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

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a null model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. Furthermore, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization.Fil: Daleo, Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Alberti, Juan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Jumpponen, Ari. Kansas State University; Estados UnidosFil: Veach, Allison. Kansas State University; Estados UnidosFil: Ialonardi, Florencia Emilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Iribarne, Oscar Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Silliman, Brian Red. University Of Duke. Nicholas School Of Environment. Marine Science And Conservation División; Estados Unido

Effect of four plant species on soil 15N-access and herbage yield in temporary agricultural grasslands

Positive plant diversity-productivity relationships have been reported for experimental semi-natural grasslands (Cardinale et al. 2006; Hector et al. 1999; Tilman et al. 1996) as well as temporary agricultural grasslands (Frankow-Lindberg et al. 2009; Kirwan et al. 2007; Nyfeler et al. 2009; Picasso et al. 2008). Generally, these relationships are explained, on the one hand, by niche differentiation and facilitation (Hector et al. 2002; Tilman et al. 2002) and, on the other hand, by greater probability of including a highly productive plant species in high diversity plots (Huston 1997). Both explanations accept that diversity is significant because species differ in characteristics, such as root architecture, nutrient acquisition and water use efficiency, to name a few, resulting in composition and diversity being important for improved productivity and resource use (Naeem et al. 1994; Tilman et al. 2002). Plant diversity is generally low in temporary agricultural grasslands grown for ruminant fodder production. Grass in pure stands is common, but requires high nitrogen (N) inputs. In terms of N input, two-species grass-legume mixtures are more sustainable than grass in pure stands and consequently dominate low N input grasslands (Crews and Peoples 2004; Nyfeler et al. 2009; Nyfeler et al. 2011). In temperate grasslands, N is often the limiting factor for productivity (Whitehead 1995). Plant available soil N is generally concentrated in the upper soil layers, but may leach to deeper layers, especially in grasslands that include legumes (Scherer-Lorenzen et al. 2003) and under conditions with surplus precipitation (Thorup-Kristensen 2006). To improve soil N use efficiency in temporary grasslands, we propose the addition of deep-rooting plant species to a mixture of perennial ryegrass and white clover, which are the most widespread forage plant species in temporary grasslands in a temperate climate (Moore 2003). Perennial ryegrass and white clover possess relatively shallow root systems (Kutschera and Lichtenegger 1982; Kutschera and Lichtenegger 1992) with effective rooting depths of <0.7 m on a silt loamy site (Pollock and Mead 2008). Grassland species, such as lucerne and chicory, grow their tap-roots into deep soil layers and exploit soil nutrients and water in soil layers that the commonly grown shallow-rooting grassland species cannot reach (Braun et al. 2010; Skinner 2008). Chicory grown as a catch crop after barley reduced the inorganic soil N down to 2.5 m depth during the growing season, while perennial ryegrass affected the inorganic soil N only down to 1 m depth (Thorup-Kristensen 2006). Further, on a Wakanui silt loam in New Zealand chicory extracted water down to 1.9 m and lucerne down to 2.3 m soil depth, which resulted in greater herbage yields compared with a perennial ryegrass-white clover mixture, especially for dryland plots (Brown et al. 2005). There is little information on both the ability of deep- and shallow-rooting grassland species to access soil N from different vertical soil layers and the relation of soil N-access and herbage yield in temporary agricultural grasslands. Therefore, the objective of the present work was to test the hypotheses 1) that a mixture comprising both shallow- and deep-rooting plant species has greater herbage yields than a shallow-rooting binary mixture and pure stands, 2) that deep-rooting plant species (chicory and lucerne) are superior in accessing soil N from 1.2 m soil depth compared with shallow-rooting plant species, 3) that shallow-rooting plant species (perennial ryegrass and white clover) are superior in accessing soil N from 0.4 m soil depth compared with deep-rooting plant species, 4) that a mixture of deep- and shallow-rooting plant species has greater access to soil N from three soil layers compared with a shallow-rooting two-species mixture and that 5) the leguminous grassland plants, lucerne and white clover, have a strong impact on grassland N acquisition, because of their ability to derive N from the soil and the atmosphere

One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR

Some fungi with pleomorphic life-cycles still bear two names despite more than 20 years of molecular phylogenetics that have shown how to merge the two systems of classification, the asexual “Deuteromycota” and the sexual “Eumycota”. Mycologists have begun to flout nomenclatorial regulations and use just one name for one fungus. The International Code of Botanical Nomenclature (ICBN) must change to accommodate current practice or become irrelevant. The fundamental difference in the size of fungi and plants had a role in the origin of dual nomenclature and continues to hinder the development of an ICBN that fully accommodates microscopic fungi. A nomenclatorial crisis also looms due to environmental sequencing, which suggests that most fungi will have to be named without a physical specimen. Mycology may need to break from the ICBN and create a MycoCode to account for fungi known only from environmental nucleic acid sequence (i.e. ENAS fungi)

Microbiology of the phyllosphere: a playground for testing ecological concepts

Many concepts and theories in ecology are highly debated, because it is often difficult to design decisive tests with sufficient replicates. Examples include biodiversity theories, succession concepts, invasion theories, coexistence theories, and concepts of life history strategies. Microbiological tests of ecological concepts are rapidly accumulating, but have yet to tap into their full potential to complement traditional macroecological theories. Taking the example of microbial communities on leaf surfaces (i.e. the phyllosphere), we show that most explorations of ecological concepts in this field of microbiology focus on autecology and population ecology, while community ecology remains understudied. Notable exceptions are first tests of the island biogeography theory and of biodiversity theories. Here, the phyllosphere provides the unique opportunity to set up replicated experiments, potentially moving fields such as biogeography, macroecology, and landscape ecology beyond theoretical and observational evidence. Future approaches should take advantage of the great range of spatial scales offered by the leaf surface by iteratively linking laboratory experiments with spatial simulation models

Environmental metabarcoding reveals contrasting belowground and aboveground fungal communities from poplar at a Hg phytomanagement site

Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps

Endophytic and epiphytic phyllosphere fungal communities are shaped by different environmental factors in a mediterranean ecosystem

The online version of this article (https://doi.org/10.1007/s00248-018-1161-9) contains supplementary material, which is available to authorized users.The diversity and factors influencing fimgal assemblages in phyllosphere of Mediterranean tree species have been barely studied, especially when endophytic and epiphytic communities are simultaneously considered. In this work, the endophytic and epiphytic fungal communities from olive tree phyllosphere were studied. This tree species is natural from the Mediterranean region and adapted to grow under adverse climatic conditions. The main objectives were to determine whether there are differences between both fungal communities and to examine whether different abiotic (climate-related) and biotic (plant organs) factors play a pivotal role in structuring these communities. Both communities differed in size and composition, with epiphytic community being richer and more abundant, displaying also a dominance of melanized fungi. Season was the major driver of community composition, especially of epiphytes. Other drivers shaping epiphytes were wind speed and temperature, while plant organ, rainfall, and temperature were the major drivers for endophytic composition. In contrast, canopy orientation caused slight variations in community composition of fungi, but with distinct effects in spring and autumn seasons. In conclusion, epiphytic and endophytic communities are not driven by the same factors. Several sources of variation undergo complex interactions to form and maintain phyllosphere fungal community in Mediterranean climates. Climatic parameters have influence on these fungal communities, suggesting that they are likely to be affected by climate changes in a near future.This work is funded by FEDER funds through COMPETE (Programa Operacional Factores de Competitividade) and by national funds by FCT (Fundacao para a Ciencia e a Tecnologia) within the framework of the project EXCL/AGR-PRO/0591/2012. T. Gomes thanks FCT, POPH-QREN, and FSE for PhD SFRH/BD/98127/2013 grant

Serpentine Soils Do Not Limit Mycorrhizal Fungal Diversity

Background: Physiologically stressful environments tend to host depauperate and specialized biological communities. Serpentine soils exemplify this phenomenon by imposing well-known constraints on plants; however, their effect on other organisms is still poorly understood. Methodology/Principal Findings: We used a combination of field and molecular approaches to test the hypothesis that serpentine fungal communities are species-poor and specialized. We conducted surveys of ectomycorrhizal fungal diversity from adjacent serpentine and non-serpentine sites, described fungal communities using nrDNA Internal Transcribed Spacer (ITS) fragment and sequence analyses, and compared their phylogenetic community structure. Although we detected low fungal overlap across the two habitats, we found serpentine soils to support rich fungal communities that include representatives from all major fungal lineages. We failed to detect the phylogenetic signature of endemic clades that would result from specialization and adaptive radiation within this habitat. Conclusions/Significance: Our results indicate that serpentine soils do not constitute an extreme environment for ectomycorrhizal fungi, and raise important questions about the role of symbioses in edaphic tolerance and the maintenanc

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

<p>Abstract</p> <p>Background</p> <p>Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems.</p> <p>Results</p> <p>Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian <it>Poa </it>grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.</p> <p>We applied this method to a group of sympatric Australian alpine <it>Poa </it>species, which we discovered to share an allopolyploid ancestor with a group of American <it>Poa </it>species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the <it>trn</it>H-<it>psb</it>A marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group.</p> <p>Conclusions</p> <p>Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.</p