ORCID Profile
0000-0001-7810-9696
Current Organisation
Flinders University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Population, Ecological and Evolutionary Genetics | Conservation and Biodiversity | Genetics | Marine and Estuarine Ecology (incl. Marine Ichthyology) | Gene Expression (incl. Microarray and other genome-wide approaches) | Ecological Impacts of Climate Change | Ecology | Environmental Science and Management | Ecological Applications | Evolutionary Biology | Terrestrial Ecology | Plant Physiology | Natural Resource Management | Environmental Rehabilitation (excl. Bioremediation) | Biogeography and Phylogeography | Biological Adaptation
ANZSRC Socio-Economic Objective (SEO)
Ecosystem Adaptation to Climate Change | Marine Flora, Fauna and Biodiversity | Flora, Fauna and Biodiversity at Regional or Larger Scales | Forest and Woodlands Flora, Fauna and Biodiversity | Effects of Climate Change and Variability on Australia (excl. Social Impacts) | Climate Change Adaptation Measures | Rehabilitation of Degraded Forest and Woodlands Environments | Rehabilitation of Degraded Mining Environments | Rehabilitation of Degraded Coastal and Estuarine Environments | Expanding Knowledge in the Environmental Sciences | Expanding Knowledge in the Biological Sciences |
Related Links
Publications
Putting provenance into perspective: the relative importance of restoration site conditions over seed sourcing
Publisher: Wiley
Date: 08-08-2023
DOI: 10.1111/REC.13989
Abstract: Post‐mining scenarios present challenges for restoration in a wide range of environments, especially in the context of climate change. The source of seed for restoration has been an issue of intense focus, as seed provenance can impact plant fitness and restoration outcomes. However, post‐mining landscapes require substrate reconstruction prior to vegetation re‐establishment. Critically, the relative importance of provenance and substrate in ecosystem recovery has been rarely quantified in a statistically rigorous framework. We established a large provenance trial with Banksia attenuata and Eucalyptus todtiana at two Western Australian mine sites in post‐mining reconstructed and adjoining un‐mined substrates. We show that site and substrate were 4 and 26 times more important than provenance in explaining survival for B. attenuata and E. todtiana , respectively. At one site, there was 100% mortality in the post‐mining substrate but high survival and no clear provenance effect in the un‐mined substrate. At the second site, there was again no clear provenance effect, but E. todtiana survival was higher in the post‐mining than un‐mined substrate. Our results show that post‐mining substrate changes can overwhelm provenance issues. Consequently, where substrates are highly impacted, alternative restoration targets and/or greater investment in substrate research are needed to improve restoration outcomes. Due to the thousands of mines across the world, this is an internationally relevant finding with important implications for investment into global ecosystem recovery.
Opportunities and challenges for microbiomics in ecosystem restoration
Publisher: Elsevier BV
Date: 08-2023
Gut microbiota composition does not associate with toxoplasma infection in rats
Publisher: Wiley
Date: 12-06-2022
DOI: 10.1111/MEC.16552
Abstract: Toxoplasma infection in intermediate host species closely associates with inflammation. This association has led to suggestions that the behavioural changes associated with infection may be indirectly driven by the resulting sustained inflammation rather than a direct behavioural manipulation by the parasite. If this is correct, sustained inflammation in chronically infected rodents should present as widespread differences in the gastrointestinal microbiota due to the dependency between the composition of these microbiota and sustained inflammation. We conducted a randomized controlled experiment in rats that were assigned to a Toxoplasma ‐treatment, placebo‐treatment or negative control group. We euthanised rats during the chronic phase of infection, collected their caecal stool s les and sequenced the V3‐V4 region of the 16S rRNA gene to characterize the bacterial community in these s les. Toxoplasma infection did not induce widespread differences in the bacterial community composition of the gastrointestinal tract of rats. Rather, we found sex differences in the bacterial community composition of rats. We conclude that it is unlikely that sustained inflammation is the mechanism driving the highly specific behavioural changes observed in Toxoplasma ‐positive rats.
Clarifying climate change adaptation responses for scattered trees in modified landscapes
Publisher: Wiley
Date: 23-02-2011
Local and non‐local soil microbiota impede germination of the endangered Acacia whibleyana
Publisher: Wiley
Date: 08-01-2023
DOI: 10.1111/AEC.13275
Abstract: Inoculating soils with microbiota that benefit the germination and growth of endangered plant species could improve their revegetation success and conservation status. While ecosystem degradation can disrupt beneficial plant–soil‐microbial interactions, the prospect of reintroducing native plant‐associated soil microbiota during revegetation could help to restore these important ecological links and assist the recovery of key species. We address the role of soil microbiota on germination and seedling fitness traits of the endangered Acacia whibleyana (Fabaceae) through a 17‐week greenhouse experiment. Soil treatments included local soil, potting medium, three inoculation ratios (3:1, 1:1, 1:3 local soil: potting medium), sterilized local soil and sterilized potting medium. Soil sterilization reduced the time to first seed germination, indicating a role of soil microbiota on germination. The 1:1 whole soil inoculation saw reduced germination rates compared with either pure local or potting‐medium treatments, and the slower germination times observed in live soils confirmed the strong influence of soil microbiota on the timing of germination. We report evidence that poor inoculation strategies can adversely impact germination of this endangered Acacia . Furthermore, our findings suggest that careful assessment of microbiota associated with A. whibleyana could help to improve germination and recruitment during its revegetation and conservation management.
How well do revegetation plantings capture genetic diversity?
Publisher: The Royal Society
Date: 10-2019
Abstract: Revegetation plantings are a key management tool for ecological restoration. Revegetation success is usually measured using ecological traits, however, genetic ersity should also be considered as it can influence fitness, adaptive capacity and long-term viability of revegetation plantings and ecosystem functioning. Here we review the global literature comparing genetic ersity in revegetation plantings to natural stands. Findings from 48 studies suggest variable genetic outcomes of revegetation, with 46% demonstrating higher genetic ersity in revegetation than natural stands and 52% demonstrating lower ersity. Levels of genetic ersity were most strongly associated with the number of source sites used—where information was available, 69% of studies showing higher genetic ersity in revegetation reported using multiple provenances, compared with only 33% for those with lower ersity. However, with a few exceptions, it was unclear whether differences in genetic ersity between revegetation and natural stands were statistically significant. This reflected insufficient reporting of statistical error and metadata within the published studies, which limited conclusions about factors contributing to patterns. Nonetheless, our findings indicate that mixed seed sourcing can contribute to higher genetic ersity in revegetation. Finally, we emphasize the type of metadata needed to determine factors influencing genetic ersity in revegetation and inform restoration efforts.
Opportunities and challenges of macrogenetic studies
Publisher: Springer Science and Business Media LLC
Date: 18-08-2021
Tissue-specific transcriptome profiles identify functional differences key to understanding whole plant response to life in variable salinity
Publisher: The Company of Biologists
Date: 15-08-2022
DOI: 10.1242/BIO.059147
Abstract: Plants endure environmental stressors via adaptation and phenotypic plasticity. Studying these mechanisms in seagrasses is extremely relevant as they are important primary producers and functionally significant carbon sinks. These mechanisms are not well understood at the tissue level in seagrasses. Using RNA-seq, we generated transcriptome sequences from tissue of leaf, basal leaf meristem and root organs of Posidonia australis, establishing baseline in situ transcriptomic profiles for tissues across a salinity gradient. S les were collected from four P. australis meadows growing in Shark Bay, Western Australia. Analysis of gene expression showed significant differences between tissue types, with more variation among leaves than meristem or roots. Gene ontology enrichment analysis showed the differences were largely due to the role of photosynthesis, plant growth and nutrient absorption in leaf, meristem and root organs, respectively. Differential gene expression of leaf and meristem showed upregulation of salinity regulation processes in higher salinity meadows. Our study highlights the importance of considering leaf meristem tissue when evaluating whole-plant responses to environmental change. This article has an associated First Person interview with the first author of the paper.
Is the genomics ‘cart’ before the restoration ecology ‘horse’? Insights from qualitative interviews and trends from the literature
Publisher: Cold Spring Harbor Laboratory
Date: 06-08-2021
DOI: 10.1101/2021.08.05.455206
Abstract: Harnessing new technologies is vital to achieve global imperatives to restore degraded ecosystems. We explored the potential of genomics as one such tool. We aimed to understand barriers hindering the uptake of genomics, and how to overcome them, via exploratory interviews with leading scholars in both restoration and its sister discipline of conservation – a discipline that has successfully leveraged genomics. We also conducted an examination of research trends to explore some insights that emerged from the interviews, including publication trends that have used genomics to address restoration and conservation questions. Our qualitative findings revealed varied perspectives in harnessing genomics. For ex le, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasised the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to bio erse and functional ecosystems.
Macrogenetic studies must not ignore limitations of genetic markers and scale
Publisher: Wiley
Date: 22-03-2021
DOI: 10.1111/ELE.13732
Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity
Publisher: Springer Science and Business Media LLC
Date: 04-05-2021
DOI: 10.1038/S41598-021-89065-Y
Abstract: Exposure to bio erse aerobiomes supports human health, but it is unclear which ecological factors influence exposure. Few studies have investigated near-surface green space aerobiome dynamics, and no studies have reported aerobiome vertical stratification in different urban green spaces. We used columnar s ling and next generation sequencing of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate urban green space aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial ersity and network complexity. We observed aerobiome vertical stratification and network complexity that was contingent on habitat type. Tree density, closer proximity, and canopy coverage associated with greater aerobiome alpha ersity. Grassland aerobiomes exhibited greater proportions of putative pathogens compared to scrub, and also stratified vertically. We provide novel insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace. This has important implications for managing urban landscapes for the regulation of aerobiome exposure.
Existing and emerging uses of drones in restoration ecology
Publisher: Wiley
Date: 26-06-2022
Abstract: In the absence of effective and scalable human intervention, up to 95% of the world's ecosystems will be affected by anthropogenic degradation by 2050. Therefore, immediate and large‐scale ecological restoration is imperative to stem bio ersity loss and ecosystem decline. Ecologists must draw upon the most effective and efficient tools available to achieve successful restoration goals. Drones (i.e., unmanned aerial vehicles) are a valuable set of tools in the environmental, forestry, and agriculture sectors however, there has been limited uptake in restoration ecology. Here, we aim to highlight the existing and emerging uses of drones in restoration science and practice. We discuss the strengths and weaknesses of these applications and provide a roadmap for increasing the utilisation of drones to refine and enhance restoration objectives. Our article is presented with the restoration continuum in mind, including sections for restoration planning, implementation and monitoring. We also take a novel approach by describing how drones relate to a globally recognised restoration tool published by the Society for Ecological Restoration . Drones are used in several restoration scenarios from mapping habitats and managing wildfires, to monitoring the effectiveness of restoration interventions. Many applications in other disciplines can also be transferred to restoration scenarios. However, the use of drones will be context‐dependent, and several technical and practical constraints need to be addressed. Drones have considerable potential to improve the science and practice of restoration at all stages of a restoration project, which is vital to realising the goals of the UN Decade on Ecosystem Restoration.
Standardized genetic diversity-life history correlates for improved genetic resource management of Neotropical trees
Publisher: Wiley
Date: 07-02-2018
DOI: 10.1111/DDI.12716
Biodiversity and Human Health: A Scoping Review and Case Studies on Underrepresented Linkages
Publisher: MDPI AG
Date: 19-10-2022
DOI: 10.20944/PREPRINTS202210.0275.V1
Abstract: Mounting evidence supports the connections between exposure to environment types& ndash & ndash such as green spaces and bio ersity& ndash & ndash and human health. However, the mechanistic links that connect bio ersity (the variety of life) and human health, plus the level of supporting evidence, are less clear. Here, we undertook a scoping review to map the links between bio ersity and human health and summarise the levels of associated evidence using an established weight of evidence framework. Distinct from other reviews, we provide additional context regarding the environment-microbiome-health axis, evaluate the environmental buffering pathway (e.g., bio ersity impacts on air pollution), and draw upon expert opinion to provide case studies on three underrepresented linkages. The case studies include (1) bio ersity and Indigenous Peoples& rsquo health, (2) bio ersity and urban social equity, and (3) bio ersity and COVID-19. We observed a moderate level of evidence to support the environmental microbiota-human health pathway and a moderate-high level of evidence to support broader nature pathways (e.g., green space) to various health outcomes, from stress reduction to enhanced wellbeing and improved social cohesion. However, studies of broader nature pathways did not typically include specific bio ersity metrics, indicating clear research gaps. Further research is required to understand the connections and causative pathways between bio ersity (e.g., using metrics such as taxonomy, ersity/richness, structure, and function) and health outcomes. There are well-established frameworks to assess the effects of broad classifications of nature on human health. These can assist future research in linking bio ersity metrics to human health outcomes. Our case studies on underrepresented linkages highlight the roles of bio ersity and its loss on urban lived experiences, infectious diseases, and Indigenous Peoples& rsquo sovereignty and livelihoods. More research and awareness of these socioecological interconnections are needed.
Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets
Publisher: Elsevier BV
Date: 05-2022
DOI: 10.1016/J.JENVMAN.2022.114748
Abstract: In post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (>25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that numerous alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states.
Which provenance and where? Seed sourcing strategies for revegetation in a changing environment
Publisher: Springer Science and Business Media LLC
Date: 02-11-2013
Revegetation rewilds the soil bacterial microbiome of an old field
Publisher: Wiley
Date: 08-04-2017
DOI: 10.1111/MEC.14081
Abstract: Ecological restoration is a globally important and well-financed management intervention used to combat bio ersity declines and land degradation. Most restoration aims to increase bio ersity towards a reference state, but there are concerns that intended outcomes are not reached due to unsuccessful interventions and land-use legacy issues. Monitoring bio ersity recovery is essential to measure success however, most projects remain insufficiently monitored. Current field-based methods are hard to standardize and are limited in their ability to assess important components of ecosystems, such as bacteria. High-throughput licon sequencing of environmental DNA (metabarcoding of eDNA) has been proposed as a cost-effective, scalable and uniform ecological monitoring solution, but its application in restoration remains largely untested. Here we show that metabarcoding of soil eDNA is effective at demonstrating the return of the native bacterial community in an old field following native plant revegetation. Bacterial composition shifted significantly after 8 years of revegetation, where younger sites were more similar to cleared sites and older sites were more similar to remnant stands. Revegetation of the native plant community strongly impacted on the belowground bacterial community, despite the revegetated sites having a long and dramatically altered land-use history (i.e. >100 years grazing). We demonstrate that metabarcoding of eDNA provides an effective way of monitoring changes in bacterial communities that would otherwise go unchecked with conventional monitoring of restoration projects. With further development, awareness of microbial ersity in restoration has significant scope for improving the efficacy of restoration interventions more broadly.
Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy
Publisher: MDPI AG
Date: 11-06-2021
DOI: 10.3390/LIFE11060553
Abstract: Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population ersity and ergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. S les identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other s les and likely form a separate, range-restricted species. Remaining s les formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic ersity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.
Higher levels of greenness and biodiversity associate with greater subjective wellbeing in adults living in Melbourne, Australia
Publisher: Elsevier BV
Date: 05-2019
DOI: 10.1016/J.HEALTHPLACE.2019.05.006
Abstract: Natural environments may be important for subjective wellbeing, yet evidence is sparse and measures of nature are unspecific. We used linear regression models to investigate the relationship between greenness, bio ersity and blue space and subjective wellbeing in 4,912 adults living in metropolitan Melbourne, Australia. Greenness (overall, private and public) and bio ersity associated with subjective wellbeing. In particular, we highlight the importance of the private greenness-subjective wellbeing association. Our work has implications for urban policy and planning in the context of increased urban densification.
Increased plant species richness associates with greater soil bacterial diversity in urban green spaces
Publisher: Elsevier BV
Date: 05-2021
The sound of restored soil: Measuring soil biodiversity in a forest restoration chronosequence with ecoacoustics
Publisher: Cold Spring Harbor Laboratory
Date: 23-01-2023
DOI: 10.1101/2023.01.23.525240
Abstract: Forest restoration requires monitoring to assess changes in above- and below-ground communities, which is challenging due to practical and resource limitations. With emerging sound recording technologies, ecological acoustic survey methods—also known as ‘ecoacoustics’—are increasingly available. These provide a rapid, effective, and non-intrusive means of monitoring bio ersity. Above-ground ecoacoustics is increasingly widespread, but soil ecoacoustics has yet to be utilised in restoration despite its demonstrable effectiveness at detecting meso- and macrofauna acoustic signals. This study applied ecoacoustic tools and indices (Acoustic Complexity Index, Normalised Difference Soundscape Index, and Bioacoustic Index) to measure above- and below-ground bio ersity in a forest restoration chronosequence. We hypothesised that higher acoustic complexity, ersity and high-frequency to low-frequency ratio would be detected in restored forest plots. We collected n = 198 below-ground s les and n = 180 ambient and controlled s les from three recently degraded (within 10 years) and three restored (30-51 years ago) deciduous forest plots across three monthly visits. We used passive acoustic monitoring to record above-ground biological sounds and a below-ground s ling device and sound-attenuation chamber to record soil communities. We found that restored plot acoustic complexity and ersity were higher in the sound-attenuation chamber soil but not in situ or above-ground s les. Moreover, we found that restored plots had a significantly greater high-frequency to low-frequency ratio for soil, but no such association for above-ground s les. Our results suggest that ecoacoustics has the potential to monitor below-ground bio ersity, adding to the restoration ecologist’s toolkit and supporting global ecosystem recovery. This is the first known study to assess the sounds of soil bio ersity in a forest restoration context, paving the way for more comprehensive studies and practical applications to support global ecosystem recovery. Soil ecoacoustics has the potential to support restoration ecology/bio ersity assessments, providing a minimally intrusive, cost-effective and rapid surveying tool. The methods are also relatively simple to learn and apply. Ecoacoustics can contribute toward overcoming the profound challenge of quantifying the effectiveness (i.e., success) of forest restoration interventions in reinstating target species, functions and so-called ‘services’ and reducing disturbance.
Revegetation of urban green space rewilds soil microbiotas with implications for human health and urban design
Publisher: Wiley
Date: 17-05-2020
DOI: 10.1111/REC.13175
Invasive Rosa rugosa populations outperform native populations, but some populations have greater invasive potential than others
Publisher: Springer Science and Business Media LLC
Date: 10-04-2018
DOI: 10.1038/S41598-018-23974-3
Abstract: Increased performance of invasive plant species in their introduced range vs. their native range has been previously documented. However, performance differences among invasive populations have rarely been explored, despite this information being central to understanding the evolution of invasiveness as well as being a useful basis to inform management of invasive species. To examine variation in performance among populations of Rosa rugosa in its introduced range, and whether introduced populations perform better than native populations, we quantified growth and reproductive traits in five invasive populations in northwest Europe and two native and declining populations in China. Overall, we found that the introduced R. rugosa populations we s led performed significantly better than the s led native populations for growth and reproductive traits (2 to 4 fold increase). However, there was significant variation for most traits among the five invasive populations, demonstrating that some introduced populations we s led were more successful invaders than others. Our findings provide a useful foundation for management of invasive R. rugosa in Europe, and support the recent call for more intra-species research in invasive species biology.
Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD
Publisher: Springer Science and Business Media LLC
Date: 22-04-2021
Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia
Publisher: Oxford University Press (OUP)
Date: 08-2020
Abstract: Populations at the edges of their geographical range tend to have lower genetic ersity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic ersity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal ersity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic ersity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic ersity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.
Walking Ecosystems in Microbiome-Inspired Green Infrastructure: An Ecological Perspective on Enhancing Personal and Planetary Health
Publisher: MDPI AG
Date: 16-11-2018
Abstract: Principles of ecology apply at myriad scales, including within the human body and the intertwined macro and microscopic ecosystems that we depend upon for survival. The conceptual principles of dysbiosis (‘life in distress’) also apply to different realms of life—our microbiome, the macro environment and the socioeconomic domain. Viewing the human body as a holobiont—a host plus billions of microbial organisms working symbiotically to form a functioning ecological unit—has the potential to enhance personal and planetary health. We discuss this ecological perspective in our paper. We also discuss the proposals to rewild the microbiome, innovative microbiome-inspired green infrastructure (MIGI) and the basis of prescribing ‘doses of nature’. Particular emphasis is given to MIGI—a collective term for the design and management of innovative living urban features that could potentially enhance public health via health-inducing microbial interactions. This concept builds upon the microbiome rewilding hypothesis. Mounting evidence points to the importance of microbial ersity in maintaining favorable health. Moreover, connecting with nature—both physically and psychologically–has been shown to enhance our health and wellbeing. However, we still need to understand the underlying mechanisms, and optimal types and levels of exposure. This paper adds to other recent calls for the inclusion of the environment-microbiome-health axis in nature–human health research. Recognizing that all forms of life—both the seen and the unseen—are in some way connected (ecologically, socially, evolutionarily), paves the way to valuing reciprocity in the nature–human relationship. It is with a holistic and symbiotic perspective that we can begin to integrate strategies and address connected issues of human and environmental health. The prospective strategies discussed in our paper focus on enhancing our connections with the natural world, and ultimately aim to help address the global challenge of halting and reversing dysbiosis in all its manifestations.
Pollen flow in fragmented landscapes maintains genetic diversity following stand-replacing disturbance in a neotropical pioneer tree, Vochysia ferruginea Mart
Publisher: Springer Science and Business Media LLC
Date: 09-10-2015
DOI: 10.1038/HDY.2013.95
Increasing aridity strengthens core bacterial rhizosphere associations in the pan-palaeotropical C4 grass, Themeda triandra
Publisher: Authorea, Inc.
Date: 11-09-2023
Ecotypic differentiation and phenotypic plasticity combine to enhance the invasiveness of the most widespread daisy in Chile, Leontodon saxatilis
Publisher: Springer Science and Business Media LLC
Date: 08-05-1970
DOI: 10.1038/S41598-017-01457-1
Abstract: Dispersal and reproductive traits of successful plant invaders are expected to undergo strong selection during biological invasions. Numerous Asteraceae are invasive and display dimorphic fruits within a single flower head, resulting in differential dispersal pathways - wind-dispersed fruits vs. non-dispersing fruits. We explored ecotypic differentiation and phenotypic plasticity of seed output and fruit dimorphisms in exotic Chilean and native Spanish populations of Leontodon saxatilis subsp. rothii . We collected flower heads from populations in Spain and Chile along a rainfall gradient. Seeds from all populations were planted in reciprocal transplant trials in Spain and Chile to explore their performance in the native and invasive range. We scored plant biomass, reproductive investment and fruit dimorphism. We observed strong plasticity, where plants grown in the invasive range had much greater biomass, flower head size and seed output, with a higher proportion of wind-dispersed fruits, than those grown in the native range. We also observed a significant ecotype effect, where the exotic populations displayed higher proportions of wind-dispersed fruits than native populations. Together, these patterns reflect a combination of phenotypic plasticity and ecotypic differentiation, indicating that Leontodon saxatilis has probably increased propagule pressure and dispersal distances in its invasive range to enhance its invasiveness.
Plants, position and pollination: Planting arrangement and pollination limitation in a revegetated eucalypt woodland
Publisher: Wiley
Date: 05-07-2019
DOI: 10.1111/EMR.12382
Increasing Antimicrobial Resistance and Potential Human Bacterial Pathogens in an Invasive Land Snail Driven by Urbanization
Publisher: American Chemical Society (ACS)
Date: 25-04-2023
Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment
Publisher: The Royal Society
Date: 06-2022
Abstract: Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis . This seagrass is at the northern extent of its natural geographic range and experiences extremes in temperature and salinity. Our genomic and cytogenetic assessments of 10 meadows identified geographically restricted, diploid clones (2 n = 20) in a single location, and a single widespread, high-heterozygosity, polyploid clone (2 n = 40) in all other locations. The polyploid clone spanned at least 180 km, making it the largest known ex le of a clone in any environment on earth. Whole-genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clone probably formed in shallow waters after the inundation of Shark Bay less than 8500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.
Pollen diversity matters: Revealing the neglected effect of pollen diversity on fitness in fragmented landscapes
Publisher: Wiley
Date: 18-10-2012
DOI: 10.1111/MEC.12056
Abstract: Few studies have documented the impacts of habitat fragmentation on plant mating patterns together with fitness. Yet, these processes require urgent attention to better understand the impact of contemporary landscape change on bio ersity and for guiding native plant genetic resource management. We examined these relationships using the predominantly insect-pollinated Eucalyptus socialis. Progeny were collected from trees located in three increasingly disturbed landscapes in southern Australia and were planted out in common garden experiments. We show that in idual mating patterns were increasingly impacted by lower conspecific density caused by habitat fragmentation. We determined that reduced pollen ersity probably has effects over and above those of inbreeding on progeny fitness. This provides an alternative mechanistic explanation for the indirect density dependence often inferred between conspecific density and offspring fitness.
Constraints to and conservation implications for climate change adaptation in plants
Publisher: Springer Science and Business Media LLC
Date: 24-09-2016
A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri)
Publisher: Springer Science and Business Media LLC
Date: 30-08-2022
DOI: 10.1007/S10592-022-01468-0
Abstract: Understanding population structure and genetic ersity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy ( Acanthocladium dockeri ) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting in iduals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and ersity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic ersity, and there was no evidence of inter-population gene flow. In iduals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic ersity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.
Evidence of endemic hendra virus infection in flying-foxes (pteropus conspicillatus)-implications for disease risk management
Publisher: Public Library of Science (PLoS)
Date: 14-12-2011
Higher levels of multiple paternities increase seedling survival in the long-lived tree eucalyptus gracilis
Publisher: Public Library of Science (PLoS)
Date: 28-02-2014
Global meta-analysis shows progress towards recovery of soil microbiota following revegetation
Publisher: Elsevier BV
Date: 08-2022
Spatial assortment of soil organisms supports the size-plasticity hypothesis
Publisher: Springer Science and Business Media LLC
Date: 19-10-2022
DOI: 10.1038/S43705-022-00185-6
Abstract: The size-plasticity hypothesis posits that larger size organisms are less plastic in their metabolic rates and, therefore, are more strongly environmental-filtered than smaller organisms. Many studies have supported this hypothesis by evaluating the relative roles of environmental filtration and dispersal for different taxonomic groups of soil organisms. Most observations are made at large spatial scales, which are assumed to have a wide array of varying habitats. However, since urbanization causes habitat fragmentation at smaller regional scales, testing the size-plasticity hypothesis at this scale would help better understand the spatial assortment of urban soil organisms which, in turn, would help to develop improved management and conservation strategies for urban soil health. Here, we used DNA metabarcoding on five groups of soil biota (bacteria, fungi, protists, nematodes, and invertebrates) to assess the relative importance of dispersal and environmental filters to examine the size-plasticity hypothesis at this spatial scale in an urban environment. We observed strong distance-decay of community similarities associated with higher levels of stochastic changes in bacteria, nematode, and protist communities but not fungal or invertebrate communities. Bacterial communities occupied the widest niche followed by protists and nematodes, potentially because of their higher dispersal abilities compared to the larger soil organisms. Null deviation of communities varied with taxonomic groups where bacteria and nematodes were mainly driven by homogenizing dispersal, protists and fungi by drift, and soil invertebrates by environmental selection. We further identified a small percentage of locally-adapted taxa (2.1%) that could be focal taxa for conservation and restoration efforts by, for ex le, restoring their habitats and enhancing their regional connectivity. These results support the size-plasticity hypothesis at the relatively unexplored regional scale in an urbanization context, and provide new information for improving urban soil health and sustainable city models.
Exposure to greenspaces could reduce the high global burden of pain
Publisher: Elsevier BV
Date: 08-2020
Exposure to Airborne Bacteria Depends upon Vertical Stratification and Vegetation Complexity
Publisher: Cold Spring Harbor Laboratory
Date: 11-11-2020
DOI: 10.1101/2020.11.11.377630
Abstract: Exposure to bio erse aerobiomes may support human health, but it is unclear which ecological factors influence exposure. Few studies have investigated near-surface green space aerobiome dynamics, and no studies have investigated aerobiome vertical stratification in different green spaces. We used columnar s ling and next generation sequencing of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial ersity and network complexity. We observed aerobiome vertical stratification and network complexity that was contingent on habitat type. Tree density, closer proximity, and canopy coverage associated with greater aerobiome alpha ersity. Grassland aerobiomes exhibited greater proportions of putative pathogens compared to scrub, and also stratified vertically. We provide new insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace.
Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere
Publisher: Elsevier BV
Date: 04-2018
DOI: 10.1016/J.FUNBIO.2017.12.013
Abstract: Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by lification and sequencing of the fungal barcode region ITS2. Fungal species ersity was found to decrease from bulk soil to rhizosphere to endosphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere s les suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.
Creating testable questions in practical conservation
Publisher: Department of Zoology, University of Cambridge
Date: 2022
Abstract: It is now clear that the routine embedding of experiments into conservation practice is essential for creating reasonably comprehensive evidence of the effectiveness of actions. However, an important barrier is the stage of identifying testable questions that are both useful but also realistic to carry out without a major research project. We identified approaches for generating such suitable questions. A team of 24 participants crowdsourced suggestions, resulting in a list of a hundred possible tests of actions.
Does aggression and explorative behaviour decrease with lost warning coloration?
Publisher: Oxford University Press (OUP)
Date: 05-11-2013
Rare genera differentiate urban green space soil bacterial communities in three cities across the world
Publisher: Microbiology Society
Date: 27-01-2022
Abstract: Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial bio ersity to benefit human health. Exposure to urban microbial bio ersity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via bio ersity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e. ersity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK Haikou, China and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil s les and assessing bacterial ersity. We characterized these green spaces as having ‘low’ or ‘high’ vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and ersity around the world. Within cities, we observed significantly different alpha and beta ersities between vegetation complexities however, these results varied between cities. Rare genera ( % relative abundance in idually, on average 35% relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.
Erratum: The resilience of forest fragmentation genetics-no longer a paradox-we were just looking in the wrong place (Heredity (2015) 115 (97-99) DOI: 10.1038/hdy.2015.40)
Publisher: Springer Science and Business Media LLC
Date: 10-02-2016
DOI: 10.1038/HDY.2015.86
Twenty Important Research Questions in Microbial Exposure and Social Equity
Publisher: American Society for Microbiology
Date: 22-02-2022
DOI: 10.1128/MSYSTEMS.01240-21
Abstract: Social and political policy, human activities, and environmental change affect the ways in which microbial communities assemble and interact with people. These factors determine how different social groups are exposed to beneficial and/or harmful microorganisms, meaning microbial exposure has an important socioecological justice context.
Rare genera differentiate urban green space soil bacterial communities in three cities across the world
Publisher: Cold Spring Harbor Laboratory
Date: 22-02-2021
DOI: 10.1101/2021.02.21.432167
Abstract: Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial bio ersity to benefit human health. Exposure to urban microbial bio ersity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via bio ersity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e., ersity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK Haikou, China and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil s les and assessing bacterial ersity. We characterized these green spaces as having ‘low’ or ‘high’ vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and ersity around the world. Within cities, we observed significantly different alpha and beta ersities between vegetation complexities however, these results varied between cities. Rare genera ( 1 % relative abundance in idually, on average 35 % relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.
Does revegetation cause soil microbiota recovery? Evidence from revisiting a revegetation chronosequence 6 years after initial sampling
Publisher: Wiley
Date: 03-2022
DOI: 10.1111/REC.13635
Abstract: The global bio ersity and land degradation crises have brought about an urgent need and great demand for restoration actions. However, restoration outcomes are often less than ideal, indicating a need for improved restoration practices. Soil microbiota are extremely erse and functionally important and should be further considered in restoration. However, despite their importance, there remains a gap in understanding of how soil microbiota respond following native plant revegetation. Several studies have used cross‐sectional study designs of restoration chronosequences to infer that revegetation causes the recovery of soil microbiota, but it is near‐impossible to determine cause and effect relationships with cross‐sectional study designs. Here we used high‐throughput licon sequencing of the bacterial 16s rRNA gene from soil s les collected at two timepoints, 6 years apart, at a revegetation chronosequence in South Australia. Our results show some indications of recovery but not the additional recovery in bacterial community composition toward the reference sites as expected after this 6‐year period—a result that appears at odds to the expected patterns of revegetation causing recovery of soil microbiota. Spatially dependent factors (e.g. soil chemistry), biotic and abiotic barriers, seasonal differences in s ling, and variability among the ecological reference sites could each help explain this apparent lack of additional microbial recovery. More detailed longitudinal and/or experimental manipulation work is required to further examine the cause‐effect relationships. Our study contributes important new information and highlights knowledge gaps in how soil microbiota respond to revegetation, and we urge caution when attempting to infer causation from cross‐sectional chronosequence studies.
Effective population size remains a suitable, pragmatic indicator of genetic diversity for all species, including forest trees
Publisher: Elsevier BV
Date: 2021
Mainstreaming microbes across biomes
Publisher: Oxford University Press (OUP)
Date: 17-06-2020
Abstract: Bacteria, fungi, and other microorganisms in the environment (i.e., environmental microbiomes) provide vital ecosystem services and affect human health. Despite their importance, public awareness of environmental microbiomes has lagged behind that of human microbiomes. A key problem has been a scarcity of research demonstrating the microbial connections across environmental biomes (e.g., marine, soil) and between environmental and human microbiomes. We show in the present article, through analyses of almost 10,000 microbiome papers and three global data sets, that there are significant taxonomic similarities in microbial communities across biomes, but very little cross-biome research exists. This disconnect may be hindering advances in microbiome knowledge and translation. In this article, we highlight current and potential applications of environmental microbiome research and the benefits of an interdisciplinary, cross-biome approach. Microbiome scientists need to engage with each other, government, industry, and the public to ensure that research and applications proceed ethically, maximizing the potential benefits to society.
Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure
Publisher: Elsevier BV
Date: 12-2020
Introducing BASE: The Biomes of Australian Soil Environments soil microbial diversity database
Publisher: Oxford University Press (OUP)
Date: 28-09-2021
Restoration, soil organisms, and soil processes: emerging approaches
Publisher: Wiley
Date: 09-2020
DOI: 10.1111/REC.13237
A guide to minimize contamination issues in microbiome restoration studies
Publisher: Wiley
Date: 29-03-2021
DOI: 10.1111/REC.13358
Abstract: Many restoration ecology studies now incorporate an environmental microbiome component, made possible mainly via advanced DNA sequencing technologies. Environmental microbiomes are important for successful restoration as they support many ecosystem functions and services that are a target of restoration interventions. However, since microbes are ubiquitous in most environments, including laboratories and researchers, there are contamination risks. If these risks are not adequately managed, the conclusions drawn from these microbiome restoration studies could be compromised. Here, we provide a user guide for restoration ecologists on how to navigate microbiome contamination risks at each stage of a study, from planning and s ling to data analysis and publishing. The two main categories of contamination we discuss are cross‐contamination —contamination between s les—and external contamination —contamination from reagents and environmental sources. We also consider the impact of batch effects , where s ling and/or processing order could leave a signal in the data. Without adequate control, these contamination issues can undermine the results of microbiome restoration studies. We hope that this guide will help minimize the effect of contamination and improve the quality of data and studies going forward.
Ecosystem restoration - a public health intervention
Publisher: Springer Science and Business Media LLC
Date: 23-06-2020
The eco-evolutionary risks of not changing seed provenancing practices in changing environments
Publisher: Authorea, Inc.
Date: 02-06-2023
DOI: 10.22541/AU.168570191.19000524/V1
Abstract: Rapidly changing environments combined with increasing global restoration initiatives require improved seed sourcing strategies for native revegetation. Sourcing seed from local populations (local provenancing) has been the long-standing default for native revegetation for numerous eco-evolutionary reasons including local adaptation and species co-evolution. However, the evidence-base has shifted, revealing risks for both non-local and local provenancing in changing environments. As alternative strategies gain interest, we argue for effective decision-making that weighs the risks of changing and not changing seed sourcing strategies in a changing environment that transcends a default position and the polarising local vs. non-local debate.
Microbiome-Inspired Green Infrastructure: A Toolkit for Multidisciplinary Landscape Design
Publisher: Elsevier BV
Date: 12-2020
Functional acclimation across microgeographic scales in Dodonaea viscosa
Publisher: Oxford University Press (OUP)
Date: 05-2018
Networked and embedded scientific experiments will improve restoration outcomes
Publisher: Wiley
Date: 07-05-2018
DOI: 10.1002/FEE.1810
Characterising the soil fungal microbiome in metropolitan green spaces across a vegetation biodiversity gradient
Publisher: Elsevier BV
Date: 10-2020
Asymmetrical habitat coupling of an aquatic predator—The importance of individual specialization
Publisher: Wiley
Date: 23-02-2019
DOI: 10.1002/ECE3.4973
Soil DNA chronosequence analysis shows bacterial community re‐assembly following post‐mining forest rehabilitation
Publisher: Wiley
Date: 18-05-2022
DOI: 10.1111/REC.13706
Abstract: Mining activities modify both aboveground and belowground ecological communities, presenting substantial challenges for restoration. The soil microbiome is one of these impacted communities and performs important ecosystem functions but receives limited focus in restoration. Sequencing soil DNA enables accurate and cost‐effective assessment of soil microbiota, allowing for comparisons across land use, environmental, and temporal gradients. We used licon sequencing of the bacterial 16s rRNA gene extracted from soil s les across a 28‐year post‐mining rehabilitation chronosequence to assess soil bacterial composition and ersity following rehabilitation at a bauxite mine in Western Australia's jarrah forest. We show that while bacterial alpha ersity did not differ between reference and rehabilitated sites, bacterial community composition changed dramatically across the chronosequence, suggesting strong impacts by mining and rehabilitation activities. Bacterial communities generally became increasingly similar to unmined reference sites with time since rehabilitation. Soil from sites rehabilitated as recently as 14 years ago did not have significantly different communities to reference sites. Overall, our study provides evidence indicating the recovery of soil bacterial communities toward reference states following rehabilitation. Including several ecological reference sites revealed substantial natural variability in bacterial communities from within a single mine site. We urge future restoration chronosequence studies to s le reference sites that geographically span the restored sites and/or are spatially paired with restored sites to ensure this variability is captured and to improve any inferences on recovery.
Building a plant DNA barcode reference library for a diverse tropical flora: an example from Queensland, Australia
Publisher: MDPI AG
Date: 29-02-2016
DOI: 10.3390/D8010005
The Lovebug Effect
Publisher: Elsevier BV
Date: 06-2020
Assessing the benefits and risks of translocations in changing environments: A genetic perspective
Publisher: Wiley
Date: 18-06-2011
Multispecies Sustainability
Publisher: Cambridge University Press (CUP)
Date: 2020
DOI: 10.1017/SUS.2020.28
Abstract: The sustainability concept seeks to balance how present and future generations of humans meet their needs. But because nature is viewed only as a resource, sustainability fails to recognize that humans and other living beings depend on each other for their well-being. We therefore argue that true sustainability can only be achieved if the interdependent needs of all species of current and future generations are met, and propose calling this ‘multispecies sustainability’. We explore the concept through visualizations and scenarios, then consider how it might be applied through case studies involving bees and healthy green spaces.
Soil bacterial community differences along a coastal restoration chronosequence
Publisher: Springer Science and Business Media LLC
Date: 13-11-2020
Urban habitat restoration provides a human health benefit through microbiome rewilding
Publisher: Wiley
Date: 11-10-2017
DOI: 10.1111/REC.12610
Abstract: Restoration aims to return ecosystem services, including the human health benefits of exposure to green space. The loss of such exposure with urbanization and industrialization has arguably contributed to an increase in human immune dysregulation. The Bio ersity and Old Friends hypotheses have described the possible mechanisms of this relationship, and suggest that reduced exposure to erse, beneficial microorganisms can result in negative health consequences. However, it is unclear whether restoration of bio erse habitat can reverse this effect, and what role the environmental microbiome might have in such recovery. Here, we propose the Microbiome Rewilding Hypothesis , which specifically outlines that restoring bio erse habitats in urban green spaces can rewild the environmental microbiome to a state that enhances primary prevention of human disease. We support our hypothesis with ex les from allied fields, including a case study of active restoration that reversed the degradation of the soil bacterial microbiome of a former pasture. This case study used high‐throughput licon sequencing of environmental DNA to assess the quality of a restoration intervention in restoring the soil bacterial microbiome. The method is rapid, scalable, and standardizable, and has great potential as a monitoring tool to assess functional outcomes of green‐space restoration. Evidence for the Microbiome Rewilding Hypothesis will help motivate health professionals, urban planners, and restoration practitioners to collaborate and achieve co‐benefits. Co‐benefits include improved human health outcomes and investment opportunities for bio ersity conservation and restoration.
Bolivar Wastewater Treatment Plant provides an important habitat for South Australian ducks and waders
Publisher: BirdLife Australia, Ltd.
Date: 2020
DOI: 10.20938/AFO37190199
Abstract: The populations of South Australian duck and wader species have recently decreased considerably, but their abundance at Bolivar Wastewater Treatment Plant in metropolitan Adelaide is poorly known. To help assess the importance of this site for ducks and waders, we made 25 trips to Bolivar between December 2018 and July 2020, during most of which time south-eastern Australia was experiencing a long dry period. On each trip, we observed between 11 and 26 species of ducks and waders, with a mean total of 9804 (range 2437–15,653) in iduals per trip. At times, we observed several thousand Pink-eared Ducks Malacorhynchus membranaceus, Grey Teal Anas gracilis, and Australian Shelducks Tadorna tadornoides, with occasionally up to 1200 Blue-billed Ducks Oxyura australis and 2000 Hardheads Aythya australis. Several wader species that largely breed in Australia’s semi-arid and arid zones were also observed, including occasionally Red-necked Avocets Recurvirostra novaehollandiae. Five species of waders that breed in the Northern Hemisphere were also recorded fairly regularly in the summer of both 2018–2019 and 2019–2020, including up to ~2000 Sharp-tailed Sandpipers Calidris acuminata, 2000 Red-necked Stints C. ruficollis and 150 Curlew Sandpipers C. ferruginea. These observations indicate that this wastewater treatment plant is a critically important refuge site for several species of ducks and waders. Every effort should thus be made to maintain this site for the conservation of these species in the future.
Four Islands EcoHealth Network
Publisher: Wiley
Date: 05-2021
DOI: 10.1111/REC.13382
Abstract: Reversing the spiraling trajectory of ecological degradation requires a profound paradigm shift that more explicitly links human and ecosystem health. Human health, as used here, includes well‐being and livelihoods, which are largely determined by socio‐cultural, economic, and environmental drivers. Ecological restoration and related restorative activities can contribute substantially to human health. However, restoration projects differ widely and health impacts can be difficult to quantify. Interdisciplinary restoration networks are important for investigating the complex socio‐cultural, economic, and environmental dynamics that characterize restoration practice and related health outcomes. We present the Four Islands EcoHealth Network (FIEN) as an exemplar for establishing interdisciplinary project connectivity to clarify intersections between ecosystem restoration and human health. FIEN is a cooperative regional restoration network within Australia and Aotearoa New Zealand which aims to research and devise strategies for restoration to simultaneously improve human health and repair native ecosystems. FIEN will operate collaboratively at local and regional scales to expand interdisciplinary research and outreach by linking research with experience‐based and Traditional Ecological Knowledge‐based restoration activities. The group's primary focus is value‐adding to the efforts of its constituent organizations by sharing expertise and methodologies to enable large‐scale analysis and comparison across adjacent regions, ultimately disseminating collective results through impactful science communication. We consider explicitly linking human and ecosystem health the best way forward to reverse the current downward trajectory of ecological degradation and declining human health, and propose FIEN as an approach which other restoration‐minded groups and coalitions might follow.
Post-pit optimization strategic alignment
Publisher: Academy of Science of South Africa
Date: 2016
Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective
Publisher: Frontiers Media SA
Date: 13-09-2018
Spatial assortment of soil organisms supports the size-plasticity hypothesis
Publisher: Research Square Platform LLC
Date: 30-08-2022
DOI: 10.21203/RS.3.RS-1896194/V1
Abstract: The size-plasticity hypothesis posits that larger size organisms are less plastic in their metabolic rates and therefore are more strongly environmental-filtered than smaller organisms. Many studies have supported this hypothesis by evaluating the relative roles of environmental filtration and dispersal for different taxonomic groups of soil organisms. Most observations are made at large spatial scales, which are assumed to have a wide array of varying habitats. However, since urbanization causes habitat fragmentation at smaller regional scales, testing the size-plasticity hypothesis at this scale would help better understand the spatial assortment of urban soil organisms which, in turn, would help to develop improved management and conservation strategies of urban soil health. Here, we used DNA metabarcoding on five groups of soil biota (bacteria, fungi, protists, nematodes, and soil invertebrates) to assess the relative importance of dispersal and environmental filters to examine the size-plasticity hypothesis at this spatial scale in an urban environment. We observed strong distance-decay of community similarities associated with higher levels of stochastic changes in bacteria, nematode and protist communities but not fungal or invertebrate communities. Bacterial communities occupied the widest niche followed by protists and nematodes, potentially because of their higher dispersal abilities compared to the larger soil organisms. Null deviation of communities varied with taxonomic groups where bacteria and nematodes were mainly driven by homogenizing dispersal, protists and fungi by drift and soil invertebrates by environmental selection. We further identified a small percentage of locally-adapted taxa (2.1%) that could be focal taxa for conservation and restoration efforts by, for ex le, restoring their habitats and enhancing their regional connectivity. These results support the size-plasticity hypothesis at the relatively unexplored regional scale in an urbanization context, and provide new information for improving urban soil health and sustainable city models and urban soil health.
Spatially designed revegetation—why the spatial arrangement of plants should be as important to revegetation as they are to natural systems
Publisher: Wiley
Date: 14-03-2018
DOI: 10.1111/REC.12690
Green Prescriptions and Their Co-Benefits
Publisher: MDPI AG
Date: 17-01-2019
Abstract: There is a growing recognition of the links between the increasing prevalence of noncommunicable diseases, environmental concerns including bio ersity loss and ecosystem degradation, and socioecological issues such as ecological (in)justice. This has encouraged a number of recent calls for the development of integrative approaches aimed at addressing these issues—also known as nature-based solutions. An ex le of an emerging nature-based solution is a ‘green prescription’, broadly defined as a nature-based health intervention. Green prescriptions are typically designed for patients with a defined need and they have the potential to supplement orthodox medical treatments, particularly those aimed at addressing noncommunicable diseases. It is also thought that green prescriptions could bring about significant environmental, economic, and social co-benefits. However, researchers have recently expressed concerns over taking the ‘dose of nature’ approach, in that it may be too reductionistic for the complex social settings in which it is provided. Here we frame a holistic philosophical perspective and discuss green prescribing logic, types, mechanisms and fundamental remaining questions and challenges. We place a significant emphasis on the potential co-benefits of green prescriptions, and the importance of taking a planetary health approach. More research is needed to determine how this potential can be realised, and to further understand the complexities of the nature–human health relationship. However, with additional research and support, there is huge potential for green prescriptions to contribute to both reactive (health care) and proactive (health promoting) public health solutions whilst enhancing the natural environment.
Urban greenspaces shape soil protist communities in a location-specific manner
Publisher: Elsevier BV
Date: 10-2023
Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt
Publisher: Springer Science and Business Media LLC
Date: 28-11-2015
DOI: 10.1038/HDY.2012.72
Priority Actions to Improve Provenance Decision-Making
Publisher: Oxford University Press (OUP)
Date: 13-06-2018
Continental-scale insights into the soil microbial co-occurrence networks of Australia and their environmental drivers
Publisher: Elsevier BV
Date: 11-2023
Cities, biodiversity and health
Publisher: Informa UK Limited
Date: 29-11-2018
Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics
Publisher: Springer Science and Business Media LLC
Date: 04-09-2015
DOI: 10.1038/HDY.2013.48
The sound of restored soil
Publisher: Wiley
Date: 22-05-2023
DOI: 10.1111/REC.13934
Abstract: Forest restoration requires monitoring to assess above‐ and belowground communities, which is challenging due to practical and resource limitations. Ecological acoustic survey methods––also known as “ecoacoustics”––are increasingly available and provide a rapid, effective, and non‐intrusive means of monitoring bio ersity. Aboveground ecoacoustics is widespread, but soil ecoacoustics has yet to be utilized in restoration despite its demonstrable effectiveness at detecting soniferous soil meso‐ and macrofauna. This study applied ecoacoustic tools and indices (Acoustic Complexity Index, Normalized Difference Soundscape Index, and Bioacoustic Index) to measure belowground (and aboveground as secondary) bio ersity in a forest restoration site spanning two age classes. We collected n = 198 belowground acoustic s les and n = 180 aboveground s les from three recently deforested (felled years ago) and three deciduous forest plots undergoing restoration (for the last 30–51 years) across three monthly visits in South Yorkshire, U.K. We used a belowground s ling device and sound‐attenuation chamber to record soil communities and passive acoustic monitoring to record aboveground sounds. We found that restored plot acoustic complexity and ersity were significantly higher than deforested plots in the sound‐attenuation chamber, but there were no inter‐plot differences in in‐situ soil or aboveground s les. We also found that restored plots had a significantly greater high‐frequency to low‐frequency ratio (suggesting higher biophony to anthrophony ratios) for in‐situ and sound chamber soil but no association for aboveground s les. Our results suggest that ecoacoustics has immense potential to monitor belowground bio ersity, adding to the restoration ecologist's toolkit and supporting global ecosystem recovery.
Restoration
Publisher: Springer Science and Business Media LLC
Date: 25-05-2016
DOI: 10.1038/533469D
Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species
Publisher: Wiley
Date: 21-08-2016
DOI: 10.1111/MEC.13750
Abstract: Teasing apart neutral and adaptive genomic processes and identifying loci that are targets of selection can be difficult, particularly for nonmodel species that lack a reference genome. However, identifying such loci and the factors driving selection have the potential to greatly assist conservation and restoration practices, especially for the management of species in the face of contemporary and future climate change. Here, we focus on assessing adaptive genomic variation within a nonmodel plant species, the narrow-leaf hopbush (Dodonaea viscosa ssp. angustissima), commonly used for restoration in Australia. We used a hybrid-capture target enrichment approach to selectively sequence 970 genes across 17 populations along a latitudinal gradient from 30°S to 36°S. We analysed 8462 single-nucleotide polymorphisms (SNPs) for FST outliers as well as associations with environmental variables. Using three different methods, we found 55 SNPs with significant correlations to temperature and water availability, and 38 SNPs to elevation. Genes containing SNPs identified as under environmental selection were erse, including aquaporin and abscisic acid genes, as well as genes with ontologies relating to responses to environmental stressors such as water deprivation and salt stress. Redundancy analysis demonstrated that only a small proportion of the total genetic variance was explained by environmental variables. We demonstrate that selection has led to clines in allele frequencies in a number of functional genes, including those linked to leaf shape and stomatal variation, which have been previously observed to vary along the s led environmental cline. Using our approach, gene regions subject to environmental selection can be readily identified for nonmodel organisms.
Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health?
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.ENVINT.2019.05.011
Abstract: Understanding how microbial communities change with environmental degradation and restoration may offer new insights into the understudied ecology that connects humans, microbiota, and the natural world. Immunomodulatory microbial ersity and 'Old Friends' are thought to be supplemented from bio erse natural environments, yet deficient in anthropogenically disturbed or degraded environments. However, few studies have compared the microbiomes of natural vs. human-altered environments and there is little knowledge of which microbial taxa are representative of ecological restoration-i.e. the assisted recovery of degraded ecosystems typically towards a more natural, bio erse state. Here we use novel bootstrap-style res ling of site-level soil bacterial 16S rRNA gene environmental DNA data to identify genus-level indicators of restoration from a 10-year grassy eucalypt woodland restoration chronosequence at Mt Bold, South Australia. We found two key indicator groups emerged: 'opportunistic taxa' that decreased in relative abundance with restoration and more stable and specialist, 'niche-adapted taxa' that increased. We validated these results, finding seven of the top ten opportunists and eight of the top ten niche-adapted taxa displayed consistent differential abundance patterns between human-altered vs. natural s les elsewhere across Australia. Extending this, we propose a two-dimensional mapping for ecosystem condition based on the proportions of these ergent indicator groups. We also show that restoring a more bio erse ecosystem at Mt Bold has increased the potentially immune-boosting environmental microbial ersity. Furthermore, environmental opportunists including the pathogen-containing genera Bacillus, Clostridium, Enterobacter, Legionella and Pseudomonas associated with disturbed ecosystems. Our approach is generalizable with potential to inform DNA-based methods for ecosystem assessment and help target environmental interventions that may promote microbiota-mediated human health gains.
The potential of outdoor environments to supply beneficial butyrate-producing bacteria to humans
Publisher: Elsevier BV
Date: 07-2021
Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs ) for genetic composition
Publisher: Wiley
Date: 12-04-2022
DOI: 10.1111/BRV.12852
Abstract: Bio ersity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how bio ersity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying bio ersity data. A major challenge is that bio ersity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Bio ersity Observation Network (GEO BON) has developed the Essential Bio ersity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret bio ersity observation data from erse sources. Mapping and analyzing EBVs can help to evaluate how aspects of bio ersity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of bio ersity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic bio ersity monitoring with respect to theory, s ling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: ( i ) Genetic Diversity ( ii ) Genetic Differentiation ( iii ) Inbreeding and ( iv ) Effective Population Size ( N e ). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for bio ersity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all bio ersity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic bio ersity monitoring regionally and globally.
Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction
Publisher: MDPI AG
Date: 30-07-2020
DOI: 10.3390/D12080299
Abstract: In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, ersity, and historical inbreeding across all known stands of the species s ling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic ersity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic ersity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species.
Ecosystem restoration is integral to humanity's recovery from COVID-19
Publisher: Elsevier BV
Date: 09-2022
High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration
Publisher: Elsevier BV
Date: 2018
Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium
Publisher: Springer Science and Business Media LLC
Date: 02-2017
DOI: 10.1038/SREP41367
Abstract: The Adelaide geosyncline, a mountainous region in central southern Australia, is purported to be an important continental refugium for Mediterranean and semi-arid Australian biota, yet few population genetic studies have been conducted to test this theory. Here, we focus on a plant species distributed widely throughout the region, the narrow-leaf hopbush, Dodonaea viscosa ssp. angustissima , and examine its genetic ersity and population structure. We used a hybrid-capture target enrichment technique to selectively sequence over 700 genes from 89 in iduals across 17 s ling locations. We compared 815 single nucleotide polymorphisms among in iduals and populations to investigate population genetic structure. Three distinct genetic clusters were identified a Flinders/Gammon ranges cluster, an Eastern cluster, and a Kangaroo Island cluster. Higher genetic ersity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations. We discuss these findings and consider the historical range dynamics of these populations. We also provide methodological considerations for population genomics studies that aim to use novel genomic approaches (such as target capture methods) on non-model systems. The application of our findings to restoration of this species across the region are also considered.
Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved
Publisher: Elsevier BV
Date: 08-2020
Light-dark cycles influence soil bacterial composition in situ
Publisher: Authorea, Inc.
Date: 07-06-2023
DOI: 10.22541/AU.168614476.62136224/V1
Abstract: Soil bacterial taxa have important functional roles in ecosystems (e.g., nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover type (e.g., remnant vegetation, agriculture, urban parks) and plant-soil feedbacks being two well studied factors. However, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We s led surface soils in situ across 24-hour light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA licon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial ersity, with soils under native vegetation expressing 15.41-16.42% lower alpha ersity but 4.92-10.67% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at phylum level was 16.0% higher in the early morning hours compared to the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on the composition of soil bacterial communities in situ and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when s ling soil bacteria.
Drivers of seedling establishment success in dryland restoration efforts
Publisher: Springer Science and Business Media LLC
Date: 22-07-2021
The potential of genomics for restoring ecosystems and biodiversity.
Publisher: Springer Science and Business Media LLC
Date: 12-07-2019
DOI: 10.1038/S41576-019-0152-0
Abstract: Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.
A practical guide for restoration ecologists to manage microbial contamination risks before laboratory processes during microbiota restoration studies
Publisher: Wiley
Date: 05-04-2023
DOI: 10.1111/REC.13687
Abstract: Environmental microbiota are becoming more conventional components of restoration ecology studies due to their functional importance in ecosystems. Studying these microbiota offers insight into how they respond to, and potentially drive, ecosystem restoration. However, microbes are everywhere and therefore they pose a risk to s le integrity via uncontrolled contamination, and many of these risks are introduced before entering a molecular facility. Field ecologists who have limited experience in microbial and/or molecular studies may lack the knowledge on how to mitigate microbial contamination risks and, accordingly, may find rigorous collection of microbial s les a daunting task. Here, we present a practical guide that builds on our previous paper to help manage the risks of microbial contamination when undertaking a microbiota restoration study prior to entering a molecular facility. We cover study design and planning, undertaking field s ling, and s le transport and storage. We hope to provide a useful and practical guide to restoration ecologists who wish to include a microbiota component in their studies. If done well, this inclusion offers improved research quality and ultimately enhanced restoration outcomes.
Trapped in desert springs: phylogeography of Australian desert spring snails
Publisher: Wiley
Date: 22-06-2012
Disentangling the evolutionary history of three related shrub species using genome-wide molecular markers
Publisher: Springer Science and Business Media LLC
Date: 30-05-2019
Harnessing soil biodiversity to promote human health in cities
Publisher: Springer Science and Business Media LLC
Date: 14-02-2023
DOI: 10.1038/S42949-023-00086-0
Abstract: Bio ersity is widely linked to human health, however, connections between human health and soil bio ersity in urban environments remain poorly understood. Here, we stress that reductions in urban soil bio ersity elevate risks to human health, but soil bio ersity can improve human health through pathways including suppressing pathogens, remediating soil, shaping a beneficial human microbiome and promoting immune fitness. We argue that targeted enhancement of urban soil bio ersity could support human health, in both outdoor and indoor settings. The potential of enhanced urban soil bio ersity to benefit human health reflects an important yet understudied field of fundamental and applied research.
The aerobiome-health axis
Publisher: Elsevier BV
Date: 07-2023
Ambient soil cation exchange capacity inversely associates with infectious and parasitic disease risk in regional Australia
Publisher: Elsevier BV
Date: 06-2018
DOI: 10.1016/J.SCITOTENV.2018.01.077
Abstract: Human contact with soil may be important for building and maintaining normal healthy immune defence mechanisms, however this idea remains untested at the population-level. In this continent-wide, cross-sectional study we examine the possible public health benefit of ambient exposures to soil of high cation exchange capacity (CEC), a surrogate for potential immunomodulatory soil microbial ersity. We compare distributions of normalized mean 2011/12-2012/13 age-standardized public hospital admission rates (cumulative incidence) for infectious and parasitic diseases across regional Australia (representing an average of 29,516 patients/year in 228 local government areas), within tertiles of socioeconomic status and soil exposure. To test the significance of soil CEC, we use probabilistic in idual-level environmental exposure data (with or without soil), and group-level variables, in robust non-parametric multilevel modelling to predict disease rates in unseen groups. Our results show that in socioeconomically-deprived areas with high CEC soils, rates of infectious and parasitic disease are significantly lower than areas with low CEC soils. Also, health inequality (relative risk) due to socioeconomic status is significantly lower in areas with high CEC soils compared to low CEC soils (Δ relative risk = 0.47 95% CI: 0.13, 0.82). Including soil exposure when modelling rates of infectious and parasitic disease significantly improves prediction performance, explaining an additional 7.5% (Δ r
Achieving more with less – linking ecological restoration investments with ecological restoration research infrastructure
Publisher: CSIRO
Date: 2018
Changes in abundance and reproductive activity of small arid-zone murid rodents on an active cattle station in central Australia
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/WR16152
Abstract: Context Boom and bust population cycles are characteristic of many arid-zone rodents, but it is unknown to what extent these dynamics might be influenced by the presence of invasive rodents, such as the house mouse (Mus musculus) in Australia. Aim To determine whether the presence of M. musculus can have negative consequences on the population abundance and reproduction of two old Australian endemic rodents (the spinifex hopping mouse, Notomys alexis, and sandy inland mouse, Pseudomys hermannsburgensis). Methods The study took place on the sand dunes of a cattle station in central Australia. Population abundance was estimated as the number of in iduals caught in small mammal traps, and female reproductive condition by external examination and, in a few cases, euthanasia and inspection of the reproductive tract. Key results Two synchronous periods of high abundance of N. alexis and M. musculus occurred several months after significant rainfall events, whereas the abundance of P. hermannsburgensis was consistently low. No reproduction took place in N. alexis or M. musculus when populations had reached high abundance. During low-rainfall periods, M. musculus was not detected on the sand dunes, and the two endemic species were sparsely distributed, with reproduction occasionally being evident. Conclusions During dry periods, M. musculus contracted back to refuges around the homestead and, after significant rainfall, it expanded onto the sand dunes and became abundant at the same time as did N. alexis. In contrast, and unlike in areas where M. musculus was generally rare, P. hermannsburgensis always remained at a low abundance. These patterns suggest that in areas of the natural environment close to human-modified sites, populations of at least one species of an old endemic rodent are supressed by the presence of M. musculus. Reproduction did not occur in the old endemics at times of high M. musculus abundance, but did take place in spring/early summer, even in some dry years. Implications The spread of M. musculus into the Australian arid zone may have had negative impacts on the population dynamics of P. hermannsburgensis. These findings suggest that the presence of human settlements has resulted in refuges for house mice, which periodically spread out into the natural environment during ‘boom’ times and adversely affect the natural population cycle of ecologically similar species such as P. hermannsburgensis.
Towards the biogeography of butyrate-producing bacteria
Publisher: Cold Spring Harbor Laboratory
Date: 08-10-2022
DOI: 10.1101/2022.10.07.510278
Abstract: Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, few (if any) studies have examined the macroecological influences on their large-scale biogeographical distribution. Here we aimed to characterise their global biogeography together with key explanatory climatic, geographic, and physicochemical variables. Global, and the Australian continent 2005-2020 Butyrate-producing bacteria We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic ( n =13,078) and Australia-wide soil 16S rRNA ( n =1,331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest BPC scores were found in anoxic and fermentative environments, including the human and non-human animal gut, and in some plant-soil systems. Within plant-soil systems, roots and rhizospheres had the highest BPC scores. Among soil s les, geographic and climatic variables had the strongest overall influence on BPC scores, with human influence also making key contributions. Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas, and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils follow complex ecological patterns influenced by geography, climate, soil chemistry, and hydrological fluctuations. Human population density and soil iron also play substantial roles, and their effects are dependent on a combination of ecological variables. These new biogeographical insights further our understanding of the global ecology patterns of butyrate-producing bacteria, with implications for emerging microbially-focussed ecological and human health policies.
The resilience of forest fragmentation genetics-no longer a paradox-we were just looking in the wrong place
Publisher: Springer Science and Business Media LLC
Date: 15-07-2015
DOI: 10.1038/HDY.2015.40
Genetic bottlenecks in time and space: Reconstructing invasions from contemporary and historical collections
Publisher: Public Library of Science (PLoS)
Date: 05-09-2014
Erratum: Introducing BASE: The Biomes of Australian Soil Environments soil microbial diversity database [GigaScience. 5, 1, (2016) (1-11)] DOI: 10.1186/s13742-016-0126-5
Publisher: Oxford University Press (OUP)
Date: 05-2017
Clumped planting arrangements improve seed production in a revegetated eucalypt woodland
Publisher: Wiley
Date: 10-12-2019
DOI: 10.1111/REC.12905
Global change community ecology beyond species-sorting: a quantitative framework based on mediterranean-biome examples
Publisher: Wiley
Date: 20-04-2014
DOI: 10.1111/GEB.12184
Degree of urbanization and vegetation type shape soil biodiversity in city parks
Publisher: Elsevier BV
Date: 11-2023
Author Correction: Drivers of seedling establishment success in dryland restoration efforts
Publisher: Springer Science and Business Media LLC
Date: 28-07-2021
A soil archaeal community responds to a decade of ecological restoration
Publisher: Wiley
Date: 05-11-2020
DOI: 10.1111/REC.13033
Abstract: Large‐scale restoration efforts are underway globally to mitigate the impact of decades of land degradation by returning functional and bio erse ecosystems. Revegetation is a heavily relied upon restoration intervention, and one that is expected to result in associated bio ersity returns. However, the outcome of such restoration interventions rarely considers recovery to the soil microbiome, a mega‐ erse and functionally important ecosystem component. Here we examine the archaeal component of the soil microbiome and track community change after a decade of eucalypt woodland restoration in southern Australia. We employed DNA metabarcoding to show that archaeal community composition, richness, and ersity shifted significantly, and towards a restored state 10 years after the restoration intervention. Changes in soil pH and nitrate associated with changes to the archaeal community, potentially relating to the pH responsive properties and close relationship with the nitrogen cycle of some archaea. Our study helps shed light on archaeal community dynamics, as no other study has used DNA metabarcoding to study archaeal responses across a restoration chronosequence. Our results provide great promise for the development of molecular monitoring of the soil microbiome as a future restoration monitoring tool.
Relating urban biodiversity to human health with the 'Holobiont' concept
Publisher: Frontiers Media SA
Date: 26-03-2019
Naturally-diverse airborne environmental microbial exposures modulate the gut microbiome and may provide anxiolytic benefits in mice
Publisher: Elsevier BV
Date: 2020
DOI: 10.1016/J.SCITOTENV.2019.134684
Abstract: Growing epidemiological evidence links natural green space exposure with a range of health benefits, including for mental health. Conversely, greater urbanisation associates with increased risk of mental health disorders. Microbiomes are proposed as an important but understudied link that may help explain many green space-human health associations. However, there remains a lack of controlled experimental evidence testing possible beneficial effects from passive exposure to natural bio ersity via airborne microbiota. Previous mouse model studies have used unrealistic environmental microbial exposures-including excessive soil and organic matter contact, feed supplements and injections-to demonstrate host microbiota, immune biomarker, and behavioural changes. Here, in a randomised controlled experiment, we demonstrate that realistic exposures to trace-level dust from a high bio ersity soil can change mouse gut microbiota, in comparison to dust from low bio ersity soil or no soil (control) (n = 54 total mice, comprising 3 treatments × 18 mice, with 9 females + 9 males per group). Furthermore, we found a nominal soil-derived anaerobic spore-forming butyrate-producer, Kineothrix alysoides, was supplemented to a greater extent in the gut microbiomes of high bio ersity treatment mice. Also, increasing relative abundance of this rare organism correlated with reduced anxiety-like behaviour in the most anxious mice. Our results point to an intriguing new hypothesis: that bio erse soils may represent an important supplementary source of butyrate-producing bacteria capable of resupplying the mammalian gut microbiome, with potential for gut health and mental health benefits. Our findings have potential to inform cost-effective population health interventions through microbiome-conscious green space design and, ultimately, the mainstreaming of bio ersity into health care.
Indigenous Knowledge and the Microbiome—Bridging the Disconnect between Colonized Places, Peoples, and the Unseen Influences That Shape Our Health and Well-Being
Publisher: American Society for Microbiology
Date: 23-02-2023
DOI: 10.1128/MSYSTEMS.00875-22
Abstract: Indigenous Peoples have a rich and long-standing connection with the environments that they descend from—a connection that has informed a deep and multifaceted understanding of the relationship between human well-being and the environment. Through cultural narratives and practices, much of this knowledge has endured despite the ongoing effects that colonization has had on many Indigenous peoples across the world.
Shifts in reproductive assurance strategies and inbreeding costs associated with habitat fragmentation in Central American mahogany
Publisher: Wiley
Date: 03-2012
Bioclimatic transect networks: Powerful observatories of ecological change
Publisher: Wiley
Date: 19-05-2017
DOI: 10.1002/ECE3.2995
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