A high-quality draft genome sequence of Neonectria faginata, causative agent of beech bark disease of Fagus grandifolia

DATA AVAILABILITY : This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAULBG000000000. The version described in this paper is version JAULBG010000000. Raw sequence data are available at NCBI SRA under project number PRJNA994555. Sequences of TEF1- and RPB2 are deposited in GenBank under accession numbers OR338330 and OR338331.The draft genome of Neonectria faginata was sequenced with Oxford Nanopore and Illumina 250 bp paired-end sequencing technologies. The assembled genome was 42.9 Mb distributed over 24 contigs, with N50 of 4.4 Mb and 98.6% BUSCO completeness. This genome sequence will aid in understanding N. faginata population structure and ecology.Partial funding was provided by the New Hampshire Agricultural Experiment Station. Supported by the USDA National Institute of Food and Agriculture McIntire-Stennis, the state of New Hampshire and a USDA National Institute of Food and Agriculture postdoctoral fellowship.https://journals.asm.org/journal/mrahj2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyNon

Defining invasiveness and invasibility in ecological networks

The success of a biological invasion is context dependent, and yet two key concepts—the invasiveness of species and the invasibility of recipient ecosystems—are often defined and considered separately. We propose a framework that can elucidate the complex relationship between invasibility and invasiveness. It is based on trait-mediated interactions between species and depicts the response of an ecological network to the intrusion of an alien species, drawing on the concept of community saturation. Here, invasiveness of an introduced species with a particular trait is measured by its per capita population growth rate when the initial propagule pressure of the introduced species is very low. The invasibility of the recipient habitat or ecosystem is dependent on the structure of the resident ecological network and is defined as the total width of an opportunity niche in the trait space susceptible to invasion. Invasibility is thus a measure of network instability. We also correlate invasibility with the asymptotic stability of resident ecological network, measured by the leading eigenvalue of the interaction matrix that depicts trait-based interaction intensity multiplied by encounter rate (a pairwise product of propagule pressure of all members in a community). We further examine the relationship between invasibility and network architecture, including network connectance, nestedness and modularity. We exemplify this framework with a trait-based assembly model under perturbations in ways to emulate fluctuating resources and random trait composition in ecological networks. The maximum invasiveness of a potential invader (greatest intrinsic population growth rate) was found to be positively correlated with invasibility of the recipient ecological network. Additionally, ecosystems with high network modularity and high ecological stability tend to exhibit high invasibility. Where quantitative data are lacking we propose using a qualitative interaction matrix of the ecological network perceived by a potential invader so that the structural network stability and invasibility can be estimated from the literature or from expert opinion. This approach links network structure, invasiveness and invasibility in the context of trait-mediated interactions, such as the invasion of insects into mutualistic and antagonistic networks

Forest insect population dynamics

Most insect species are rare most of the time, but populations of certain taxa exhibit dramatic fluctuations in abundance across years. These fluctuations range from highly regular, cyclical dynamics to mathematical chaos. Peaks in abundance, or “population outbreaks” are notable both for the damage they can cause in natural and planted forests and for the rich body of research and theory they have inspired focused on elucidating drivers of population fluctuations across time and space. This chapter explores some of the key mechanisms that explain the population dynamics of outbreaking species, including variation in intrinsic growth rates, lagged endogenous feedbacks linked to top-down and/or bottom-up effects, nonlinearities in the density dependent relationship, and the existence of multiple stable and unstable equilibria, among others. We explore some basic mathematical and graphical approaches to modeling and representing these dynamics and provide a suite of empirical examples from the recent and historical literatur

Species and environmental matrix

This file contains three spreadsheets (1) the presence/absence data of Phytophthora species by site (2) the environmental matrix/categories and (3) the species informatio

Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity

The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with insufficient taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths

Data from: Predictors of Phytophthora diversity and community composition in natural areas across diverse Australian ecoregions

Comprehensive understanding of the patterns and drivers of microbial diversity at a landscape scale is in its infancy, despite the recent ease by which soil communities can be characterized using massively parallel amplicon sequencing. Here we report on a comprehensive analysis of the drivers of diversity distribution and composition of the ecologically and economically important Phytophthora genus from 414 soil samples collected across Australia. We assessed 22 environmental and seven categorical variables as potential predictors of Phytophthora species richness, αandβ diversity, including both phylogenetically and non‐phylogenically explicit methods. In addition, we classified each species as putatively native or introduced and examined the distribution with respect to putative origin. The two most widespread species, P. multivora and P. cinamomi, are introduced, though five of the ten most widely distributed species are putatively native. Introduced taxa comprised over 54% of Australia's Phytophthora diversity and these species are known pathogens of annual and perennial crop habitats as well as urban landscapes and forestry. Patterns of composition were most strongly predicted by bioregion (R2=0.29) and ecoregion (R2=0.26) identity; mean precipitation of warmest quarter, mean temperature of the wettest quarter and latitude were also highly significant and described approximately 21%, 14% and 13% of variation in NMDS composition, respectively. We also found statistically significant evidence for phylogenetic over‐dispersion with respect to key climate variables.This study provides a strong baseline for understanding biogeographical patterns in this important genus as well the impact of key plant pathogens and invasive Phytophthora species in natural ecosystems

seq.fna.zip

Sequences obtained from Ion Torrent Amplicon sequencing of the fungal community of Eucalyptus grandis in South Africa

Demography of an invading forest insect reunited with hosts and parasitoids from its native range

The Sirex woodwasp Sirex noctilio Fabricius (Hymenoptera: Siricidae), a widespread invasive pest of pines in the Southern Hemisphere, was first detected in North America in 2004. This study assessed the impacts of life history traits, host resistance and species interactions on the demography of S. noctilio in New York, Pennsylvania and Vermont, then compared key metrics to those found in the native range in Galicia, Spain. Many trees naturally attacked by S. noctilio in North America produced no adult woodwasps, with 5 of 38 infested trees (13%) sampled across six sites yielding 64% of emerging insects. Reproductive success was highest in the introduced host scots pine, Pinus sylvestris, but native red pine, Pinus resinosa, produced larger insects. Sirex noctilio required one or sometimes two years to develop and sex ratios were male biased, 1:2.98 ♀:♂. Body size and fecundity were highly variable, but generally lower than observed in non-native populations in the Southern Hemisphere. Hymenopteran parasitoids killed approximately 20% of S. noctilio larvae and 63% of emerging adults were colonized by the parasitic nematode Deladenus siricidicola, although no nematodes entered eggs. Demographic models suggested that S. noctilio in the northeastern USA have a higher potential for population growth than populations in the native range: estimated finite factor of increase, λ, was 4.17–4.52 (depending on tree species colonized), compared to λ = 1.57 in Spain

Mean family richness.

<p>Mean family richness for the parameter settings (‘perfect match’, ‘fuzzy match’, ‘no primer’) and OTU sequence similarity values (90%, 95%, 97%).</p