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COVID-19 has devastated global communities and economies. The pandemic has exposed socioeconomic disparities and weaknesses in health systems worldwide. Long-term health effects and economic recovery are major concerns. Ecosystem restoration—ie, the repair of ecosystems that have been degraded—relates directly to tackling the health and socioeconomic burdens of COVID-19, because stable and resilient ecosystems are fundamental determinants of health and socioeconomic stability. Here, we use COVID-19 as a case study, showing how ecosystem restoration can reduce the risk of infection and adverse sequelae and have an integral role in humanity’s recovery from COVID-19.The next decade will be crucial for humanity’s recovery from COVID-19 and for ecosystem repair. Indeed, in the absence of effective, large-scale restoration, 95% of the Earth’s land could be degraded by 2050. The UN Decade on Ecosystem Restoration (2021–30) declaration reflects the growing urgency and scale at which we should repair ecosystems. Importantly, ecosystem restoration could also help to combat the health and socioeconomic issues that are associated with COVID-19, yet it is poorly integrated into current responses to the disease. Ecosystem restoration can be a core public health intervention and assist in COVID-19 recovery if it is closely integrated with socioeconomic, health, and environmental policies. Refereed/Peer-reviewed

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 samples and sequenced the V3-V4 region of the 16S rRNA gene to characterize the bacterial community in these samples. 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.

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 diverse 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 samples 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 diversity. Two mitochondrial DNA analysis approaches were explored to detect the presence of human DNA. Trace eDNA from these low biomass samples demonstrated sample 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.

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.

AimButyrate-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.LocationGlobal, and the Australian continentTime period2005-2020Major taxa studiedButyrate-producing bacteriaMethodsWe 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.ResultsThe 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 samples, 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.Main conclusionsAbundances 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.

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 changes 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 sacrificed rats during the chronic phase of infection, collected their cecal stool samples and sequenced the V3-V4 region of the 16S rRNA gene to characterise the bacterial community in these samples. Toxoplasma infection did not induce widespread changes in the bacterial community composition of the gastrointestinal tract of rats. Rather, we found sex differences in the bacterial community composition and only minor changes in Toxoplasma infected rats. We conclude that it is unlikely that sustained inflammation is the mechanism driving the highly specific behavioural changes observed in Toxoplasma-positive rats.

Background There is a growing body of evidence that exposure to greenspace is good for our health: spending time in greenspace can improve depressive symptoms, obesity, and sleep problems, and reduce the risk of breast and prostate cancer. We also know that exposure to outdoor artificial light at night (O-ALAN) is associated with increased risk of breast and prostate cancer, and can worsen depression, obesity and sleep problems. As both greenspace exposure and O-ALAN have been implicated in the same health outcomes, we aimed to establish if O-ALAN was itself correlated with greenspace, potentially confounding spatial epidemiological studies of greenspace and health outcomes (and vice versa). Methods We investigated the correlation between greenspace diversity (Shannon diversity index of National Vegetation Information System’s vegetation classes within 3 km radius buffer zones), and night-time light data (NOAA/NCEI Nighttime Visible Infrared Imaging Radiometer Suite Day/Night Band 2015 Annual Composite product), in Australian major cities. Results We identified an inverse correlation between O-ALAN and greenspace diversity. Conclusions The finding makes intuitive sense because more developed areas are likely to have fewer trees and more artificial light, which is consistent with our hypothesis that that O-ALAN could be confounding studies of the relationship between greenspace and health. Without considering the potential confounding effects of O-ALAN, public health-driven initiatives such as greenspace conservation and restoration in urban environments may not be optimised for health benefits. Key messages Spatial epidemiological studies of greenspace exposure and health should include O-ALAN as a potential confounder (and vice versa).

Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, as they are central to important ecological functions including the support of plant communities. High throughput sequencing of environmental DNA used to characterise soil microbiota offers promise to monitor ecological progress towards reference states. 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. We analysed patterns of surface soil bacterial community similarity to reference (9rehabilitation trajectory9) data from three long-term (> 25 year) post-mining rehabilitation chronosequence case studies from south-west Western Australia. We examined the influence of different ecological distance measures, sequence grouping approaches, and eliminating rare taxa on rehabilitation trajectories and predicted recovery times. We also explored the issue of spatial autocorrelation in our rehabilitation trajectory assessments and trialled a first-pass approach for correcting its undue influence. We found considerable variation in bacterial communities among reference sites within each case study minesite, providing valuable context for setting targets and evaluating recovery. Median Bray-Curtis similarities among references within each minesite ranged from 30-36%, based on amplicon sequence variant-level data. Median predicted times for rehabilitated sites to recover to these levels ranged from around 40 to over 100 years. We discuss strengths and limitations of the different approaches and offer recommendations to improve the robustness of this assessment method. Synthesis and applications. We demonstrate a proof-of-concept, complexity-reducing application of soil eDNA sequence-based surveys of bacterial communities in restoration chronosequence studies to quantitatively assess progress towards reference communities and corresponding rehabilitation targets. Our method provides a step towards developing microbiota-based SMART metrics for measuring rehabilitation success in post-mining, and potentially other, restoration contexts. Our approach enables prediction of recovery time, explicitly including uncertainty in assessments, and assists examination of potential barriers to ecological recovery, including biologically-associated variation in soil properties.

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 sampling to data analysis and publishing. The two main categories of contamination we discuss are cross‐contamination—contamination between samples—and external contamination—contamination from reagents and environmental sources. We also consider the impact of batch effects, where sampling 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.

Exposure to green space has been associated with a range of human health benefits, largely in spatial epidemiological studies. Green space and artificial light at night are both associated with breast and prostate cancer, depressive symptoms, obesity, and sleep problems, and are both influenced by the built environment and urbanisation. We identified a negative correlation between green space diversity and outdoor artificial light at night for Australian major cities. Outdoor artificial light at night is therefore a potential, but overlooked, confounder in spatial epidemiological studies of green space exposure and human health, and should be incorporated into future models.

The vegetation and soil microbiome within urban green spaces is increasingly managed to help conserve biodiversity and improve human health concurrently. However, the effects of green space management on urban soil ecosystems is poorly understood, despite their importance. Across 40 urban green spaces in metropolitan Adelaide, South Australia, we show that soil bacterial communities are strongly affected by urban green space type (incl. sport fields, community gardens, parklands and revegetated areas), and that plant species richness is positively associated with soil bacterial diversity. Importantly, these microbiome trends were not affected by geographic proximity of sample sites. Our results provide early evidence that urban green space management can have predictable effects on the soil microbiome, at least from a diversity perspective, which could prove important to inform policy development if urban green spaces are to be managed to optimise population health benefits.

Background:\ud \ud Exposure to a diverse environmental microbiome is thought to play an important role in “educating” the immune system and facilitating competitive exclusion of pathogens to maintain human health. Vegetation and soil are key sources of airborne microbiota––the aerobiome. A limited number of studies have attempted to characterize the dynamics of near surface green space aerobiomes, and no studies to date have investigated these dynamics from a vertical perspective. Vertical stratification in the aerobiome could have important implications for public health and for the design, engineering, and management of urban green spaces.\ud \ud \ud \ud Objectives:\ud \ud The primary objectives of this study were to: a) assess whether significant vertical stratification in bacterial species richness and evenness (alpha diversity) of the aerobiome occurred in a parkland habitat in Adelaide, South Australia; b) assess whether significant compositional differences (beta diversity) between sampling heights occurred; and c) to preliminarily assess whether there were significant altitudinal differences in potentially pathogenic and beneficial bacterial taxa.\ud \ud \ud \ud Methods:\ud \ud We combined an innovative columnar sampling method at soil level, 0.0, 0.5, 1.0, and 2.0m, using passive petri dish sampling to collect airborne bacteria. We used a geographic information system (GIS) to select study sites, and we used high-throughput sequencing of the bacterial 16S rRNA gene to assess whether significant vertical stratification of the aerobiome occurred.\ud \ud \ud \ud Results:\ud \ud Our results provide evidence of vertical stratification in both alpha and beta (compositional) diversity of airborne bacterial communities, with diversity decreasing roughly with height. We also found significant vertical stratification in potentially pathogenic and beneficial bacterial taxa.\ud \ud \ud \ud Discussion:\ud \ud Although additional research is needed, our preliminary findings point to potentially different exposure attributes that may be contingent on human height and activity type. Our results lay the foundations for further research into the vertical characteristics of urban green space aerobiomes and their implications for public health and urban planning.

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.

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 biodiversity 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 biodiversity soil can change mouse gut microbiota, in comparison to dust from low biodiversity 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 biodiversity 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 biodiverse 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 biodiversity into health care.

A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.

Butyrate is an important mediator of human health and disease. The mechanisms of action of butyrate are becoming increasingly well-known. Many commensal bacteria that inhabit the human gut can synthesise butyrate, which is then absorbed into the human host. Simultaneously, several immune- and inflammatory-mediated diseases are being linked to insufficient exposure to beneficial microbes from our environment, including butyrate-producing bacteria. However, the role of outdoor environmental exposure to butyrate-producing bacteria remains poorly understood. Here we review the literature on the human exposure pathways to butyrate-producing bacteria, with a particular focus on outdoor environmental sources (e.g. associated with plants, plant-based residues, and soil), and the health implications of exposure to them. Emerging evidence suggests that environmental butyrate-producers may help supplement the human gut microbiota and represent an important component of the Biodiversity and Old Friends hypotheses. Improving our understanding of potential sources, precursors, and exposure pathways of environmental butyrate-producers that influence the gut microbiota and butyrate production offers promise to advance multiple disciplines of health and environmental science. We outline research priorities to address knowledge gaps in the outdoor environment-butyrate-health nexus and build knowledge of the potential pathways to help optimise exposure to human-beneficial butyrate-producing bacteria from the outdoor environment during childhood and adulthood.

International audience; Digital Soil Mapping and Assessment (DSMA) has progressed from challenging traditional soil science paradigms, through small scale prototyping, to large-scale implementation capturing quantitative measures of soil attributes and functions. This paper considers the future for DSMA in the context of a highly uncertain world where high-quality knowledge of soil dynamics will be important for responding to the challenges of sustainability. Irrespective of whether the need is for survival, increased productivity or broadening the services provided from land management, or simply securing the soil itself, we see DSMA as a fundamental approach and essential tool. With a broadening need and a strong foundation in the practice of DSMA now in place, the theory, tools and technology of DSMA will grow significantly. We explore expected changes in covariate data, the modelling process, the nature of base data generation and product delivery that will lead to tracking and forecasting a much wider range of soil attributes and functions at finer spatial and temporal resolutions over larger areas, particularly globally. Equally importantly, we expect the application and impact of DSMA to broaden and be used, directly and collaterally, in the analysis of land management issues in coming decades. It has the capacity to provide the background to a soil and landscape ‘digital twin’ and the consequent transformation in monitoring and forecasting the impacts of land management practices. We envision the continued growth of DSMA skills amongst soil scientists and a much broader community of practice involved in developing and utilizing DSMA products and tools. Consequently, there will be a widening and deepening role of public-private partnerships in this development and application.

Plant-soil feedbacks not only shape plant communities but also the abiotic and biotic nature of soils. These feedbacks are well-studied in natural and agricultural landscapes, but poorly studied in cities. Here, we investigated soil fungal communities, vegetation and soil abiotic properties in five urban green space types within urban Adelaide, South Australia. We surveyed eight, spatially-independent replicates of Sport Fields, Community Gardens, Parklands, Young Revegetation, and Old Revegetation sites. Vegetation strongly associated with soil fungal abundance and diversity. Revegetated urban green spaces had appreciably higher fungal diversity than other spaces, as well as greater richness in saprotrophic and pathotrophic fungi. We suggest that restoration of urban green space fungal microbiomes appears possible via replanting the native vegetation community. Such revegetation interventions will likely have positive outcomes for not only biodiversity conservation but also human health, via re-creating a biodiverse environmental microbiome.

Retrospective evaluation has consistently shown that soil information has value beyond the investment used to produce it. Digital soil mapping and assessment (DSMA) is the new paradigm for soil survey and a key source of soil and land information. It promises increased utility and flexibility for the users of soil information. Does DSMA methodology add value? What are some of the outcomes and emerging impacts? Seven examples from the burgeoning use of DSMA in and near Australia have been explored to determine the nature and extent of outcomes and impact achieved. The analysis began with a workshop of key soil scientists, involved a survey of the use of DSMA and attitudes to impact amongst practitioners of DSMA and looked at each of the seven examples in the context of the systems they seek to influence. There is evidence of progress along impact pathways in each case. In the simpler systems, the products of DSMA are being used as envisaged and change is occurring. In more complex systems, the role of soil information meshes with many other influences and impact is harder to discern. Importantly, we find that few practitioners using DSMA explicitly identify impact pathways and design projects at the outset to optimise the chance of more extensive impact. Thus, an approach to planning for impact in DSMA is proposed that could improve the chance of impact and allow for iteration as our understanding of the systems in which change is expected improves through our interaction with them.

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 diversity. 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 statusand soil exposure. To test the significance of soil CEC, we use probabilistic individual-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 r2 = 0.075; 95% CI: 0.05, 0.10) of variation in disease risk, in local government areas that were not used for model building. Our findings suggest that exposure to high CEC soils (typically high soil biodiversity) associates with reduced risk of infectious and parasitic diseases, particularly in lower socioeconomic areas.Science of the Total Environment. Volume 626, 1 June 2018, Pages 117-125

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 diversity and ‘Old Friends’ are thought to be supplemented from biodiverse 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, biodiverse state. Here we use novel bootstrap-style resampling 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 samples elsewhere across Australia. Extending this, we propose a two-dimensional mapping for ecosystem condition based on the proportions of these divergent indicator groups. We also show that restoring a more biodiverse ecosystem at Mt Bold has increased the potentially immune-boosting environmental microbial diversity. 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. Keywords: Bacterial indicators, Biodiversity hypothesis, Ecological restoration, Environmental health, Merged-sample bootstrap, Restoration genomics

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 example 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 examples 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.

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.

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 example 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.