Craig Liddicoat

• PhD Bioscience; B Env Sc (ecology); BE Mech (1st class hons)
• Research Fellow at Flinders University

Background Type 2 diabetes (T2D) is a complex metabolic disease with uncertain pathogenesis, including recognized influences from gut microbiome-host interactions and environmental factors. Meanwhile, soil microbiomes are known to shift in their composition and functional capacities with ecosystem condition, and represent an important environmental...

The interrelationship between climate change, pollution and the aerobiome (the microbiome of the air) is a complex ecological dynamic with profound implications for human and ecosystem health. This mini‐review explores the multifaceted relationships among these factors. By synthesising existing research and integrating interdisciplinary perspective...

Ecoacoustics—or acoustic ecology—aids in monitoring elusive and protected species in several ecological contexts. For example, passive acoustic monitoring (PAM), which involves autonomous acoustic sensors, is widely used to detect various taxonomic groups in terrestrial and aquatic ecosystems, from birds and bats to fish and cetaceans. Here, we ill...

Soil microbiota can colonise plant roots via a two-step selection process, which involves the recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species, which is surprising given its fundamental role in plant and soil ecology. Here we examined...

Soil microbiota underpin ecosystem functionality yet are rarely targeted during ecosystem restoration. Soil microbiota recovery following native plant revegetation can take years to decades, while the effectiveness of soil inoculation treatments on microbiomes remains poorly explored. Therefore, innovative restoration treatments that target soil mi...

Soil microbiota are important components of healthy ecosystems. Greater consideration of soil microbiota in the restoration of biodiverse, functional, and resilient ecosystems is required to address the twin global crises of biodiversity decline and climate change. In this review, we discuss available and emerging practical applications of soil mic...

Butyrate‐producing bacteria colonise the gut of humans and non‐human animals, where they produce butyrate, a short‐chain fatty acid with known health benefits. Butyrate‐producing bacteria also reside in soils and soil bacteria can drive the assembly of airborne bacterial communities (the aerobiome). Aerobiomes in urban greenspaces are important res...

Understanding belowground plant-microbial interactions is fundamental to predicting how plant species respond to climate change, particularly in global drylands. However, these interactions are poorly understood, especially for keystone grass species like the pan-palaeotropical Themeda triandra. Here, we used 16S rRNA amplicon sequencing to charact...

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, the macroecological influences on their biogeographical distribution remain poorly resolved....

Urban development has profoundly reduced human exposure to biodiverse environments, which is linked to a rise in human disease. The 'biodiversity hypothesis' proposes that contact with diverse microbial communities (microbiota) benefits human health, as exposure to microbial diversity promotes immune training and regulates immune function. Soils an...

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 types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant–soil feedbacks being well-studied factors. However,...

Indigenous health interventions have emerged in New Zealand aimed at increasing human interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. H...

Growing evidence suggests that exposure to microbial biodiversity is important for human immunoregulation and health. Urban greenspaces harbour airborne bacterial communities (aerobiomes) with the potential to transfer beneficial bacteria to humans. However, limited studies have examined the ecological influences of soil, vegetation, and rainfall o...

Ecosystem restoration in post-agricultural landscapes is a critical response to agricultural land abandonment, climate change, and the escalating biodiversity crisis. However, effective restoration of these landscapes can be hampered by land-use legacies that create biotic and abiotic barriers to ecosystem recovery, particularly in ancient Tertiary...

Microbiomes are critical to the health and functioning of humans and ecosystems. Defining ‘healthy microbiomes’, however, remains elusive. More advanced knowledge exists on health associations for the compounds used or produced by microbes. Because microbes, their feedstocks and micro-environments interact synchronously, using functional genes to f...

Interactions between soil microbiota and keystone plant species in grassland ecosystems are poorly understood, yet these interactions are fundamental to grassland ecosystem dynamics (e.g., responses to climate change). Here, we used 16S rRNA amplicon sequencing to characterise microbiota in rhizospheres and bulk soils associated with the keystone g...

Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant–soil–microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessibl...

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 communit...

Biodiversity is widely linked to human health, however, connections between human health and soil biodiversity in urban environments remain poorly understood. Here, we stress that reductions in urban soil biodiversity elevate risks to human health, but soil biodiversity can improve human health through pathways including suppressing pathogens, reme...

Aim 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 bi...

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...

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 contamina...

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 socioeconom...

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 whil...

The global declines in biodiversity and ecosystem integrity demand effective restoration. Soil microbiota are fundamentally linked to biodiversity and ecosystem restoration, as they are central to important ecological functions (e.g., nutrient cycling) and are extremely species rich. Their importance, plus the growing affordability of high-throughp...

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...

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 inflammat...

Mining activities modify both above- and below-ground 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 mic...

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 sample integrity via u...

The global biodiversity 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 diverse and functionally important, and should be further considered in restorati...

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 inflammat...

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...

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...

Exposure to biodiverse 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 sampling and next generation sequencing of...

Background: 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 and/or designed and managed to enhance health-promoting interactions between humans and environmenta...

Background: 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 and/or designed and managed to enhance health-promoting interactions between humans and environmenta...

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 identifi...

Butyrate is an important mediator of human health and disease. The mechanisms of action of Simultaneously, several immune- and inflammatory-mediated diseases are being linked to 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. insuf...

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 ub...

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 knowled...

Background: 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 dyna...

Exposure to biodiverse 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 sampling and next generation sequencing o...

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 s...

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, Sou...

Australia has advanced the science and application of Digital Soil Mapping (DSM). Over the past decade, DSM in Australia has evolved from being purely research focused to become 'operational', where it is embedded into many soil-agency land resource assessment programs around the country. This has resulted from a series of 'drivers', such as an inc...

Vertical Stratification in Urban Green Space Aerobiomes - proof-of-concept study (pre-print). Evidence of vertical stratification in both alpha and beta (compositional) diversity of airborne bacterial communities, with alpha diversity decreasing with height. Vertical stratification in known pathogenic and beneficial bacterial taxa suggests potent...

Retrospective (or ex post) 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 DSM...

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....

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 devel...

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 anthr...

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, whos...

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 p...

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, biodiversity and human health may offer new...

Microbiota from environmental sources overlap and interact with human microbiota, contribute to human microbial diversity, and provide beneficial immunomodulatory stimuli. Meanwhile, reduced diversity in human microbiota and immune dysregulation have been associated with a range of diseases. Emerging evidence suggests landscape-scale drivers of mic...

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 know...

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...