Microfungal Communities Research Articles

Spatiotemporal dynamics of culturable microfungi in soil of Mount Hermon, Israel

We examined the spatiotemporal structure of culturable mycobiota in terra rossa soil of the Israeli part of Mount Hermon, along an altitudinal gradient from 1310 to 1720 m. A total of 155 species representing 65 genera was isolated using the soil dilution plate method. Soil microfungal communities from the studied area are characterized by: (i) the dominance of Penicillium species in sites under canopies; (ii) the prevalence of melanized microfungi in vegetation-free sites, and (iii) a lower heterogeneity and evenness of microfungal communities under canopies due to the overdominance of Penicillium simplicissimum. Abundance of melanized fungi correlated with seasonal abiotic extremes (high solar radiation, high soil temperatures – about 40°C – and low soil moisture – about 4.5% – in summer, and low temperature – about 0°C – in water-saturated soil under snow cover in winter). The effects of altitude on both community structure and diversity characteristics were smaller than the variation found between open sites and sites under tree cover at the same altitude. These findings support the idea that edaphic micro-environmental parameters, such as soil moisture, temperature, and organic matter content, may affect diversity of soil microfungal communities to a higher extent than macroenvironmental (climatic) factors.

Changes in Microfungal Community in Cherrapunji—The Wettest Patch on Earth as Influenced by Heavy Rain and Soil Degradation

As part of a long time analysis to examine the ecological impacts of heavy rain coupled to soil degradation, soil fungal communities from two closely spaced sites bearing distinct ecology—one receiving heaviest rainfall but degraded patch on earth and the other pristine sacred grove forest were investigated over a period of three years. Cherrapunji besides being highest rainfall receiving area, is characterized by complete deforestation and soil erosion with sparse grasses forming the surface growth, whereas the sacred forests are conserved in their pristine nature due to religious beliefs of the indigenous tribes. The effect of deforestation and land degradation on soil microbes, soil organic carbon, soil nitrate nitrogen, soil pH, soil temperature, and fungal CFU/g were investigated from the two contrasting sites. The sites showed great variability in physical and chemical parameters including soil composition, temperature, pH, soil carbon, nitrogen content, water availability and enzyme activities. The population count of fungi was higher in sacred forest soil than degraded land of Cherrapunji. In both soil types, Penicillium perpurogenum markedly dominated and the co-dominant species (Aspergillus sp., Fusarium sp. and Trichoderma sp.) were common in both virgin and degraded soils. A total of 63 species were identified during the study period. The species composition between the two sites showed some variation as Syncephalastrum sp., S. chartarum, Gliocladium sp., Eupenicillium osmophilum and Eurotium sp. were not present in Cherrapunji. The undisturbed sacred forest fungal communities had significantly higher Simpson, Shannon and evenness indices than that of degraded soil of Cherrapunji. The prolonged anthropogenic activity in the area leading to degradation coupled with heavy rainfall has decreased the diversity level of fungal communities and masked the pristine differentiating effect of soil on the fungal community.

Ecology of microfungal communities in gardens of fungus-growing ants (Hymenoptera: Formicidae): a year-long survey of three species of attine ants in Central Texas

We profiled the microfungal communities in gardens of fungus-growing ants to evaluate possible species-specific ant-microfungal associations and to assess the potential dependencies of microfungal diversity on ant foraging behavior. In a 1-year survey, we isolated microfungi from nests of Cyphomyrmex wheeleri, Trachymyrmex septentrionalis and Atta texana in Central Texas. Microfungal prevalence was higher in gardens of C. wheeleri (57%) than in the gardens of T. septentrionalis (46%) and A. texana (35%). Culture-dependent methods coupled with a polyphasic approach of species identification revealed diverse and changing microfungal communities in all the sampling periods. Diversity analyses showed no obvious correlations between the number of observed microfungal species, ant species, or the ants' changing foraging behavior across the seasons. However, both correspondence analysis and 5.8S-rRNA gene unifrac analyses suggested structuring of microfungal communities by ant host. These host-specific differences may reflect in part the three different environments where ants were collected. Most interestingly, the specialized fungal parasite Escovopsis was not isolated from any attine garden in this study near the northernmost limit of the range of attine ants, contrasting with previous studies that indicated a significant incidence of this parasite in ant gardens from Central and South America. The observed differences of microfungal communities in attine gardens suggest that the ants are continuously in contact with a diverse microfungal species assemblage.

Spatiotemporal distribution of soil microfungi in the Makhtesh Ramon area, central Negev desert, Israel

Abstract We examined the spatiotemporal pattern of soil mycobiota structure in the area of Makhtesh Ramon – a unique erosion cirque located in the central Negev desert, Israel. A total of 185 species from 76 genera were isolated using the soil dilution plate method. Most microfungal communities from sunny open localities were characterized by a dominance of melanin-containing species with large, thick-walled and multi-celled conidia increasing in the summer. By contrast, in the shrub communities, dark-colored species with comparatively small one-celled conidia prevailed. Aspergilli (mainly Aspergillus fumigatus) and teleomorphic ascomycetes comprised a basic part of thermotolerant mycobiota obtained at a temperature of 37 °C. Diversity (heterogeneity, evenness) was highest in the edaphically extreme localities and decreased in the climatically extreme summer season. The results demonstrated that the soil of the Makhtesh Ramon area maintained comparatively rich microfungal diversity subjected to spatiotemporal variations apparently adaptively influenced by variations in microclimatic and edaphic conditions.

Microfungal communities in soil polluted with fluoride

There have been identified three zones according to the degree of soil pollution with fluoride in the impact area of air emissions of the Kandalaksha Aluminium Smelter (Russia): zone of maximum pollution up to 2.5 km from the emission source with the content of fluoride from 5000 to 1200 mg/kg, zone of strong pollution up to 13 km from the plant with the content of fluoride between 1200-400 mg/kg and zone of moderate pollution up to 20 km from the source with content of fluoride between 400-200 mg/kg. Emissions of the aluminium plant have reduced the number and the diversity of fungi and have caused an increase in fungal communities that are potentially pathogenic fungi. The biomass of fungi has decreased in the organic horizon of the maximum polluted soil from 5.4 to 3.6 mg/g. As a whole, emissions from the aluminium plant in the Murmansk region are less toxic for the environment, than emissions of copper-nickel enterprises.

Microfungal communities in soil polluted with fluoride

There have been identified three zones according to the degree of soil pollution with fluoride in the impact area of air emissions of the Kandalaksha Aluminium Smelter (Russia): zone of maximum pollution up to 2.5 km from the emission source with the content of fluoride from 5000 to 1200 mg/kg, zone of strong pollution up to 13 km from the plant with the content of fluoride between 1200-400 mg/kg and zone of moderate pollution up to 20 km from the source with content of fluoride between 400-200 mg/kg. Emissions of the aluminium plant have reduced the number and the diversity of fungi and have caused an increase in fungal communities that are potentially pathogenic fungi. The biomass of fungi has decreased in the organic horizon of the maximum polluted soil from 5.4 to 3.6 mg/g. As a whole, emissions from the aluminium plant in the Murmansk region are less toxic for the environment, than emissions of copper-nickel enterprises.

The addition of labile carbon alters litter fungal communities and decreases litter decomposition rates

Many field and laboratory studies have demonstrated that the addition of easily available carbon can increase rates of decomposition of plant litter or humified soil organic matter, though opposite trends are also common. In boreal forests, a large part of labile carbon enters soil via tree roots and ectomycorrhizal (EM) network. The influence of increased C availability and the presence of EM roots on litter decomposition was studied in a long-term field experiment in a 50-year-old Picea abies plantation. Litterbags containing litter of three species ( Populus tremula, Quercus robur, or P. abies) were buried to the depth of ca. 2.5 cm. The experiment was set up in a full-factorial design with carbon availability and presence of roots as factors. Carbon was added as an aqueous sucrose solution (50 g C m −2) every second week during snow-free period. Spruce roots around and underneath experimental plots were cut once a month. Subsets of litterbags were analysed after 12, 21 and 24 months. The serial dilution technique was used to assess the fungal community composition. The addition of labile carbon led to a strong decrease in litter decomposition rates, associated with consistent shifts in the composition of saprotrophic microfungal communities, and to an increase in the overall density of culturable fungal species ( r-strategists), but not of specialized cellulolytic microfungi ( K-strategists), isolated on Hutchinson agar. Sucrose addition did not affect the number of species isolated but the dominance structure was shifted toward the domination of the 2–4 most abundant species. The presence of EM roots significantly reduced moisture content in decomposing litter but had only weak and inconsistent effect on the decomposition rates and on the community composition of saprotrophic microfungi; these effects did not depend on the level of carbon availability.

Comparative mycobiotic and edaphic analyses of two neighboring soil profiles on different lithologies in Upper Galilee, Israel

Microfungal communities from two profiles of the neighboring pale rendzina and basaltic vertisoil in the Upper Galilee area, Israel, were analyzed and compared. The bedrock lithology determines the key differences in mineralogical composition of the contrasting soils on chalk and basaltic rocks. Pale rendzina on chalk is strongly calcareous while the basaltic soil profile is leached from carbonates below the 5–8 cm depth and is significantly magnetically enhanced. The soils also differ in CEC, exchangeable cations, and in microstructure. In parallel, mycobiota isolated by the soil dilution plate method (124 species) displays different patterns both in distribution along the contrasting profiles and in structure of the communities at definite depths. The basaltic mycobiota is significantly richer (87 vs. 69 species in the rendzina) being less heterogeneous and even at a 5–50 cm depth. According to all estimated mycobiotic characteristics, at 15–18 cm depth the differences between the basaltic and rendzina soils are mostly pronounced. Excellent aeration of the basaltic soil in contrast to the rendzina may account at least partly for the peak of mycobiotic differences at this depth. No single edaphic parameter is responsible for the greatest level of variations in the mycobiotic characteristics indicating that co-influence of soil biotic/abiotic factors determined distribution of microfungi throughout the profiles.

Indigenous microfungi and plants reduce soil nonylphenol contamination and stimulate resident microfungal communities

Nonylphenol, the most abundant environmental pollutant with endocrine disrupting activity, is also toxic to plants and microorganisms, but its actual impact in the field is unknown. In this study, diversity of culturable soil microfungal and plant communities was assessed in a disused industrial estate, at three sites featuring different nonylphenol pollution. Although soil microfungal assemblages varied widely among the sites, no significant correlation was found with point pollutant concentrations, thus suggesting indirect effects of soil contamination on microfungal assemblages. The potential of indigenous fungi and plants to remove nonylphenol was assessed in mesocosm experiments. Poplar plants and a fungal consortium consisting of the most abundant strains in the nonylphenol-polluted soil samples were tested alone or in combination for their ability to reduce, under greenhouse conditions, nonylphenol levels either in a sterile, artificially contaminated sand substrate, or in two non-sterile soils from the original industrial area. Introduction of indigenous fungi consistently reduced nonylphenol levels in all substrates, up to ca. 70% depletion, whereas introduction of the plant proved to be effective only with high initial pollutant levels. In native non-sterile soil, nonylphenol depletion following fungal inoculation correlated with biostimulation of indigenous fungi, suggesting positive interactions between introduced and resident fungi.

The mycological properties of medieval culture layers as a form of soil ‘biological memory’ about urbanization

The mycological properties of soil can offer information about ancient human–landscape interaction, including urbanization. This preposition has been confirmed in our study of the habitation deposits in the medieval Russian settlements (eighth to fourteenth centuries A.D.). The mycobiota of profiles of anthropogenically transformed soil of excavated medieval settlements were examined in different climate conditions in the European part of Russia. The fungal biomass and biomass structure were evaluated using luminescent microscopy. The isolation and enumeration of microfungi were performed using the method of serial dilutions of soil samples and plating them out on the number of solid media. The isolation of keratinolytic microfungi was performed by hear-bite technique. It was established that in ancient urban soils, the mycobiota may have properties different from those of zone fungal communities. The examined cultural layers of ancient settlements differ from the horizons of the surrounding natural soils because of a bigger rate of fungal spores in fungal biomass, more mosaic distribution of microfungal communities, different species composition and dominant microfungal species, increased incidence of some ecological, and trophic fungal groups (for example, keratinophilic, potentially pathogenic microfungi). The mycological characteristics of anthropogenic deposits in the excavated medieval settlements were found to be mainly similar to mycological properties of modern urban soils. These properties of habitation deposits can be interpreted as a kind of “soil mycological memory” of the ancient urban impact. Soil mycological characteristics could be used in paleoecological reconstructions and biomonitoring of urban impacts

Determining species diversity of microfungal communities in forest tree roots by pure-culture isolation and DNA sequencing

Pure-culture isolation from roots was compared with transformation of total DNA from roots followed by sequence analysis of ITS 1/2 rDNA of representative clones as methods for determining the abundance and composition of microbiota in roots of Betula pendula, Fagus sylvatica, Larix decidua, Prunus serotina and Quercus petraea. The results from the two methods differed greatly, with no overlap between the taxa identified. Pure-culture isolation revealed greater species diversity (47 taxa), the most frequent fungi being Ascomycota, including Penicillium spp., Phialocephala fortinii, Pochonia bulbillosa, Sesquicillium candelabrum and Trichoderma spp. Transformation of total DNA and sequencing revealed less diversity (22 taxa), the most frequent taxa being Basidiomycota, including Coprinus fissolanatus and Mycena spp., and Ascomycota, including Podospora– Schizothecium spp., Helgardia anguioides and Microdochium sp. Communities characterized by either method showed slightly greater fungal diversity and less species dominance on F. sylvatica than on roots of other trees, whilst DNA sequencing showed least diversity and greatest species dominance on Q. petraea.

Vertical divergence of microfungal communities in soil profiles of “Evolution Canyon” I, Lower Nahal Oren, Mount Carmel, Israel

In the present study, species composition, the contribution of major groupings to community structure, and diversity level (species richness, heterogeneity, and evenness) were examined in their distribution in a soil depth of 0 – 43 cm in two opposite slopes at “Evolution Canyon” I, Nahal Oren, Mount Carmel, Israel. A total of 90 species from 35 genera belonging to Zygomycota (2 species), teleomorphic Ascomycota (12), and anamorphic Ascomycota (76) were isolated. In the soil profile of the xeric “African” south-facing slope (AS), melanin-containing fungi and teleomorphic species remarkably decreased their abundance with depth, while Penicillium spp. and Aspergillus spp. increased their contribution to the community structure. These variations were accompanied by a decrease in heterogeneity and evenness of the microfungal communities. In contrast, on the mesic “European” north-facing slope (ES), a sharp decrease in abundance of penicilli was observed with soil depth, followed by increasing diversity level of the communities. The variations in community structure through soil profiles were associated with variations in edaphic conditions (increasing soil moisture) together with escape from solar radiation on the AS and a decrease of organic matter content on the ES.

Diversity of cultured microfungal communities in surface horizons of soils on different lithologies in Upper Galilee, Israel

Topsoil microfungal communities from two closely spaced sites on different lithologies in the Upper Galilee area, Israel, were analyzed and compared. The sites are located in a pasture, with pristine Mediterranean maquis completely destroyed, presumably, about 2000 years ago. The bedrock lithology in the area determines the key differences in mineralogical composition of the soils on chalk and basaltic rocks. Because of destroyed natural maquis/forest associations, the runoff from the chalk-based watershed following winter rains reaches the lower lying basaltic areas. This results in high calcareous topsoil on basalt and similar, slightly alkaline pH in both soils, irrespective of season and locality (under or between shrubs). Differences between the culturable fractions of microfungal communities studied by the soil dilution plate method (in composition and diversity level) in the open and shrub localities on the same lithology were more pronounced than those between different lithologies. In all localities, one species— Penicillium simplicissimum—markedly dominated and this fungus, as well as its co-dominant species, are common both in virgin and arable soils. We assume that prolonged agricultural activity in the area might decrease the diversity level of microfungal communities and mask the pristine differentiating effect of soil diversity on these communities.

Soil microfungal communities of ‘Evolution Canyons’ in Israel - extreme differences on a regional scale

On a regional scale, we compared the local adaptive patterns of soil mycobiota revealed in four ‘Evolution Canyons’ located in the northern and southern parts of Israel. These microsites were chosen according to the framework of the Institute of Evolution, University of Haifa programme, focusing on the effect of interslope environmental divergence on biodiversity patterns. The comparative analysis demonstrated remarkable differences in spatiotemporal structure of the microfungal communities and their biodiversity level (species richness, heterogeneity and equitability). In the desert ‘Evolution Canyon’, stress-selected, slow-reproducing, dark-coloured species with large, multicelled conidia were dominant. At the same time, in the forest localities of the northern canyons, as well as in the agriculturally disturbed locality with soil degradation, ruderal-selected, fast-reproducing Penicillium species predominated. Environmental natural selection appeared to be the major factor affecting adaptive diversity patterns of soil microfungi in the studied area. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 157–163.

Influence of soil compaction on microfungal community structure in two soil types in Bartin Province, Turkey

Soil compaction negatively influences physical properties of soil (bulk density and pore space), and may consequently limit soil microfungi, which are significant for nutrient bioavailability. We measured microfungal community responses to compaction in a sandy loam and a clay loam soil at picnic sites. Soil bulk density increased significantly in the compacted samples. However, microfungal numbers and community composition were unrelated to changes in soil bulk density. With increases in bulk density from 1.22 to 1.37 g cm(-3) in the clay soil and from 1.38 to 1.54 g cm(-3) in the sandy loam soil, the total number of fungi declined or showed insignificant increases. In the compacted samples as well as the control sites, the most frequently occurring genera in the clay soil were Penicillium, Aspergillus, and Gliocladium. However, the most prominent feature occurring within the sandy loam soil was the exhibition of the greatest increase in the frequency of the Fusarium genus. When comparing compacted and control soils, fungal community composition corresponded more closely within each soil texture. The two microfungal soil communities, therefore, tolerated compaction. In contrast, a difference occurred in the fungal communities between the two soil textures. This is more likely due to the variability in the controlling factors of microfungal abundance and composition, such as soil characteristics, tree species, and competitive ability of fungal genera.

Influence of mineral and organic fertilization on soil fungi, enzyme activities and humic substances in a long-term field experiment

Changes in microfungal communities, fungal activities and humic substances (HS) in agricultural soils kept under different fertilization regimes were observed and their causal relationships were investigated in a long-term field experiment. Fertilization did not change the abundance of HS-utilizing microfungi and, except for organic amendment alone, total culturable microfungi were also unaffected by this factor. Organic fertilization increased activities of manganese peroxidase (MnP) and proteinase, but decreased endo-1,4-beta-glucanase activity compared to the corresponding control without organic fertilization. In soils treated with mineral fertilizers, the activities of MnP, endo-1,4-beta-glucanase and proteinase were higher than in control without any mineral treatment. Both the aromaticity of fulvic acid and the molar mass of humic acid was lower in soil with organic fertilization, which may be a result of oxidative degradation mediated by higher MnP activity observed in treatments with organic fertilization.

Microfungal community structure from forest soils in Northern Thrace Region, Turkey

The soil fungi in the pure stand of oak (Quercus petraea), beech (Fagus orientalis), and pine (Pinus nigra) were investigated by the dilution plate method at Yildiz Mountain in Thrace region. The mycobiota, as well as the number of isolates per plate, was determined at various soil depths. Principal component analysis of the soil profiles indicated that there was variation in mycobiota composition and the variation was attributed to differences among the ecosystems. When comparing conifer and hardwood soils, using Sorenson’s similarity index, fungal community composition corresponded more closely between the hardwood stands than with the conifer stand. Fungal community composition appears to be influenced by the organic compounds entering soil from plant litter.

Plant community influences on soil microfungal assemblages in boreal mixed-wood forests

We studied the relationships between assemblages of soil microfungi and plant communities in the southern boreal mixed-wood forests of Quebec. Sampling took place in 18,100 m2 plots from an existing research site. Plots were separated into three categories based on dominant overstory tree species: (i) trembling aspen, (ii) white birch and (iii) a mixture of white spruce and balsam fir. Within each plot a 1 m2 subplot was established in which the understory herbaceous layer was surveyed and soil cores were collected. Microfungi were isolated from soil cores with the soil-washing technique and isolates were identified morphologically. To support our morphological identifications DNA sequences were obtained for the most abundant microfungi. The most frequently occurring microfungal species were Penicillium thomii, P. spinulosum, P. janthinellum, Penicillium sp., P. melinii, Trichoderma polysporum, T. viride, T. hamatum, Mortierella ramanniana, Geomyces pannorum, Cylindrocarpon didymum, Mortierella sp. and Mucor hiemalis. Multivariate analyses (redundancy analysis followed by variance partitioning) revealed that most of the variation in microfungal communities was explained by understory plant species composition as opposed to soil chemistry or overstory tree species. In this floristically diverse system saprophytic microfungal assemblages were not correlated with the overstory tree species but were significantly correlated with the main understory herbs, thereby reflecting differences at a smaller spatial scale.

Plant community influences on soil microfungal assemblages in boreal mixed-wood forests

We studied the relationships between assemblages of soil microfungi and plant communities in the southern boreal mixed-wood forests of Québec. Sampling took place in 18 100 m2 plots from an existing research site. Plots were separated into three categories based on dominant overstory tree species: (i) trembling aspen, (ii) white birch and (iii) a mixture of white spruce and balsam fir. Within each plot a 1 m2 subplot was established in which the understory herbaceous layer was surveyed and soil cores were collected. Microfungi were isolated from soil cores with the soil-washing technique and isolates were identified morphologically. To support our morphological identifications DNA sequences were obtained for the most abundant microfungi. The most frequently occurring microfungal species were Penicillium thomii, P. spinulosum, P. janthinellum, Penicillium sp., P. melinii, Trichoderma polysporum, T. viride, T. hamatum, Mortierella ramanniana, Geomyces pannorum, Cylindrocarpon didymum, Mortierella sp. and Mucor hiemalis. Multivariate analyses (redundancy analysis followed by variance partitioning) revealed that most of the variation in microfungal communities was explained by understory plant species composition as opposed to soil chemistry or overstory tree species. In this floristically diverse system saprophytic microfungal assemblages were not correlated with the overstory tree species but were significantly correlated with the main understory herbs, thereby reflecting differences at a smaller spatial scale.

Adaptive spatiotemporal distribution of soil microfungi in ‘Evolution Canyon’ III, Nahal Shaharut, extreme southern Negev Desert, Israel

We examined adaptive spatiotemporal mycobiota structure in the soil of ‘Evolution Canyon’ III, Nahal Shaharut, in the extreme southern Negev, Israel. A total of 223 species representing 80 genera were isolated using the soil dilution plate method. The microfungal communities in all localities and seasons were characterized by a superdominance of dark-coloured species with large multicelled conidia: Ulocladium atrum, U. botrytis, Alternaria alternata, and Al. chlamydospora. Species of the genus Aspergillus (mainly As. fumigatus) and teleomorphic ascomycetes comprised a basic part of the thermotolerant mycobiota obtained at a temperature of 37 °C. Isolate density displayed high positive dependence on organic matter content. Density was subject to drastic spatiotemporal (especially spatial) fluctuations, with maximum levels found in the shady valley bottom locality. The lowest biodiversity indices were estimated in localities under shrubs and in the most stressful summer and spring. The results demonstrated a clear effect of harsh desert climatic and edaphic selection on the adaptive variation of the mycobiota studied. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90, 263–277.