Biology subjects

Caruso, T.

Publications and source records attributed to Caruso, T..

10 recordsLinked to original sources

bioRxiv2026

Bidirectional changes in seabird populations drive terrestrial ecosystem function and biodiversity

Seabird populations fluctuate dramatically in response to perturbations and human activity, such as the current highly pathogenic avian influenza (HPAI) panzootic and fishery practices. Seabirds vector marine nutrients into terrestrial and coastal environments causing cascading effects through ecosystems, but quantifying the inter-related mechanisms underpinning marine-terrestrial cascades in response to changes in seabird populations is challenging. Here we simulate decreases and increases in seabird density, as have occurred due to HPAI and fishing practices respectively, through turf transplant experiments and stratified surveys to quantify marine nutrient cascades and show how they regulate terrestrial ecosystem processes and biodiversity. We use structural equation modelling to quantify the relative strengths of each hypothesised mechanistic pathway in the ecological network. This analysis identified that seabirds shape terrestrial plant and invertebrate biodiversity primarily indirectly, through modifying soil nutrient availability. Our findings highlight the ecosystem changes that are likely occurring, and the pathways through which they operate, due to acute declines and chronic increases in seabirds caused by HPAI, fishing practices or other drivers.

ecology↗

bioRxiv2026

Unveiling Hidden Endophytes by Optimising Identification of Endophytic Bacterial Communities from Wild Grassland Plant Roots

Endophytic bacteria are increasingly recognised for their roles in plant health through symbiosis. However, methodological challenges, such as inconsistent root sterilisation, inefficient microbial DNA extraction, and co-amplification of plant organellar DNA, limit accurate characterisation of these communities, especially in wild grassland plants and non model plant in general. To address this, we developed and tested a streamlined protocol for bacterial endophyte detection from wild grassland plant roots, encompassing surface sterilisation of roots, DNA extraction, clamping of plant internal mitochondrial and chloroplast DNA, and 16S rRNA amplicon sequencing. Our approach minimises plant DNA contamination and yields high-quality microbial profiles. The protocol is adaptable and specific to grassland plant species, offering a standardised foundation for endophyte studies in wild and non-model plants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=141 HEIGHT=200 SRC="FIGDIR/small/706108v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@157df36org.highwire.dtl.DTLVardef@1ff645aorg.highwire.dtl.DTLVardef@1580ecorg.highwire.dtl.DTLVardef@1c31b89_HPS_FORMAT_FIGEXP M_FIG C_FIG (Haskins and Ajaz, 2026) https://BioRender.com/47gd2xr

plant biology↗

bioRxiv2026

Maximum entropy networks predict fluctuations and stability of food web energetics

A central goal of ecology is understanding how the architecture of food webs, which represent the structural backbone of ecosystems, affects their stability. The analysis of stability in the classical sense of population dynamics (i.e. return to equilibrium) can be successful for a single instance of an empirical food web but ignores the multiplicity of alternative states in which the system could be found as a result of intrinsic variability and fluctuations. Here we propose and test a new methodology to reconstruct, from single empirical observations of a food web, the viable ensemble of alternative realizations respecting the observed resource-consumer linkages and empirical ener-getics. The reconstruction can be handled analytically within a maximum-entropy framework which predicts how empirical food webs access a multitude of alternative states with comparable stability and reactivity. The (measurable) entropy of the reconstructed ensemble directly quantifies this multiplicity and serves as a novel proxy of system resilience, that is the rate of return to equilibrium in response to an external perturbation. We show that the associated ensemble fluctuations provide explicit predictions for the expected response of food webs to external perturbations, such as anthropogenic or climate-induced stresses. We do that by validating the proposed fluctuation-response relation on empirical soil food webs subjected to experimentally controlled perturbations, confirming that intrinsic fluctuations in the unperturbed state predict responses to subsequent stresses. The perturbed states are associated with higher entropy, indicating less likely spontaneous recovery.

ecology↗

bioRxiv2025

Dominance of indirect effects of deer populations on soil biodiversity

Deer abundances and distributions have expanded at increasing rates in several regions across the globe due to human-driven land use change, uncontrolled introductions and reintroductions, and insufficient top-down control by human or natural predators. Yet, the impact of unsustainable density of deer on the belowground component of ecosystems is understudied. Ireland is a good model for anthropic environmental context in which the population of large herbivores is not regulated by large predators nor planned hunting management. Through a combination of camera trapping paired with soil and vegetation surveys conducted with high-throughput technology, we monitored 50 sites in Irish woodlands to study the effect of varying sika deer (Cervus nippon) relative densities on soil biota. Site-level deer intensity of use correlated with vegetation through an increase in litter and moss quantity and reduction in understory vegetation. Furthermore, the effect covaried with soil pH and cascaded on soil microarthropod, bacterial and fungal communities, with more opportunistic taxa linked to high relative deer densities. We also found that variation in deer intensity of use directly affects vertebrate communities, which shifted towards a dominance of foxes, squirrels, cats and dogs - species more commonly associated to human-dominated landscapes - and a reduction in birds and mustelids, which also cascaded on soil biota. Our results thus support the hypothesis that deer overabundance has a strong potential to drive the structure of soil biota mostly through indirect effects via vertebrate fauna and vegetation, acting as a powerful ecosystem engineer. Future studies will have to experimentally tease apart the mechanisms underpinning the patterns documented in this study.

ecology↗

bioRxiv2025

Litter biota and quality as drivers of litter decomposition in mature oak forests subject to drought or elevated CO2

1.) Increasing atmospheric CO2 concentrations alongside more frequent and severe droughts are key global change factors impacting litter decomposition and global carbon cycles. Yet, we have a poor understanding of how these perturbations impact interactions between initial litter chemical properties and the abiotic and biotic properties of the decomposition environment, especially under field conditions. 2.) We tested how drought and elevated atmospheric CO2 concentrations modify litter decomposition via litter properties and decomposition environment using two separate, long-term manipulative drought or elevated CO2 field experiments in mature oak woodlands. Litterbags were deployed in a reciprocal transplant design within each experiment, where we measured litter mass loss, carbon-biochemistry, C:N ratios, moisture content, and microbial and mesofaunal properties. 3.) We found that litter placed in droughted plots decomposed slower than in control plots and experimental litter derived from elevated CO2 plots decomposed slower over the first three harvests compared to control litter. Under drought, litter mass loss rates and C:N ratio was regulated by initial litter properties and the decomposition environment, while elevated CO2 impacted mass loss via changes in initial litter properties. 4.) Synthesis: We show that drought and elevated atmospheric CO2 can modify the decomposability of litter prior to litterfall and during the subsequent decomposition, highlighting the need to disentangle their individual and interactive effects to better predict how global change factors influence decomposition.

ecology↗

bioRxiv2023

Community structure of known and previously unknown endobacteria associated with spores of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are ubiquitous plant root symbionts which can house two endobacteria: Ca. Moeniiplasma glomeromycotorum (CaMg) and Ca. Glomeribacter gigasporarum (CaGg). However, little is known about their distribution and population structure in natural AMF populations and whether AMF can harbour other endobacteria. We isolated AMF from two environments and surveyed the surface-sterilized spores for endobacteria. We found that CaMg and CaGg differed significantly in distribution whereby CaMg were extremely abundant (80%) and CaGg were extremely rare (2%) in both environments. Unexpectedly, we discovered an additional and previously unknown level of bacterial diversity within AMF spores which extended beyond the known endosymbionts, with as many as 277 other bacterial taxa detected in individual spores. Detailed analysis of endobacterial communities inside AMF spores revealed that: (i)CaGg were not limited in distribution to the Gigasporacea family of AMF, as previously thought, (ii) CaMg community structure was driven by AMF host genotype, (iii) a significant inverse correlation existed between the diversity of CaMg and diversity of all other endobacteria. The latter suggests the existence of competition dynamics between different bacterial populations inside AMF spores and provides a basis for generation of testable hypotheses regarding the function of CaMg in AMF biology.

microbiology↗

bioRxiv2019

Air mass source determines airborne microbial diversity at the ocean-atmosphere interface of the Great Barrier Reef marine ecosystem

The atmosphere is the least understood biome on Earth despite its critical role as a microbial transport medium. The influence of surface cover on composition of airborne microbial communities above marine systems is unclear. Here we report evidence for a dynamic microbial presence at the ocean-atmosphere interface of a major marine ecosystem, the Great Barrier Reef, and identify that recent air mass trajectory over an oceanic or continental surface associated with observed shifts in airborne bacterial and fungal diversity. Relative abundance of shared taxa between air and coral microbiomes varied between 2.2-8.8% and included those identified as part of the core coral microbiome. We propose that this variable source of atmospheric inputs may in part contribute to the diverse and transient nature of the coral microbiome.

microbiology↗

bioRxiv2018

Microbial dispersal limitation to isolated soil habitats in the McMurdo Dry Valleys of Antarctica

Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities. Airborne microbial transport is assumed to occupy a central role in determining dispersal outcomes and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change. One of the most pertinent biomes in this regard is Antarctica given its geographic isolation and vulnerability to climate change and human disturbance. Here we report the first characterisation of microbial diversity in near-ground and high-altitude air above a typical Antarctic Dry Valley as well as that of underlying soil microbial communities. We found that persistent airborne inputs were unable to fully explain local soil community assembly. Comparison with airborne microbial diversity from non-polar sources suggests that strong selection occurs during atmospheric transport resulting in regionally isolated airborne inputs and highly specialized soil communities where fungi displayed greater isolation than bacteria from non-polar sources. Overall microbial communities from this isolated Antarctic ecosystem displayed limited connectivity to the global microbial pool. Our findings provide critical insights to forecast the potential outcomes for microbial communities of climate change-mediated shifts in air circulation to the Dry Valleys, the largest ice-free region of Antarctica.

microbiology↗

bioRxiv2017

Subsoil arbuscular mycorrhizal fungal communities in arable soil differ from those in topsoil

Arbuscular mycorrhizal fungi are recognized as important drivers of plant health and productivity in agriculture but very often existing knowledge is limited to the topsoil. With growing interest in the role of subsoil in sustainable agriculture, we used high-throughput Illumina sequencing on a set of samples encompassing drilosphere, rhizosphere and bulk soil, in both top- and subsoil. Our results show subsoil AMF communities harbor unique Operational Taxonomic Units (OTUs) and that both soil depths differ in community structure both at the OTU and family level. Our results emphasize the distinctness of subsoil AMF communities and the potential role of subsoil as a biodiversity reservoir.

ecology↗

bioRxiv2017

Unifying concepts of biological function from molecules to ecosystems.

The concept of function arises at all levels of biological study and is often loosely and variously defined, especially within ecology. This has led to ambiguity, obscuring the common structure that unites levels of biological organisation, from molecules to ecosystems. Here we build on already successful ideas from molecular biology and complexity theory to create a precise definition of biological function which spans scales of biological organisation and can be quantified in the unifying currency of biomass, enabling comparisons of functional effectiveness (irrespective of the specific function) across the field of ecology. We give precise definitions of ecological and ecosystem function that bring clarity and precision to studies of biodiversity-ecosystem function relationships and questions of ecological redundancy. To illustrate the new concepts and their unifying power, we construct a simple community-level model with nutrient cycling and animal-plant mutualism, emphasising the importance of its network structure in determining overall functioning. This type of network structure is that of an autocatalytic set of functional relationships, which also appears at biochemical, cellular and organism levels of organisation, creating a nested hierarchy. This enables a common and unifying concept of function to apply from molecular interaction networks up to the global ecosystem.

ecology↗