ORCID Profile
0000-0002-4812-7524
Current Organisations
Department for Environment and Water
,
Flinders University
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Publisher: CRC Press
Date: 27-01-2014
DOI: 10.1201/B16500
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.
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.
Publisher: Elsevier BV
Date: 08-2023
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.
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.
Publisher: Cold Spring Harbor Laboratory
Date: 13-08-2021
DOI: 10.1101/2021.08.12.456018
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 many 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.
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.
Publisher: Elsevier BV
Date: 08-2022
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
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.
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.
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.
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.
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.
Publisher: Elsevier BV
Date: 06-2021
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.
Publisher: Cambridge University Press (CUP)
Date: 12-2021
DOI: 10.1017/S1359135522000148
Abstract: Microbiome-Inspired Green Infrastructure (MIGI) was recently proposed as an integrative system to promote healthy urban ecosystems through multidisciplinary design. Specifically, MIGI is defined as nature-centric infrastructure restored, designed, and managed to enhance health-promoting interactions between humans and environmental microbiomes while sustaining microbially mediated ecosystem functionality and resilience. MIGI also aims to stimulate a research agenda that focuses on considerations for the importance of urban environmental microbiomes. In this article, we provide details of what MIGI entails from a bioscience and biodesign perspective, highlighting the potential dual benefits for human and ecosystem health. We present ‘what is known’ about the relationship between urban microbiomes, green infrastructure, and environmental factors that may affect urban ecosystem health - taken here to mean ecosystem functionality and resilience, as well as human health. We discuss how to start operationalising the MIGI concept based on current available knowledge and present a horizon-scan of emerging and future considerations in research and practice. We conclude by highlighting challenges to implementing MIGI and propose a series of workshops to discuss multi-stakeholder needs and opportunities. This research will enable urban landscape managers to incorporate initial considerations for the microbiome in their development projects to promote human and ecosystem health. However, overcoming the challenges to operationalising MIGI will be essential to furthering its practical development. Although the research is in its infancy, there is considerable potential for MIGI to help deliver sustainable urban development driven by considerations for reciprocal relations between humans and the foundations of our ecosystems – the microorganisms.
Publisher: Elsevier BV
Date: 05-2021
Publisher: Frontiers Media SA
Date: 26-03-2019
Publisher: MDPI AG
Date: 21-06-2019
DOI: 10.3390/SU11123416
Abstract: Soil Security is an emerging sustainability science concept with global application for guiding integrated approaches to land management, while balancing ecosystem services, environmental, social, cultural, and economic imperatives. This discussion paper sets the scene for an Australian Soil Security framework as an ex le of how it might be developed for any country, defining the key issues and justification for Soil Security, as well as detailing implementation requirements and benefits two ex les of beneficial outcomes are provided in terms of facilitating decommoditization of agricultural products and the impact of urban encroachment on productive land. We highlight research gaps, where new knowledge will contribute to well-rounded approaches that reflect differing stakeholder perspectives. We also provide key nomenclature associated with a potential Soil Security framework so that future discussions may use a common language. Through this work we invite scientific and policy discourse with the aim of developing more informed responses to the myriad of competing demands placed on our soil systems.
Publisher: Elsevier BV
Date: 2018
DOI: 10.1016/J.JENVMAN.2017.10.007
Abstract: Megatrends of urbanisation and reducing contact with natural environments may pose a largely unappreciated risk to human health, particularly in children, through declining normal (healthy) immunomodulatory environmental exposures. On the other hand, building knowledge of connections between environments, bio ersity and human health may offer new integrated ways of addressing global challenges of rising population health costs and declining bio ersity. In this study we are motivated to build insight and provide context and priority for emerging research into potential protective (e.g. immunomodulatory) environmental exposures. We use respiratory health as a test case to explore whether some types and qualities of environment may be more beneficial than others, and how such exposures may compare to known respiratory health influences, via a cross-sectional ecological epidemiology study for the continent of Australia. Using Lasso penalized regression (to interpret key predictors from many candidate variables) and 10-fold cross-validation modelling (to indicate reproducibility and uncertainty), within different socio-geographic settings, our results show surrogate measures of landscape bio ersity correlate with respiratory health, and rank amongst known predictors. A range of possible drivers for this relationship are discussed. Perhaps most novel and interesting of these is the possibility of protective immunomodulatory influence from microbial ersity (suggested by the understudied 'bio ersity hypothesis') and other bioactive agents associated with bio erse environments. If beneficial influences can be demonstrated from bio erse environments on immunomodulation and human health, there may be potential to design new cost-effective nature-based health intervention programs to reduce the risk of immune-related disease at a population level. Our approach and findings are also likely to have use in the evaluation of environment and health associations elsewhere.
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/SR14274
Abstract: It is increasingly necessary to apply quantitative techniques to legacy soil polygon maps given that legacy soil maps may be the only source of soil information over large areas. Spatial disaggregation provides a means of extracting information from legacy soil maps and enables us to downscale the original information to produce new soil class maps at finer levels of detail. This is a useful outcome in its own right however, the disaggregated soil-class coverage can also be used to make digital maps of soil properties with associated estimates of uncertainty. In this work, we take the spatially disaggregated soil-class coverage for all of Western Australia and the agricultural region of South Australia and demonstrate its application in mapping clay content at six depth intervals in the soil profile. Estimates of uncertainty are provided in the form of the 90% prediction interval. The work can be considered an ex le of harmonisation to a common output specification. The validation results highlighted areas in the landscape and taxonomic spaces where more knowledge of soil properties is necessary.
Publisher: Springer Science and Business Media LLC
Date: 20-12-2022
DOI: 10.1038/S41598-022-25196-0
Abstract: Falsified medicines are a major threat to global health. Antimalarial drugs have been particularly targeted by criminals. As DNA analysis has revolutionized forensic criminology, we hypothesized that these techniques could also be used to investigate the origins of falsified medicines. Medicines may contain erse adventitious biological contamination, and the sealed nature of blister-packages may capture and preserve genetic signals from the manufacturing processes allowing identification of production source(s). We conducted a blinded pilot study to determine if such environmental DNA (eDNA) could be detected in eleven s les of falsified and genuine artesunate antimalarial tablets, collected in SE Asia, which could be indicative of origin. Massively Parallel Sequencing (MPS) was used to characterize microbial and eukaryote ersity. Two mitochondrial DNA analysis approaches were explored to detect the presence of human DNA. Trace eDNA from these low biomass s les demonstrated s le specific signals using two target markers. Significant differences in bacterial and eukaryote DNA community structures were observed between genuine and falsified tablets and between different packaging types of falsified artesunate. Human DNA, which was indicative of likely east Asian ancestry, was found in falsified tablets. This pilot study of the ‘pharmabiome’ shows the potential of environmental DNA as a powerful forensic tool to assist with the identification of the environments, and hence location and timing, of the source and manufacture of falsified medicines, establish links between seizures and complement existing tools to build a more complete picture of criminal trade routes. The finding of human DNA in tablets raises important ethical issues that need to be addressed.
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.
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.
Publisher: Oxford University Press (OUP)
Date: 12-10-2016
Publisher: Elsevier BV
Date: 07-2021
Publisher: Elsevier BV
Date: 09-2022
Publisher: Elsevier BV
Date: 10-2020
Publisher: Elsevier BV
Date: 03-2021
Publisher: Elsevier BV
Date: 12-2020
Publisher: Authorea, Inc.
Date: 11-09-2023
Publisher: Elsevier BV
Date: 09-2020
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/SR15100
Abstract: Better understanding the spatial distribution of soil organic carbon (SOC) stocks is important for the management and enhancement of soils for production and environmental outcomes. We have applied digital soil mapping (DSM) techniques to combine soil-site datasets from legacy and recent sources, environmental covariates and expert pedological knowledge to predict and map SOC stocks in the top 0.3 m, and their uncertainty, across South Australia’s agricultural zone. In achieving this, we aimed to maximise the use of locally sourced datasets not previously considered in national soil C assessments. Practical considerations for operationalising DSM are also discussed in the context of working with problematic legacy datasets, handling large numbers of potentially correlated covariates, and meeting end-user needs for readily interpretable results and accurate maps. Spatial modelling was undertaken using open-source R statistical software over a study area of ~160 000 km2. Legacy-site SOC stock estimates were derived with inputs from an expert-derived bulk-density pedotransfer function to overcome critical gaps in the data. Site estimates of SOC were evaluated over a consistent depth range and then used in spatial predictions through an environmental-correlation regression-kriging DSM approach. This used the contemporary Least Absolute Shrinkage and Selection Operator penalised-regression method, which catered for a large number (63 numeric, four categorical, four legacy-soil mapping themes) of potentially correlated covariates. For efficient use of the available data, this was performed within a k-fold cross-validation (k = 10) modelling framework. Through this, we generated multiple predictions and variance information at every node of our prediction grid, which was used to evaluate and map the expected value (mean) of SOC stocks and their uncertainty. For the South Australian agricultural zone, expected value SOC stocks in the top 0.3 m summed to 0.589 Gt with a 90% prediction interval of 0.266–1.086 Gt.
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.
No related grants have been discovered for Craig Liddicoat.