Biology subjects

Darcy, S.

Publications and source records attributed to Darcy, S..

4 recordsLinked to original sources

bioRxiv2026

A canine brain bank for comparative neuroscience and brain aging research

Companion animal brain banking has been recognized as a valuable approach for translational aging and dementia research. However, realizing the full value of canine brain banks depends on optimizing the methods that are used to collect and preserve the tissue. Whole brain perfusion fixation is one promising approach, but it is not yet well described in dogs. Here we describe the development of methods for a canine brain bank (currently n = 55), including whole brain perfusion fixation via aortic cannulation and brain extraction. We assessed perfusion quality using gross examination, post-perfusion CT, and histological clearance of blood vessels. We found that body weight and average flow rate per body weight were each significantly correlated with perfusion quality in our cohort. To illustrate the kind of analysis the bank could facilitate, we next performed a preliminary study of brain aging, one of our primary planned research applications. Using a pixel classifier applied to whole slide images, we quantified lipofuscin burden, and in this preliminary cohort found that it increased strongly with age in both the thalamus and hippocampus. In the hippocampus, lipofuscin burden was also elevated in dogs with owner-reported cognitive dysfunction, although the current cohort is too small to determine to what extent this association is independent of age. Preliminary electron microscopy studies also confirmed that perfusion fixed tissue from the bank is amenable to ultrastructural analysis. This work describes one approach for canine brain perfusion fixation and introduces a brain tissue resource that may help support future neuroscience research.

neuroscience↗

bioRxiv2024

Strong family- and guild-specific responses of arbuscular mycorrhizal fungi to long-term deficiencies and imbalances of N, P and K

O_LIMany agroecosystems face nitrogen (N), phosphorus (P) or potassium (K) deficiencies due to imbalanced or insufficient nutrient replenishment after plant biomass harvest. How this affects the symbiosis between plants and arbuscular mycorrhizal fungi (AMF), and the abundance of exploration-based AMF guilds (i.e., rhizophilic, edaphophilic, ancestral) remains largely unknown. C_LIO_LIWe studied a 70-year nutrient-deficiency experiment in a managed grassland in central Austria, where aboveground biomass was harvested three times annually. N, P and K were fully, partially, or not replenished, causing long-term nutrient deficiencies and imbalances. We analysed AMF communities in soil and roots by DNA/RNA amplicon sequencing and fatty-acid biomarkers, alongside soil and plant community properties. C_LIO_LISoil AMF communities were affected by N and P deficiencies, while root AMF communities were most susceptible to K deficiency, showing a 50% biomass reduction. We observed distinct guild- and family-specific responses: The edaphophilic guild declined with N deficiency, while the rhizophilic guild decreased with P and K deficiencies. Families within each guild, particularly in the ancestral guild, showed differential responses, indicating complementary nutrient specializations at the family level. C_LIO_LIOur findings underscore the previously unrecognized role of K deficiency in AMF symbiosis and suggest the existence of nutrient-related functional subgroups within exploration-based AMF guilds. C_LI

ecology↗

bioRxiv2024

Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates

Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogenous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre-scale. In this study, we examined whether bacteria, archaea, and fungi organise into distinct communities in individual 2-millimetre-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate-communities displayed exceptionally high beta-diversity, with 3-4 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20-30% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.

ecology↗

bioRxiv2021

From Diversity to Complexity: Microbial Networks in Soils

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.

ecology↗