Biology subjects

Finch, J.

Publications and source records attributed to Finch, J..

3 recordsLinked to original sources

bioRxiv2025

Five years of national airborne pollen monitoring in South Africa: Biome-specific calendars to inform allergy diagnosis and prevention

Pollen monitoring is crucial for understanding seasonal patterns, supporting allergy diagnosis and informing early-warning tools to mitigate allergic diseases. The Southern Hemisphere lacks long-term data on pollen seasons, with extremely few from Africa. We present pollen calendars based on five-year data from the South African Pollen Monitoring Network (SAPNET). Airborne pollen from 2019 to 2024 in biomes across South Africa was collected using Hirst-type volumetric spore traps and standard protocols. Daily concentrations were analysed by light microscopy. The five-year mean annual pollen integral (APIn, pollen grains/m3 per year) was calculated for each site. The five-year mean APIn was highest in the Grassland Biome (Bloemfontein, 11654 pg/m3; range 8515 to 14454 pg/m3) and lowest in the Albany Thicket Biome (Gqeberha, 1372; range 853 to 2010 pg/m3). The Grassland Biome (Johannesburg) had the highest averaged tree pollen concentration (7558; range 6575 to 8803 pg/m3). The Savanna Biome (Kimberley) had the highest average grass pollen concentration (3150; 1826 to 3785 pg/m3). The grass family (Poaceae) was the most common pollen type across all biomes. Other common contributing taxa were exotic trees Cupressaceae, Platanus, Morus and Betula. Tree seasons were July to September, whilst grass and weed pollen seasons varied across the different biomes. These five-year pollen calendars provide the first biome-specific national reference for airborne pollen exposure in South Africa. The findings provide baseline data for the clinical management of allergic disease.

ecology↗

bioRxiv2025

Large-scale culturing of the tree microbiome enables targeted disease suppression

The tree microbiome is essential for host health and pathogen suppression. Synthetic microbial communities (SynComs) are emerging as important tools to understand microbiome dynamics and engineer microbiomes to harness beneficial properties. However, while the rational design, assembly and application of SynComs requires representative microbiota isolate collections combined with functional information, microbial culture collections from tree species such as oak (Quercus) are critically lacking. Here, we generated an oak microbiota culture collection comprising >30,000 isolates from 150 oak trees across Britain, belonging to key bacterial and fungal taxa that represented 61% of the total bacterial sequences and 87% of total fungal sequences as determined by culture-independent sequencing. Over 22,000 isolates were screened for suppression of bacterial species associated with degradation of live stem tissue in trees affected by Acute Oak Decline (AOD), identifying 341 bacterial isolates that suppressed oak pathogens. In vitro screening of 40 randomly assembled SynComs demonstrated that oak microbiota SynComs can suppress oak pathogenic bacteria associated with AOD. Inoculation of a disease-suppressive SynCom into the stem of oak seedlings and logs prior to pathogen challenge reduced the quantities of the bacteria, Brenneria goodwinii and Gibbsiella quercinecans, by 56% and 87%, respectively, in seedlings, and 71% and 95% in logs. This work demonstrates that the tree microbiome can be engineered using disease suppressive SynComs.

microbiology↗

bioRxiv2025

Environment and disease have tissue-specific effects on the tree microbiome

Trees are essential for ecosystem function, but due to their long lifespan, are disproportionately impacted by climate change and disease. Tree-associated microbiota are critical for tree health and resilience, but the composition and function of tree microbiomes across different tissue types, and how environmental factors and disease impact tree microbiomes, is poorly understood. Oak trees are major constituents of forests of the Northern hemisphere, but are increasingly impacted by climate and disease. Here, we studied the oak microbiome across Britain, combining 16S rRNA gene and ITS microbial community profiling and shotgun metagenomics of leaf, stem and root/rhizosphere samples, and developed a three-level occupancy model to describe microbiota distribution across the landscape. We show that oak leaf, stem and root/rhizosphere tissues harbour taxonomically and functionally distinct microbiota and identified differences in tissue-specific effects of environmental variables (e.g. temperature, rainfall, ion deposition) on microbiome composition and function. We generated 1657 bacterial, archaeal and fungal metagenome-assembled genomes representing key members of the oak microbiome. Furthermore, the stem microbiome of oak trees with symptoms of Acute Oak Decline, a complex decline disease driven by abiotic and biotic stressors, exhibited reduced bacterial and fungal richness and altered microbiome function. This work represents the most comprehensive microbiome study of a tree species to date. Understanding how tree-associated microbiota respond to environmental change and disease across different tissues is crucial to predict future climate and disease impacts on tree microbiome function, and inform translational approaches to modulate tree microbiomes for plant health.

microbiology↗