Mycobiome of the Bat White Nose Syndrome (WNS) Affected Caves and Mines reveals High Diversity of Fungi and Local Adaptation by the Fungal Pathogen Pseudogymnoascus (Geomyces) destructans

The investigations of the bat White Nose Syndrome (WNS) have yet to provide answers as to how the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) first appeared in the Northeast and how a single clone has spread rapidly in the US and Canada. We aimed to catalogue Pd and all other fungi (mycobiome) by the culture-dependent (CD) and culture-independent (CI) methods in four Mines and two Caves from the epicenter of WNS zoonotic. Six hundred sixty-five fungal isolates were obtained by CD method including the live recovery of Pd. Seven hundred three nucleotide sequences that met the definition of operational taxonomic units (OTUs) were recovered by CI methods. Most OTUs belonged to unidentified clones deposited in the databases as environmental nucleic acid sequences (ENAS). The core mycobiome of WNS affected sites comprised of 46 species of fungi from 31 genera recovered in culture, and 17 fungal genera and 31 ENAS identified from clone libraries. Fungi such as Arthroderma spp., Geomyces spp., Kernia spp., Mortierella spp., Penicillium spp., and Verticillium spp. were predominant in culture while Ganoderma spp., Geomyces spp., Mortierella spp., Penicillium spp. and Trichosporon spp. were abundant is clone libraries. Alpha diversity analyses from CI data revealed that fungal community structure was highly diverse. However, the true species diversity remains undetermined due to under sampling. The frequent recovery of Pd indicated that the pathogen has adapted to WNS-afflicted habitats. Further, this study supports the hypothesis that Pd is an introduced species. These findings underscore the need for integrated WNS control measures that target both bats and the fungal pathogen.Comment: 59 pages, 7figure

Fungal Traits Important for Soil Aggregation

Soil structure, the complex arrangement of soil into aggregates and pore spaces, is a key feature of soils and soil biota. Among them, filamentous saprobic fungi have well-documented effects on soil aggregation. However, it is unclear what properties, or traits, determine the overall positive effect of fungi on soil aggregation. To achieve progress, it would be helpful to systematically investigate a broad suite of fungal species for their trait expression and the relation of these traits to soil aggregation. Here, we apply a trait-based approach to a set of 15 traits measured under standardized conditions on 31 fungal strains including Ascomycota, Basidiomycota, and Mucoromycota, all isolated from the same soil. We find large differences among these fungi in their ability to aggregate soil, including neutral to positive effects, and we document large differences in trait expression among strains. We identify biomass density, i.e., the density with which a mycelium grows (positive effects), leucine aminopeptidase activity (negative effects) and phylogeny as important factors explaining differences in soil aggregate formation (SAF) among fungal strains; importantly, growth rate was not among the important traits. Our results point to a typical suite of traits characterizing fungi that are good soil aggregators, and our findings illustrate the power of employing a trait-based approach to unravel biological mechanisms underpinning soil aggregation. Such an approach could now be extended also to other soil biota groups. In an applied context of restoration and agriculture, such trait information can inform management, for example to prioritize practices that favor the expression of more desirable fungal traits

Root-associated fungal communities colonizing two dominant semiarid grasses: Hilaria sp. and Stipa sp.

We conducted a preliminary survey of the fungal communities associated with roots of Stipa hymenoides and Hilaria jamesii, two grasses native to the southwestern United States. Root samples from 10 different plants were collected at a semiarid grassland in Utah. Fungal communities were assessed using microscopic and molecular methods. Roots were cleared with KOH and stained using blue ink to visualize mycorrhizal and endophytic fungi. A total of 100 root segments were surface sterilized and plated on malt extract agar with antibiotics. Fungal endophytes were identified using nrITS primers.

Results/Conclusions

Microscopic analyses showed that all root samples from both Hillaria and Stipa were colonized by dark septate and arbuscular mycorrhizal fungi. Vesicles and hyaline hyphae also were observed in all the roots. Sclerotia, a characteristic structure of some dark septate fungi were also found. Approximately 75 fungi were isolated representing at least 45 morphotypes. Molecular identification showed that both grasses are colonized by endophytes in the orders Pleosporales, Hypocreales, and Sordariales commonly found in semiarid grasses, liverworts, and mosses

Micro-eukaryotic diversity in hypolithons from Miers Valley, Antarctica

The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts

The largest reservoir of mitochondrial introns is a relic of an ancestral split gene

In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms (ref. 1-4). Large introns (0.1 to 5 kbp) are frequent in mitochondrial genomes of plant and fungi (ref. 1,5) but scarce in Metazoa, despite these organisms are grouped with fungi among Opisthokonts. Introns are classified in two main groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism (ref. 5,6). Most of the group I introns carry a "Homing Endonuclease Gene" (ref. 7-9) encoding a DNA endonuclease acting in the transfer and site specific integration "homing") and allowing the intron spreading and gain after lateral transfer even between species from different kingdoms (ref. 10,11). Opposite to this "late intron" paradigm, the "early intron" theory indicates that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss (ref. 12,13).

Here we report the sequence of the cox1 gene of the button mushroom _Agaricus bisporus_, the most worldwide cultivated mushroom. This gene is both the longest mitochondrial gene (29,902 nt) and the largest Group I intron reservoir reported to date. An analysis of the group I introns available in _cox1_ genes shows that they are ancestral mobile genetic elements, whose frequent events of loss (according to the "late theory") and gain by lateral transfer ("early theory") must be combined to explain their wide and patchy distribution extending on several kingdoms. This allows the conciliation of the "early" and "late intron" paradigms, which are still matters of much debate (ref. 14,15). The overview of the intron distribution indicates that they evolve towards elimination. In such a landscape of eroded and lost intron sequences, the _A. bisporus_ largest intron reservoir, by its singular dynamics of intron keeping and catching, constitutes the most fitted relic of an early split gene

Managing with fire: effects of recurring prescribed fire on soil and root-associated fungal communities

Master of ScienceDepartment of BiologyAri JumpponenPrescribed fire is a necessary management tool used to reduce fuel loads and to maintain fire-adapted ecosystems over time. Although the effects of fire on vegetation and soil properties are well understood, the long-term impacts of different fire regimes on soil fungi, root-inhabiting and ectomycorrhizal (ECM) fungi remain largely unknown. Previous studies show that high intensity wildfires reduce soil fungal biomass and alter fungal communities, however the effects of repeated low intensity prescribed fires are less understood. Studies described in this thesis took advantage of a long-term (>25 years) fire management regime in southern yellow pine stands in the southeastern United States to analyze the effects of repeated prescribed fires on soil fungi, root-associated and ECM fungal communities. The fire management regimes included five fire treatments varying in season (winter and summer) and interval length (two-year, three-year, six-year, and unburned control) allowing us to address effects of burn season and fire frequency on these fungal communities. We used 454-pyrosequencing to analyze ECM roots to specifically focus on the root-associate fungi and ECM. After a pilot study comparing the use of non-proofreading and proofreading polymerases to generate deep high throughput sequence data on soil fungal communities using Illumina MiSeq technology, proofreading polymerase was chosen to create amplicon libraries to minimize overestimation of community richness and underestimation of community evenness. We found that season had no or only minimal effect on diversity and community composition on any of these fungal communities. However, both soil and root-associated fungi responded compositionally to frequent fire intervals. In contrast, we observed no effects of recurring fire on ECM communities. Indicator taxon analyses identified many taxa in each dataset (soil, root-associated, and ECM fungi) that represent potentially fire suppressed or fire adapted taxa. These findings indicate that frequent recurring prescribed fires result in distinct fire adapted/tolerant soil and root-associated fungal communities that are correlated with the desired fire-adapted plant communities. However, the ECM symbionts colonizing these hosts remain largely unaffected