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The adaptive radiation of Pseudomonas fluorescens SBW25 populations in static liquid microcosms results in the appearance of the biofilm–forming Wrinkly Spreader. This adaptive mutant is able to colonise the high O2-rich region at the top of the liquid column established by the metabolic activity of earlier wild-type colonists, and by doing so, enjoys a significant fitness advantage over non-biofilm–forming competitors including the ancestral Pf. SBW25. Although the underlying molecular biology and evolutionary ecology of the Wrinkly Spreader is well understood, we have recently questioned the need for expensive biofilm–formation to colonise the air-liquid (A-L) interface, as O2-directed flagella-mediated swimming (aerotaxis) should be sufficient to maintain cells in this region. Our investigations show that swimming can overcome displacement by Brownian diffusion and microcurrents within the liquid column. However, it is not sufficient to explain the high levels of enrichment at the A-Linterface shown by Wrinkly Spreader cells. A comparison of the liquid surface tension of wild-type and Wrinkly Spreader cultures, supernatants, and washed cells, suggests that the Wrinkly Spreader produces a surface-active compound weakly associated with the cell which helps penetration of the A-L interface and allows cells to remain in the high-O2 region without further expenditure of energy. Our results suggest that this penetration is key to the following biofilm–formation which supports higher populations at the A-L interface and that this explains the adaptive advantage of the Wrinkly Spreader.

The fungi comprise a separate kingdom of life and epitomise the indeterminate growth form. Very little is known about the factors that influence the nature of fungal diversity and the link between individual behaviour and the structure and function of fungal communities is particularly poorly understood. Here, we present a theoretical framework that is capable of elucidating this link. An individual-based model for fungal community dynamics is introduced that has been developed from a physiologically based model for the fungal phenotype. The model is used to explore the role of individual interactions, the production of an external inhibitor field and the quality of the external environment on the structure and diversity of the resulting community. We show that traits relating to growth rate, autophagic behaviour and the production of inhibitors are key in influencing the success of a particular genotype in a community. The species richness increases with the amount of available resource. This is the first model of fungal community dynamics that introduces the concept of a biomass-based abundance distribution function that can be described by the log-normal form which typically corresponds to communities in equilibrium. The species abundance curve was stable to changes in the relative location of inocula, although the ranked abundance of the individuals was not. We present the first attempt to identify the traits that affect the form of that curve. Future studies should examine the role of environmental heterogeneity and spore dispersal.

This contribution, based on a Special Interest Group session held during IMC9, focuses on physiological based models of filamentous fungal colony growth and interactions. Fungi are known to be an important component of ecosystems, in terms of colony dynamics and interactions within and between trophic levels. We outline some of the essential components necessary to develop a fungal ecology: a mechanistic model of fungal colony growth and interactions, where observed behaviour can be linked to underlying function; a model of how fungi can cooperate at larger scales; and novel techniques for both exploring quantitatively the scales at which fungi operate; and addressing the computational challenges arising from this highly detailed quantification. We also propose a novel application area for fungi which may provide alternate routes for supporting scientific study of colony behaviour. This synthesis offers new potential to explore fungal community dynamics and the impact on ecosystem functioning.

Using an existing fungal growth model that captures the physiological processes of vegetative growth and development of a fungal colony, and in particular incorporates, for the first time, a recycling of biomass mechanism, we explore the effects of recycling in various environmental contexts. Here we test whether resource density thresholds exist, below which finite colony expansion occurs, in three dimensions based on the number of randomly removed resource sites. We then test the effect of recycling on resource density thresholds. Modelled soil structure, derived from experiments, is combined with the fungal growth model. The effect of recycling on foraging efficiency is investigated for resource distributed homogeneously and heterogeneously throughout the modelled soil structure. The simulated results show that resource density thresholds do exist in three dimensions and that the recycling mechanism decreases the threshold value. Our results indicate that recycling promotes persistence and a recycling mechanism is crucial for those fungi that reside in a resource patchy and limited environment.

The role of fungi in shaping ecosystems is well evidenced and there is growing recognition of their importance among scientists and the general public. Establishing and separating the role of key local (soil chemical, biological, and physical properties) and global (climate, dispersal limitation) drivers in fungal community structure and functioning is currently a source of frustration to mycologists. The quest to determine niche processes and environmental characteristics shaping fungal community structure, known to be important for plant and animal communities, is proving difficult, resulting in the acknowledgment that niche neutral processes (climate, dispersal limitations) may dominate. The search for predictable patterns in fungal community structure may have been restricted as the "appropriate" scales at which to measure community structure and characterize the environment have not been fully determined yet, and the focus on taxonomy makes it difficult to link environmental characteristics to fungal traits. While key determinants of microbial community composition have been uncovered for some functional groups, the differential response of functional groups is largely unknown. Before we can truly understand what drives the development of microbial community structure, an understanding of the autecology of major fungal taxa and how they interact with their immediate environment (from the micro- up to kilometer scale) is urgently needed. Furthermore, key information and empirical data is missing at the microscale due to experimental difficulties in mapping this heterogeneous and opaque environment. We therefore present a framework that would help generate this much-needed empirical data and information at the microscale, together with modeling approaches to link the spatial and temporal scales. The latter is important as we propose that there is much to be gained by linking our understanding of fungal community responses across scales, in order to develop species and community-environment-function predictive models.

Polyaromatic hydrocarbons (PAHs) present a challenge to bioremediation because they are hydrophobic, thus influencing the water availability and repellency of soil. The addition of different concentrations of the PAH, anthracene, showed it to induce moderate levels of repellency. We investigated the efficacy of three basidiomycete fungal species on improving the wettability of soil by reducing repellency caused by contamination of soil with 7 ppm anthracene. A microcosm system was used that enabled determination of the impact of fungi on wettability at three locations down a 30 mm deep repacked soil core. Before incubation with fungi, the contaminated soil had a repellency of R = 3.12 ± 0.08 (s.e.). After 28 days incubation, Coriolus versicolor caused a significant reduction in repellency to R = 1.79 ± 0.35 (P < 0.001) for the top section of the soil in a microcosm. Phanerochaete chrysosporium and Phlebia radiata did not influence repellency. None of the fungi had an effect at 20 mm depth.

Fungi are thought to affect soil slaking resistance and bypass flow by inducing low levels of water repellency on soil pore surfaces. This was investigated in a laboratory study on arable field soil by selectively inhibiting fungi and/or bacteria with biocides and adding ground barley shoot substrate (2 mg g − 1 soil) to half of the samples. The fungicide Captan and the bactericide Bronopol were used alone and in combination at a concentration of 1 mg g − 1 , resulting in different levels of microbial respiration and active fungal biomass (ergosterol) after 8 days of incubation. Repellency was measured on the surface and on an internal fracture of the soil cores. Wet–dry cycles were applied to some samples to investigate the persistence of water repellency. Substrate addition caused the greatest increase to water repellency after incubation, suggesting that microbial activity affects repellency. The drying surface of the soil had greater repellency than the internal fracture surface. No clear trends could be found between the level of fungal biomass and repellency; this was most evident in soils treated with bactericide and substrate. Despite having the highest fungal biomass ( P P > 0.05). Wetting and drying cycles caused significant changes to repellency and structure. Ethanol sorptivity indicates pore structure and its value changed least in the soil that had the greatest fungal biomass (i.e. bactericide treated with substrate), indicating that fungal populations protected soil structures from slaking stresses. Given the poor relationship found between fungal biomass and water repellency, these results suggest that other microbial or physico-chemical processes were involved. Our findings do not support previous research that reported a close link between water repellency and fungal biomass. However, given the strong evidence of fungal-produced hydrophobins and the close links between soil structural stability, repellency and fungal biomass found in field studies, the effectiveness of the biocides used in this study or the influence of different fungal species could have influenced the results and thus requires greater investigation.

Fungi are one of the most important and widespread components of the biosphere, and are essential for the growth of over 90% of all vascular plants. Although they are a separate kingdom of life, we know relatively little about the origins of their ubiquitous existence. This reflects a wider ignorance arising from their status as indeterminate organisms epitomized by extreme phenotypic plasticity that is essential for survival in complex environments. Here we show that the fungal phenotype may have its origins in the defining characteristic of indeterminate organisms, namely their ability to recycle locally immobilized internal resources into a mobilized form capable of being directed to new internal sinks. We show that phenotype can be modelled as an emergent phenomenon resulting from the interplay between simple local processes governing uptake and remobilization of internal resources, and macroscopic processes associated with their transport. Observed complex growth forms are reproduced and the sensitive dependence of phenotype on environmental context may be understood in terms of nonlinearities associated with regulation of the recycling apparatus.

The role of fungi in shaping ecosystems is well evidenced and there is growing recognition of their importance among scientists and the general public. Establishing and separating the role of key local (soil chemical, biological, and physical properties) and global (climate, dispersal limitation) drivers in fungal community structure and functioning is currently a source of frustration to mycologists. The quest to determine niche processes and environmental characteristics shaping fungal community structure, known to be important for plant and animal communities, is proving difficult, resulting in the acknowledgment that niche neutral processes (climate, dispersal limitations) may dominate. The search for predictable patterns in fungal community structure may have been restricted as the "appropriate" scales at which to measure community structure and characterize the environment have not been fully determined yet, and the focus on taxonomy makes it difficult to link environmental characteristics to fungal traits. While key determinants of microbial community composition have been uncovered for some functional groups, the differential response of functional groups is largely unknown. Before we can truly understand what drives the development of microbial community structure, an understanding of the autecology of major fungal taxa and how they interact with their immediate environment (from the micro- up to kilometer scale) is urgently needed. Furthermore, key information and empirical data is missing at the microscale due to experimental difficulties in mapping this heterogeneous and opaque environment. We therefore present a framework that would help generate this much-needed empirical data and information at the microscale, together with modeling approaches to link the spatial and temporal scales. The latter is important as we propose that there is much to be gained by linking our understanding of fungal community responses across scales, in order to develop species and community-environment-function predictive models.

Relationships between Serpula lacrymans and S. himantioides isolates of ‘wild’ Himalayan woodland and building (European and Australian) origin were examined using RAPD-PCR and ITS rDNA sequence comparison. GelCompar analysis of the genetic fingerprints of eighteen isolates using four RAPD-primer combinations clearly distinguished S. lacrymans and S. himantioides. Little intraspecific variation was observed in S. lacrymans (including isolates of Himalayan woodland origin), relative to S. himantioides. Despite previously reported differences in growth rates and decay capabilities of ‘wild’ Himalayan woodland S. lacrymans isolates and those from buildings, RAPD fingerprints and ITS sequences indicated they were genetically similar. Interspecific ITS sequence polymorphisms were consistent with other studies and clearly demonstrated S. himantioides and S. lacrymans were distinct taxa. Evolutionary questions regarding the origins of S. lacrymans are discussed.

A stochastic cellular automaton for modelling the dynamics of a two-species fungal microcosm is presented. The state of each cell in the automaton depends on the state of a predefined neighbourhood via a set of conditional probabilities derived from experiments conducted on pairwise combinations of species. The model is tested by detailed comparison with larger-scale experimental microcosms. By employing different hypotheses which relate the pairwise data to the conditional probabilities in the model, the nature of the local and non-local interactions in the community is explored. The hypothesis that the large-scale dynamics are a consequence of independent interactions between species in a local neighbourhood can be excluded at the 5% significance level. The form of the interdependencies is determined and it is shown that the outcome of the interactions at the local neighbourhood-scale depends on the community-scale patterning of individuals. The dynamics of the microcosm are therefore an emergent property of the system of interacting mycelia that cannot be deduced from a study of the components in isolation.

The community dynamics of two- and three-fungal species interactions derived for a tessellated agar model system are described. The microcosm allows for the varied prescription of: (1) the number of fungal species interacting; (2) the spatial configuration (patchiness) of the distribution of individuals; (3) the magnitude of scale of spatial occupation by different fungal individuals; and (4) the operation of antagonistic mechanisms based on contact or longer range diffusible components. Stepwise logistic regressions for two-species interactions are used to inform the design of the multi-species interaction tessellations. The model prescribes and investigates complex parameters, such as spatiotemporal heterogeneity and microcosm scale (e.g. population patchiness and crossing times). Data are quantified as proportion, interface class and state transition class of viable fungal species. Spatiotemporal heterogeneity is represented using a novel application of principal component analysis which shows good intuitive agreement with visual assessment of the interaction outcome patterns, and allows effective comparison of the data as a whole. The model demonstrates the influence of the complex and coordinated behaviour of fungal mycelia on community development: interaction outcome of three-species interactions cannot be directly extrapolated from the relevant binary component interactions; interaction outcomes of the multi-species tessellations appears to be neither random nor fully deterministic; a degree of stochasticity is apparent in all tessellation arrangements; the smaller scale tessellations produce more consistent interaction outcome results, probably because experimental scale affects the duration of transient behaviour; and different initial spatial configurations of inoculum (irrespective of inoculum quantity or proportion) influence community development and reproducibility.

We report the first successful culturing and confirmation of identity (via sodium dodecyl sulphate polyacrylamide gel electrophoresis, SDS–PAGE) of Serpula lacrymans (the dry rot fungus) derived from basidiomes and mycelia growing in the ‘wild’. The fungus was found growing on well decayed coniferous wood within the Narkanda region of the Western Himalayas at between 2800 and 3100 m above sea level (a.s.l.). The ‘wild’ habitat of the fungus is described, as is the isolation of Serpula himantioides also found in these regions. Temperature, osmotic potential, initial pH and air-current influenced the average colony extension rate of ‘wild’ and a selection of building isolates on 2% malt extract agar. The ‘wild’ and building isolates behaved as two separate cohorts; the ‘wild’ isolates appeared to be less affected by extremes of temperature, whereas building isolates extended more rapidly at the moderate microenvironmental regimes.

The built environment is the product of complex interactions between the external environment, the building materials, the design, the contents, the activities in the building, and the occupants, both human and commensal. To try to manipulate any one of these factors without consideration for the effects on the others can be at worst ineffective, and at best, inefficient and costly. Timber decay organisms cannot be eradicated even by the most Draconian pesticide treatments. However, they can flourish in buildings only if the environmental conditions are suitable. Even with the loss of traditional skills and the complexities introduced into building by new materials and uses, these conditions can easily be avoided with a little thought and scientific understanding. Indeed, new materials and techniques can often be used to advantage if their properties are analyzed as potential environmental controls. This more rational approach to the treatment of timber decay is really good building practice, which independent surveyors and their scientific consultants should promote in the interest of sound building and public health.

The dry-rot fungus Serpula lacrymans has a maximum growth temperature of 28°C which is an unusual feature in comparison to other Serpula species. This has led to the investigation of S. lacrymans sensitivity to higher temperature regimes with respect to increased thermotolerance and the production of heat-shock proteins (hsps). The strategy employed in this study has been to correlate protein synthesis with thermotolerance and the heat-shock response. Protein profiles generated by one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (1D SDS-PAGE) of fungal colonies exposed to optimal, supraoptimal (sublethal) and lethal temperatures were probed with rabbit anti-GRoEL serum for the presence of the 60-kDa heat-shock protein. The preliminary findings indicate that an important heat-shock protein, a GRoEL analogue, is produced by S. lacrymans and that this basidiomycete undergoes the classic heat-shock response.

The optimum (22 and 25 °C respectively), supraoptimal (sublethal) and the minimum lethal temperature regimes for Serpula lacrymans and S. himantioides were established. Exposure of S. lacrymans and S. himantioides to supraoptimal temperature regimes induced a transient tolerance to subsequent, normally lethal heat treatments (40° for 2 and 3 h respectively). An optimum thermotolerance training ‘window’ of 28° for 24 h and 25° for 48 h was appropriate for S. lacrymans , whereas thermotolerance training improved at 28 and 30° with increasing period (1–72 h) in the case of S. himantioides . The reported thermosensitivity of S. lacrymans compared to S. himantioides appears to be reflected in the contrasting thermotolerance-training profiles presented here, and may contribute to the general absence of S. lacrymans from the wild in temperate Europe.

Les hommes construisent leurs habitations depuis 20 000 ans seulement, alors que les champignons destructeurs du bois existent depuis environ 300 millions d'annees. Il est donc probable, estiment les auteurs, que le champignon du bois dont souffrent actuellement les bâtiments aient evolue dans la nature en utilisant le bois comme source nutritive. Cet article parle de la decouverte de champignon du bois sauvage dans l'Himalaya, et suggere ses voies probables de propagation et domestication en Europe. Il devrait etre possible, grâce a l'elaboration de strategies non chimiques, de mieux lutter contre ce parasite.

There have been a number of advances in the understanding of the physiology of the dry rot fungus, Serpula lacrymans, in the last decade. Specifically, studies on the natural origins of the fungus, morphogenesis, toxicant tolerance, environmental sensitivity, nitrogen metabolism, utilization of non-woody materials and biological control have all contributed to this understanding and each is discussed in relation to potential control strategies for the future. In addition, molecular studies involving detection, monitoring of speciation and the heat shock response of Serpula lacrymans have provided new insights into an organism which is uniquely destructive in the built environment.

SUMMARY: The effects of different gaseous regimes on the growth rate and extracellular enzyme location in vitro of colonies of Phlebia radiata, Phlebia rufa and Coriolus versicolor are reported. The two Phlebia species showed similar growth, extracellular enzyme and pH responses to gaseous composition (N2, O2 and CO2), but the responses of C. versicolor differed. Whilst maximum extension rates were obtained for all species under atmospheric gaseous composition, maximum biomass production occurred at 5% (v/v) O2 with 20% (v/v) CO2 for the Phlebia species and at 5% O2 with 60% CO2 for C. versicolor. The Phlebia species had a coenocytic margin (5–6 mm width) under atmospheric conditions, which increased in width with increasing percentage of CO2. Laccase and peroxidase activity were present throughout the septate region, but not in the coenocytic zone. With C. versicolor laccase and peroxidase activities appeared throughout the colony, but were more intense in the peripheral region, under all gaseous regimes. A laser densitometer, normally used to visualize proteins on electrophoresis strips, was used to estimate profiles of biomass and laccase-α-naphthol activity within colonies. Surface pH changed little in colonies of C. versicolor but dropped by over 1 pH unit from the margin inwards with the Phlebia species. The significance of these results is discussed in terms of ecological strategy and developmental versatility.

Confronted colonies of Phlebia radiata, P. rufa, Coriolus versicolor, Stereum hirsutum, Phanerochaete velutina and Hypholoma fasciculare showed spatially and temporally heterogeneous patterns of loccase-α-naphthol and peroxidase activities. These activities were coincident in axenic cultures. but were not always so during interaction. Confrontation between species resulted in induction of phenoloxidase activities, even within coenocytic colony regions of Phlebia species which were normally void of such activities in axenic culture. These events resulted in restriction of C. versicolor growth during interaction with P. rufa.

Consequences of initial spatial organisation of model fungal communities upon their spatio-temporal development were investigated. Dynamics of prescribed two- and three-species 'communities' developing on tessellated agar tile model systems were analysed in terms of literal maps, principal component analyses, or as the proportion of species extant within tiles. It was established that for two-species interactions of equal patch size, large-scale (i.e. many constituent tiles) behaviour could be extrapolated from the relevant small-scale (i.e. pairs of tiles) interactions. However, relative patch sizes (scale) of species within tessellations influenced the times taken by individuals to colonise tiles and, hence, temporal behaviour of the system. Outcome of arrangements involving three species of equal patch size and inoculum potential, and prescribed with different mixing patterns, could not be directly extrapolated by reference to the outcome of pair-wise interactions between constituent species. Three-species arrangements attempt to limit assembly of lateral aggregates of individuals (patch size) and hence any effects of tile colonisation times, so as to reveal effects of nearest neighbour context within the complex community. Such arrangements indicate that spatial configuration of inoculum influences community development and reproducibility. They also suggest that spatial distribution of species affects persistence of individuals, which would otherwise be expected to be eliminated from the system. Two-species interactions appeared generally more reproducible than those comprising three species, and the sensitivity of fungal community development to temperature was not solely associated with influence on colony extension rate.

Indeterminate organisms have received comparatively little attention in theoretical ecology and still there is much to be understood about the origins and consequences of community structure. The fungi comprise an entire kingdom of life and epitomize the indeterminate growth form. While interactions play a significant role in shaping the community structure of indeterminate organisms, to date most of our knowledge relating to fungi comes from observing interaction outcomes between two species in two-dimensional arena experiments. Interactions in the natural environment are more complex and further insight will benefit from a closer integration of theory and experiment. This requires a modelling framework capable of linking genotype and environment to community structure and function. Towards this, we present a theoretical model that replicates observed interaction outcomes between fungal colonies. The hypotheses underlying the model propose that interaction outcome is an emergent consequence of simple and highly localized processes governing rates of uptake and remobilization of resources, the metabolic cost of production of antagonistic compounds and non-localized transport of internal resources. The model may be used to study systems of many interacting colonies and so provides a platform upon which the links between individual-scale behaviour and community-scale function in complex environments can be built.

The use of OFMSW for biogas and compost production is considered as a sustainable strategy in saving valuable landfill space while producing valuable product for soil application. This study examines the effects of anaerobic and aerobic post-treatment of OFMSW on the stability of anaerobic digestate and compost and soil quality using seed germination tests. Anaerobic digestion of OFMSW was carried out for fifteen days after which the residual anaerobic digestate was subjected to aerobic post-treatment for seventy days. Seed germination tests showed that fresh feedstock and digestates collected during anaerobic digestion and during the early stages of aerobic post-treatment were phytotoxic. However, phytotoxic effects were not observed in soils amended with the fully stabilised anaerobic digestate compost, ADC. It was also found that seed germination increases with dilution and incubation time, suggesting that lower soil application rates and longer lag periods between soil application of ADC and planting can reduce the amount of biodegradable organics in the ADC, thus enhancing the benefits of ADC as soil amendment.

Timber is still a most useful structural material, and is often a major component in historic buildings. It has many structural and aesthetic properties, as well as being an energy-efficient and re...

Molecular and morphological parameters of Serpula lacrymans isolates from various sites in the built environment in Europe and Australia were compared to similar parameters of ‘wild’ isolates from India, the Sumava Mountains (Czech Republic) and Mount Shasta (USA). The Indian, Czech Republic and all of the building isolates bar one showed identity in both molecular and morphological features. The Australian and the USA isolates (BF-050 and USA’94 respectively) showed specific morphological differences and could be separated on the basis of randomly amplified polymorphic deoxyribonucleic acid polymerase chain reaction (RAPD PCR) with the USA isolate being least closely related to the S. lacrymans type strain of FPRL12C. ITS sequence data revealed two base differences between FPRL12C and BF-050 in the 673 sequenced, nine differences between FPRL12C and USA’94 and 16 differences between USA’94 and the closely related organism Serpula himantioides. The possible evolutionary relationships between the various isolates are discussed along with suggestions for the origin of S. lacrymans as a scourge of the built environment in many temperate areas of the world. > 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

A microcosm system is described which permits assessment of the progressive growth of filamentous fungi through soil. We report on its application to measure the effects of Coriolus versicolor and Phanerochaete chrysosporium upon the sorptivity and water repellence of a mineral soil, measured using a miniature infiltration device. Both fungal species caused moderate sub-critical repellence. Since the pore structure was unaffected, the repellence was probably due to hydrophobic substances of fungal origin. This is the first report of changes in soil repellence caused by the growth of potential xenobiotic bioremediating fungi. The potential consequences are discussed.

Timber represents a rich source of potential nutrients for a wide variety of macro-organisms (e.g. insects and marine borers) and micro-organisms (notably fungi and bacteria). Timber is susceptible to these agents during both production and in-service use, though degradation by them is not always inevitable and is usually associated with misuse or inappropriate use. However when timber is to be used in some types of environment, notably where relatively high levels of moisture are available, protective systems are necessary to prevent decay. Currently such systems often rely on the use of chemical treatments but alternative strategies are under development at a number of centres and these come under the headings of environmental control, biological control and the use of natural products as wood preservatives. This chapter will explore each of these systems in the context of the control of the dry rot fungus Serpula lacrymans,a wood decay basidiomycete which causes severe damage to wooden elements of buildings in temperate areas and whose natural home appears to be the Himalayan foothills. Discussion of these natural processes and products will be preceded by a description of the current wood preservation scenario and of the pressures which are bringing about change in the associated industry.