MicrobiologyBytes

Cell-cell interactions are common to all living systems. Bacteria are no exception, and numerous mechanisms that use secreted products as signaling molecules are known. Among these, the so-called “quorum sensing” systems are perhaps the best studied. In quorum sensing, all bacterial cells within a population produce secreted molecules. Only when population densities are high is there a response to these compounds, thus allowing the bacteria to coordinate their behavior. However, it is clear that there is much more to bacterial cell–cell interactions than simply counting numbers and coordinating behavior. Secreted molecules also play key roles in microbial development so that different cell fates can arise and coexist within a single-species population. In addition, in settings where multiple species coexist, their interactions often are mediated through extracellular compounds. Development in one microbe can be influenced by small molecules secreted by other species.

Almost all quorum sensing studies have been performed under laboratory conditions – far removed from how bacteria actually live. What happens in the “wild” when rival bacterial gangs contest the same territory?

Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. PNAS USA November 10 2011. doi: 10.1073/pnas.11036301
Many different systems of bacterial interactions have been described. However, relatively few studies have explored how interactions between different microorganisms might influence bacterial development. To explore such interspecies interactions, we focused on Bacillus subtilis, which characteristically develops into matrix-producing cannibals before entering sporulation. We investigated whether organisms from the natural environment of B. subtilis – the soil – were able to alter the development of B. subtilis. To test this possibility, we developed a coculture microcolony screen in which we used fluorescent reporters to identify soil bacteria able to induce matrix production in B. subtilis. Most of the bacteria that influence matrix production in B. subtilis are members of the genus Bacillus, suggesting that such interactions may be predominantly with close relatives. The interactions we observed were mediated via two different mechanisms. One resulted in increased expression of matrix genes via the activation of a sensor histidine kinase, KinD. The second was kinase independent and conceivably functions by altering the relative subpopulations of B. subtilis cell types by preferentially killing noncannibals. These two mechanisms were grouped according to the inducing strain’s relatedness to B. subtilis. Our results suggest that bacteria preferentially alter their development in response to secreted molecules from closely related bacteria and do so using mechanisms that depend on the phylogenetic relatedness of the interacting bacteria.

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One of the great advances in medical technology has unwittingly spawned a serious threat to public health. Implanted medical devices, from cardiac stents to artificial hip joints, are commonly infected with biofilms, complex microbial communities that can prove remarkably resistant to host defenses and treatment. It appears, however, that biofilms, even those arising from the same microbe species, may harbor innate differences in their response to treatments like antifungal agents. Understanding how these microbe colonies might produce structures that appear similar but have very different physical properties and functions is a critical step in figuring out how to overcome antimicrobial resistance.

In humans, Candida albicans can cause problems like oral thrush and yeast infections. Far more serious is its increasing tendency to colonize catheters, heart valves, and other medical devices, where it serves as a seeding source for potentially deadly bloodstream infections. The finding that C. albicans can form two different types of biofilm is interesting not only because it is an example of how similar structures can have very different functions, but also because it provides information about how signaling pathways may evolve by modifying preexisting signaling modules for entirely new purposes. This phenomenon may be widespread, extending beyond slimy fungal biofilms to a variety of organisms. On a practical note, when researchers are designing new methods to discourage fungal biofilms it will be useful for them to keep in mind that there are two types of biofilms being formed by C. albicans.

A Tale of Two Biofilms. 2011 PLoS Biol 9(8): e1001119. doi:10.1371/journal.pbio.1001119

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It is commonly accepted that the spread of most viruses occurs via the diffusion of ‘cell-free’ viral particles. In support of this, infectious viruses have been found in biological fluids and aerosols, and could be propagated in vitro using virus stocks produced from infected cell-culture supernatants. This mode of viral dissemination requires high numbers of stable viral particles released by the infected cell into the extracellular environment, such as the host bodily fluids. ‘Free’ viral particles were associated with a variety of components, such as lipids or proteins, which might reinforce virus envelop integrity and prevent envelope glycoprotein shedding. However, for other viruses, few viral particles are released, or they are poorly infectious when separated from infected cells. In such cases, virus propagation largely requires the presence of infected cells, suggesting that cell contacts mediate viral spread. This type of dissemination is mainly reported for enveloped viruses, such as some herpes viruses and some retroviruses, particularly deltaretroviruses such as the human T-cell leukemia virus type 1 (HTLV-1). Many aspects of this mode of virus dissemination are largely unknown, such as (i) the nature and the mechanism for forming cellular junctions that mediate cell–cell virus spread, and (ii) the nature of the infectious material transferred. Both of these factors depend on the virus and the type of infected cells.

Of note, the spread of two human retroviruses that infect leukocytes, HIV-1 and HTLV-1, occurs between mobile cells forming dynamic contacts with other cells. Both retroviruses cause severe chronic viral infections. Their transmission between individuals occurs through sexual contact and blood transfusion, and vertically from mother to child, including through breastfeeding. In addition to HTLV-1 dissemination through division of infected cells carrying viral genomes, transmission of HTLV-1 viral particles is known to occur mainly through cell contact in vitro and in vivo, with the exception of dendritic cells, which can be infected by cell-free viral particles. By contrast, HIV-1 spread can occur by both diffusion and direct cell–cell transfer. Nevertheless, compelling evidence indicates that direct spread through cell contact is the most efficient mode of HIV-1 dissemination in vitro, and might play a crucial role in vivo:

Can viruses form biofilms? Trends Microbiol. Mar 31 2011
The recent finding that the human T-cell leukemia virus type 1 (HTLV-1) encases itself in a carbohydrate-rich adhesive extracellular ‘cocoon’, which enables its efficient and protected transfer between cells, unveiled a new infectious entity and a novel mechanism of viral transmission. These HTLV-1 structures are observed at the surface of T cells from HTLV-1-infected patients and are reminiscent of bacterial biofilms. The virus controls the synthesis of the matrix, which surrounds the virions and attaches them to the T cell surface. We propose that, similar to bacterial biofilms, viral biofilms could represent ‘viral communities’ with enhanced infectious capacity and improved spread compared with ‘free’ viral particles, and might constitute a key reservoir for chronic infections.

Traditionally, research in bacterial communication and co-operation has been performed at the molecular level and less attention has been paid to evolutionary and ecological factors which govern such actions. But Steve Diggle and Roman Popat ask in this article in Microbiology Today, what is the relevance of social evolution for microbes?

Most of us at some point have had the rather unpleasant experience of putting our fingers down a plug-hole only to pull up a slimy goo. As microbiologists are now well aware, this is a large mass of microbial cells that we commonly refer to as a biofilm, and such microbial communities can be found almost everywhere. They are the pioneers of rocky shores which help enable seaweed to settle on rocks. They cause problems in industrial settings such as contamination of beer lines. Clinically, they are of huge importance, contributing to infection, colonization of medical devices and antibiotic resistance. Biofilms consist of numerous cells, often belonging to a number of diverse species surrounded by a complex exopolysaccharide matrix. They remind us that bacterial cells interact with each other and inevitably lead social lives. Recently, there has been a growing interest in studying aspects of sociality using bacteria or other microbial study systems.

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The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. This paper describes the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.

The biofilm matrix. 2010 Nature Reviews Microbiology 8: 623-633 doi:10.1038/nrmicro2415

Related:

• Can filamentous fungi form biofilms?
• Bugs Against Biofilms
• Biofilms Use Chemical Weapons

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Interspecies chemical communication in bacterial development. Ann Rev Microbiol. 2009 63: 99-118

Related:

• Communication, cooperation, competition and cheating – bacteria are just like us
• Quorum Sensing in Bacteria: We Two Are One
• Bacterial Crowd Control
• Pneumococcus: the quorum-sensing killer
• Quorum sensing in Serratia

In the past few decades our fundamental understanding of how microorganisms grow and survive in natural settings or in host tissues has changed considerably. It is now widely accepted that microbes in nature rarely survive as solitary cells, but rather grow as biofilms. In fact, the formation of biofilms is so prevalent that it is likely to be a positively selected trait that became fixed very early in microbial evolution as an important feature for survival on surfaces in diverse or changing environments.

A biofilm can be described as a microbially derived sessile community characterized by cells that are irreversibly attached to a substratum or interface or to each other, are embedded in a matrix of extracellular polymeric substances that they have produced, and exhibit an altered phenotype with respect to growth rate and gene transcription. It is important to note that not all researchers apply the term biofilm synonymously. For example, another widely accepted biofilm definition describes a “microscopic mushroom-shaped” 3D community of microbial cells held in association and firmly attached to surfaces via an extracellular polymeric matrix that is permeated by water channels allowing efficient biomass exchange between the population and the environment. This definition encompasses many examples of biofilm structures in aqueous environments, but does not include surface-associated microbial growth in environments that are not saturated in water or fluid. The range of physical or environmental conditions necessary for the formation of biofilm structures is a debated topic. For example, surface-associated microbial growth in low water environments, such as on rocks, rhizospheres or the surfaces of buildings, have been termed unsaturated, terrestrial or subaerial biofilms by some authors. As a result of these diverse definitions, differences exist in the application of the terminology to various microbial assemblages, and it is unclear whether all assemblages qualify as biofilms versus aggregates, microbial mats, flocs or microcolonies.

In a broad context, biofilm formation involves genetically programmed changes in the organization and metabolism of the solitary or planktonic forms of microorganisms. Structurally, cells leave a motile, solitary or planktonic condition and become securely attached to a surface and/or other cells within an exopolymeric matrix. The structure of individual cells is not significantly altered, but the individuals become organized into a communal structure, encased in slime, and display novel characteristics and phenotypes. One frequently measurable change in the phenotype of cells in a biofilm, as compared to their planktonic counterparts, is significantly increased tolerance to chemical, biological or physical stresses. In fact, one of the most striking and consistently reported features of microbial populations growing as biofilms is their increased intrinsic resistance to antimicrobial agents. As a result, conventional antibiotic agents and biocides often fail to eradicate infectious microorganisms from hosts or from inert hard surfaces when present in a biofilm.

It is generally assumed that filamentous fungi, some of which have a significant impact on our health or our economy, do not form biofilms. In contrast to this assumption, this paper discusses recent findings supporting the hypothesis that surface-associated filamentous fungi can form biofilms. Based on these findings and on previous models for bacterial and yeast systems, it proposes preliminary criteria and a model for biofilm formation by filamentous fungi.

Can filamentous fungi form biofilms? Trends Microbiol. Oct 13 2009

Related:

• Candida parapsilosis secreted lipase is a major virulence factor
• Bugs Against Biofilms
• Who you gonna call? Slimebusters!

A recent article in New Scientist entitled Why microbes are smarter than you thought looks at six behaviours that seem remarkably intelligent for single celled organisms. Single-celled organisms don’t have nervous systems, let alone brains, but they could be viewed as “biological computers” with internal machinery that can process and respond to information.

On MicrobiologyBytes I’ve often discussed bacterial communication – the ways in which bacteria talk to each other using chemical signals. If Bacillus subtilis cells are growing in a nutrient-poor area, they release chemicals into their surroundings which tell their neighbours “There’s not much food here, so clear off or we’ll both starve.” In response to these chemical messages, the other bacteria move away, changing the shape of the colony.

Many single-celled organisms can work out how many other bacteria of their own species are in their vicinity – something known as “quorum sensing“. Each individual bacterium releases a small amount of a chemical into the surrounding medium. If there are lots of other bacteria around, all releasing the same chemical, levels can reach a critical point and trigger a change in behaviour of the whole population. This “voting system” can be used to decide when to launch an attack on a host. Once they have grown to sufficient numbers to overwhelm the immune system, they collectively launch an assault on the body. Jamming these signals might provide us with a way to fight back.

Bacteria form communities known as biofilms, familiar as the thin layer of slime that coats the insides of water pipes, or surgical implants. Many different species live side by side in these “bacterial cities”, consuming each other’s wastes, cooperating to exploit food sources, and safeguarding one another from external threats such as antibiotics.

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Many microbes can accelerate the rate at which their genes mutate. This allows them to obtain new abilities that may be helpful when conditions get tough. Escherichia coli mutates more rapidly when under stress (Stress-induced mutagenesis in bacteria. Science. 2003 300(5624): 1404-9), and yeast can perform the same trick (Adaptive mutation in Saccharomyces cerevisiae. Crit Rev Biochem Mol Biol. 2007 42(4): 285-31).

Microbes are also pretty good at navigation. The single-celled algae Chlamydomonas swim towards light, but only if it is of a wavelength that they can use for photosynthesis. Some bacteria move according to the presence of chemicals in their environment – a behaviour called chemotaxis. Another group of bacteria align themselves to the Earth’s magnetic field, allowing them to head directly north or south, and more importantly, up or down for optimum photosynthesis.

When the amoeba Dictyostelium searches the surface of a Petri dish for food, it makes frequent turns. But it does not do so randomly. If it has just turned right, it is twice as likely to turn left as right on its next turn, and vice versa. It remembers which direction it last turned.

Remarkable though these behaviours are, we have probably only scratched the surface of what single-celled organisms can do. With so many still entirely unknown to science, there must be plenty more surprises in store.

Related:

• Quorum Sensing
• Biofilms
• It’s good to talk
• Communication, cooperation, competition and cheating – bacteria are just like us

A biofilm is a surface-associated population of microbes that is embedded in a cement of extracellular compounds. This cement is known as matrix. The two main functions of matrix are to protect cells from their surrounding environment, preventing drugs and other stresses from penetrating the biofilm, and to maintain the architectural stability of the biofilm, acting as a glue to hold the cells together. The presence of matrix is a contributing factor to the high degree of resistance to antimicrobial drugs observed in biofilms. Because biofilms have a major impact on human health, and because matrix is such a pivotal component of biofilms, it is important to understand how the production of matrix is regulated.

A group of researchers has identified a novel regulatory gene network that plays an important role in the spread of common, and sometimes deadly, fungus infections. The new findings establish the role of Zap1 protein in the activation of genes that regulate the synthesis of biofilm matrix. Candida albicans is a fungus, more specifically a yeast, which approximately 80 percent of people have in their gastrointestinal and genitourinary tract with no ill effects. However, at elevated levels it can cause non-life threatening conditions like thrush and yeast infections. C. albicans infection becomes much more serious, and can be lethal in those with compromised immune systems who have an implantable medical device such as a pacemaker or artificial joint, or who use broad-spectrum antibiotics. Central to such infections is the biofilm –  a population of microbes, in this case C. albicans cells, joined together to form a sheet of cells. The cells in the biofilm produce extracellular components such as proteins and sugars, which form a cement-like matrix. This matrix serves to protect the cells of the biofilm, preventing drugs and other stressors from attacking the cells while acting as a glue that holds the cells together. By doing this, the matrix provides an environment in which yeast cells in the biofilm can thrive, promoting infection and drug resistance.

Biofilms have a major impact on human health and matrix is such a pivotal component of biofilms. It is important to understand how the production of matrix is regulated. In the study, the scientists found that the zinc-responsive regulatory protein Zap1 prevents the production of soluble beta-1,3 glucan, a sugar that is a major component of matrix. They also identified other genes whose expression is controlled by Zap1, called Zap1 target genes. They found that these genes encode two types of enzymes, glucoamylases and alcohol dehydrogenases, which both govern the production and maturation of matrix components. Understanding this novel regulatory gene network gives us insight into the metabolic processes that contribute to biofilm formation, and the role the network plays in infection. By better understanding the mechanisms by which biofilms develop and grow, we can start to look at targets for combating infection.

Biofilm Matrix Regulation by Candida albicans Zap1. 2009 PLoS Biol 7(6): e1000133 doi:10.1371/journal.pbio.1000133
A biofilm is a surface-associated population of microorganisms embedded in a matrix of extracellular polymeric substances. Biofilms are a major natural growth form of microorganisms and the cause of pervasive device-associated infection. This report focuses on the biofilm matrix of Candida albicans, the major fungal pathogen of humans. We report here that the C. albicans zinc-response transcription factor Zap1 is a negative regulator of a major matrix component, soluble b-1,3 glucan, in both in vitro and in vivo biofilm models. To understand the mechanistic relationship between Zap1 and matrix, we identified Zap1 target genes through expression profiling and full genome chromatin immunoprecipitation. On the basis of these results, we designed additional experiments showing that two glucoamylases, Gca1 and Gca2, have positive roles in matrix production and may function through hydrolysis of insoluble b-1,3 glucan chains. We also show that a group of alcohol dehydrogenases Adh5, Csh1, and Ifd6 have roles in matrix production: Adh5 acts positively, and Csh1 and Ifd6, negatively. We propose that these alcohol dehydrogenases generate quorum-sensing aryl and acyl alcohols that in turn govern multiple events in biofilm maturation. Our findings define a novel regulatory circuit and its mechanism of control of a process central to infection.

Related:

• Candida albicans: the video
• Candida parapsilosis secreted lipase is a major virulence factor
• Bugs Against Biofilms