contrast agents such as microbubbles or polymer beads and offer potential, with some optimization, for drug-free biofilm treatment.

Host Environment Shapes S. aureus Social Behavior as Revealed by Microscopy Pattern Formation and Dynamic Aggregation Analysis

Understanding how bacteria adapt their social behavior to environmental changes is of crucial importance from both biological and clinical perspectives. Staphylococcus aureus is among the most common infecting agents in orthopedics, but its recalcitrance to the immune system and to antimicrobial treatments in the physiological microenvironment are still poorly understood. By means of optical and confocal microscopy, image pattern analysis, and mathematical modeling, we show that planktonic biofilm-like aggregates and sessile biofilm lifestyles are two co-existing and interacting phases of the same environmentally adaptive developmental process and that they exhibit substantial differences when S. aureus is grown in physiological fluids instead of common lab media. Physicochemical properties of the physiological microenvironment are proposed to be the key determinants of these differences. Besides providing a new tool for biofilm phenotypic analysis, our results suggest new insights into the social behavior of S. aureus in physiological conditions and highlight the inadequacy of commonly used lab media for both biological and clinical studies of bacterial development.

Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients

Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.

Imaging Flow Cytometry to Study Biofilm-Associated Microbial Aggregates

The aim of the research was to design an advanced analytical tool for the precise characterization of microbial aggregates from biofilms formed on food-processing surfaces. The approach combined imaging flow cytometry with a machine learning-based interpretation protocol. Biofilm samples were collected from three diagnostic points of the food-processing lines at two independent time points. The samples were investigated for the complexity of microbial aggregates and cellular metabolic activity. Thus, aggregates and singlets of biofilm-associated microbes were simultaneously examined for the percentages of active, mid-active, and nonactive (dead) cells to evaluate the physiology of the microbial cells forming the biofilm structures. The tested diagnostic points demonstrated significant differences in the complexity of microbial aggregates. The significant percentages of the bacterial aggregates were associated with the dominance of active microbial cells, e.g., 75.3% revealed for a mushroom crate. This confirmed the protective role of cellular aggregates for the survival of active microbial cells. Moreover, the approach enabled discriminating small and large aggregates of microbial cells. The developed tool provided more detailed characteristics of bacterial aggregates within a biofilm structure combined with high-throughput screening potential. The designed methodology showed the prospect of facilitating the detection of invasive biofilm forms in the food industry environment.

The role of uspE in virulence and biofilm formation by Histophilus somni

UspE is a global regulator in Escherichia coli. To study the function of Histophilus somni uspE, strain 2336::TnuspE was identified from a bank of mutants generated with EZ::Tn5™<KAN-2> Tnp Transposome™ that were biofilm deficient. The 2336::TnuspE mutant was highly attenuated in mice, the electrophoretic profile of its lipooligosaccharide (LOS) indicated the LOS was truncated, and the mutant was significantly more serum-sensitive compared to the wildtype strain. In addition to forming a deficient biofilm, exopolysaccharide (EPS) production was also compromised, but the electrophoretic profile of outer membrane proteins was not altered. RNA sequence analysis revealed that the transcription levels of some stress response chaperones, transport proteins, and a large number of ribosomal protein genes in 2336::TnuspE were significantly differentially regulated compared to strain 2336. Therefore, uspE may differentially function in direct and indirect expression of H. somni genes, but its attenuation may be linked to poor biofilm formation and rapid clearance of the bacteria resulting from a compromised LOS structure. Our results support that uspE is a global stress regulatory gene in H. somni.

Bacteria autoaggregation: how and why bacteria stick together

Autoaggregation, adherence between identical bacterial cells, is important for colonization, kin and kind recognition, and survival of bacteria. It is directly mediated by specific interactions between proteins or organelles on the surfaces of interacting cells or indirectly by the presence of secreted macromolecules such as eDNA and exopolysaccharides. Some autoaggregation effectors are self-associating and present interesting paradigms for protein interaction. Autoaggregation can be beneficial or deleterious at specific times and niches. It is, therefore, typically regulated through transcriptional or post-transcriptional mechanisms or epigenetically by phase variation. Autoaggregation can contribute to bacterial adherence, biofilm formation or other higher-level functions. However, autoaggregation is only required for these phenotypes in some bacteria. Thus, autoaggregation should be detected, studied and measured independently using both qualitative and quantitative in vitro and ex vivo methods. If better understood, autoaggregation holds the potential for the discovery of new therapeutic targets that could be cost-effectively exploited.

Atrial Natriuretic Peptide Affects Skin Commensal Staphylococcus epidermidis and Cutibacterium acnes Dual-Species Biofilms

The first evidence of the atrial natriuretic peptide (ANP) effect on mono-species and dual-species biofilms of skin commensals Cutibacterium acnes and Staphylococcus epidermidis was obtained in different model systems. Elucidation of the mechanism of action of hormones on the microbial communities of human skin is an important physiological and medical aspect. Under anaerobic conditions, ANP at a concentration of 6.5 × 10-10 M inhibits the growth of S. epidermidis biofilms and stimulates the growth of C. acnes biofilms, and a lesser effect has been demonstrated on planktonic cultures. In biofilms, ANP stimulates aggregation in C. acnes and aggregate dispersion of S. epidermidis, while in S. epidermidis, ANP also stimulates the metabolic activity of cells. Analysis of dual-species biofilms has shown the dominance of S. epidermidis, while ANP increases the ratio of C. acnes biomass in the community. ANP decreases the growth rate of S. epidermidis biofilms and increases that of C. acnes. The effect of ANP is not dependent on the surface type and probably affects other targets in microbial cells. Thus, the potential regulatory effect of human ANP on skin microbe dual-species communities has been shown, and its potential has been demonstrated to change microbiota homeostasis on the skin.