Biology subjects

Eastwood, D. C.

Publications and source records attributed to Eastwood, D. C..

3 recordsLinked to original sources

bioRxiv2021

Secondary metabolism drives ecological breadth in the Xylariaceae

Global, large-scale surveys of phylogenetically diverse plant and lichen hosts have revealed an extremely high richness of endophytes in the Xylariales, one of the largest clades of filamentous fungi and a significant source of novel secondary metabolites (SMs). Endophytes may produce host protective antimicrobial or insecticidal SMs, as well as compounds that facilitate symbiotic establishment through suppression or degradation of host immune response, but the ecological roles of most SMs are unknown. Here we characterized metabolic gene clusters in 96 genomes of endophytes and closely related saprotrophs and pathogens in two clades of Xylariales (Xylariaceae s.l. and Hypoxylaceae). Hundreds of genes appear horizontally transferred to xylarialean fungi from distantly related fungi and bacteria, including numerous genes in secondary metabolite gene clusters (SMGCs). Although all xylarialean genomes contain hyperabundant SMGCs, we show that increased gene duplications, horizontal gene transfers (HGTs), and SMGC content in Xylariaceae s.l. taxa are linked to greater phylogenetic host breadth, larger biogeographic distributions, and increased capacity for lignocellulose decomposition compared to Hypoxylaceae taxa. Overall, our results suggest that xylarialean endophytes capable of dual ecological modes (symbiotic and saprotrophic) experience greater selection to diversify SMGCs to both increase competitiveness within microbial communities and facilitate diverse symbiotic interactions.

genomics↗

bioRxiv2019

Comparison of different extraction kits to isolate microRNA from Galleria mellonella (wax moth) larvae infected with Metarhizium brunneum (ARSEF4556)

MicroRNAs (miRNAs) play an important role in regulating gene expression and are involved in developmental processes in animals, plants and fungi. To understand the role of miRNAs in a biological system, it is important to optimise the extraction procedures to obtain high quality and quantity nucleic acid that enable high throughput sequencing and expression analysis. Numerous kit-based miRNA extraction protocols have been optimised generally to single cell or tissue cultures. Fungi, however, often occupy physically and chemically complex environments which miRNA make extraction challenging, such as fungal pathogens interacting within plant or animal host tissue. We used a Galleria mellonella (wax moth) larvae and entomopathogenic fungus Metarhizium brunneum ARSEF 4556 host/pathogen model to compare commercially available miRNA extraction kits (Invitrogen PureLink miRNA Isolation Kit, Ambion mirVanamiRNA Isolation Kit and Norgen microRNA purification Kit). Our results showed reproducible and significant differences in miRNAs extraction between the kits, with the Invitrogen PureLink miRNA Isolation protocol demonstrating the best performance in terms of miRNA quantity, quality and integrity isolated from fungus-infected insect tissue.

molecular biology↗

bioRxiv2017

A mechanistic perspective of ecological networks highlights the contribution of alternative interaction strategies

O_LISpecies traits mediate ecological interaction outcomes and community structure. It is important, therefore, to identify the minimum number of traits required to characterise observed networks, i.e. the minimum dimensionality. Existing methods for estimating minimum dimensionality often lack three features commonly associated with a higher numbers of traits: a mechanistic description of observed interactions, alternative interaction modes (e.g. different feeding strategies such as active vs sit-and-wait feeding), and trait-mediated forbidden links. Omitting these features can lead to underestimation of the trait numbers involved, and therefore, minimum dimensionality. Here, we develop a minimum mechanistic dimensionality measure, accounting for these three features. C_LIO_LIThe only input required by our method is the observed network of interaction outcomes. We then assume how traits are mechanistically involved in alternative interaction modes. These unidentified traits are contrasted using pairwise performance inequalities between the interacting species. E.g. if a predator feeds upon a prey species via a typical predation mode, in each step of the predation sequence the predators performance must be greater than the preys. We construct a system of inequalities from all observed outcomes, which we attempt to solve with mixed integer linear programming. The minimum number of traits required for a feasible system of inequalities provides our dimensionality estimate. C_LIO_LIWe applied our method to 658 published empirical ecological networks including animal dominance, predator-prey, primary consumption, pollination, parasitism and seed dispersal networks, to compare with minimum dimensionality estimates when the three focal features are missing. Minimum dimensionality was typically higher when including alternative interaction modes (54% of empirical networks), forbidden interactions as trait-mediated interaction outcomes (92%), or a mechanistic perspective (81%), compared to network dimensionality estimates missing these features. C_LIO_LIOur method can reduce the risk of omitting essential traits that are involved mechanistically, in different interaction modes, or in failure outcomes. More accurate estimates will allow us to parameterise models to generate theoretical networks with a more realistic structure at the interaction outcome level. Thus, we hope our method can improve predictions of community structure and structure-dependent dynamics. C_LI

ecology↗