MicrobiologyBytes

In 1518, one of the strangest epidemics in recorded history struck the city of Strasbourg. Hundreds of people were seized by an irresistible urge to dance, hop and leap into the air. In houses, halls and public spaces, as fear paralyzed the city and the members of the elite despaired, the dancing continued with mindless intensity. Seldom pausing to eat, drink or rest, many of them danced for days or even weeks. And before long, the chronicles agree, dozens were dying from exhaustion. What was it that could have impelled as many as 400 people to dance, in some cases to death?

Medieval dancing epidemics were not unrelated events: they were linked both in time and space. Every one of the ten or so outbreaks between the late 1300s and 1518 happened along the Rhine and Mosel rivers. In 1374, for instance, the crazed dance gradually spread out from an epicentre around Aachen, Liege and Maastricht to neighbouring towns such as Ghent, Utrecht, Metz, Trier and, eventually, Strasbourg. Moreover, outbreaks of compulsive dancing virtually always struck in or close to places affected by earlier outbreaks. Maastricht, Trier, Zurich and Strasbourg each experienced two or more episodes. There are also several reports of compulsive dancing after 1518. All of these, crucially, took place close to the Rhine, and all but one within a short ride of Strasbourg itself.

How can we explain this striking epidemiological picture? One suggestion is that wild dancing formed part of the ecstatic ritual of a heretical sect, an energetic counterpart of the flagellant’s cult. There are two main difficulties with this theory. First, in lucid moments the dancers implored bystanders and priests to come to their aid. There is absolutely no evidence that the dancers wanted to dance. On the contrary, they expressed fear and desperation. Second, the authorities consistently saw the afflicted not as heretics but as the victims of diabolical possession or divine curse, and treated them accordingly. The dancers were subject to exorcisms or sent on pilgrimages. Never were they hauled before the inquisition.

Other authors have sought a chemical or biological origin for the dancing mania, and the chief contender has been ergot, a mould that grows on the stalks of damp rye. While seductively simple, this hypothesis is untenable. The chemicals contained in ergot do not allow for sustained dancing. They can certainly trigger violent convulsions and delusions, but not coordinated movements that last for days. Yet while the dancers were free from ergot, they almost certainly were delirious. Only in an altered state of consciousness could they have tolerated such extreme fatigue and the searing pain of sore, swollen and bleeding feet. Moreover, witnesses consistently spoke of the victims as being entranced, seeing terrifying visions and behaving with wild, crazy abandon. So what could have plunged hundreds of people into trances so deep that remorseless dancing became possible? Psychologists, neurologists and anthropologists have identified severe psychological distress as a factor increasing the likelihood of an individual entering an altered state. It is unlikely to be a coincidence, therefore, that in the year 1518 many people in Strasbourg were experiencing truly exceptional levels of hunger and mental anguish.

In a spin: the mysterious dancing epidemic of 1518. Endeavour. 2008 32(3): 117-121. doi: 10.1016/j.endeavour.2008.05.001

Ectomycorrhizal (ECM) fungi form a mutualistic symbiosis with tree roots and play key roles in forest ecosystems. In return for receiving nutrients and water from the soil via the roots, they receive carbohydrates as photosynthate from their host plants. As is the case for other soil fungal species, the composition of the ECM community is affected by both biotic and abiotic factors; these include climate changes, seasons, soil micro-site heterogeneity, soil and litter quality, host tree species and forest management. To describe in more detail the impact of environmental factors on community composition, long-term, year-round monitoring and a detailed spatial description of the community has to be carried out. However, analyses are very often hindered by a limited sample number and by the ephemeral or cryptic lifestyle of the fungi.

Over the last fifteen years, PCR-based molecular methods and DNA sequencing of nuclear and mitochondrial ribosomal DNA have been used routinely to identify mycorrhizal fungi. However, these methods are timeconsuming and are limited in the number of samples that can be treated in a realistic time frame. With automated molecular genotyping techniques, appropriate DNA databases and a better knowledge of internal transcribed spacer (ITS) variability within fungal species, identification of fungal taxa in environmental samples can now be expanded from the aforementioned methods to high-throughput molecular diagnostic tools, such as phylochips. So far, DNA arrays have been mainly used for genome-wide transcription profiling, but also for the identification of bacterial species from complex environmental samples or for the identification of a few genera of pathogenic fungi and Oomycetes.

Phylochips may comprise up to several thousand probes that target phylogenetic marker genes, such as 16S rRNA in bacteria or the ITS region in fungi. Phylochips have several advantages over traditional approaches, including higher specificity, cost efficiency, rapid identification and detection of target organisms, and the high numbers of samples throughput; therefore, they are increasingly used for the detection of bacterial and pathogenic fungi. In the ECM fungal ecology field, the first application of ribosomal DNA arrays was to develop a specific phylochip (on nylon membranes) to detect Suilloid fungi. Recently, this approach has also been used for truffle identification. No previous study has reported the construction and application of an ECM fungal phylochip to detect a large number of ECM fungal species that belong to various genera from environmental samples. This paper reports the first application of a custom ribosomal ITS phylochip to describe the community composition of ECM fungi on roots. The phylochip carried specific oligonucleotides for 95 fungal species that belong to 25 ECM fungal genera. The specificity of the oligonucleotides was evaluated using ITS amplicons of known reference species. The method was then used to describe ECM fungal communities that were obtained from 30-year-old spruce and beech plantations. The phylochip approach should be an attractive method for routine, accurate and reproducible monitoring of fungal species on specific sites, in which a high sample throughput is required.

Development and validation of an oligonucleotide microarray to characterise ectomycorrhizal fungal communities. BMC Microbiology 2009, 9: 241 doi:10.1186/1471-2180-9-241
In forest ecosystems, communities of ectomycorrhizal fungi (ECM) are influenced by biotic and abiotic factors. To understand their underlying dynamics, ECM communities have been surveyed with ribosomal DNA-based sequencing methods. However, most identification methods are both time-consuming and limited by the number of samples that can be treated in a realistic time frame. As a result of ongoing implementation, the array technique has gained throughput capacity in terms of the number of samples and the capacity for parallel identification of several species. Thus far, although phylochips (microarrays that are used to detect species) have been mostly developed to trace bacterial communities or groups of specific fungi, no phylochip has been developed to carry oligonucleotides for several ectomycorrhizal species that belong to different genera. We have constructed a custom ribosomal DNA phylochip to identify ECM fungi. Specific oligonucleotide probes were targeted to the nuclear internal transcribed spacer (ITS) regions from 95 fungal species belonging to 21 ECM fungal genera. The phylochip was first validated using PCR amplicons of reference species. Ninety-nine percent of the tested oligonucleotides generated positive hybridisation signals with their corresponding amplicons. Cross-hybridisation was mainly restricted at the genus level, particularly for Cortinarius and Lactarius species. The phylochip was subsequently tested with environmental samples that were composed of ECM fungal DNA from spruce and beech plantation fungal communities. The results were in concordance with the ITS sequencing of morphotypes and the ITS clone library sequencing results that were obtained using the same PCR products. To overcome cross-hybridisation problems, specific filter and evaluation strategies that used spot signal intensity were applied. Evaluation of the phylochip by hybridising environmental samples confirmed the possible application of this technology for detecting and monitoring ectomycorrhizal fungi at specific sites in a routine and reproducible manner.

Related:

• Plants, mycorrhizal fungi, and bacteria: a network of interactions
• Evolution of root nodule symbiosis with nitrogen-fixing bacteria

Amphibians such as frogs and toads are being driven to extinction by an aquatic fungus. This microbe, commonly called Bd, is spreading rapidly around the world and contributing to the decline in the biodiversity of the animals. In this article in Microbiology Today (pdf) Matthew Fisher believes that if control measures are not implemented, one-third of amphibian species could disappear:

Amphibians became the most ancient class of land-dwelling vertebrates when, 360 million years ago, Ichthyostega first hauled itself onto what was then Greenland. Since then, the amphibia have diversified into over 6,300 species that not only settled all continents except Antarctica, but also survived the catastrophic extinction events that overwhelmed their sister group, the dinosaurs. However, longevity of species is no guarantee of their future success; modern-day amphibians are suffering rates of extinction that far exceed those of any other class of vertebrates, including mammals and birds. Nearly one-third of amphibian species are threatened. The question of why amphibians are becoming extinct at these accelerated rates has puzzled scientists for three decades. While it is now clear that we are heading for a new anthropocene mass-extinction event as a consequence of human-driven planetary degradation, it has not been clear why this should be affecting amphibians more than other taxa. Further, many amphibian declines and extinctions were observed to occur in pristine environments that are relatively untouched by humans, such as rainforests and montane systems. A clue to the mystery came about when scientists working in Central America noted that the declines in amphibian biodiversity appeared to be occurring in a wave-like manner, with the initial losses being observed in Costa Rica, then spreading southwards towards the Panama Canal at rates of up to 43 km per year. These patterns of decline were suggestive of an epidemic, spreading pathogen, and in 1997 an international team of scientists discovered a new organism that appeared to be associated with many previously ‘enigmatic’ amphibian extinctions in two regions: Central America and north-eastern Australia. In 1999, the mycologist Joyce Longcore formally described this organism as new species of aquatic fungus and named it Batrachochytrium dendrobatidis.

Read more

Related:

• Chytrid fungus
• Salamander skin bacteria fight chytrid fungus
• Fungus fighter
• Frogs vs Bacteria

A mycorrhiza is a symbiotic association between a fungus and the roots of a plant. In a mycorrhizal association, the fungus may colonize the roots of a host plant, either intracellularly (arbuscular mycorrhizal fungi) or extracellularly (ectomycorrhizal fungi). These communities are important in plant growth and soil flora. This review focuses on interactions among plants, mycorrhizal fungi, and bacteria, testing the hypothesis whether mycorrhizas can be defined as tripartite associations. After summarizing the main biological features of mycorrhizas, it illustrates the different types of interaction occurring between mycorrhizal fungi and bacteria, from loosely associated microbes to endobacteria. It also discusses, in the context of nutritional strategies, the mechanisms that operate among members of the consortium and that often promote plant growth. Release of active molecules, including volatiles, and physical contact among the partners seem important for the establishment of the bacteria/mycorrhizal fungus/plant network. The potential involvement of quorum sensing and Type III secretion systems is discussed, even if the exact nature of the complex interspecies/interphylum interactions remains unclear.

Plants, mycorrhizal fungi, and bacteria: a network of interactions. Ann Rev Microbiol. 2009 63: 363-83

Related:

• Evolution of root nodule symbiosis with nitrogen-fixing bacteria

Mushroomexpert.com is a great website by Michael Kuo for anyone interested in identifying fungi, whether edible or poisonous! As well as Mushroom of the Month, the site also includes great sections on:

• Collecting for Study
• Making Spore Prints
• Descriptions & Journals
• Identifying Mushrooms
• Determining Odor and Taste
• Pronouncing Latin Names
• Testing Chemical Reactions
• Preserving Specimens
• Using a Microscope
• Mushroom Taxonomy
• Digital Photography Tips
• Scanning Mushrooms

Although they are beautiful, there is no simple way of knowing which fungi are safe to eat and which poisonous. Do not experiment with edible fungi, and get expert advice if you are in any doubt. Do not trust visual identification alone, whether from books or websites, as fungi vary tremendously in size, shape, colour and sometimes even in growing habitat.

Why not grow your own?

Related:

• All About Fungi: Part 1
• Saturday Cimema: How mushrooms can save the world
• Ancient fungus farmers
• Death of mycology – a career opportunity?

The ability of fungal pathogens to cause disease is dependent on the ability to grow within the human host environment. In general, the human host environment can be considered a slightly alkaline environment, and the ability of fungi to grow at this pH is essential for pathogenesis. The Rim101 signal transduction pathway is the primary pH sensing pathway described in the pathogenic fungi, and in Candida albicans, it is required for a variety of diseases. As more detailed analyses have been conducted studying pathogenesis at the molecular level, it has become clear that the Rim101 pathway, and pH responses in general, play an intimate role in pathogenesis beyond simply allowing the organism to grow.

The mammalian host environment can generally be considered to be at a pH slightly greater than neutral. The pH of human blood and tissues is 7.4 ± 0.1; the pH of murine blood and tissues is 7.2 ± 0.1. However, this represents a rather limited view of the host environment from a standpoint of pH, when mucosal and other sites exposed to the outside world are considered, dramatic variations from this slightly alkaline pH are found. One obvious example is the digestive track, which shows spatial variations in pH from extremely acidic (pH < 2.0) to more alkaline (pH > 8.0). Further, temporal changes in pH within a single site have been well documented, such as within the oral cavity following the fermentation of dietary sugar by endogenous microbes. The vaginal cavity is an acidic environment, pH 4; however, increases in vaginal pH occur in conjunction with menses. Thus, while fungi must be able to adapt to changes in pH within the host, most if not all pathogenic fungi must be able to thrive at neutral-alkaline pH within host tissues in order to cause disease. This paper discusses the signaling pathways required for growth and adaptation to host pH and the contributions these pathways make to pathogenesis.

Recent studies have found that the pathways responsible for sensing and responding to environmental pH have been co-opted for adaptation to the mammalian host. The pathogenic fungi, including C. albicans, C. neoformans, and A. nidulans, face physical and chemical stresses due to neutral-alkaline pH similarly to environmental fungi, such as S. cerevisiae, such as iron starvation. What has been somewhat surprising is that these pH sensing pathways also control expression of virulence traits not necessarily predicted to be associated with pH, including adhesion to host cells, tissue invasion, as well as other virulence attributes. This highlights the importance of continuing studies of these fundamental pH response pathways in pathogenic fungi in order to understand how these pathogens are adapted to the mammalian host and potentially identify new approaches for preventing or treating infections.

How human pathogenic fungi sense and adapt to pH: the link to virulence. Curr Opin Microbiol. 23 July 2009. doi:10.1016/j.mib.2009.05.006

Related:

• All About Fungi: Part 1
• All About Fungi: Infection

With football managers blaming the state of the pitch for the failure of their teams to win big matches, anything that improves the condition of turf can only be welcome. In this article in Microbiology Today (pdf) Alan Gange describes how mould diseases can devastate the sward and some work being done to exploit the power of beneficial microbes to act as “biostimulants” and improve the health of turf grasses:

April 2009: both Manchester United and Arsenal lose their FA Cup semi final matches at Wembley Stadium. Afterwards, both managers, Sir Alex Ferguson and Arsène Wenger, blamed the state of the Wembley pitch, Ferguson describing it as “spongy and dead”. A few days later, the head groundsman was sacked and the pitch re-laid at a cost approaching £100,000. This is the sixth time that the pitch has been replaced since it was first laid in 2006. Whether the pitch or the groundsman were in any way to blame for the fact that Everton scored more times in the penalty shoot-out than did United is, of course, debatable. However, these facts illustrate how important the quality of the playing surface is in sport and the vast sums of money that are spent to construct and maintain these surfaces. The highest quality turf surfaces are to be found on golf courses. There are over 2,500 golf courses in the UK and nearly 32,000 worldwide. The quality of the tees, fairways and greens is of the utmost importance and are always to blame when one’s approach shot hits the rough or that critical putt is missed! Sports turf is an unusual plant community, composed of just a few grass species. In British fairways and football pitches, the predominant grass is Lolium perenne (perennial rye). In our golf tees and greens, the desirable grasses are species of bents (Agrostis) and fescues (Festuca), with many cultivars of each species available. However, all turf systems become invaded by the weed grass Poa annua (annual meadow grass). Poa is undesirable, because it is nutrient and water hungry, susceptible to disease and provides an inferior quality playing surface. The control of Poa is the key to successful sports turf management.

Read more

Related:

• Toxins for microbial attack and plant defence
• Biological pest control of bark beetles

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

Ah, the tasty fruiting bodies of Basidiomycetes! (mushrooms to you ;-) The snag is that some are poisonous. Which ones? Well, that’s the risky bit. Taylor Lockwood is a biologist and photographer whose new DVD, The Good, the Bad, and the Deadly tries to teach you the basics about toxic mushrooms and their edible look-alikes.

Although they are beautiful, there is no simple way of knowing which fungi are safe to eat and which poisonous. Do not experiment with edible fungi, and get expert advice if you are in any doubt. Do not trust visual identification alone, whether from books or websites, as fungi vary tremendously in size, shape, colour and sometimes even in growing habitat.

Why not grow your own?

Related:

• All About Fungi: Part 1
• Saturday Cimema: How mushrooms can save the world
• Ancient fungus farmers
• Death of mycology – a career opportunity?