Prof Lynne Boddy - PhD, DSc
Foraging patterns, and nutrient uptake and translocation by fungal mycelia in soil
Funding bodies: NERC
External collaborators: Sarah C. Watkinson and Mark D. Fricker (University of Oxford), Peter Baldrian (Prague, Czech Republic)
MPhil Students: Alaa Alawi
Mycelial cord systems of Phanerochaete velutina ramifying across the floor of a mixed deciduous woodland.
Wood-decaying basidiomycete fungi are the major agents of decomposition in forests and hence crucial to nutrient cycling. On the forest floor, decay fungi that produce ‘root-like’ linear organs - termed cords, exhibit remarkable patterns of biomass and nutrient reallocation on locating new resources. They also deploy biomass differently and operate different search patterns depending on species, microclimatic regime, nutrient status of the system and surrounding soil.
We are seeking to understand how the balance between the metabolic requirements of the fungus and the need to conserve nutrients determines the patterns of mycelial system development, and the rates, routes and direction of nutrient (N, P, K) movement within mycelial systems, particularly the common woodland fungi Phanerochaete velutina, Phallus impudicus (stinkhorn), Hypholoma fasciculare (sulphur tuft) and Resinicium bicolor.
Image analysis and fractal geometry has revealed polarised growth of mycelial cord systems of P. velutina towards newly encountered resources even when these are relatively small. N, P, K status of both soil and the resource from which the fungus is growing critically affects foraging behaviour and fractal dimension, and the response of mycelia to newly encountered resources. Phosphorus is moved from existing to newly-encountered resources. However, local supply of phosphorus from soil adjacent to the new resource is up to 100 times greater than that moved in from elsewhere. In mature mycelial systems growing from a central resource with new resources added to the systems at different times, the rate of accumulation by outlying resources (translocated from a central resource) is dependent on how long they have been colonized. Amazingly, when mycelial connection between the central resource and many of the outlying resources is severed, the total phosphorus acquisition by the latter is not significantly affected! Resources no longer directly linked to the central resource receive increased quantities of phosphorus via and at the expense of directly connected resources, to which they are attached tangentially. Unravelling this dynamic interplay is ongoing.
Cords in tropical rainforest (photographed by Rory Bolton).
Translocation has been suggested as being via large vessel hyphae within mature mycelial cords, though direct evidence has not yet been presented. We are collaborating with Sarah Watkinson and Mark Fricker’s group, who are using photon counting scintillation imaging to elucidate translocation paths.
We are also seeking to understand the enzymology associated with obtaining nutrients from dead organic matter in nature. We have just begun to investigate spatial and temporal variation in enzyme activity in wood and soil associated with different regions of mycelium, with Peter Baldrian.
The complex mycelial networks that form in soil are constantly being remodelled in response to nutrient discovery and demand, changes in microclimate and destructive disturbance, e.g. by invertebrate grazers. We are currently investigating, mathematically, routes between different regions, resilience to damage, etc. using graph/network theory, in collaboration with Mark Fricker at Oxford.
Interactions between saprotrophic fungi
Funding bodies: NERC
BIOSI collaborators: Hilary J. Rogers, Carsten Müller and T. Hefin Jones
PhD students: Catherine Eyre, Timothy Rotheray, Jennifer Evans, Wafa Mufta, Nawal Elariebi
Interaction zone lines in decaying beech wood.
Somatic interactions between basidiomycetes occur both within colonized organic substrata and in soil/leaf litter during outgrowth in search of new wood resources.
The overall outcome of these interactions can be classified as deadlock - in which neither fungus gains headway over the other, or replacement - in which one fungus takes over the domain of the other. Intermediate situations also arise, where one fungus begins to replace another and is then halted, and where each fungus gains headway into the territory of the other in different regions of the interaction front.
Outcomes vary depending on species, site of interaction (i.e. in soil or wood etc.), microclimate and relative size of mycelia and resources occupied etc. Outcomes of interactions crucially affect fungal community development in wood, and distribution on the forest floor. Outcome of interactions can be affected by microclimate and resource status amongst others. Recently we (Tim Rotheray and T.Hefin Jones) have shown that soil invertebrate grazing alters mycelial interactions, dramatically.
Considerable morphological changes occur during interactions, but little is currently known about associated spatial (in the vicinity of interacting hyphae and elsewhere in the mycelium in support of the interaction front) and temporal changes in gene expression and enzyme production. We (Catherine Eyre, Peter Kille and Hilary J. Rogers) are using subtractive cDNA techniques to isolate expressed genes, and microarray technology to study their expression.
Many fungi produce volatile (VOCs) and diffusible organic compounds, and we have identified some of these and shown that during interactions these increase in quantity and additional VOCs are produced. These are part of the aggressive and defensive fungal combative mechanisms. However, our (Jennifer Evans, Tim Rotheray, T.Hefin Jones and C.T. Müller) ongoing work is revealing that some of these compounds also kill invertebrates and affect other fungi in the vicinity not directly interacting with the producers.
Saprotrophic cord-forming fungi seem to be remarkably conservative of the nutrients that they sequester, yet they must release them to enable continued primary production. We hypothesise that nutrient release largely occurs during interactions. This is currently being tested in model soil systems in the laboratory.
Interactions between saprotrophs, tree-root pathogens and mycorrhizal fungi
Funding bodies: NERC
External collaborators:Jonathan R. Leake (Sheffield)
Three functional groups of fungi play central roles in forest ecology: the biotrophic mycorrhizas, the necrotrophic pathogens and the saprotrophic wood and litter decomposers.
Through their effects on nutrient and carbon cycling, seedling establishment, and tree health and productivity these fungi are "keystone" organisms in forest ecosystems. Their mycelial systems dominate the microbial biomass of forest soils, but despite our awareness of the importance of each of these trophic groups of fungi, surprisingly little is known of the outcomes of interactions which occur between them when they meet each other in forest soil.
In our collaborative work with Jonathan Leake, we have refined and developed microcosm systems, previously used independently to study ectomycorrhizal and saprotrophic mycelial networks, to enable the study of interactions between these major groups of fungi in soil. In these microcosms intact mycorrhizal mycelial networks, growing in association with seedlings of their normal host plants in non-sterile natural soil, can be interacted with mycelia or spores of other microorganisms and their responses be non-invasively studied.
We employ a novel combination of time-sequence photography with digital image analysis and fractal geometry to enable effects on the patterns of growth and structure of the mycelial networks in soil to be quantified. At the same time the functioning of these interacting mycelial networks (in terms of nutrient and carbon uptake, translocation and allocation) can be determined by the use of radioactive tracers (14C and 33P) and non-destructive quantitative digital autoradiography. This enables study of the dynamic patterns of allocation of the radioisotope tracers simultaneously throughout whole mycelial networks.
Our recent studies have shown that when ectomycorrhizal mycelium encounters mycelium of saprotrophic wood- and litter-decomposing basidiomycetes in natural soil there is intense territorial conflict. Extension of mycelial cords of the aggressive saprotroph Phanerochaete velutina was halted by dense mycelium of the ectomycorrhizal fungus Paxillus involutus symbiotic with Betula pendula. The cords rapidly become truncated (low fractal dimension), and their apices turned brown and senesced. Deflection of growth of the saprotroph by the advancing ectomycorrhizal mycelium was dramatic, often restricting access to ectomycorrhiza-occupied regions.
On the other hand, the growth and allocation of host plant-derived carbon within the external mycorrhizal mycelium was markedly reduced in the part with most intimate contact with the saprotroph and, in some cases (e.g. Suillus bovinus vs P. velutina), the growth of the whole mycorrhizal mycelium was reduced.
Fungal invertebrate interactions
Funding bodies: NERC
BIOSI collaborators: T. Hefin Jones and Carsten Müller
PhD students: Timothy Rotheray
Folsomia candida grazing upon fungal mycelium in soil microcosms. Photograph courtesy of GM Tordoff.
Mycelial cord systems of Phanerochaete velutina ramifying across the floor of a mixed deciduous woodland.
Many invertebrates are attracted to fungal mycelia and fruit bodies, upon which they may graze and in which they may breed. The mycelial morphology and physiological/biochemical functioning of saprotrophic soil basidiomycetes can alter dramatically in the presence of nematodes, collembola and other invertebrates. Detailed studies of the effects of collembola on saprotrophic cord-forming fungi have revealed dramatic changes to mycelial patterns. These changes depend both on invertebrate grazer species and on fungal species. Collembola fecundity is also variable depending both on fungal species grazed and collembola species. As well as changes to fungal morphology, rate of wood decomposition was also affected by grazing on extra-resource mycelium.
Priorities are now to investigate effects of: (1) Grazing on nutrient release from mycelia; (2) Attraction of invertebrates to mycelia; (3) Grazing on mature, large mycelia.
Ecology of endangered woodland basidiomycetes
Funding bodies:Natural England, Forestry Commision
External collaborators:A. Martyn Ainsworth (Natural England)
BIOSI collaborator: Hilary J. Rogers
Post-docs: David Parfitt, Julie Hunt
PhD student: Martha Crockatt
Hericium coralloides in snow. Copyright Martyn Ainsworth.
Fungi in the genus Hericium (hedgehog fungi) are decomposers of wood and other plant litter. H. erinaceum is a UK BAP priority species, and H. coralloides appears even rarer, H. cirrhatum is also uncommon. Knowledge of the ecology of these species is essential to underpin future management and conservation; and their study will provide valuable information on the establishment of fungi at early stages of community development in large standing and fallen mature trees.
This project seeks to determine how these fungi establish in wood (e.g. latently in xylem, as wound parasites or as saprotrophs in non-functional sapwood), their basic ecophysiology, population biology and outcome of interaction with early and later-stage decomposer basidiomycetes and xylariaceous ascomycetes. In a similar project on Piptoporus quercinus – the rare oak polypore, we have found that populations appear to be inbred, sexual spores rarely germinate, but thick-walled asexual spores allow survival under adverse microclimate.
Having now developed specific PCR primers for these BAP fungi we are now in a position to discover whether they are really rare or whether they just produce visible fruit bodies infrequently.
Some mycorrhizal basidiomycetes are also rare or endangered, particularly stipitate hydnoids. These fungi are not currently culturable and fruit bodies of some species are often hard to distinguish from those of others. Before we can investigate their ecology we need to be able to identify them (both as fruit bodies and as mycelia). Currently we are using molecular approaches to separate taxa, and to construct species specific PCR primers.
Detection, distribution and identification of pioneer fungi latently present in functional sapwood
Funding bodies: NERC
BIOSI collaborator: Hilary J. Rogers
Post-docs: David Parfitt, Julie Hunt
Wood decomposition and fungal community development begins while branches are still in the canopy and trunks still standing. In at least eight angiosperm tree species, extensive (several to many metres) decay columns develop in less that one growing season. These decay columns are much longer than could be achieved by a fungus extending by mycelial growth from a single inoculum point. Instead, we suggest that fungal propagules are extensively but sparsely distributed throughout the sap stream, but do not develop overtly because of the high water content. Thus, if the high water content (low O2, low nutrient availability) of functional sapwood is removed then mycelia will develop from these propagules, will quickly meet and if they are the same genotype they will fuse and act as a single individual. This has been shown to be the case in all broadleaved trees tested (aspen, European beech, American beech, birch, ash, hazel, oak, sycamore) so far, though with some species genetic differences in mycelia resulted in long decay columns containing several or sometimes many different fungal individuals.
Many questions remain, and to attempt to answer these we need sensitive techniques. Thus, we are using PCR-based approaches to begin to test the following hypotheses, which is essential to understand fully the early stages of tree death and wood decay in the natural environment:
- Most woodland angiosperm trees contain wood decay fungi latently present within functional sapwood.
- Fungi latently present in one tree species have a much wider distribution in other species than has been shown to date by conventional methodologies, i.e. are not host-specific.
- Conversely fungal species only suspected to be latently present, are in fact present, despite not being found by culturing (e.g. Eutypa spinosa on beech).
- In addition to known and suspected latent fungi, there are many other fungal species, which have not been identified as such.
- The spatial distribution of latently present fungi varies between fungal species.
Fungus-bacteria interactions
BIOSI Collaborators: Eshwar Mahenthiralingam
External Collaborators: Wietse de Boer (Hetersen, The Netherlands) and Peter Baldrian ( Prague, Czech Republic)
Being ubiquitous, bacteria must frequently interact with fungal mycelia in nature, yet hitherto this has received very little attention. We have recently shown that saprotrophic mycelial cords growing in woodlands have a variety of bacteria closely associated with them, including members of the Burkholderiaceae. Laboratory soil microcosm studies have revealed that fungal mycelia have species specific effects on the adhering microbial community, and also that bacteria are rapidly suppressed during fungal colonization of wood.
Climate change effects on fungi
External Collaborators: Alan Gange (Royal Holloway, University of London), Ted Gange (Salisbury, Wiltshire), Tim Sparks (Centre for Ecology and Hydrology, Monks Wood), Hävard Kauserud (University of Oslo, Norway)
Hypholoma fasciculare in snow. Copyright Martyn Ainsworth.
Fungi provide vital ecosystem services through decomposition, nutrient cycling and soil aggregation, yet they have been ignored during consideration of ecosystem responses to global change. We (A. Gange, E. Gange & T. Sparks) are analysing a data set of over 52,000 individual fungal fruiting records, from nearly 1,400 localities, in southern England during 1950-2005. From information on 315 autumnal fruiting species, each recorded in at least 20 y, we have revealed that the first fruiting date averaged across all species has become significantly earlier, while average last fruiting date has become significantly later, resulting in the whole fruiting season now being 75d – double that in the 1950’s. Earlier fruiting is correlated with elevated August temperatures and later fruiting with both elevated August temperature and October rainfall since 1975. Moreover, many fungi, especially wood decayers, now also fruit in spring as well as autumn. These changes are not only important in terms of extending the duration of production of fungal sexual spores, but more significantly fungi are now active over much longer periods, hence effecting decomposition.
There are differences depending on ecological group. Perhaps most importantly fruiting period of fungi that form ectomycorrhizas (EM) differs depending on whether fungi are associated with deciduous or coniferous trees. Eight (of 11) EM fungi that have both deciduous and coniferous hosts showed a delay in last fruiting date in the former but not in the latter, indicating that there have been changes in the temporal allocation of nutrients to deciduous tree toots, but not to coniferous roots.
We are now extending our analyses to: (1) look more closely at different ecological groups of fungi; (2) determine whether ‘host preferences’ have changed; (3) determine whether there are changes in patterns of fruiting of fungi whose ecology is closely linked, e.g. host/parasite and predecessor/successors in community development. Further, we are joining with Norwegian mycologists (Håvard.Kauserud) to investigate effects of global changes on fungi across larger geographic areas – UK and Norway. Also, changes in the phenology of fruiting is likely to have large effects on the organisms which feed upon them, and we (A.Gange) are just starting to investigate this.
Application of artificial neural networks to biological identification and ecological modelling
External collaborators: Colin W Morris (University of Glamorgan), Michele Denise (Oceanography Centre, Marseille)
It is now well appreciated that artificial neural networks (ANNs) are eminently suitable for biological applications, where data are often very noisy or exhibit complex underlying relationships. There are many different types, but for identification Multilayer perceptrons (MLPs; back propagation ANNs) are most commonly used.
We have, however, shown that other networks may often be superior, e.g. Radial basis function (RBF) ANNs are easier to optimize and train more rapidly. Importantly, when used for identification, RBF ANNs are able to deal with novel taxa either by rejecting them as unknown or by retraining to allow for them. Where it is necessary to incorporate these new taxa, retraining a neural network may be time consuming and/or impossible. Also, in some situations there is the need only to look for the presence or absence of a few taxa against a community of many hundreds.
Further, biological problems are often unbounded, so we are developing strongly partitioned RBF networks and Support Vector Machines (SVMs) for discrimination of single species against a background of N other species. The latter are a type of network developed for discriminating only two groupings, and preliminary studies indicate that they may be more effective than RBFs at discrimination of single species against a background of N other species.
Much of our work centres around identification of phytoplankton from flow cytometry data. Cells are analysed at a rate of about 10 3 cells sec -1. We have developed a neural network and clustering software package to analyse these data (and which is broadly applicable to other areas)
Research into clustering, self-organising maps, and obtaining training data is ongoing, and we are getting closer to being able to analyse field samples at sea in near real time.
Grants
- NERC
Detection, distribution and identification of pioneer fungi latently present in functional sapwood. - NERC
Resource-related redistribution of nitrogen in woodland fungi (with Sarah Watkinson, Oxford). - NERC
Attraction of invertebrates to zones of interactions between basidiomycete mycelia.
Collaborations
Dr A. Martyn Ainsworth (Natural England)
"Ecology and taxonomy of rare species".
Dr Peter Baldrian (Institute of Microbiology of the ASCR, Czech Republic) “Interactions between bacteria and basidiomycetes” and Extracellular enzyme production by mycelia in soil”.
Dr Wietse de Boer (NIOO-KNAW Centre for Terrestrial Ecology, Netherlands)
“Interactions between bacteria and basidiomycetes”.
Dr Juliet Frankland (CEH Lancaster)
"Distribution of woodland fungi using molecular and traditional approaches".
Dr Mark D. Fricker (University of Oxford)
“Networking of fungal mycelia”.
Professor Alan Gange (Royal Holloway, London) “Effects of global change on fungal fruiting”.
Dr Christian Kampichler (Free University of Berlin)
"Interactions between saprotrophic cord-forming fungi and soil invertebrates".
Dr Håvard Kauserud (University of Oslo) “Effects of global change on fungal fruiting”.
Dr Jonathan Leake (University of Sheffield)
"Interactions between ectomycorrhizal, saprotrophic and root-pathogenic fungal mycelia".
Mr Colin Morris (University of Glamorgan)
"Application of artificial neural networks to biological data analysis" and "image processing for biological identification".
Dr Sarah C. Watkinson (University of Oxford)
"Nutrient translocation in mycelial cords".
Affiliated Staff: 2000 - present
2005-present
Effect of cold stress and grazing on fungal mycelia
Arnaud Autret
2000-2003
Analysis of phytoplankton data using support vector Machines (jointly with Colin Morris, based at the University of Glamorgan).
Martha Crockatt
2004-present
Ecology of rare species of Hericium and Piptoporus quercinus
Damian Donnelly
1997-2005
Interactions between ectomycorrhizal mycelium, saprotrophs and tree-root pathogens in forest soil: impact on tree seedling establishment and mycorrhizal functioning (jointly with Jonathan Leake, University of Sheffield).
2006-present
Gene expression and production of fungal volatiles during interspecific interactions (jointly with Hilary J. Rogers and Carsten Müller).
2003-present
Gene expression during mycelial interactions
Sam Hardy
2000
Cluster analysis of phytoplankton data (based at the University of Glamorgan with Colin Morris).
Melanie Harris
1997-2004
Cultured cord-forming fungi.
Jacob Heilman-Clausen
2000
Interactions between late-stage decay fungi.
Julie Hunt
1999-2003,2007
Fungal diversity in grasslands using molecular techniques (jointly with Peter Randerson, Hilary Rogers, Jon Winder (Gwent Wildlife Trust).
Juliet Hynes (née Preston-Mafham)
2000-2006
Functional diversity in grasslands (jointly with Peter Randerson, Hilary Rogers, Jon Winder (Gwent Wildlife Trust).
Nutrient translocation in saprotrophic cord-forming basidiomycetes (jointly with Sarah Watkinson and Mark Fricker, University of Oxford).
Attraction of invertebrates to interacting basidiomycete mycelia (jointly with T. Hefin Jones and Carsten Müller, Cardiff University).
David Parfitt
2005-present
Locating latent fungi in functional sapwood of trees, and detection of rare fungi.
2007-present
Gene expression during mycelial interactions (jointly with Hilary J. Rogers and Carsten Müller)
2007-present
Production of volatile organic compounds during mycelial interactions (jointly with Carsten Müller)
2004-present
Effect of collembola grazing on mycelial interactions
Deborah Simpson
2005
Discrimination of stipitate hydnoid fungi
Laurienne Tibbles
1999-2004
Attraction of flies to basidiomycetes (jointly with Mark Jervis, Carsten Müller & Phil White (HRI Wellesbourne).
George Tordoff
2002-2006
Effects of collembola grazing on mycelial foraging.
Paul Wald
2000-2004
Ecology of rare species of Hericium (jointly with Martyn Ainsworth (Fungus Forum), Carl Borges (English Nature).
John Wells
1995-2002
Nutrient translocation and release by saprotrophic cord-forming fungi.
Elizabeth Wilberforce
1999-2003
Distribution of Fusarium in managed and unmanaged Grasslands (jointly with Gareth Griffith, based at Aberystwyth University).
Malcolm Wilkins
1997-2000
Identification of phytoplankton by artificial neural networks.
Ab Jamil Zakari
1996-2000
Ecology of cord-forming fungi.