Charlotte Armstrong’s research while affiliated with Ministry for the Environment, New Zealand and other places

Background Pollen is a crucial source of nutrients and energy for pollinators. It also provides a unique habitat and resource for microbiota. Previous research on the microbiome of pollen has largely focused on angiosperm systems, with limited research into coniferous gymnosperms. This study characterises the pollen microbiome and metabolome associated with one of the world’s most widely grown tree species, Pinus radiata . Trees were sampled from locations across Canterbury, New Zealand. Repeated collections were undertaken in 2020 and 2021. Results 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 ρ-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 ecological filtering of microbiome communities on pollen. The P. radiata pollen microbiome was richer in fungal taxa compared with bacteria, which differs from many angiosperm species. Geographic range and annual variation were evaluated as drivers of microbiome assembly. Neither sampling location (geographic range) nor annual variation significantly influenced the fungal community which exhibited remarkable conservation across samples. However, some bacterial taxa exhibited sensitivity to geographic distances and yearly variations, suggesting a secondary role of these factors for some taxa. 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. Conclusion 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.

Bradyrhizobium sp. Ash2021 is a free-living soil bacterium isolated from a Pinus radiata forest in Canterbury, New Zealand. The genome comprises of a 9,328,819 bp chromosome and a 375,468 bp plasmid. The chromosome harbors biosynthesis pathways for auxins, thiazole-oxazole-modified microcins, and polyketide synthase. The plasmid harbors lactate and GlcNAc metabolism genes.

Temperate forest soils are considered significant methane (CH4) sinks, but other methane sources and sinks within these forests, such as trees, litter, deadwood, and the production of volatile organic compounds are not well understood. Improved understanding of all CH4 fluxes in temperate forests could help mitigate CH4 emissions from other sources and improve the accuracy of global greenhouse gas budgets. This review highlights the characteristics of temperate forests that influence CH4 flux and assesses the current understanding of the CH4 cycle in temperate forests, with a focus on those managed for specific purposes. Methane fluxes from trees, litter, deadwood, and soil, as well as the interaction of canopy-released volatile organic compounds on atmospheric methane chemistry are quantified, the processes involved and factors (biological, climatic, management) affecting the magnitude and variance of these fluxes are discussed. Temperate forests are unique in that they are extremely variable due to strong seasonality and significant human intervention. These features control CH4 flux and need to be considered in CH4 budgets. The literature confirmed that temperate planted forest soils are a significant CH4 sink, but tree stems are a small CH4 source. CH4 fluxes from foliage and deadwood vary, and litter fluxes are negligible. The production of volatile organic compounds could increase CH4’s lifetime in the atmosphere, but current in-forest measurements are insufficient to determine the magnitude of any effect. For all sources and sinks more research is required into the mechanisms and microbial community driving CH4 fluxes. The variability in CH4 fluxes within each component of the forest, is also not well understood and has led to overestimation of CH4 fluxes when scaling up measurements to a forest or global scale. A roadmap for sampling and scaling is required to ensure that all CH4 sinks and sources within temperate forests are accurately accounted for and able to be included in CH4 budgets and models to ensure accurate estimates of the contribution of temperate planted forests to the global CH4 cycle.

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 world's 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 ρ-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.

Abstract The assembly and function of the phyllosphere microbiome is important to the overall fitness of plants and, thereby, the ecosystems they inhabit. Presently, model systems for tree phyllosphere microbiome studies are lacking, yet forests resilient to pests, diseases, and climate change are important to support a myriad of ecosystem services impacting from local to global levels. In this study, we extend the development of model microbiome systems for trees species, particularly coniferous gymnosperms, by undertaking a structured approach assessing the phyllosphere microbiome of Pinus radiata. Canopy sampling height was the single most important factor influencing both alpha- and beta-diversity of bacterial and fungal communities (p

Forest soils are fundamental in regulating the global carbon (C) cycle; their capacity to accumulate large stores of C means they form a vital role in mitigating the effects of climate change. Understanding the processes that regulate forest soil C dynamics and stabilisation is important to maximise the capacity and longevity of C sequestration. Compared with surface soil layers, little is known about soil C dynamics in subsoil layers, sensu those below 30 cm depth. This knowledge gap creates large uncertainties when estimating the distribution of global soil C stocks and assessing the vulnerability of soil C reserves to climate change. This study aimed to dive deep into the subsoils of Puruki Experimental Forest (New Zealand) and characterise the changes in soil C dynamics and the soil microbiome down to 1 m soil depth. ITS and 16S rRNA sequencing and quantitative real-time PCR were used to measure changes in soil microbial diversity, composition, and abundance. Stable (δ13C) and radioactive (14C) C analyses were performed to assess depth-driven changes in the stability and age of soil C. Our research identified large declines in microbial diversity and abundance with soil depth, alongside significant structural shifts in community membership. Importantly, we conservatively estimate that more than 35 % of soil C stocks are present in subsoil layers below 30 cm. Although the age of soil C steadily increased with depth, reaching a mean radiocarbon age of 1571 yr BP (years before present) in the deepest soil layers, the stability of soil C varied between different subsoil depth increments. These research findings highlight the importance of quantifying subsoil C stocks for accurate C accounting. By performing a broad range of analytical measures, this research has comprehensively characterised the abiotic and biotic properties of a subsoil environment – a frequently understudied but significant component of forest ecosystems.

Forest soils are fundamental in regulating the global carbon (C) cycle; their capacity to accumulate large stores of C means they are vital in mitigating the effects of climate change. Understanding the processes that regulate forest soil organic C (SOC) dynamics and stabilisation is important to maximise the capacity and longevity of C sequestration. Compared to surface soil layers, little is known about the SOC dynamics in subsoil layers, sensu those below 30 cm depth. This knowledge gap creates large uncertainties when estimating the global distribution and vulnerability of SOC reserves to climate change. This study aimed to dive deep into the subsoils of Puruki Experimental Forest (New Zealand) and characterise the incremental changes in SOC dynamics and the soil microbiome down to 1 metre soil depth. ITS and 16S rRNA sequencing and quantitative real-time PCR were used to measure changes in soil microbial diversity, composition, and abundance. Stable (δ13C) and radioactive (14C) C analyses were performed to assess depth-driven changes in SOC stability and age. We conservatively estimate more than 35 % of total C stocks are present in subsoil layers below 30 cm. Although C age steadily increased with depth, reaching a mean radiocarbon age of 1571 yBP (years before present) in the deepest soil layers, the stability of SOC varied between different subsoil depth increments. Declines in soil carbon were associated with lower microbial diversity, abundance, and significant shifts in community membership. These research findings highlight the importance of quantifying subsoil C stocks for accurate systems-level global and local C budgets and modeling. Furthermore, performing a broad range of analytical measures (i.e. 13C & 14C natural abundance, and microbiome analysis) is vital to assess the vulnerability of subsoil C to climate change.

Dermacoccus strain Tok2021 (Actinobacteria) is a soil bacterium, isolated from commercial Pinus radiata forest soil from Tokoiti, New Zealand. The bacterium has a draft genome size of 3,101,786 bp and harbors genes involved in antibiotic production, siderophore production, and N2 fixation.