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Fungal Ecology
Abstract
Saprophytic fungi have evolved to exploit every possible habitat on earth, wherever degradable organic matter exists. Fungi occupy terrestrial and aquatic environments (both marine and freshwater) in tropical, temperate and polar regions. There are fungi characteristic of forests, pastures, heaths and bogs, and within these habitats fungi form distinct but overlapping ecological groups associated with various resources. Some exploit the leanest of resources and grow in the most inhospitable of environments such as the microcolonial ascomycetes of rock surfaces in arid deserts (Staley, Palmer and Adams, 1982; Palmer et al., 1987).
A través de un Sistema de Información geográfica (SIG) y con datos de suelo, clima, vegetación etc.. se establece el potencial micológico de toda la provincia de Guadalajara y se relaciona con sus posibilidades de aprovechamiento turístico así como las medidas necesarias para desarrollar el sector sin poner en peligro la conservación de las especies
Coprophilous species of Ascobolus and Saccobolus from Brazil are poorly known. Fourteen species were identified from fresh herbivore dung recently collected in Pernambuco, Northeastern Brazil, and eight exsiccatti sets were revised from the Pe. Camille Torrend (URM) and Dárdano de Andrade Lima (IPA) herbaria. Ascobolus elegans and S. beckii are reported for the first time in South America, while Ascobolus americanus and Saccobolus saccoboloides are reported for the first time in Brazil. Saccobolus infestans is neotypified. Information regarding the distribution and substrate preference of these species is presented. Descriptions and plates are provided, along with an identification key to all known species of Ascobolus and Saccobolus in Brazil.
Fungi play fundamental ecological roles in terrestrial ecosystems. However, their distribution and diversity remain poorly described in natural communities, particularly in arid and semiarid ecosystems. In order to identify environmental factors determining fungal community structure in these systems, we assessed their diversity in conjunction with soil physicochemical characteristics in a semiarid ecosystem in Baja California, Mexico, endemic for Coccidioidomycosis (Valley Fever). Two different microhabitats, burrows (influenced by rodent activity) and topsoil, were compared in winter and summer. Using a metagenomic approach, the ITS1 region of nuclear ribosomal DNA was used as barcode. A total of 1,940 OTUs were identified from 362,332 ITS1 sequences obtained by 454 pyrosequencing. Differences in fungal composition between seasons were clearly identified. Moreover, differences in composition between microhabitats were mainly correlated to significant differences in environmental factors, such as moisture and clay content in topsoil samples, and temperature and electrical conductivity in burrow samples. Overall, the fungal community structure (dominated by Ascomycota and Basidiomycota) was less variable between seasons in burrow than in topsoil samples. Coccidioides spp. went undetected by pyrosequencing. However, a nested PCR approach revealed its higher prevalence in burrows.
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Some natural ecosystems near industrialized and agricultural areas receive atmospheric nitrogen inputs that are an order of magnitude greater than those presumed for preindustrial times. Because nitrogen (N) often limits microbial growth on dead vegetation, increased N input can be expected to affect the ecosystem process of decomposition. We found that extracellular enzyme responses of a forest-floor microbial community to chronically applied aqueous NH4NO3 can explain both increased and decreased litter decomposition rates caused by added N. Microbes responded to N by increasing cellulase activity in decaying leaf litter of flowering dogwood, red maple, and red oak, but in high-lignin oak litter, the activity of lignin-degrading phenol oxidase declined substantially. We believe this is the first report to reduced ligninolytic enzyme activity caused by chronic N addition in an ecosystem. This result provides evidence that ligninolytic enzyme suppression can be an important mechanism explaining decreased decay rates of plant matter seen in this and other N-addition experiments. Since lignin and cellulose are the two most abundant organic resources on earth, these altered enzyme responses signal that atmospheric N deposition may be affecting the global carbon cycle by influencing the activities of microbes and their carbon-acquiring enzymes - especially the unique ligninolytic enzymes produced by white-rot fungi - over broad geographic areas.
As a first attempt to investigate evolutionary patterns of spore size in Agarics, I tested whether this trait was correlated to the size of the fruit-body (basidiocarp). Based on phylogenetically independent contrasts, it was shown that big mushroom species had on average 9% longer, 9% wider and 33% more voluminous spores (all with P < 0.05, one-tailed tests) than small congeneric species (a three-fold difference in cap diameter was used to discriminate big and small mushrooms). It is argued that larger spore size does not consistently confer higher fitness in fungi, owing to aerodynamic constraints. Surprisingly, the cap–spore correlation was strongly lineage-specific. Thus, spore volume correlated significantly with cap diameter in five of 16 large genera (four positive and one negative correlation). Positive cap–spore correlations are interpreted in terms of developmental constraints, mediated by hyphal swelling during cap expansion. The possible mechanisms which can account for the breakdown of this constraint in the majority of genera investigated are discussed.
Three greenhouses and the Central Garden of The Botanical Garden of Pavia were monitored for 1 year with the objective of investigating the occurrence of both airborne fungal spores and phylloplane fungi. By using an SAS air sampler, the higher fungal spore concentrations were detected in tropical and Mediterranean greenhouses. A total of 72 species belonging to 42 genera, some of which are related to the presence of plants ex situ, were isolated from Petri plates after exposure. Some airborne fungi, such as Aspergillus spp., Penicillium spp. and Conidiobolus spp., which are responsible for human allergies and respiratory problems, were also detected. Forty-four genera of phylloplane fungi were identified from leaves randomly collected from greenhouse plants. Most of the aerial fungal taxa isolated were also detected from the phylloplane. Some phytopathogenic taxa, as exemplified by Gliocladium vermoeseni, Graphium sp., Peronospora sp., and Zygosporium oscheoides, were isolated only from the phylloplane. The information obtained from qualitative and quantitative analysis of fungi can be a useful tool in the control of indoor air quality, thereby guaranteeing ex situ plant conservation and occupational health safety.
A survey of the patterns of wood decaying fungi as to occurrence of sporocarps on naturally fallen logs of Norway spruce (Picea abies) was undertaken in two nearby forest stands with different histories of management. One stand was an old-growth forest with few signs of logging, and the other stand was selectively logged 60–80 years ago. Altogether 118 species were found. Forest management had a negative impact on the species diversity. Newly fallen and weakly decayed logs in a natural forest had a higher species richness, more red-listed species, as well as more indicator species compared to similar logs in a managed forest. The importance of dead wood for species diversity of wood inhabiting fungi was clearly demonstrated. Presence of logs in later stages of decomposition increased the total species number in a natural forest stand with 42 (63 %), compared to a survey of only newly fallen and weakly decayed logs. Presence of logs in later stages of decomposition also increased the diversity of the species pool colonising newly fallen and weakly decayed logs. The highest number of fruiting species was found on intermediately decayed logs and on logs lying in contact with the ground. The fungal gradient as revealed in a DCA ordination was primarily related to decay. A successional pathway based on the primary decayer Fomitopsis pinicola was not detected.
It has previously been hypothesized that low rates of attack by natural enemies may contribute to the invasiveness of exotic plants.
We tested this hypothesis by investigating the influence of pathogens on survival during a critical life‐history stage: the seed bank. We used fungicide treatments to estimate the impacts of soil fungi on buried seeds of a taxonomically broad suite of congeneric natives and exotics, in both upland and wetland meadows.
Seeds of both natives and exotics were recovered at lower rates in wetlands than in uplands. Fungicide addition reduced this difference by improving recovery in wetlands, indicating that the lower recovery was largely attributable to a higher level of fungal mortality. This suggests that fungal pathogens may contribute to the exclusion of upland species from wetlands.
The effects of fungicide on the recovery of buried seeds did not differ between natives and exotics. Seeds of exotics were recovered at a higher rate than seeds of natives in uplands, but this effect was not attributable to fungal pathogens.
Fungal seed pathogens may offer poor prospects for the management of most exotic species. The lack of consistent differences in the responses of natives vs. exotics to fungicide suggests few aliens owe their success to low seed pathogen loads, while impacts of seed‐pathogenic biocontrol agents on non‐target species would be frequent.
Peat drainage, a common land-use practice in Europe, has been associated with habitat degradation and increased particulate and dissolved carbon release. In the UK, peatland drain blockage has been encouraged in recent years as a management practice to preserve peatland habitats and to reduce fluvial carbon loss and municipal water discoloration. Drain blockage has, however, been found to increase drain-water dissolved organic carbon (DOC) concentrations and coloration in the short term. In order to investigate the contribution of changes in extracellular phenol oxidase activity to the increase in water coloration following peatland drain blockage, cores collected from a riparian peatland in North Wales were incubated under impeded drainage conditions. Impeded drainage resulted in the stimulation of peat extracellular phenol oxidase activity and heightened soluble phenolic concentrations, suggesting that changes in extracellular phenol oxidase activity may be a key driver of increases in DOC and water coloration following peatland drain blockage. An increase in peat pH with impeded drainage was also observed that may have contributed to the heightened soluble phenolic concentrations – directly (through effects on solubility) and/or indirectly as a driver of the elevated extracellular phenol oxidase activity.
Endophytes are microorganisms that live inside plant tissues without causing symptoms of disease. They are a largely unexplored component of biodiversity, especially in the tropics. In this study, leaves from two populations of Guarea guidonia trees (Meliaceae) in the Luquillo region, Puerto Rico, were screened for diversity and composition of en‐dophytic fungal communities. A total of 268 leaf fragments from 14 trees were surveyed. Thirty‐eight morphospecies of endophytes were found. Phomopsis, Colletotrichum, Xylaria, and Rhizoctonia‐iike fungi were the most abundant taxa. Over 95 percent of the leaf pieces had endophytes. Communities had a few abundant species and many species with few individuals. The fungal community from the Guarea population in a forest preserve was more diverse than that from a disturbed area. Fungal communities were stratified according to height within a tree, but no differences were found between blade, petiolule, and rachis. The data suggest that the smaller and the more scattered the plant fragments sampled, the higher the probability of approaching real diversity values of endophytic fungal communities.
RESUMES
Los endófitos son microorganismos que viven dentro de las tejidos vegetales sin manifestarse patológicamente. Ellos constituyen un componente poco explorado de la biodiversidad, especialmente en las zonas tropicales. En este trabajo se estudió la diversidad y composición de las comunidades de hongos endófitos en hojas de dos poblaciones del árbol Guarea guidonia (Meliaceae), en la región de Luquillo, Puerto Rico. Un total de 268 fragmentos provenientes de 14 árboles fueron muestreados, encontrándose 38 morfoespecies de hongos endófitos. Los taxones más abundantes fueron Phomopsis, Colletotrichum, Xylaria, y Rhizoctonia. Más del 95 por ciento de los fragmentos presentó endófitos; las comunidades tenían pocas especies abundantes y muchas especies raras. De las dos poblaciones de G. guidonia estudiadas, la situada en una zona más conservada fue más diversa en cuanto a su comunidad de endófitos. Se observó estratificación de acuerdo con la altura del árbol, pero no se observaron diferencias entre la lámina, el peció1ulo, y el raquis de las hojas. Los datos sugieren que entre más pequeños y esparcidos scan los fragmentos muestreados, mayor será la probabilidad de aproximarse a los valores reales de diversidad de las comunidades de hongos endófitos.
Wood represents the defining feature of forest systems, and often the carbon in woody debris has a long residence time. Globally, coarse dead wood contains 36–72 Pg C, and understanding what controls the fate of this C is important for predicting C cycle responses to global change. The fate of a piece of wood may include one or more of the following: microbial decomposition, combustion, consumption by insects, and physical degradation. The probability of each fate is a function of both the abiotic environment and the wood traits of the species. The wood produced by different species varies substantially in chemical, micro- and macro-morphological traits; many of these characteristics of living species have ‘afterlife’ effects on the fate and turnover rate of dead wood. The colonization of dead wood by microbes and their activity depends on a large suite of wood chemical and anatomical traits, as well as whole-plant traits such as stem-diameter distributions. Fire consumption is driven by a slightly narrower range of traits with little dependence on wood anatomy. Wood turnover due to insects mainly depends on wood density and secondary chemistry. Physical degradation is a relatively minor loss pathway for most systems, which depends on wood chemistry and environmental conditions. We conclude that information about the traits of woody plants could be extremely useful for modeling and predicting rates of wood turnover across ecosystems. We demonstrate how this trait-based approach is currently limited by oversimplified treatment of dead wood pools in several leading global C models and by a lack of quantitative empirical data linking woody plant traits with the probability and rate of each turnover pathway. Explicitly including plant traits and woody debris pools in global vegetation climate models would improve predictions of wood turnover and its feedback to climate.
To determine whether host species influence the composition of fungal communities, the ascomycetes and basidiomycetes present on three tree species (Prioria copaifera (Fabaceae), Quararibea asterolepis (Bombacaceae), and Trichilia tuberculata (Meliaceae)) were sampled on the 50-ha Forest Dynamics Project plot in lowland moist tropical forest on Barro Colorado Island, Panama. The most abundant fungal morphotypes of both ascomycetes and basidiomycetes were generalists found on all three hosts, but detrended correspondence analysis revealed distinct differences in fungal community composition among host trees. These differences among hosts were constant across census years. Randomization tests revealed that there were significantly fewer host-generalist fungi than expected for ascomycetes but not for basidiomycetes. These results indicate that host composition plays a role in structuring both ascomycete and basidiomycete fungal communities, but that the most successful fungal morphotypes are capable of colonizing multiple host species.
The microbiota at industrial full-scale composting plants has earlier been fragmentarily studied with molecular methods. Here, fungal communities from different stages of a full-scale and a pilot-scale composting reactors were studied before and after wood ash amendment.
The portion of fungal biomass, determined using phospholipid fatty acid analysis, varied between 6.3% and 38.5% in different composting phases. The fungal internal transcribed spacer (ITS) area was cloned and sequenced from 19 samples representing different stages of the composting processes. Altogether 2986 sequenced clones were grouped into 166 phylotypes from which 35% had a close match in the sequence databases. The fungal communities of the samples were related with the measured environmental variables in order to identify phylotypes typical of certain composting conditions. The fungal phylotypes could be grouped into those that dominated the mesophilic low pH initial phases (sequences similar to genera Candida, Pichia and Dipodascaceae) and those found mostly or exclusively in the thermophilic phase (sequences clustering to Thermomyces, Candida and Rhizomucor), but a few were also present throughout the whole process.
The community composition was found to vary between suboptimally and optimally operating processes. In addition, there were differences in fungal communities between processes of industrial and pilot scale.
The results of this study reveal the fungal diversity with molecular methods in industrial composting process. This is also one of the first studies conducted with samples from an industrial biowaste composting process.
Less than 1% of the estimated number of fungal species have been investigated concerning the transport of low-molecular-weight nutrients and metabolites through the plasma membrane. This is surprising if one considers the importance of the processes at the plasma membrane for the cell: this membrane mediates between the cell and its environment. Concentrating on filamentous fungi, in this review emphasis is placed on relating results from biophysical chemistry, membrane transport, fungal physiology, and fungal ecology. Among the treated subjects are the consequences of the small dimension of hyphae, the habitat and membrane transport, the properties of the plasma membrane, the efflux of metabolites, and the regulation of membrane transport. Special attention is given to methodological problems occurring with filamentous fungi. A great part of the presented material relies on work with Neurospora crassa, because for this fungus the most complete picture of plasma membrane transport exists. Following the conviction that we need "concepts instead of experiments", we delineate the lively network of membrane transport systems rather than listing the properties of single transport systems.
Membrane overcultures of Rhizopus oligosporus were shifted from 37 to 50 degrees C for 10 h and then returned to 37 degrees C, mimicking the temporal temperature profiles which typically occur in SSF due to heat transfer limitations. Analysis with a modified two-phase growth model suggests that the temperature upshift causes a 48% decrease in the number of actively extending hyphal tips, and that the first order death rate constant of tips increases from 0. 059 to 0.073 h(-1). The fungus did not immediately recover when the temperature was returned to 37 degrees C. The model assumed that the specific growth rate constant microgram(g) was not affected by the increase of temperature, although contradictory data was obtained from radial growth rate experiments.
Competition is often considered a fundamental process influencing assemblage structure, yet little is known about competition among ectomycorrhizal (EM) fungi. Here, we examine competitive interactions between Rhizopogon occidentalis and Rhizopogon salebrosus in a 6-month microcosm study. Pinus muricata seedlings were grown in three EM treatments: R. occidentalis, R. salebrosus, and R. occidentalis and R. salebrosus. At 2, 4, and 6 months, five seedlings per treatment were harvested and the EM root tip biomass of each species was determined. Root tips in the two-species treatment were identified using molecular techniques. R. occidentalis had similar EM root tip biomass when grown alone or in the presence of R. salebrosus. By contrast, R. salebrosus had significantly lower EM root tip biomass when grown with R. occidentalis than when grown alone, indicating it was a competitive inferior under the conditions tested. Competition was driven by differences in timing of colonization resulting in a strong priority effect for R. occidentalis. Our results, together with two earlier studies, indicate competition may play a more important role in EM interactions than previously recognized.
Some cyclic peptides and depsipeptides are synthesized in microorganisms by large multienzymes called nonribosomal peptide synthetases. The structures of peptide products originating in this way are complex and diverse and are microorganism-specific. This work proposes the use of fungal cyclic peptides and depsipeptides as extremely specific markers of fungal infections. Since a reliable molecular tool for diagnosing fungal infections at an early stage is still missing, we present mass spectrometry as a new, modern, broadband (with respect to fungal strain) and specific tool for clinical mycologists. More than 40 different fungal species can be rapidly characterized according to specific families of cyclic peptides, and in some cases, a particular fungal strain can be identified on the basis of its cyclopeptide profile. This paper is also aimed at initiating discussion on the biological role of these secondary metabolites, especially of those synthesized by medically important strains. Proven cytotoxic, anti-inflammatory or immunosuppressive activities of some cyclic peptides indicate that these molecules may contribute to the synergistic array of fungal virulence factors and support microbial invasion during fungal infection. In addition to an overview on recent mass spectrometric protocols for cyclic peptide sequencing, the structures of new peptides from Paecilomyces and Pseudallescheria are presented.
Fungi are of fundamental importance in terrestrial ecosystems playing important roles in decomposition, nutrient cycling, plant symbiosis and pathogenesis, and have significant potential in several areas of environmental biotechnology such as biocontrol and bioremediation. In all of these contexts, the fungi are growing in environments exhibiting spatio-temporal nutritional and structural heterogeneities. In this work, a discrete mathematical model is derived that allows detailed understanding of how events at the hyphal level are influenced by the nature of various environmental heterogeneities. Mycelial growth and function is simulated in a range of environments including homogeneous conditions, nutritionally-heterogeneous conditions and structurally-heterogeneous environments, the latter emulating porous media such as soils. Our results provide further understanding of the crucial processes involved in fungal growth, nutrient translocation and concomitant functional consequences, e.g. acidification, and have implications for the biotechnological application of fungi.
Coarse woody debris (CWD) is a key habitat for many species in forest ecosystems. To ensure the long-term survival of such species, forest management regimes must include measures that promote dead wood dynamics similar to those of natural forests. Thus, information on CWD dynamics under natural conditions is required, including data pertaining to the underlying agents of disturbance. This study examines modes of mortality, decay rates, and temporal patterns in the availability of Picea abies logs in a Swedish old-growth forest affected by internal, small-scale disturbance. All 684 logs in a 6.6-ha plot were mapped and classified into one of six decay classes. Logs in the early stages of decay were examined for the presence of heart-rot fungi. Six years later all logs were re-inventoried, including newly formed logs. Matrix models based on the transition rates between decay classes showed that it took about 60 years for 90% of the logs to decay beyond class 6 (a deformed trunk with soft wood). Large logs (> 26 cm) decayed 40% more slowly than small logs (< 25 cm). The initial volume of logs was 37.6 m3/ha but increased to 44.8 m3/ha after six years. In addition, there was a large shift in the decay-class distribution. The volume of logs in early and late decay classes increased by 71% and 45%, respectively, while the volume of logs in the intermediate decay classes decreased by 32%. The fluctuations appear to result from pulses in mortality, driven by a combination of strong winds and the heart-rot fungus, Phellinus chrysoloma, which was present in more than 30% of all logs at an early stage of decay. These results show that large temporal fluctuations in dead wood also occur in the absence of large-scale disturbance, and that heart-rot fungi are important factors driving the overall dynamics of dead wood. Since many wood-inhabiting species are naturally rare and have very specific substrate demands, such temporal variability in dead wood availability may have effects on biodiversity and should be taken into account when designing small, protected forest areas.
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