Biology subjects

Gallagher, R. V.

Publications and source records attributed to Gallagher, R. V..

12 recordsLinked to original sources

bioRxiv2026

Revegetation following grazing cessation drives sequential shifts in soil microbial functions and life-history strategies over decadal time scales

Revegetation is a key strategy for restoring degraded lands globally. While this process can reshape belowground microbial communities, the extent to which such changes restore soil ecosystem functions, and whether different microbial traits recover synchronously or on distinct timescales remains less clear. Understanding this is essential for evaluating restoration success, as different microbial traits underpin distinct ecosystem services, from carbon storage to plant growth promotion, and the sequence in which these are restored can inform restoration targets and provide meaningful indicators of long-term ecological recovery. To address this, we applied deep metagenomic sequencing to characterise soil microbial responses following revegetation (spanning 1-31 years prior to sampling) on grazing agricultural lands. We find that revegetation following grazing cessation drove significant and sequential shifts in dominant microbial functions and life-history strategies. Functional changes occurred in distinct phases: an early, rapid restructuring of core soil health processes, detectable as early as three years, including enrichment of nutrient retention and carbon fixation pathways, followed by a more gradual development of plant growth-promoting traits as the plant community matures. Genome-resolved analyses of nearly 500 metagenome-assembled genomes revealed a fundamental shift in dominant microbial life history strategies: from a resource-scavenging and stress tolerance profile in grazing soils to strategies that prioritise biosynthesis and growth yields in revegetated soils. These lifestyle shifts have important implications for enhancing the microbial biomass and carbon sink potential of soils. Together, these findings show that microbial functional shifts following revegetation are temporally structured - informing expectations for when key restoration targets may be achieved, and providing a practical framework for monitoring ecosystem recovery.

microbiology↗

bioRxiv2024

Detecting ecosystem trends in response to climate and disturbance across continental plot networks: a power analysis

Plant communities are dynamic: cyclical, directional and stochastic changes in species composition make interpretation of responses complex. The multi-dimensionality of ecological change is reduced by ecosystem indicators that quantify functional responses to environmental drivers. However, thresholds of detectable change in indicators may vary by ecosystem or the spatial configuration of monitoring sites within regions. We quantified the power of a continental terrestrial ecosystem plot network (TERN Ausplots, Australia) to detect change in ecological indicators linked to disturbance and climate: community temperature index (CTI), proportional abundance of photosynthetic pathways (C4%), and species abundance distribution (SAD). We simulated trend and noise scenarios and calculated power and effect size across spatial clusters of plots using linear mixed effects models. We then assessed factors that influenced change detection capacity. Power varied substantially across the network. Trends with a minimum magnitude of 0.5-3.0{degrees}C in CTI, 0.01-0.3 in C4% and 0.1-0.5 in the SAD sigma were detectable, depending on cluster identity and noise. Increased plot replication within a spatial cluster increased power and lower variance among baseline replicates increased effect size for CTI and C4% but not SAD. Latitudinal patterns in change detection capacity emerged for CTI and C4%. The effect size of increasing CTI was greater in the tropics due to lower among-plot variance, while power to detect increasing C4% was higher in the temperate south, where C4 is rare. Indicators reveal trends in complex ecological data that can inform decision-making. Increasing spatial replication and minimising spatial variation by stratifying plots to the same ecological community enhance change detection, albeit with different effectiveness by indicator. The results suggest change detection differs by location, irrespective of sampling factors such as number of plots. Strategies and thresholds for change detection may therefore apply unequally across environments and should be considered by region and response parameter.

ecology↗

bioRxiv2024

A-Islands: A plant dataset for biodiversity research and species monitoring on Australian islands

Australias coastline is fringed by more than 8,000 continental islands. These islands feature a diverse array of landforms, rock and soil types and geological origins. Some of these islands are among the least invaded, most pristine habitats in Australia and support high plant diversity. Here, we present a new Australia-wide curated dataset for plant species occurrences on islands. Combining information from 1,349 species lists and floras, A-Islands includes data on >6,500 plant species from 844 islands ranging in size from 18 m2 to 4,400 km2, exhibiting different degrees of isolation from the mainland, and spanning all major Australian climate zones. Of these, 251 islands have been repeatedly sampled up to 11 times making it possible to investigate temporal compositional change. A-Islands is open access and will be continuously updated. Its simple data structure consisting of three comma separated files allows easy integration with other Australian and global plant-occurrence databases and can serve as a repository for island research in Australia. Knowing which species occur on Australia's islands will provide opportunities for future research, including studying changes in biodiversity and species-turnover within and among archipelagos, tests of classical island biogeography theory and as a baseline for ecological monitoring and conservation.

ecology↗

bioRxiv2024

traits.build: a data model, workflow and R package for building harmonised ecological trait databases

Trait databases have proliferated over the past decades, facilitating research on the ecology, evolution, and conservation of taxa across the Tree of Life. Typically, teams of independent researchers build these databases, and each must develop their own workflow and output structure. This divests research hours from downstream tasks such as trait-based analysis and interpretation and the resultant datasets are often difficult to integrate due to disparate database structures. Here we introduce the {traits.build} package, which offers a generalised workflow for building trait databases. {traits.build} contains bespoke functions for propagating metadata files, extensive tutorials, and sample configuration files, allowing researchers to efficiently build a new trait database using open source tools. In addition, the {traits.build} output structure is fully documented by a data model, ensuring the meaning of each variable and sematic relationship between variables is transparent and consistent. The data standard links to terms in previously published data standards, drawing strongly on DarwinCore and the Ecological Trait-data Standard, but also includes the ability to fully map location and context properties absent from these vocabularies., It is the first published database-building workflow that adheres to the Extensible Observation Ontology. Simultaneously developing a generalised workflow and publishing a data standard for the workflow provides {traits.build} users a straightforward pathway to build a new trait database that achieves the FAIR principles. The meaning of all variables in a {traits.build} database are already documented, allowing further integration with either other {traits.build} databases or indeed any other database with a documented data model. This follows the vision of the Open Traits Network to build trait databases whose data can be easily integrated for further analysis.

bioinformatics↗

bioRxiv2023

Drivers of thermal tolerance breadth of plants across contrasting biomes: do mean or seasonality in climate indices matter more?

O_LIThe climate variability hypothesis (CVH) predicts that species from environments with more variable temperatures should have wider thermal tolerance breadth. This hypothesis has not yet been tested thoroughly across diverse plants. Here, we asked how local climate predictors (including precipitation, mean and extreme temperatures and thermal variability) are associated with species physiological thermal limits. C_LIO_LIMeasures of lower (Tcrit-cold) and upper (Tcrit-hot) photosystem II thermal tolerance thresholds were used to determine thermal tolerance breadth (TTB), along with ice nucleation temperature (Tnucleation, freezing tolerance) of 69 plant species sampled from the field across three contrasting biomes: alpine, desert and coastal temperate rainforest. C_LIO_LIAll measured thermal tolerance metrics (Tcrit-cold, Tnucleation, Tcrit-hot and TTB) differed among biomes. Notably, desert species had the most cold and heat tolerant leaves, and therefore the widest TTB, whereas species in alpine and temperate biomes had similar TTB. For plants in all biomes, TTB exceeded the thermal range of their local climate. C_LIO_LIOverall, two Principal Component axes of local climate drivers explained substantial variation in all tolerance metrics. Extreme hot, dry climates improved freezing and heat tolerance. High thermal variability and low minimum temperatures also improved freezing tolerance but were unrelated to heat tolerance or TTB. Species explained a significant amount of variation among all metrics, but this was not due to phylogenetic relatedness. We discuss how the remaining variation could be due to microclimate-driven plasticity, leaf traits or thermoregulatory mechanisms. C_LIO_LISynthesis. Our results provide partial support for the climate variability hypothesis in plants: photosystem thermal tolerance breadth was greatest in more thermally variable biomes. This relationship was largely driven by cold tolerance, with variation in heat tolerance explained better by mean and extreme temperatures. Therefore, we conclude that the CVH alone is not sufficient to explain variation in plant thermal tolerance, with many other aspects of climate, environment and biology being potentially important drivers. C_LI

ecology↗

bioRxiv2023

Revisiting the role of mean annual precipitation in shaping functional trait distributions at a continental scale

1Mean annual precipitation (MAP) plays an undisputed role in determining the spatial distribution of the vegetative ecosystems on Earth. Nevertheless, the relationship between MAP and plant functional traits remains unclear. Here, we test the relationship between eight key functional traits and MAP. Our analysis reveals a strong, coordinated response of several plant traits including leaf mass per area, leaf nitrogen, the leaf carbon isotope ratio and plant height from resource-conservative to resource-acquisitive values as MAP increased. These results establish an important role for MAP in driving trait selection across space and, therefore, a need for these effects to be included in future theoretical frameworks.

ecology↗

bioRxiv2023

The AusTraits Plant Dictionary

Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. Reanalysis of data from a single database, or analyses that integrate data across multiple databases, can only occur if researchers are confident the trait concepts are consistent within and across sources. The lack of a unified, comprehensive resource for plant trait definitions has previously limited the utility of trait databases. Here we describe the AusTraits Plant Dictionary (APD), which extends the trait definitions included in the new trait database AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait meta-data; and publication in both human and machine-readable forms. Trait definitions include keywords, references and links to related trait concepts in other databases, and the traits are grouped into a hierarchy for easy searching. As well as improving the usability of AusTraits, the Dictionary will foster the integration of trait data across global and regional plant trait databases.

ecology↗

bioRxiv2022

Transcriptome Mining Reveals a Spectrum of RNA Viruses in Primitive Plants

Current knowledge of plant viruses stems largely from those affecting economically important plants. Yet, plant species in cultivation represent a small and bias subset of the plant kingdom. Here, we describe virus diversity and abundance from a survey of 1079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analysing open-source data from the One Thousand Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% comprised single-stranded positive-sense RNA viruses across eight orders, including members of the Hepelivirales, Tymovirales, Cryppavirales, Martellivirales and Picornavirales. One-third of the newly described viruses comprised double-stranded RNA viruses from the orders Durnavirales and Ghabrivirales. The remaining were negative-sense RNA viruses from the Rhabdoviridae, Aspiviridae, Yueviridae, Phenuiviridae and the newly proposed Viridisbunyaviridae. Our analysis considerably expands the known host range of 13 virus families to include lower plants (e.g., Benyviridae and Secoviridae) and four virus families to include algae hosts (e.g., Tymoviridae and Chrysoviridae). The discovery of the first 30 kDa movement protein in a non-vascular plant, suggests that the acquisition of plant virus movement proteins occurred prior to the emergence of the plant vascular system. More broadly, however, a co-phylogeny analysis revealed that the evolutionary history of these families is largely driven by cross-species transmission events. Together, these data highlight that numerous RNA virus families are associated with older evolutionary plant lineages than previously thought and that the scarcity of RNA viruses found in lower plants to date likely reflects a lack of investigation rather than their absence. ImportanceOur knowledge of plant viruses is mainly limited to those infecting economically important host species. In particular, we know little about those viruses infecting primitive plant lineages such as the ferns, lycophytes, bryophytes and charophytes. To expand this understanding, we conducted a broad-scale viral survey of species across the breadth of the plant kingdom. We find that primitive plants harbour a wide diversity of RNA viruses including some that are sufficiently divergent to comprise a new virus family. The primitive plant virome we reveal offers key insights into the evolutionary history of core plant virus gene modules and genome segments. More broadly, this work emphasises that the scarcity of viruses found in these species to date likely reflects the absence of research in this area.

microbiology↗

bioRxiv2021

Climate shapes flowering periods across plant communities

AimClimate shapes the composition and function of plant communities globally, but it remains unclear how this influence extends to floral traits. Flowering phenology, or the time period in which a species flowers, has well-studied relationships with climatic signals at the species level but has rarely been explored at a cross-community and continental scale. Here, we characterise the distribution of flowering periods (months of flowering) across continental plant communities encompassing six biomes, and determine the influence of climate on community flowering period lengths. LocationAustralia TaxonFlowering plants MethodsWe combined plant composition and abundance data from 629 standardised floristic surveys (AusPlots) with data on flowering period from the AusTraits database and additional primary literature for 2,983 species. We assessed abundance-weighted community mean flowering periods across biomes and tested their relationship with climatic annual means and the predictability of climate conditions using regression models. ResultsCombined, temperature and precipitation (annual mean and predictability) explain 29% of variation in continental community flowering period. Plant communities with higher mean temperatures and lower mean precipitation have longer mean flowering periods. Moreover, plant communities in climates with predictable temperatures and, to a lesser extent, predictable precipitation have shorter mean flowering periods. Flowering period varies by biome, being longest in deserts and shortest in alpine and montane communities. For instance, desert communities experience low and unpredictable precipitation and high, unpredictable temperatures and have longer mean flowering periods, with desert species typically flowering at any time of year in response to rain. Main conclusionsOur findings demonstrate the role of current climate conditions in shaping flowering periods across biomes, with implications under climate change. Shifts in flowering periods across climatic gradients reflect changes in plant strategies, affecting patterns of plant growth and reproduction as well as the availability of floral resources across the landscape.

ecology↗

bioRxiv2021

Climate-change risk analysis for global urban forests

Urban forests (i.e. all vegetation present in urban areas), provide environmental and socioeconomic benefits1 to more than half of the global population2. Projected climate change threatens these benefits to society3-5. Here, we assess vulnerability to climate change of 16,006 plant species present in the urban forests of 1,010 cities within 93 countries, using three vulnerability metrics: exposure, safety margin and risk. Exposure expresses the magnitude of projected changes in climate in a given area, safety margin measures species sensitivity to climate change, and risk is the difference between exposure and safety margin6. We identified 9,676 (60.5%) and 8,344 (52.1%) species exceeding their current climatic tolerance (i.e. safety margin) for mean annual temperature (MAT) and annual precipitation (AP), respectively. By 2050, 13,479 (84.2%) and 9,960 (62.2%) species are predicted to be at risk from projected changes in MAT and AP, respectively, with risk increasing in cities at lower latitudes. Our results can aid evaluation of the impacts of climate change on urban forests and identify the species most at risk. Considering future climates when selecting species for urban plantings will enhance the long-term societal benefits provided by urban forests, including their contribution to mitigating the magnitude and impacts of climate change.

ecology↗

bioRxiv2020

Areas of global importance for terrestrial biodiversity, carbon, and water

Summary paragraphTo meet the ambitious objectives of biodiversity and climate conventions, countries and the international community require clarity on how these objectives can be operationalized spatially, and multiple targets be pursued concurrently1. To support governments and political conventions, spatial guidance is needed to identify which areas should be managed for conservation to generate the greatest synergies between biodiversity and natures contribution to people (NCP). Here we present results from a joint optimization that maximizes improvements in species conservation status, carbon retention and water provisioning and rank terrestrial conservation priorities globally. We found that, selecting the top-ranked 30% (respectively 50%) of areas would conserve 62.4% (86.8%) of the estimated total carbon stock and 67.8% (90.7%) of all clean water provisioning, in addition to improving the conservation status for 69.7% (83.8%) of all species considered. If priority was given to biodiversity only, managing 30% of optimally located land area for conservation may be sufficient to improve the conservation status of 86.3% of plant and vertebrate species on Earth. Our results provide a global baseline on where land could be managed for conservation. We discuss how such a spatial prioritisation framework can support the implementation of the biodiversity and climate conventions.

ecology↗

bioRxiv2020

Global shortfalls in extinction risk assessments for endemic flora

The Global Strategy for Plant Conservation (GSPC) ambitiously calls for an assessment of extinction risk for all recognised plant taxa by 20201. It is now clear that this target will not be met in the short-term; only 21-26% of known plant species have been assessed2 - a monumental shortfall in anticipated knowledge. Yet the need for risk assessments has never been more urgent. Plants are rapidly going extinct3,4 and face threats such as climate change5 and permanent deforestation6. Extinction risk assessments continue to provide the critical foundation to inform protection, management and recovery of plant species7,8, the loss of which will have clear consequences for maintaining planetary systems and human well-being9. Here, we rank countries of the world based on progress towards assessing the extinction risk to their endemic flora. Overall, 67% of country-based endemic species do not have an extinction risk assessment completed (143,294 species). We show that some of the worlds wealthiest nations, which also have relatively strong species protections, are failing to protect their unique flora by not systematically assessing risks to their endemic species.

ecology↗