Biology subjects

Wakelin, S. A.

Publications and source records attributed to Wakelin, S. A..

3 recordsLinked to original sources

bioRxiv2024

genomesizeR: An R package for genome size prediction

The genome size of organisms present in an environment can provide many insights into evolutionary and ecological processes at play in that environment. The genomic revolution has enabled a rapid expansion of our knowledge of genomes in many living organisms, and most of that knowledge is classified and readily available in the databases of the National Center for Biotechnology Information (NCBI). The genomesizeR tool leverages the wealth of taxonomic and genomic information present in NCBI databases to infer the genome size of Archeae, Bacteria, or Eukaryote organisms identified at any taxonomic level. This R package uses statistical modelling on data from the most up-to-date NCBI databases and provides three statistical methods for genome size prediction of a given taxon, or group of taxa. A straightforward weighted mean method identifies the closest taxa with available genome size information in the taxonomic tree, and averages their genome sizes using weights based on taxonomic distance. A frequentist random effect model uses nested genus and family information to output genome size estimates. Finally a third option provides predictions from a distributional Bayesian multilevel model which uses taxonomic information from genus all the way to superkingdom, therefore providing estimates and uncertainty bounds even for under-represented taxa. All three methods use: O_LIA list of queries; a query being a taxon or a list of several taxa. The package was designed to make it easy to use with data coming from environmental DNA experiments, but works with any table of taxa. C_LIO_LIA reference database containing all the known genome sizes, built from the NCBI databases, with associated taxa, provided in an archive to download. C_LIO_LIA taxonomic tree structure as built by the NCBI, provided in the same archive. C_LI genomesizeR retrieves the taxonomic classification of input queries, estimates the genome size of each query, and provides 95% confidence intervals for each estimate.

bioinformatics↗

bioRxiv2024

Pollen Partners: The Symbiotic Microbes of Pinus radiata Pollen

Pollen, a crucial source of nutrients and energy for pollinators. It also provides a unique habitat for ecological microbiota. Previous research on the microbiome of pollen has largely focussed on angiosperm systems, with limited research into coniferous gymnosperms. This study characterises the pollen microbiome associated with one of the worlds most widely grown tree species, Pinus radiata. Trees were sampled from locations across Canterbury, New Zealand, with repeated collections in 2020 and 2021. Metabolomic analysis revealed the main compounds present on P. radiata pollen to be amino acids (principally proline), and carbohydrates (fructose, glucose, and sucrose). Although phenolic compounds such as {rho}-coumaric acid and catechin, and terpenoids such as dehydroabietic acid, were present at low concentrations, their strong bioactive natures mean they may be important in filtering of microbiome communities on pollen. Pinus radiata pollen was found to host a microbiome dominated by fungi; this directly contrasts with those for many angiosperm species. Geographic range and sampling years were evaluated as secondary drivers of microbiome assembly. Neither sampling location nor annual variation had a significant impact on the fungal component of the pine pollen microbiome, which was remarkably stable/conserved among samples. However, some bacterial taxa exhibited sensitivity to geographic distances and yearly variations, suggesting a secondary role for some. A core microbiome was identified in P. radiata pollen, characterized by a consistent presence of specific fungal and bacterial taxa across samples. While the dominant phyla, Proteobacteria and Ascomycota, align with findings from other pollen microbiome studies, unique core members were unidentified at genus level. This tree species-specific microbiome assembly emphasizes the crucial role of the host plant in shaping the pollen microbiome. These findings contribute to a deeper understanding of pollen microbiomes in gymnosperms, shedding light on the need to look further at their ecological and functional roles.

ecology↗

bioRxiv2023

Is it what's inside that matters? A conserved microbiome in woody tissues of Pinus radiata

Understanding the interaction of endophytic microbiomes and their tree hosts may provide insights into wood formation and quality. Given the role of wood in carbon and nutrient cycling, this will provide valuable insights for forest growth and carbon cycling globally. Furthermore, the management of these interactions may add new value to wood-and fibre-based forest products. We assessed the microbiome of outer and inner bark, cambium tissue, year 2-8 wood increments, and the pith of 11 Pinus radiata trees, a widely planted, model conifer species. Diverse prokaryotic and fungal microbiomes were present in all trees, with communities structured by tissue type (p<0.001). Inner and outer bark tissues had high richness and the most distinct communities. Microbiome richness was lowest in year 2 through to year 8 wood, and the communities in these samples had similar composition. Prokaryote communities were dominated by Alpha-Beta-, and Gamma-proteobacteria, Actinobacteria, Firmicutes (Clostridia and Bacilli). Within fungal communities, Sordariomycetes comprised over 90% of the taxa present. Microbiomes of cambial and pith tissues were distinct to those niches. Overall, we provide further support that the wood of conifers is host to distinct microbiome communities. Microbiomes in these niches are profoundly placed to impact tree physiology, health, and fitness, through to ecosystem function and global carbon cycles.

microbiology↗