Genetic signatures of variation in population size in a native fungal pathogen after the recent intensive plantation of its host tree

Historical fluctuations in forests’ distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that hypothesis by reconstructing the demographic history of Armillaria ostoyae, one of the major pathogens of the maritime pine (Pinus pinaster), in the largest monospecific pine planted forest in Europe (south-western France). Genetic structure analyses and approximate Bayesian computation approaches revealed that a single pathogen population underwent a severe reduction in effective size (12 times lower) 1080–2080 generations ago, followed by an expansion (4 times higher) during the last 4 generations. These results are consistent with the history of the maritime pine forest in the region characterized by a strong recession during the last glaciation (~19 000 years ago) and massive plantations during the second half of the nineteenth century. Results suggest that recent and intensive plantations of a host tree population have offered the opportunity for a rapid spread and adaptation of their pathogens

Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology

Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration

Phylogenetic affinities and in vitro seed germination of the threatened New Zealand orchid Spiranthes novae-zelandiae

The New Zealand ladies' tresses Spiranthes novae-zelandiae is a terrestrial orchid currently classified as Threatened - Nationally Vulnerable. Although considered endemic to New Zealand, morphological similarity with the widespread Eurasian Spiranthes sinensis has cast doubt on its taxonomic and biogeographic status. Habitat destruction is the main threat to the survival of S.novae-zelandiae. Unfortunately, lack of information regarding its symbiotic fungal associates and technical expertise within New Zealand with symbiotic seed germination techniques have hindered its propagation from seed. In this study we examined the phylogenetic affinities of S.novae-zelandiae using nuclear (internal transcribed spacer) and chloroplast (trnL, trnS-G and matK) DNA sequences. We also explored the diversity of fungal symbionts associated with S.novae-zelandiae and identified the fungal symbiont that promotes seed germination and seedling development using DNA sequences and in vitro seed germination experiments. Bayesian Inference analyses showed that S.novae-zelandiae is nested within S.sinensis along with Spiranthes australis and Spiranthes aff. novae-zelandiae (CHR 518297; Motutangi), a morphological variant of uncertain taxonomic status from northern New Zealand. These results support earlier suggestions that a broader concept of S.sinensis is needed to include S.novae-zelandiae and many other taxa segregated from S.sinensis. Nine fungal Operational Taxonomic Units were isolated from the roots of S.novae-zelandiae but only one promoted seed germination and seedling development. DNA sequence analyses confirmed that this isolate was a strain of Tulasnella (anamorph: Epulorhiza); a widespread mycorrhizal fungus previously found in S.australis and S.sinensis. Lastly, we describe the germination process and the steps we followed to obtain flowering plants after 2 years of seed inoculation

Phylogenetic affinities and <i>in vitro</i> seed germination of the threatened New Zealand orchid <i>Spiranthes novae-zelandiae</i>

<p>The New Zealand “ladies’ tresses” <i>Spiranthes novae-zelandiae</i> is a terrestrial orchid currently classified as Threatened – Nationally Vulnerable. Although considered endemic to New Zealand, morphological similarity with the widespread Eurasian <i>Spiranthes sinensis</i> has cast doubt on its taxonomic and biogeographic status. Habitat destruction is the main threat to the survival of <i>S. novae-zelandiae</i>. Unfortunately, lack of information regarding its symbiotic fungal associates and technical expertise within New Zealand with symbiotic seed germination techniques have hindered its propagation from seed. In this study we examined the phylogenetic affinities of <i>S</i>.<i> novae-zelandiae</i> using nuclear (internal transcribed spacer) and chloroplast (<i>trn</i>L, <i>trn</i>S-G and <i>mat</i>K) DNA sequences. We also explored the diversity of fungal symbionts associated with <i>S. novae-zelandiae</i> and identified the fungal symbiont that promotes seed germination and seedling development using DNA sequences and <i>in vitro</i> seed germination experiments. Bayesian Inference analyses showed that <i>S. novae-zelandiae</i> is nested within <i>S. sinensis</i> along with <i>Spiranthes australis</i> and <i>Spiranthes</i> aff. <i>novae-zelandiae</i> (CHR 518297; Motutangi), a morphological variant of uncertain taxonomic status from northern New Zealand. These results support earlier suggestions that a broader concept of <i>S. sinensis</i> is needed to include <i>S. novae-zelandiae</i> and many other taxa segregated from <i>S. sinensis</i>. Nine fungal Operational Taxonomic Units were isolated from the roots of <i>S. novae-zelandiae</i> but only one promoted seed germination and seedling development. DNA sequence analyses confirmed that this isolate was a strain of <i>Tulasnella</i> (anamorph: <i>Epulorhiza</i>); a widespread mycorrhizal fungus previously found in <i>S. australis</i> and <i>S. sinensis</i>. Lastly, we describe the germination process and the steps we followed to obtain flowering plants after 2 years of seed inoculation.</p

Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants.

Comparisons of phylogenetic patterns between coevolving symbionts can reveal rich details about the evolutionary history of symbioses. The ancient symbiosis between fungus-growing ants, their fungal cultivars, antibiotic-producing bacteria and cultivar-infecting parasites is dominated by a pattern of parallel coevolution, where the symbionts of each functional group are members of monophyletic groups. However, there is one outstanding exception in the fungus-growing ant system, the unidentified cultivar grown only by ants in the Apterostigma pilosum group. We classify this cultivar in the coral-mushroom family Pterulaceae using phylogenetic reconstructions based on broad taxon sampling, including the first mushroom collected from the garden of an ant species in the A. pilosum group. The domestication of the pterulaceous cultivar is independent from the domestication of the gilled mushrooms cultivated by all other fungus-growing ants. Yet it has the same overall assemblage of coevolved ant-cultivar-parasite-bacterium interactions as the other ant-grown fungal cultivars. This indicates a pattern of convergent coevolution in the fungus-growing ant system, where symbionts with both similar and very different evolutionary histories converge to functionally identical interactions

Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae

Eukaryotic genetic interaction networks (GINs) are extensively described in the Saccharomyces cerevisiae S288C model using deletion libraries, yet being limited to this one genetic background, not informative to individual drug response. Here we created deletion libraries in three additional genetic backgrounds. Statin response was probed with five queries against four genetic backgrounds. The 20 resultant GINs representing drug-gene and gene-gene interactions were not conserved by functional enrichment, hierarchical clustering, and topology-based community partitioning. An unfolded protein response (UPR) community exhibited genetic background variation including different betweenness genes that were network bottlenecks, and we experimentally validated this UPR community via measurements of the UPR that were differentially activated and regulated in statin-resistant strains relative to the statin-sensitive S288C background. These network analyses by topology and function provide insight into the complexity of drug response influenced by genetic background.status: publishe

Identification and Bioactivity of 3-<i>epi</i>-Xestoaminol C Isolated from the New Zealand Brown Alga <i>Xiphophora chondrophylla</i>

We report here the bioassay-guided isolation of a new 1-deoxysphingoid, 3-<i>epi</i>-xestoaminol C (<b>1</b>), isolated from the New Zealand brown alga <i>Xiphophora chondrophylla</i>. This is the first report of a 1-deoxysphingoid from a brown alga. We describe the isolation and full structure elucidation of this compound, including its absolute configuration, along with its bioactivity against mycobacteria and mammalian cell lines and preliminary mechanism of action studies using yeast chemical genomics

Bioactivity-Guided Metabolite Profiling of Feijoa (<i>Acca sellowiana</i>) Cultivars Identifies 4‑Cyclopentene-1,3-dione as a Potent Antifungal Inhibitor of Chitin Synthesis

Pathogenic fungi continue to develop resistance against current antifungal drugs. To explore the potential of agricultural waste products as a source of novel antifungal compounds, we obtained an unbiased GC-MS profile of 151 compounds from 16 commercial and experimental cultivars of feijoa peels. Multivariate analysis correlated 93% of the compound profiles with antifungal bioactivities. Of the 18 compounds that significantly correlated with antifungal activity, 5 had not previously been described from feijoa. Two novel cultivars were the most bioactive, and the compound 4-cyclopentene-1,3-dione, detected in these cultivars, was potently antifungal (IC₅₀ = 1–2 μM) against human-pathogenic <i>Candida</i> species. Haploinsufficiency and fluorescence microscopy analyses determined that the synthesis of chitin, a fungal-cell-wall polysaccharide, was the target of 4-cyclopentene-1,3-dione. This fungal-specific mechanism was consistent with a 22–70-fold reduction in antibacterial activity. Overall, we identified the agricultural waste product of specific cultivars of feijoa peels as a source of potential high-value antifungal compounds