Tallgrass prairie soil fungal communities are resilient to climate change

Climate models for central United States predict increasing temperatures and greater variability in precipitation. Combined, these shifts in environmental conditions impact many ecosystem properties and services. Long‐term climate change experiments, such as the Rainfall Manipulation Plots (RaMPs), can be used to address soil community responses to simultaneous manipulation of temperature and temporal variability in precipitation. The RaMPs experiment is located in a native tallgrass prairie at the Konza Prairie Biological Station and has been operational since 1998 providing the potential to address responses to long‐term environmental manipulations. To test whether community composition, richness, or diversity respond to environmental change, more than 40,000 fungal amplicons were analyzed from soil samples collected in 2006. The data suggest that soil fungal communities are compositionally resilient to predicted environmental change. This is the case both for the community composition overall as inferred from ordination analyses as well as analyses of variance for each of the most common Operational Taxonomic Units (OTUs). However, while this study suggests compositional resilience, further studies are required to address functional attributes of these communities and their responses to environmental manipulations

Mutualism-parasitism paradigm synthesized from results of root-endophyte models

Citation: Mandyam, K. G., & Jumpponen, A. (2015). Mutualism-parasitism paradigm synthesized from results of root-endophyte models. Frontiers in Microbiology, 5, 13. doi:10.3389/fmicb.2014.00776Plant tissues host a variety of fungi. One important group is the dark septate endophytes (DSEs) that colonize plant roots and form characteristic intracellular structures melanized hyphae and microsclerotia. The DSE associations are common and frequently observed in various biomes and plant taxa. Reviews suggest that the proportion of plant species colonized by DSE equal that colonized by AM and microscopic studies show that the proportion of the root system colonized by fungi DSE can equal, or even exceed, the colonization by AM fungi. Despite the high frequency and suspected ecological importance, the effects of DSE colonization on plant growth and performance have remained unclear. Here, we draw from over a decade of experimentation with the obscure DSE symbiosis and synthesize across large bodies of published and unpublished data from Arabidopsis thaliana and Allium porrum model systems as well as from experiments that use native plants to better resolve the host responses to DSE colonization. The data indicate similar distribution of host responses in model and native plant studies, validating the use of model plants for tractable dissection of DSE symbioses. The available data also permit empirical testing of the environmental modulation of host responses to DSE colonization and refining the "mutualism-parasitism-continuum" paradigm for DSE symbioses. These data highlight the context dependency of the DSE symbioses: not only plant species but also ecotypes vary in their responses to populations of conspecific DSE fungi environmental conditions further shift the host responses similar to those predicted based on the mutualism-parasitism-continuum paradigm. The model systems provide several established avenues of inquiry that permit more detailed molecular and functional dissection of fungal endophyte symbioses, identifying thus likely mechanisms that may underlie the observed host responses to endophyte colonization

Fungi and algae co-occur in snow: an issue of shared habitat or algal facilitation of heterotrophs?

Citation: Brown, S. P., Olson, B., & Jumpponen, A. (2015). Fungi and algae co-occur in snow: an issue of shared habitat or algal facilitation of heterotrophs? Arctic Antarctic and Alpine Research, 47(4), 729-749. doi:10.1657/aaar0014-071Late season alpine snows are often colonized by psychrophilic snow algae that may provide a source of nutrients for microbes. Such late season snows are a harsh environment, but support a diverse and complex fungal community. We used culture independent methods (Illumina MiSeq) to test if the presence of snow algae influences fungal communities. We compared algae-colonized snows to adjacent (3 m distant) noncolonized snows in a paired experimental design. Our data indicate that several fungi are locally enriched in algae colonized snows. Although many such fungi were basidiomycetous yeasts, our analyses identified a large number of snow-borne members of phylum Chytridiomycota. While the ecology and function of these Chytridiomycetes remain unclear, we hypothesize that their enrichment in the algal patches suggests that they depend on algae for nutrition. We propose that these chytrids are important components in snow ecosystems, highlighting the underestimation of their diversity and importance. Taken together, our data strongly indicate that fungal communities are heterogeneous in snow even among adjacent samples. Further, fungal and algal communities may be influenced by similar environmental drivers resulting in their co-occurrence in snow

A community of clones: Snow algae are diverse communities of spatially structured clones

Citation: Brown, S. P., Ungerer, M. C., & Jumpponen, A. (2016). A community of clones: Snow algae are diverse communities of spatially structured clones. International Journal of Plant Sciences, 177(5), 432-439. doi:10.1086/686019Premise of research. Snow algae are cosmopolitan and often colonize late-season snowpacks. These snow algae do not occur in isolation; rather, visible algal blooms consist of multispecies communities. Although several of these common snow algae have been characterized taxonomically, their inter- and intraspecific diversity remains unknown. Further, the phylogeographic and biogeographic structuring of snow algal species is poorly understood. Methodology. Algal communities were censused by sequencing the variable internal transcribed spacer 2 locus using Illumina MiSeq. We further analyzed two of the most common and abundant algal operational taxonomic units (OTUs) for biogeographic haplotype diversity. Pivotal results. Our data show that the communities are diverse and taxonomically broad (orders: Chlamydomonadales [74% of OTUs], Microthamniales [20% OTUs], and Chlorellales [6% OTUs]). We demonstrate that the two most common species (best nucleotide basic local alignment search tool match to Coenochloris sp. and Chlamydomonas sp.) have distinct haplotype distributions locally and regionally. Each sampled algal colony was dominated by one and only one haplotype, with negligible intraspecific haplotype diversity. Conclusions. Our results suggest that snow algae are communities of clones within a discrete patch yet are heterogeneous across the landscape. Thus, these communities are likely structured via strong priority effects, intense kin competition, and dispersal limitations. © 2016 by The University of Chicago. All rights reserved

Ectomycorrhizal Fungal Communities in Urban Parks Are Similar to Those in Natural Forests but Shaped by Vegetation and Park Age

Ectomycorrhizal (ECM) fungi are important mutualists for the growth and health of most boreal trees. Forest age and its host species composition can impact the composition of ECM fungal communities. Although plentiful empirical data exist for forested environments, the effects of established vegetation and its successional trajectories on ECM fungi in urban greenspaces remain poorly understood. We analyzed ECM fungi in 5 control forests and 41 urban parks of two plant functional groups (conifer and broadleaf trees) and in three age categories (10, similar to 50, and > 100 years old) in southern Finland. Our results show that although ECM fungal richness was marginally greater in forests than in urban parks, urban parks still hosted rich and diverse ECM fungal communities. ECM fungal community composition differed between the two habitats but was driven by taxon rank order reordering, as key ECM fungal taxa remained largely the same. In parks, the ECM communities differed between conifer and broadleaf trees. The successional trajectories of ECM fungi, as inferred in relation to the time since park construction, differed among the conifers and broadleaf trees: the ECM fungal communities changed over time under the conifers, whereas communities under broadleaf trees provided no evidence for such age-related effects. Our data show that plant-ECM fungus interactions in urban parks, in spite of being constructed environments, are surprisingly similar in richness to those in natural forests. This suggests that the presence of host trees, rather than soil characteristics or even disturbance regime of the system, determine ECM fungal community structure and diversity. IMPORTANCE In urban environments, soil and trees improve environmental quality and provide essential ecosystem services. ECM fungi enhance plant growth and performance, increasing plant nutrient acquisition and protecting plants against toxic compounds. Recent evidence indicates that soil-inhabiting fungal communities, including ECM and saprotrophic fungi, in urban parks are affected by plant functional type and park age. However, ECM fungal diversity and its responses to urban stress, plant functional type, or park age remain unknown. The significance of our study is in identifying, in greater detail, the responses of ECM fungi in the rhizospheres of conifer and broadleaf trees in urban parks. This will greatly enhance our knowledge of ECM fungal communities under urban stresses, and the findings can be utilized by urban planners to improve urban ecosystem services.Peer reviewe

Over twenty years farmland reforestation decreases fungal diversity of soils, but stimulates the return of ectomycorrhizal fungal communities

Although soil-inhabiting fungi can affect tree health and biomass production in managed and pristine forests, little is known about the sensitivity of the plant-fungal associations to long-term changes in land use. We aimed to investigate how reforestation of farmlands change soil characteristics and affected the recovery of soil fungal functional guilds. We examined edaphic conditions and fungal communities (Illumina Sequencing) in three land-use types: primary forests (PF), secondary forests (SF, established over two decades ago) and active farmlands during May, July and September in Wuying, China. Edaphic conditions and general fungal communities varied with land-use. Interestingly, overall fungal diversity was higher in soils at the farmland than at the forested sites, possibly as a result of recurring disturbances (tilling) allowing competitive release as described by the intermediate disturbance hypothesis. Although ectomycorrhizal fungal diversity and richness were marginally higher in PF than in SF, the latter still hosted surprisingly diverse and abundant ectomycorrhizal fungal communities. Reforestation largely restored fungal communities that were still in transition, as their composition in SF was distinct from that in PF. Our results highlight the ability of fungi grown in previously strongly managed agricultural land to rapidly respond to reforestation and thus provide support for forest trees.Peer reviewe

Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials

Background. Polycyclic aromatic hydrocarbons (PAHs) accumulate in urban soils, and PAH contamination can change soil microbial community composition. Environmental microbiota is associated with human commensal microbiota, immune system and health. Therefore, studies investigating the degradation of PAHs, and the consequences of soil pollution on microbial communities in urban landscaping materials, are crucial. Methods. Four landscaping materials (organic matter 1, 2, 13 and 56%) were contaminated with PAHs commonly found at urban sites (phenanthrene, fluoranthene, pyrene, chrysene and benzo(b)fluoranthene) in PAH concentrations that reflect urban soils in Finland (2.4 mu g g(-1) soil dry weight). PAHs were analyzed initially and after 2, 4, 8 and 12 weeks by gas chromatography-mass spectrometry. Half-lives of PAHs were determined based on 12-weeks degradation. Bacterial communities were analyzed at 1 and 12 weeks after contamination using Illumina MiSeq 16S rRNA gene metabarcoding. Results. Half-lives ranged from 1.5 to 4.4 weeks for PAHs with relatively low molecular weights (phenanthrene, fluoranthene and pyrene) in landscaping materials containing 1-2% organic matter. In contrast, in materials containing 13% and 56% organic matter, the half-lives ranged from 2.5 to 52 weeks. Shorter half-lives of phenanthrene and fluoranthene were thus associated with low organic matter content. The half-life of pyrene was inversely related to the relative abundance of Beta-, Delta- and Gammaproteobacteria, and diversity of Bacteroidetes and Betaprotebacteria. Compounds with higher molecular weights followed compound-specific patterns. Benzo(b)fluoranthene was resistant to degradation and half-life of chrysene was shorter when the relative abundance of Betaproteobacteria was high. Temporal microbiota changes involved increase in the relative abundance of Deltaproteobacteria and decrease in genera Flavobacterium and Rhodanobacter. Exposure to PAHs seems to adjust microbial community composition, particularly within class Beta- and Deltaproteobacteria. Conclusions. In this study, PAH degradation depended on the organic matter content and bacterial community composition of landscaping materials. Contamination seems to alter bacterial community composition in landscaping materials depending on material type. This alteration includes changes in bacterial phyla associated with human health and immune system. This may open new possibilities for managing urban environments by careful selection of landscaping materials, to benefit health and wellbeing.Peer reviewe

Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem

Prescribed burning is a common management tool to control fuel loads, ground vegetation, and facilitate desirable game species. We evaluated soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia and utilized deep Internal Transcribed Spacer Region 1 (ITS1) amplicon sequencing afforded by the recent Ion Torrent Personal Genome Machine (PGM). These deep sequence data (19,000+ reads per sample after subsampling) indicate that frequent fires (3 year fire interval) shift soil fungus communities whereas infrequent fires (6 year fire interval) permit system resetting to a state similar to that without prescribed fire. Furthermore, in nonmetric multidimensional scaling analyses, primarily ectomycorrhizal taxa were correlated with axes associated with long fire intervals whereas soil saprobes tended to be correlated with the frequent fire recurrence. We conclude that 1) multiplexed Ion Torrent PGM analyses allow deep cost effective sequencing of fungal communities, but may suffer from short read lengths and inconsistent sequence quality adjacent to the sequencing adaptor; 2) frequent prescribed fires elicit a shift in soil fungal communities; and, 3) such shifts do not occur when fire intervals are longer. Our results emphasize the general responsiveness of these forests to management, and the importance of fire return intervals in meeting management objectives

Analyses of Sporocarps, Morphotyped Ectomycorrhizae, Environmental ITS and LSU Sequences Identify Common Genera that Occur at a Periglacial Site

Abstract: Periglacial substrates exposed by retreating glaciers represent extreme and sensitive environments defined by a variety of abiotic stressors that challenge organismal establishment and survival. The simple communities often residing at these sites enable their analyses in depth. We utilized existing data and mined published sporocarp, morphotyped ectomycorrhizae (ECM), as well as environmental sequence data of internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal RNA gene to identify taxa that occur at a glacier forefront in the North Cascades Mountains in Washington State in the USA. The discrete data types consistently identified several common and widely distributed genera, perhaps best exemplified by Inocybe and Laccaria. Although we expected low diversity and richness, our environmental sequence data included 37 ITS and 26 LSU operational taxonomic units (OTUs) that likely form ECM. While environmental surveys of metabarcode markers detected large numbers of targeted ECM taxa, both the fruiting body and the morphotype datasets included genera that were undetected in either of the metabarcode datasets. These included hypogeous (Hymenogaster) and epigeous (Lactarius) taxa, some of which may produce large sporocarps but may possess small and/or spatially patchy genets. We highlight the importance of combining various data types to provide a comprehensive view of a fungal community, even in an environment assumed to host communities of low species richness and diversity.Peer reviewe

Twenty years of research on fungus-microbe-plant interactions on Lyman Glacier forefront – lessons learned and questions yet unanswered

Retreating glaciers and the periglacial areas they vacate for organismal colonization produce a harsh environment of extreme radiation, nutrient limitations, and temperature oscillations. They provide a model system for studying mechanisms that drive establishment and early assembly of communities. Here, we synthesize more than twenty years of research at the Lyman Glacier forefront in the North Cascades Mountains, comparing the results and conclusions for plant and microbial communities. Compared to plant communities, the trajectories and processes of microbial community development are difficult to deduce. However, the combination of high throughput sequencing, more revealing experimental designs, and analyses of phylogenetic community provide insights into mechanisms that shape early microbial communities. While the inoculum is likely randomly drawn from regional pools and accumulates over time, our data provide no support for increases in richness over time since deglaciation as is commonly observed for plant communities. Re-analyses of existing datasets suggest that microbial, particularly fungal, communities are insensitive to time since substrate exposure from underneath the retreating glacier but responsive to plant establishment both in biomass and community composition. Further research on functional aspects, organismal activity, or ecosystem services in early successional environments will provide deeper appreciation for the dynamics of these communities.Keywords: community assembly, glacier forefront, mycorrhizae, community divergence, propagule, community trajectory, establishment, community convergenc