Abstract:Biofilm is the dominant lifestyle of microbes in various ecological niches. A group of microorganisms form biofilms through sticking each other by extracellular polymeric substances consisting of polysaccharides, extracellular DNA, and proteins. When living in biofilms, the microbial cells employ small chemicals as “language” to communicate mutually, and exhibit remarkable differences in physiology compared to those live as planktonic state. It has been proved that the development of biofilm is subject to the regulation of c-di-GMP, an important second messenger found in prokaryotes. Considering the essential roles of biofilms in microbial infection, industry, plant-microbe interactions and administration of polluted environments, it is one of the state-of-art areas in microbiology. This special issue of “Biofilm and c-di-GMP” systematically reviews the current progress in the multiple research frontiers, including biotechnology, infectious diseases, environmental microbiology and plant pathology, with special reference to the application of novel study skills. We hope that the issue will inspire the new-generation of young scientists to enter this exciting area.

Abstract:Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous nucleotide second messenger present in a wide variety of bacteria. It regulates many important bacterial physiological functions such as biofilm formation, motility, adhesion, virulence and extracellular polysaccharide synthesis. It binds with many different proteins or RNA receptors, one of which is called riboswitch that is usually located at the 5′-untranslational region (5′-UTR) in some mRNA. Riboswitch usually comprises a specific ligand-binding (sensor) domain (named aptamer domain, AD), as well as a variable domain, termed expression platform (EP), to regulate expression of downstream coding sequences. When a specific metabolite concentration exceeds its threshold level, it will bind to its cognate riboswitch receptor to induce a conformational change of 5′-UTR, leading to modulation of downstream gene expression. Two classes of c-di-GMP-binding riboswitches (c-di-GMP-Ⅰ and c-di-GMP-Ⅱ) have been discovered that bind with this second messenger with high affinity to regulate diverse downstream genes, underscoring the importance of this unique RNA receptor in this pathway. Class Ⅰ c-di-GMP riboswitches are present in a wide variety of bacteria, and are most common in the phyla Firmicutes and Proteobacteria, while class Ⅱ c-di-GMP riboswitches typically function as allosteric ribozymes, binding to c-di-GMP to induce folding changes at atypical splicing site junctions to modulate downstream gene expression. This review introduces the discovery, classification, function, and also the affected downstream genes of c-di-GMP riboswitches.

Abstract:Bacterial biofilm plays an important role in persistent microbial infection. Delineation of the formation and development of bacterial biofilm would provide a promising strategy to treat recalcitrant infection. c-di-AMP (Cyclic diadenosine monophosphate) is a recently identified second messenger of bacteria and involved in plethora of bacterial activities, including cell growth, cell wall homeostasis, biofilm formation and microbial pathogenicity. Here we review the recent literature pertinent to the role and molecular mechanisms of c-di-AMP in regulating biofilm formation of bacteria. The potential application of c-di-AMP and its related proteins in the development of novel antimicrobial therapeutics has also been discussed.

Abstract:cyclic di-GMP (c-di-GMP) is a universal second messenger in bacterial cells. It regulates various biological processes such as biofilm development, pathogenicity, motility, exopolysaccharide (EPS) production and cell cycle. The second messenger exerts its function by binding to effectors, such as riboswitches and proteins. However, due to the diverse conformations of c-di-GMP, its effectors are hardly to be predicted by homology search. Identification of c-di-GMP effectors is the initial step to investigate its regulatory function in bacterial signal transduction, however, it remains to be a technically difficult task. Here we reviewed the mechanism of biofilm development controlled by c-di-GMP through binding to various types of protein effectors, and summarized the screening strategies, including genetics analysis, protein pull-down combined with LC/MS/MS identification, DRaCALA systematic screening and molecular docking-based prediction. We also summarized experimental methods for verifying protein-c-di-GMP interaction, including isothermal titration calorimetry, surface plasmon resonance, microscale thermophoresis etc. In addition, we discussed the advantages and disadvantages of these strategies and methods. The present review aims to facilitate the future investigations that are focused on regulatory role of novel c-di-GMP effectors.

Abstract:It was known that bacteria adhere to surfaces and form sessile colonies called biofilms. Biofilms Show potential applications for biodegradation and biocatalysis, whilst they also cause healthy and environmental problems. In particular, they lead to human infections and biofouling problems in industry. Physical properties of biofilms reflect the architecture and mechanical stability of biofilms that are highly related to their resistance to environmental challenges and their survival. In this article, we reviewed the physical properties involved in the development of biofilms and the related characterization techniques. The surface adhesion of bacteria plays a crucial role in the biofilm formation, which is determined by the motion of bacteria near a surface as well as the interaction between the bacteria and the surface. As far as the biofilms become mature, they behave like a polymer glassy material revealed by rheological measurements.

Abstract:Because of the nanometre resolution, piconewton force sensitivity, label-free technique and the ability to operate in liquid environments, atomic force microscopy (AFM) has emerged as a powerful tool to explore the biofilm development processes. AFM provides three-dimensional topography and structural details of biofilm surfaces under in-situ conditions. It also helps to generate key information on the mechanical properties of biofilm surfaces, such as elasticity and stickiness. Additionally, single-molecule and single-cell force spectroscopies can be applied to measure the strength of adhesion, attraction, and repulsion forces between cell-solid and cell-cell surfaces. This paper outlined the basic principle of AFM technique and introduced recent advances in the application of AFM for the investigation of ultra-morphological, mechanical and interactive properties of biofilms. Furthermore, the existing problems and future prospects were discussed.

Abstract:Biofilms are surface-attached complex aggregates consisting of bacteria cells and extracellular polymeric substances. Cells in biofilms show strong resistance to antibiotics and immune-escape capabilities. Their motility and metabolic activities are quite different from those when they are in planktonic style. In recent years, applications of new image-capturing techniques together with new image-processing methods, have greatly advanced the development of bacterial studies. This review focuses on bacterial tracking techniques. We first present an overview of recent progress in applications of those techniques in biofilm research, especially in the areas of bacterial motility and biofilm regulation, including swimming, twitching, swarming and typical regulatory signaling pathways for biofilms. Then we give a prospect for future applications of bacterial tracking in other related microbial fields.

Abstract:Biofilm is a bacterial lifestyle ubiquitously in natural environments. Bacterial biofilm leads to drug resistance, a main reason why many infectious diseases are difficult to control. Due to the prominent points of biofilms implicated in infectious disease and the spread of multi-drug resistance, it is urgent to discover new antibacterial agents that can regulate biofilm formation and development. This review introduces chemical agents that could modulate bacterial biofilm formation and development.

Abstract:The cyclic dinucleotide c-di-GMP is known as an important second messenger in bacteria, which controls various important cellular processes, such as cell differentiation, biofilm formation and virulence factors production. It is extremely vital for the development of new antibacterial agents by virtue of blocking c-di-GMP signal conduction. Current research indicates that there are three potential targets for discovering new antibacterial agents based on c-di-GMP regulated signal pathway, which are c-di-GMP synthases, c-di-GMP degrading enzymes and c-di-GMP receptors. Herein, we review small molecules that have been developed to inhibit c-di-GMP related enzymes and indicate perspectives of c-di-GMP inhibitors.

Abstract:Zn lactate and SnF2 were used as active compounds in the dentifrice. Here, their anti-biofilm effects were evaluated on Pseudomonas aeruginosa, Acinetobacter baumannii and Streptococcus mutans. The biofilm prevention/ dispersal assay of P. aeruginosa PAO1 demonstrated that Zn lactate and SnF2 can inhibit biofilm formation independently or by combined treatment. Zn lactate disrupted extracellular polysaccharides matrix formation and SnF2 reduced the biomass of biofilm. Most importantly, the combination of Zn lactate and SnF2 thoroughly abolished the biofilm formation of all three strains.

Abstract:Biofilms are surface-associated communities of microorganisms embedded within self-secreted extracellular polymeric substances, and a major cause of chronic and persistent infections. Respiratory Pseudomona aeruginosa infection is the leading reason for morbidity and mortality in cystic fibrosis patients. The formation of biofilms by P. aeruginosa in the airway is thought to increase persistence and antibiotic resistance during infection. Biofilm formation of P. aeruginosa is regulated by complicated signaling systems including quorum sensing and two-component systems that control the synthesis of extracellular polymeric substances. Furthermore, iron is an essential and scarce nutrient for bacteria and an important signal factor. P. aeruginosa has developed multiple iron uptake systems to sequester enough iron for its survival, with important regulatory roles in both release of virulence factors and formation of biofilms. In this review, we summarize recent advances in biofilm formation and its regulation along with the iron-uptake strategies in P. aeruginosa, to provide new insights and understanding to fight bacterial biofilms.

Abstract:Yersinia pestis, the cause of plague, is transmitted by flea bite. Y. pestis forms a biofilm in the proventriculus of its flea vector to enhance transmission. Biofilm formation in Y. pestis is positively regulated by the intracellular levels of the second messenger cyclic diguanylate (c-di-GMP). The c-di-GMP in Y. pestis is synthesized by two diguanylate cyclases (DGC), HmsT and HmsD, and degraded by phosphodiesterase (PDE), HmsP. Here we summarized the regulators that modulate c-di-GMP metabolism and biofilm formation in Y. pestis and discussed their regulatory mechanism.

Abstract:Although most microbes are not readily cultured in the lab, microbial DNA can be extracted directly from an environmental sample and be functionally expressed in a suitable host for natural products discovery, and this approach has been termed “metagenomics”. An E’mei Mountain soil metagenomic library was constructed using an Escherichia coli-Streptomyces shuttle vector for functional based screening of anti-bacterial clones in Streptomyces albus host. Two active clones were obtained and their fermentation broths were studied for the inhibitory effect on Staphylococcus aureus biofilm. Their fermentation products have a good inhibitory effect on the formation of S. aureus biofilm, and the inhibitory effect could exceed 90% when the concentration of sample was 2 MIC (Minimum Inhibitory Concentration). In addition, two samples had significantly effect on S. aureus biofilm dispersal, and the clearance rate of EM110 was higher than EM123. In conclusion, substances with strong bioactivities on biofilm formation and dispersal of S. aureus could be discovered by using metagenomics technology.

Abstract:Biofilm associated Vibrio cholerae exhibits hypervirulence and supreme fitness against the harsh stresses during its infectious cycle. It is important to study the relationships between the regulation mechanism of V. cholerae biofilm development and its environmental adaption in host niche and aquatic habitat. Here, we summarize the recent advances in V. cholerae biofilm, including biofilm compositions, development and regulation. Particularly, we extensively discuss how V. cholerae fosters its biofilm architecture and assembly via sensing and responding various environmental determinants, such as bacterium self-produced molecules, natural environment components and host factors.

Abstract:Dental biofilms are composed of hundreds of bacterial species, among which Streptococcus mutans is widely recognized as the major pathogen of dental caries. The cariogenic potential of S. mutans is related to its ability to form a robust biofilm on the tooth surface and its acidogenic and acid-tolerant properties. Co-evolution of S. mutans with the host has resulted in the diversity of secondary metabolism of S. mutans in strain level. A variety of secondary metabolites, including 10 bacteriocins (mutacins) and one hybrid Polyketide/Non-Ribosomal Peptide type compound, have been characterized. Studies on these secondary metabolites indicate that they play a significant role either in interspecies or in inter-kingdom interactions in the dental biofilm. As more S. mutans strains are isolated and sequenced, additional secondary metabolites with novel functions will be discovered. The study of secondary metabolites in S. mutans is anticipated to be helpful for oral disease treatment and prevention by providing new strategies.

Abstract:Fungal pathogens represent an important group of human pathogenic microbes that lead to an unacceptably severe global burden especially due to exceptionally high mortality. For many fungal pathogens, they are widespread saprophytes and human host is not the exclusive niche for their proliferation. Their exceptional capability to survive and thrive within infected host likely stems from their sophisticated strategies in adaptation to diverse biotic and abiotic stressors from natural niches or predators. Among these ‘environmental pathogens’, Cryptococcus neoformans as a model organism claims the lives of more than half a million annually. Some recent studies indicate that cryptococcal survival both inside and outside of hosts can be coordinated by a combination of social behaviors. In this review, we describe and discuss the social behaviors employed by C. neoformans and address their significant impact on biofilm formation, sexual reproduction and pathogenicity.

Abstract:Candida albicans is an important opportunistic fungal pathogen of humans. Phenotypic plasticity is a typical biological feature of C. albicans, which is associated with pathogenicity, host adaptation, and sexual reproduction. Biofilm of C. albicans is a complex community formed by different morphological types of cells (yeast, hyphae and pseudohyphae) and secreted extracellular matrix. C. albicans biofilms are intrinsically resistant to antifungal drugs, the host immune system, and environmental stresses. Biofilm is an important virulence factor and a major clinical challenge. With the development of new technologies in global gene expression profiles and genetic manipulation, the regulatory mechanisms that govern C. albicans biofilm development and drug resistance become more and more clear. Major regulatory mechanisms involve the MAPK and cAMP signaling pathways and transcriptional regulators such as Bcr1 and Tec1. In addition, morphological transitions and sexual reproduction are also involved in the regulation of biofilm development. In this review, we focus on the genetic regulatory mechanisms of biofilm including the roles of cell-wall related proteins, transcription factors, and the MTL locus. In the last section, we also summarize the mechanisms of drug resistance of biofilm in C. albicans.

Abstract:Myxococcus xanthus is a Gram-negative soil bacterium capable of performing sophisticated cellular behaviors and growing one of the most intricate bacterial single-species biofilms in nature. During the process of biofilm formation, social behaviors of M. xanthus cells dominate key steps of the biofilm establishment, e.g., cellular motility on solid surface, predatory behavior by the grouped cells, kin recognition in the community, fruiting body development, myxospore differentiation, and programmed cell death. This review introduces the recent research progress about the M. xanthus biofilms.

Abstract:Studies on biofilm regulation based on Lux type quorum sensing system in wastewater treatment have attracted much attention. The intervention of quorum sensing system includes both mechanisms of positive and negative control. The positive invigorating effect improves the efficiency of biofilm wastewater treatment, promotes the production of extracellular polymeric substance (EPS) and soluble microbial products (SMP), and increases the yield of biofilm. The negative weakening effect of quorum sensing can decompose the signal molecules needed in the process of biofilm formation, interrupts the gene expression process of biofilm formation, and inhibits the formation of biofilm on MBR membrane surface effectively. The further study of the structure and mechanism of N-acyl homoserine lactone (AHLs), the immobilization technology and application of quorum quenching bacteria, the synergistic effect verification of different biofouling control methods and the application feasibility of quorum sensing system based technology in more wastewater treatment fields are the next important researches to explore.

Abstract:Twitching motility is very important for Pseudomonas aeruginosa in the adaptation of surface environment and in the 3-D structure formation of mature biofilm. To quantitatively characterize twitching motility in situ, we developed a method by combining high-throughput data acquisition, automatic image processing and database establishment. This method is based on single cell analysis and big data visualization. A periodic relaxation of 0.9 second was resolved during slingshot motility analysis. Twitching motilities of bacteria under addition of two quorum sensing signaling molecules were studied, cells moved faster after signal addition. This method may help understand the molecular mechanism and regulatory circuits of twitching motility.

Abstract:Quorum sensing (QS) is a cell-cell communication mechanism that allows bacterial populations to coordinate gene expression in response to cell density. N-acylhomoserine lactones (AHL) are used as quorum-sensing signal molecules by many Gram negative bacteria. Acinetobacter sp. 77, an AHL-degrading bacterium, was isolated in our previous work. The gene aidE for AHL inactivation was cloned in this study by screening a genomic DNA library. The deduced protein AidE is 268 amino acids in length and shares a high identity (95%) with the beta-lactamase family protein in Acinetobacter gyllenbergii CIP110306, but low identities with known AHL-degrading enzymes. HPLC analysis of the AidE-degraded C6-HSL products revealed that AidE functioned as an AHL lactonase. Sequences alignment suggested that the aidE gene is not conserved in Acinetobacter species, flanking sequences of aidE and their arrangement are specific in Acinetobacter sp. 77 genome, and some IS insertion sequences were found downstream of the aidE gene. These evidences indicated that the aidE gene might be foreign DNA taken up via horizontal gene transferring or had changed its relative location due to the genome rear-arrangement. Expression of the aidE gene in Pectobacterium carotovorum subsp. carotovorum Z3-3 significantly reduced its AHL production as well as the pathogenicity on host plants, indicating that AidE was able to effectively quench quorum sensing-dependent functions in bacteria. In conclusion, aidE is a newfound AHL-lactonase with a potential for suppression of bacterial infections.

Abstract:Biofilms are complex three-dimensional bacterial assemblages that attach to biotic or abiotic solid surfaces, and frequently embed within a self-produced matrix of extracellular polymeric substances. Biofilm formation is a microbial defense response to biotic and abiotic stresses, and a key factor for survival in adverse environments. A wide variety of microorganisms can colonize distant tissues of higher plants, such as leaves, vascular network and roots, and adhere to the surface of the tissues to form biofilms. The dynamic processes in forming biofilms in response to plant internal environment are key steps required for full virulence of phytopathogenic bacteria. Exploring the mechanisms involved in regulation of bacterial biofilms is important for understanding the plant-pathogens interactions. In this review, we summarized the research progresses related to the biofilms of bacterial phytopathogens, including biofilm characteristics, essential regulatory mechanisms and key signals affecting the transition between a planktonic lifestyle and multicellular behavior.