Distinct Fungal Communities Research Articles

Arbuscular mycorrhizal fungal communities and root colonisation differ in relation to plant host and soil nutrients

<p>• Field samples from two coexisting plant species were examined to see whether they were colonised by distinct fungal communities, and whether the colonisation pattern differed between the two plant species.</p><p>• Two plant species, <em>Agrostis capillaris</em> and <em>Ranunculus acris</em> from four mountain slopes in the Faroe Islands were examined for percentage root length colonisation (%RLC) including the amount of arbuscules and vesicles, and the arbuscular mycorrhizal (AM) fungal types in the roots identified by cloning and sequencing.</p><p>• Fewer AM fungal types were found in <em>Ranunculus acris</em> than in <em>Agrostis capillaris,</em> but the %RLC was greater in <em>Ranunculus acris</em>, which also showed seasonal variability. Vesicles were more abundant in <em>Ranunculus acris.</em></p><p>• Statistical analysis suggested that the AM fungal communities colonising the two plant species were distinct. The root colonisation in <em>Ranunculus acris</em> responded to other soil nutrients than the root colonisation in <em>Agrostis capillaris.</em></p>

Forest Management Type Influences Diversity and Community Composition of Soil Fungi across Temperate Forest Ecosystems.

Fungal communities have been shown to be highly sensitive toward shifts in plant diversity and species composition in forest ecosystems. However, little is known about the impact of forest management on fungal diversity and community composition of geographically separated sites. This study examined the effects of four different forest management types on soil fungal communities. These forest management types include age class forests of young managed beech (Fagus sylvatica L.), with beech stands age of approximately 30 years, age class beech stands with an age of approximately 70 years, unmanaged beech stands, and coniferous stands dominated by either pine (Pinus sylvestris L.) or spruce (Picea abies Karst.) which are located in three study sites across Germany. Soil were sampled from 48 study plots and we employed fungal ITS rDNA pyrotag sequencing to assess the soil fungal diversity and community structure. We found that forest management type significantly affects the Shannon diversity of soil fungi and a significant interaction effect of study site and forest management on the fungal operational taxonomic units richness. Consequently distinct fungal communities were detected in the three study sites and within the four forest management types, which were mainly related to the main tree species. Further analysis of the contribution of soil properties revealed that C/N ratio being the most important factor in all the three study sites whereas soil pH was significantly related to the fungal community in two study sites. Functional assignment of the fungal communities indicated that 38% of the observed communities were Ectomycorrhizal fungi (ECM) and their distribution is significantly influenced by the forest management. Soil pH and C/N ratio were found to be the main drivers of the ECM fungal community composition. Additional fungal community similarity analysis revealed the presence of study site and management type specific ECM genera. This study extends our knowledge on the impact of forest management type on general and ectomycorrhizal fungal diversity and community structure in temperate forests. High plasticity across management types but also study site specific spatial distribution revealed new insights in the ECM fungal distribution patterns.

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1) with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from different patients, providing a poignant example of parallel evolution. Together, this combined clinical-genomic approach provides a high-resolution portrait of the fungal microbiome of cystic fibrosis patient lungs and identifies a genetic basis of pathogen adaptation.

The distribution of polypore fungi in endemism centres in Brazilian Amazonia

Abstract Amazonia is covered by the largest, best-preserved tropical forest in the world, almost 50% of which is in Brazil. The Amazonian region has the highest biodiversity of the planet, distributed, at least for the fauna and flora communities, in eight distinct centres of endemism. However, there is little information about the fungal distribution in the region. In this study, the abundance, species richness and composition of species of poroid fungi were investigated in three Amazonian centres of endemism in order to test the hypothesis whether these centres also have distinct fungal communities. One hundred and twenty four unit samples in three centres of endemism were visited from 2006 to 2011, resulting in 2303 collections representing 153 species of poroid fungi. The fungal communities did not form distinct groups in relation to the centres of endemism when the Analysis of Similarity (ANOSIM) was used and the hypothesis was rejected.

Impacts of root symbiotic associations on interspecific variation in sugar exudation rates and rhizosphere microbial communities: a comparison among four plant families

Symbiotic associations between rhizobia and arbuscular mycorrhyzal fungi (AMF) influence changes in carbon allocation to plant roots and alter the exudation of signal molecules in their host plants. In this study, we examined the impacts of bacterial and fungal symbiotic associations on the variation in sugar exudation rates from plant roots, and in rhizosphere microbial community structure, by comparing four plant families (e.g., Asteraceae, Brassicaceae, Fabaceae, and Poaceae) with different bacterial and fungal symbiotic associations. We determined sugar exudation rates of 23 plant species by regressions of exuded sugars against root mass through periodic samplings of plants grown in pots. Banding patterns from PCR-DGGE analyses of 28 plant species were evaluated by ordination scores relative to their rhizosphere bacterial and fungal community structures. Plant family was the most important source of variation in sugar exudation rates and microbial community structure between plant species. Brassicaceae, which lacks a root symbiotic association, had the lowest sugar exudation rate, the lowest rhizosphere microbial mass, and a distinct fungal community structure relative to the other plant families. Fabaceae had a different bacterial community structure relative to the other plant families. These results demonstrate that root symbiotic associations have great impacts on the rate of sugar exudation and free-living microbial communities that inhabit the rhizosphere.

Metabarcoding analysis of home composts reveals distinctive fungal communities with a high number of unassigned sequences.

Home composting has been strongly advocated in the UK, Europe and North America to divert organic waste away from conventional waste processing. Despite this, little attention has been given to microbial communities and their diversity in these systems. In this study, we examined the diversity of fungal species in 10 different domestic composts by 454 tag-encoded pyrosequencing. We report the recovery of 478 different molecular operational taxonomic units (MOTUs) from the 10 composts with a mean of 176.7 ± 19.6 MOTUs per compost and a mean of 12.9 ± 3.8 unique MOTUs per sample. Microascales (17.21 %), Hypocreales (16.76 %), Sordariales (14.89 %), Eurotiales (11.25 %) and Mortierellales (7.38 %) were the dominant orders in the community, with Pseudallescheria (9.52 %), Penicillium (8.43 %), Mortierella (3.60 %) and Fusarium (3.31 %) being the most abundant genera. Fungal communities in home composts were substantially different to large-scale commercial composts, with thermophilic and thermotolerant fungi present in much lower numbers. Significantly, 46.2 % of all sequences were identified as uncultured fungi or could not be assigned above the family level, suggesting there are a high number of new genera and species in these environments still to be described.

Residual soil DNA extraction increases the discriminatory power between samples.

Forensic soil analysis relies on capturing an accurate and reproducible representation of the diversity from limited quantities of soil; however, inefficient DNA extraction can markedly alter the taxonomic abundance. The performance of a standard commercial DNA extraction kit (MOBIO PowerSoil DNA Isolation kit) and three modified protocols of this kit: soil pellet re-extraction (RE); an additional 24-h lysis incubation step at room temperature (RT); and 24-h lysis incubation step at 55°C (55) were compared using high-throughput sequencing of the internal transcribed spacer I ribosomal DNA. DNA yield was not correlated with fungal diversity and the four DNA extraction methods displayed distinct fungal community profiles for individual samples, with some phyla detected exclusively using the modified methods. Application of a 24 h lysis step will provide a more complete inventory of fungal biodiversity, and re-extraction of the residual soil pellet offers a novel tool for increasing discriminatory power between forensic soil samples.

Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests.

Climate change has important implications on the abundance and range of insect pests in forest ecosystems. We studied responses of root-associated fungal communities to defoliation of mountain birch hosts by a massive geometrid moth outbreak through 454 pyrosequencing of tagged amplicons of the ITS2 rDNA region. We compared fungal diversity and community composition at three levels of moth defoliation (intact control, full defoliation in one season, full defoliation in two or more seasons), replicated in three localities. Defoliation caused dramatic shifts in functional and taxonomic community composition of root-associated fungi. Differentially defoliated mountain birch roots harbored distinct fungal communities, which correlated with increasing soil nutrients and decreasing amount of host trees with green foliar mass. Ectomycorrhizal fungi (EMF) abundance and richness declined by 70-80% with increasing defoliation intensity, while saprotrophic and endophytic fungi seemed to benefit from defoliation. Moth herbivory also reduced dominance of Basidiomycota in the roots due to loss of basidiomycete EMF and increases in functionally unknown Ascomycota. Our results demonstrate the top-down control of belowground fungal communities by aboveground herbivory and suggest a marked reduction in the carbon flow from plants to soil fungi following defoliation. These results are among the first to provide evidence on cascading effects of natural herbivory on tree root-associated fungi at an ecosystem scale.

Heart rot hotel: fungal communities in red-cockaded woodpecker excavations

Tree-cavity excavators such as woodpeckers are ecosystem engineers that have potentially complex but poorly documented associations with wood decay fungi. Fungi facilitate cavity excavation by preparing and modifying excavation sites for cavity excavators. Associations between fungi and endangered red-cockaded woodpeckers (RCWs) are particularly interesting because these are the only birds that specialize in excavating into the heartwood of living pines, a process that takes years to complete. Using molecular methods, we examined fungal communities in complete and incomplete RCW excavations, and non-cavity control trees. In addition to finding a high diversity of fungi, we found three groupings of fungal communities corresponding to the three groups of trees sampled. We show that trees selected for cavity excavation by RCWs are infected by distinct fungal communities, and propose two hypotheses to explain this outcome: the bird facilitation hypothesis and the tree selection hypothesis.

Minor changes in soil bacterial and fungal community composition occur in response to monsoon precipitation in a semiarid grassland.

Arizona and New Mexico receive half of their annual precipitation during the summer monsoon season, making this large-scale rain event critical for ecosystem productivity. We used the monsoon rains to explore the responses of soil bacterial and fungal communities to natural moisture pulses in a semiarid grassland. Through 454 pyrosequencing of the 16S rRNA gene and ITS region, we phylogenetically characterized these communities at 22 time points during a summer season. Relative humidity increased before the rains arrived, creating conditions in soil that allowed for the growth of microorganisms. During the course of the study, the relative abundances of most bacterial phyla showed little variation, though some bacterial populations responded immediately to an increase in soil moisture once the monsoon rains arrived. The Firmicutes phylum experienced over a sixfold increase in relative abundance with increasing water availability. Conversely, Actinobacteria, the dominant taxa at our site, were negatively affected by the increase in water availability. No relationship was found between bacterial diversity and soil water potential. Bacterial community structure was unrelated to all environmental variables that we measured, with the exception of a significant relationship with atmospheric relative humidity. Relative abundances of fungal phyla fluctuated more throughout the season than bacterial abundances did. Variation in fungal community structure was unrelated to soil water potential and to most environmental variables. However, ordination analysis showed a distinct fungal community structure late in the season, probably due to plant senescence.

Can bioinformed design promote healthy indoor ecosystems?

Can bioinformed design promote healthy indoor ecosystems?

Ectomycorrhizal-dominated boreal and tropical forests have distinct fungal communities, but analogous spatial patterns across soil horizons.

Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0–20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling.

A distinctive fungal community inhabiting cryoconite holes on glaciers in Svalbard

Cryoconite holes on glacier surfaces are ice-cold hot spots of microbial diversity and activity but still little is known about their fungal inhabitants. We provide the first report of distinctive fungal communities in cryoconite debris from three valley glaciers at Kongsfjorden, Svalbard. Multivariate analysis of terminal-restriction fragment length polymorphism (T-RFLP) profiles of rRNA ITS amplicons revealed that quite distinct fungal communities were found in cryoconite holes compared with soils from adjacent moraine and tundra sites, and that communities on glaciers with contrasting ice-surface hydrology also differed. Most of the fungi cultured from cryoconite sediment were basidiomycetous yeasts or filamentous Ascomycota (Helotiales/Pleosporales). The latter included aeroaquatic fungi, such as Articulospora and Varicosporium, implying a role for these important freshwater decomposers in the carbon dynamics of cryoconite holes. Matching of the dominant peaks from T-RFLP analysis to predicted peaks of cultured isolates confirmed the abundance of these aeroaquatic fungi but also revealed that most of the dominant T-RFLP peaks did not match any cultured isolates. Considering the prevalence and endangerment of glacial environments worldwide, these findings would suggest that their potential as reservoirs of fungal diversity should not be overlooked.

Culture-Free Survey Reveals Diverse and Distinctive Fungal Communities Associated with Developing Figs (Ficus spp.) in Panama

The ancient association of figs (Ficus spp.) and their pollinating wasps (fig wasps; Chalcidoidea, Hymenoptera) is one of the most interdependent plant-insect mutualisms known. In addition to pollinating wasps, a diverse community of organisms develops within the microcosm of the fig inflorescence and fruit. To better understand the multipartite context of the fig-fig wasp association, we used a culture-free approach to examine fungal communities associated with syconia of six species of Ficus and their pollinating wasps in lowland Panama. Diverse fungi were recovered from surface-sterilized flowers of all Ficus species, including gall- and seed flowers at four developmental stages. Fungal communities in syconia and on pollinating wasps were similar, dominated by diverse and previously unknown Saccharomycotina, and distinct from leaf- and stem endophyte communities in the same region. Before pollination, fungal communities were similar between gall- and seed flowers and among Ficus species. However, fungal communities differed significantly in flowers after pollination vs. before pollination, and between anciently diverged lineages of Ficus with active vs. passive pollination syndromes. Within groups of relatively closely related figs, there was little evidence for strict-sense host specificity between figs and particular fungal species. Instead, mixing of fungal communities among related figs, coupled with evidence for possible transfer by pollinating wasps, is consistent with recent suggestions of pollinator mixing within syconia. In turn, changes in fungal communities during fig development and ripening suggest an unexplored role of yeasts in the context of the fig-pollinator wasp mutualism.

Distinctive fungal and bacterial communities are associated with mats formed by ectomycorrhizal fungi

The distinct rhizomorphic mats formed by ectomycorrhizal Piloderma fungi are common features of the organic soil horizons of coniferous forests of the Pacific Northwest. These mats have been found to cover 25–40% of the forest floor in some Douglas-fir stands, and are associated with physical and biochemical properties that distinguish them from the surrounding non-mat soils. In this study, we examined the fungal and bacterial communities associated with Piloderma mat and non-mat soils. Each mat and non-mat area was repeatedly sampled at four times throughout the year. Characterization of the mat activity and community was achieved using a combination of N-acetylglucosaminidase (NAGase) enzyme assays, and molecular analysis of fungal and bacterial communities using T-RFLP profiles, clone libraries, and quantitative PCR. Piloderma mats had consistently greater NAGase activity across all dates, although the magnitude of the difference varied by season. Furthermore, we found distinct fungal and bacterial communities associated with the Piloderma mats, yet the size of the microbial populations differed little between the mat and non-mat soils. Significant temporal variation was seen in the NAGase activity and in the sizes of the fungal and bacterial populations, but the community composition remained stable through time. Our results demonstrate the presence of two distinct microbial communities occupying the forest floor of Douglas-fir stands, whose populations and activities fluctuate seasonally but with little change in composition, which appears to be related to the physiochemical nature of mat and non-mat habitats.

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite’s impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C3 perennial grasses, C4 midgrasses, C4 shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.

Analyzing salt-marsh fungal diversity: comparing ARISA fingerprinting with clone sequencing and pyrosequencing

Abstract In a previous study from our laboratory we used automated ribosomal intergenic spacer analysis (ARISA) to assess salt-marsh fungal diversity ( Torzilli et al. 2006 ). The results demonstrated that different salt-marsh plants harbor distinct fungal communities, thereby supporting the hypothesis that substratum type is an important factor in determining fungal community composition. However, ARISA of several pure cultures of salt-marsh fungi indicated that an operational taxonomic unit (OUT) in an ARISA community profile may represent more than one taxon. To assess the extent to which such ambiguity might have affected the interpretation of our ARISA fingerprinting, we have now fingerprinted and sequenced clones derived from the same fungal DNA used for our ARISA community profiles. Results from this confirmed that an ARISA OTU may represent multiple taxa and that a given taxon may be represented by more than one OTU. Nonetheless, sequencing still confirmed the importance of substratum in determining community composition, and indicated that despite ambiguities associated with OTU's, ARISA may be used to provide a quick snapshot of diversity which can be further refined using sequencing methods. In addition, we compared the fungal diversity from short-form Spartina alterniflora as revealed by clone sequencing with that obtained from pyrosequencing, which avoids the cloning biases of traditional sequencing, and provide greatly expanded depth of coverage. Pyrosequencing significantly enhanced the characterization of fungal diversity compared to traditional clone sequencing.

Arbuscular mycorrhizal fungal community structures differ between co-occurring tree species of dry Afromontane tropical forest, and their seedlings exhibit potential to trap isolates suited for reforestation

The diversity of arbuscular mycorrhizal (AM) fungi and their broad or narrow association with distinct plant species in natural environments are crucial information in the understanding of the ecological role of AM fungi on plant co-existence. This knowledge is also needed for appropriate mycorrhization of nursery-grown seedlings for forestation efforts. Here, we report results from comparative studies on three co-occurring indigenous tree species of the dry Afromontane forests of Ethiopia and their seedlings grown under controlled conditions in soil collected from the sites. AM fungal SSU rDNA fragment was amplified and sequenced from mycorrhizas of adult plants and seedlings of Olea europaea subsp. cuspidata and Prunus africana, and from Podocarpus falcatus seedlings. AM fungal identity, diversity and community structure were analyzed based on sequence types defined by the NS31-AM1 SSU rDNA fragment similarity in order to compare with data from other habitats. A total of 409 sequences, grouped in 32 sequence types, belonging to Glomeraceae, Diversisporaceae and Gigasporaceae were found. Some sequence types are close to the widespread Glomus intraradices, G. hoi, G. etunicatum, G. cf. etunicatum and Gigaspora margarita. However, the majority (59%) of sequence types are so far specific for the sites including 11 new types when compared with previous data from the same area. The AM fungal community associated with adult plants, including data previously obtained from adult Podocarpus falcatus seedlings, and seedlings of a host species differed significantly, where seedlings trapping a surprising large number of native fungi. AM fungal community structure also differed significantly between host species and sites, respectively. The results confirm previous results from the same area indicating distinct fungal communities associated with the diverse tree species and suggests the potential of these indigenous tree seedlings to trap a wide range of AM fungi appropriate for successful afforestation.

Plant–fungal symbiosis en gros and en détail

Plant–fungal symbiosis <i>en gros</i> and <i>en détail</i>

Arbuscular mycorrhizal communities in tropical forests are affected by host tree species and environment.

Arbuscular mycorrhizal (AM) fungi are mutualists with plant roots that are proposed to enhance plant community diversity. Models indicate that AM fungal communities could maintain plant diversity in forests if functionally different communities are spatially separated. In this study we assess the spatial and temporal distribution of the AM fungal community in a wet tropical rainforest in Costa Rica. We test whether distinct fungal communities correlate with variation in tree life history characteristics, with host tree species, and the relative importance of soil type, seasonality and rainfall. Host tree species differ in their associated AM fungal communities, but differences in the AM community between hosts could not be generalized over life history groupings of hosts. Changes in the relative abundance of a few common AM fungal species were the cause of differences in AM fungal communities for different host tree species instead of differences in the presence and absence of AM fungal species. Thus, AM fungal communities are spatially distinguishable in the forest, even though all species are widespread. Soil fertility ranging between 5 and 9 Mg/ha phosphorus did not affect composition of AM fungal communities, although sporulation was more abundant in lower fertility soils. Sampling soils over seasons revealed that some AM fungal species sporulate profusely in the dry season compared to the rainy season. On one host tree species sampled at two sites with vastly different rainfall, relative abundance of spores from Acaulospora was lower and that of Glomus was relatively higher at the site with lower and more seasonal rainfall.