Childcare centre soil microbiomes are influenced by substrate type and surrounding vegetation condition

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 and sandpits in urban childcare centres may provide exposure to diverse microbiota that support immunoregulation at a critical developmental stage in a child's life. However, the influence of outdoor substrate (i.e., sand vs. soil) and surrounding vegetation on these environmental microbiota in urban childcare centres remains poorly understood. Here, we used 16S rRNA amplicon sequencing to examine the variation in bacterial communities in sandpits and soils across 22 childcare centres in Adelaide, Australia, plus the impact of plant species richness and habitat condition on these bacterial communities. We show that sandpits had distinct bacterial communities and lower alpha diversity than soils. In addition, we found that plant species richness in the centres' yards and habitat condition surrounding the centres influenced the bacterial communities in soils but not sandpits. These results demonstrate that the diversity and composition of childcare centre sandpit and soil bacterial communities are shaped by substrate type, and that the soils are also shaped by the vegetation within and surrounding the centres. Accordingly, there is potential to modulate the exposure of children to health-associated bacterial communities by managing substrates and vegetation in and around childcare centres.

Restoring soil biodiversity

Soil health is crucial for all terrestrial life, supporting, among other processes, food production, water purification and carbon sequestration. Soil biodiversity - the variety of life within soils - is key to these processes and thus key to soil restoration. Human activities that degrade ecosystems threaten soil biodiversity and associated ecosystem processes. Indeed, 75% of the world's soils are affected by degradation - a figure that could rise to 90% by 2050 if deforestation, overgrazing, urbanisation and other harmful practices persist. Restoring soil biodiversity is a prerequisite for planetary health, and it comes with many challenges and opportunities. Soil directly supports around 60% of all species on Earth, and land degradation poses a major problem for this biodiversity and the ecosystem services that sustain human populations. Indeed, 98% of human calories come from soil, and earthworms alone underpin 6.5% of the world's grain production. Moreover, the total carbon in terrestrial ecosystems is around 3,170 gigatons (1 gigaton (Gt) = 1 billion metric tons), of which approximately 80% (2,500 Gt) is found in soil. Therefore, restoring soil biodiversity is not just a human need but an ecological and Earth-system imperative. It is pivotal for maintaining ecosystem resilience, sustaining agricultural productivity and mitigating climate change impacts.

The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity

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. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). 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 followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.

Biodiversity and human health: A scoping review and examples of underrepresented linkages

Mounting evidence supports the connections between exposure to environmental typologies(such as green and blue spaces)and human health. However, the mechanistic links that connect biodiversity (the variety of life) and human health, and the extent of supporting evidence remain less clear. Here, we undertook a scoping review to map the links between biodiversity and human health and summarise the levels of associated evidence using an established weight of evidence framework. Distinct from other reviews, we provide additional context regarding the environment-microbiome-health axis, evaluate the environmental buffering pathway (e.g., biodiversity impacts on air pollution), and provide examples of three under- or minimally-represented linkages. The examples are (1) biodiversity and Indigenous Peoples' health, (2) biodiversity and urban social equity, and (3) biodiversity and COVID-19. We observed a moderate level of evidence to support the environmental microbiota-human health pathway and a moderate-high level of evidence to support broader nature pathways (e.g., greenspace) to various health outcomes, from stress reduction to enhanced wellbeing and improved social cohesion. However, studies of broader nature pathways did not typically include specific biodiversity metrics, indicating clear research gaps. Further research is required to understand the connections and causative pathways between biodiversity (e.g., using metrics such as taxonomy, diversity/richness, structure, and function) and health outcomes. There are well-established frameworks to assess the effects of broad classifications of nature on human health. These can assist future research in linking biodiversity metrics to human health outcomes. Our examples of underrepresented linkages highlight the roles of biodiversity and its loss on urban lived experiences, infectious diseases, and Indigenous Peoples' sovereignty and livelihoods. More research and awareness of these socioecological interconnections are needed.

Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort

Indigenous health interventions have emerged in New Zealand aimed at increasing people's 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. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.

Probiotic Cities: microbiome-integrated design for healthy urban ecosystems

Combining microbiome science and biointegrated design offers opportunities to help address the intertwined challenges of urban ecosystem degradation and human disease. Biointegrated materials have the potential to combat superbugs and remediate pollution while inoculating landscape materials with microbiota can promote human immunoregulation and biodiverse green infrastructure, contributing to 'probiotic cities'.

Policy implications of the microbiota-gut-brain axis

The microbiota-gut-brain axis facilitates communication between the gut microbiota and the brain. It has implications for health and environmental policy. Microbiota are linked to neurological and metabolic disorders, and our exposure to health-promoting microbiota depends on environmental quality. Microbiota-gut-brain axis interventions could inform policy initiatives to address systemic health issues.

Light-dark cycles may influence in situ soil bacterial networks and diurnally-sensitive taxa

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, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils in situ across 24-h 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 amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% 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 the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on 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 sampling soil bacteria.

Urban greenspaces shape soil protist communities in a location-specific manner

The impacts of urbanization on aboveground biodiversity are well studied, and its impact on soil microorganisms are also receiving increased attention. However, the impact of urbanization on the soil protists are hardly investigated. Here, we studied how urbanization and distinct urban greenspaces affect protist communities. We used amplicon sequencing of the18 S rRNA gene of samples from five types of urban greenspaces (parks, greenbelts, industrial areas, residential areas and hospital lawns), neighboring natural forests and agricultural ecosystems in Ningbo, China. We found that urban greenspaces harbored higher protist α-diversity than forests, while protist β-diversity increased from agricultural systems to urban greenspaces to forests. Among the studied driving factors, soil bacterial α- and β-diversity best predicted phagotrophic protist α- and β-diversity in urban greenspaces, while differences in α- and β-diversity of phototrophic protists were best explained by soil carbon-to-nitrogen ratio and fungal β-diversity, respectively. Abiotic factors i.e., total phosphorus and carbon-to-nitrogen ratio, best predicted the α- and β-diversity of protist parasites in urban greenspaces, respectively. The results revealed that the composition and drivers of protist communities vary between functional groups and urban ecosystems. Overall, our findings contribute to a better understanding of drivers of soil protist communities and indicate that soil protist communities and associated soil functions could be managed in predictable ways in urban greenspaces.

Opportunities and challenges for microbiomics in ecosystem restoration

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 accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.

Degree of urbanization and vegetation type shape soil biodiversity in city parks

Urbanization negatively impacts aboveground biodiversity, such as bird and insect communities. City parks can reduce these negative impacts by providing important habitat. However, it remains poorly understood how the degree of urbanization and vegetation types within city parks (e.g., lawns, woodland) impact soil biodiversity. Here we investigated the impact of the degree of urbanization (urban vs. suburban) and vegetation type (lawn, shrub-lawn, tree-lawn and tree-shrub mixtures) on soil biodiversity in parkland systems. We used eDNA metabarcoding to characterize soil biodiversity of bacteria, fungi, protists, nematodes, meso- and macrofauna across park vegetation types in urban and suburban regions in Xiamen, China. We observed a strong effect of the degree of urbanization on the richness of different soil biota groups, with higher species richness of protists and meso/macrofauna in urban compared to suburban areas, while the richness of bacteria and fungi did not differ, and the difference of nematode richness depended on vegetation type. At the functional level, increased degree of urbanization associated with greater species richness of bacterivores, plant pathogens and animal parasites. These urbanization effects were at least partly modulated by higher soil phosphorous levels in urban compared to suburban sites. Also, the vegetation type impacted soil biodiversity, particularly fungal richness, with the richness of pathogenic and saprotrophic fungi increasing from lawn to tree-shrub mixtures. Tree-shrub mixtures also had the highest connectedness between biotas and lowest variation in the soil community structure. Overall, we show that soil biodiversity is strongly linked to the degree of urbanization, with overall richness increasing with urbanization, especially in bacterivores, plant pathogens and animal parasites. Targeted management of vegetation types in urban areas should provide a useful way to help mitigate the negative effect of urbanization on soil biodiversity.

The aerobiome-health axis: a paradigm shift in bioaerosol thinking

Historically, a primary aim of bioaerosol research has been to understand and prevent 'unhealthy' human exposures to pathogens and allergens. However, there has been a recent paradigm shift in thinking about bioaerosols. Exposure to a diverse aerobiome - the microbiome of the air - is now considered necessary to be healthy.

Increasing Antimicrobial Resistance and Potential Human Bacterial Pathogens in an Invasive Land Snail Driven by Urbanization

Our understanding of the role urbanization has in augmenting invasive species that carry human bacterial pathogens and antimicrobial resistance (AMR) remains poorly understood. Here, we investigated the gut bacterial communities, antibiotic resistance genes (ARGs) and potential antibiotic-resistant pathogens in giant African snails (Achatina fulica) collected across an urbanization gradient in Xiamen, China (n = 108). There was a lack of correlation between the microbial profiles of giant African snails and the soils of their habitats, and the resistome and human-associated bacteria were significantly higher than those of native snails as well as soils. We observed high diversity (601 ARG subtypes) and abundance (1.5 copies per 16S rRNA gene) of giant African snail gut resistome. Moreover, giant African snails in more urban areas had greater diversity and abundance of high-risk ARGs and potential human bacterial pathogens (e.g., ESKAPE pathogens). We highlight that urbanization significantly impacted the gut microbiomes and resistomes of these invasive snails, indicating that they harbor greater biological contaminants such as ARGs and potential human bacterial pathogens than native snails and soils. This study advances our understanding of the effect of urbanization on human bacterial pathogens and AMR in a problematic invasive snail and should help combat risks associated with invasive species under the One Health framework.

Spatial assortment of soil organisms supports the size-plasticity hypothesis

The size-plasticity hypothesis posits that larger size organisms are less plastic in their metabolic rates and, therefore, are more strongly environmental-filtered than smaller organisms. Many studies have supported this hypothesis by evaluating the relative roles of environmental filtration and dispersal for different taxonomic groups of soil organisms. Most observations are made at large spatial scales, which are assumed to have a wide array of varying habitats. However, since urbanization causes habitat fragmentation at smaller regional scales, testing the size-plasticity hypothesis at this scale would help better understand the spatial assortment of urban soil organisms which, in turn, would help to develop improved management and conservation strategies for urban soil health. Here, we used DNA metabarcoding on five groups of soil biota (bacteria, fungi, protists, nematodes, and invertebrates) to assess the relative importance of dispersal and environmental filters to examine the size-plasticity hypothesis at this spatial scale in an urban environment. We observed strong distance-decay of community similarities associated with higher levels of stochastic changes in bacteria, nematode, and protist communities but not fungal or invertebrate communities. Bacterial communities occupied the widest niche followed by protists and nematodes, potentially because of their higher dispersal abilities compared to the larger soil organisms. Null deviation of communities varied with taxonomic groups where bacteria and nematodes were mainly driven by homogenizing dispersal, protists and fungi by drift, and soil invertebrates by environmental selection. We further identified a small percentage of locally-adapted taxa (2.1%) that could be focal taxa for conservation and restoration efforts by, for example, restoring their habitats and enhancing their regional connectivity. These results support the size-plasticity hypothesis at the relatively unexplored regional scale in an urbanization context, and provide new information for improving urban soil health and sustainable city models.

Ecosystem restoration is integral to humanity's recovery from COVID-19

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.

A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri)

Understanding population structure and genetic diversity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy (Acanthocladium dockeri) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting individuals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and diversity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic diversity, and there was no evidence of inter-population gene flow. Individuals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic diversity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.

Is the genomics 'cart' before the restoration ecology 'horse'? Insights from qualitative interviews and trends from the literature

Harnessing new technologies is vital to achieve global imperatives to restore degraded ecosystems. We explored the potential of genomics as one such tool. We aimed to understand barriers hindering the uptake of genomics, and how to overcome them, via exploratory interviews with leading scholars in both restoration and its sister discipline of conservation-a discipline that has successfully leveraged genomics. We also conducted an examination of research trends to explore some insights that emerged from the interviews, including publication trends that have used genomics to address restoration and conservation questions. Our qualitative findings revealed varied perspectives on harnessing genomics. For example, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasized the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to biodiverse and functional ecosystems. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

Tissue-specific transcriptome profiles identify functional differences key to understanding whole plant response to life in variable salinity

Plants endure environmental stressors via adaptation and phenotypic plasticity. Studying these mechanisms in seagrasses is extremely relevant as they are important primary producers and functionally significant carbon sinks. These mechanisms are not well understood at the tissue level in seagrasses. Using RNA-seq, we generated transcriptome sequences from tissue of leaf, basal leaf meristem and root organs of Posidonia australis, establishing baseline in situ transcriptomic profiles for tissues across a salinity gradient. Samples were collected from four P. australis meadows growing in Shark Bay, Western Australia. Analysis of gene expression showed significant differences between tissue types, with more variation among leaves than meristem or roots. Gene ontology enrichment analysis showed the differences were largely due to the role of photosynthesis, plant growth and nutrient absorption in leaf, meristem and root organs, respectively. Differential gene expression of leaf and meristem showed upregulation of salinity regulation processes in higher salinity meadows. Our study highlights the importance of considering leaf meristem tissue when evaluating whole-plant responses to environmental change.

This article has an associated First Person interview with the first author of the paper.

Summary: Differences in seagrass leaf, meristem and root transcriptomes across variable salinities are due to tissue-specific processes. Leaf meristem contained the broadest process range, indicating preferential use for inferring plant-wide activity.

Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment

Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extremes in temperature and salinity. Our genomic and cytogenetic assessments of 10 meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and a single widespread, high-heterozygosity, polyploid clone (2n = 40) in all other locations. The polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole-genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clone probably formed in shallow waters after the inundation of Shark Bay less than 8500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.

Gut microbiota composition does not associate with Toxoplasma infection in rats

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.

Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets

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.

Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (N_e). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.

Rare genera differentiate urban green space soil bacterial communities in three cities across the world

Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial biodiversity to benefit human health. Exposure to urban microbial biodiversity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via biodiversity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e. diversity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK; Haikou, China; and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil samples and assessing bacterial diversity. We characterized these green spaces as having ‘low’ or ‘high’ vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and diversity around the world. Within cities, we observed significantly different alpha and beta diversities between vegetation complexities; however, these results varied between cities. Rare genera (<1% relative abundance individually, on average 35% relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.

The potential of outdoor environments to supply beneficial butyrate-producing bacteria to humans

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.

Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy

Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.

Correction to: Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9

Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity

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 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 diversity 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 diversity. 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.

Increased plant species richness associates with greater soil bacterial diversity in urban green spaces

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.

Macrogenetic studies must not ignore limitations of genetic markers and scale

Millette et al. (Ecology Letters, 2020, 23:55-67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.

Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure

BACKGROUND

In industrialized countries, non-communicable diseases have been increasing in prevalence since the middle of the 20th century. While the causal mechanisms remain poorly understood, increased population density, pollution, sedentary behavior, smoking, changes in diet, and limited outdoor exposure have all been proposed as significant contributors. Several hypotheses (e.g. Hygiene, Old Friends, and Biodiversity Hypotheses) also suggest that limited environmental microbial exposures may underpin part of this rise in non-communicable diseases. In response, the Microbiome Rewilding Hypothesis proposes that adequate environmental microbial exposures could be achieved by restoring urban green spaces and could potentially decrease the prevalence of non-communicable diseases. However, the microbial interactions between humans and their surrounding environment and the passaging of microbes between both entities remains poorly understood, especially within an urban context.

RESULTS

Here, we survey human skin (n = 90 swabs) and nasal (n = 90 swabs) microbiota of three subjects that were exposed to air (n = 15), soil (n = 15), and leaves (n = 15) from different urban green space environments in three different cities across different continents (Adelaide, Australia; Bournemouth, United Kingdom; New Delhi, India). Using 16S ribosomal RNA metabarcoding, we examined baseline controls (pre-exposure) of both skin (n = 16) and nasal (n = 16) swabs and tracked microbiota transfer from the environment to the human body after exposure events. Microbial richness and phylogenetic diversity increased after urban green space exposure in skin and nasal samples collected in two of the three locations. The microbial composition of skin samples also became more similar to soil microbiota after exposure, while nasal samples became more similar to air samples. Nasal samples were more variable between sites and individuals than skin samples.

CONCLUSIONS

We show that exposure to urban green spaces can increase skin and nasal microbial diversity and alter human microbiota composition. Our study improves our understanding of human-environmental microbial interactions and suggests that increased exposure to diverse outdoor environments may increase the microbial diversity, which could lead to positive health outcomes for non-communicable diseases.

Vertical Stratification in Urban Green Space Aerobiomes

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 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.

OBJECTIVES

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.

METHODS

We combined an innovative columnar sampling method at soil level, 0.0, 0.5, 1.0, and 2.0 m , 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.

RESULTS

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.

DISCUSSION

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. https://doi.org/10.1289/EHP7807.

Exposure to greenspaces could reduce the high global burden of pain

Painful conditions are among the leading causes of years lived with disability, and may increase following the coronavirus pandemic, which has led to temporary closure of some healthcare services for people with chronic pain. To reduce this burden, novel, cost-effective and accessible interventions are required. We propose that greenspace exposure may be one such intervention. Drawing on evidence from neuroscience, physiology, microbiology, and psychology, we articulate how and why exposure to greenspaces could improve pain outcomes and reduce the high global burden of pain. Greenspace exposure potentially provides opportunities to benefit from known or proposed health-enhancing components of nature, such as environmental microbiomes, phytoncides, negative air ions, sunlight, and the sights and sounds of nature itself. We review the established and potential links between these specific exposures and pain outcomes. While further research is required to determine possible causal links between greenspace exposure and pain outcomes, we suggest that there is already sufficient evidence to help reduce the global burden of pain by improving access and exposure to quality greenspaces.

Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia

Populations at the edges of their geographical range tend to have lower genetic diversity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic diversity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal diversity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic diversity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic diversity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.

Mainstreaming Microbes across Biomes

Bacteria, fungi, and other microorganisms in the environment (i.e., environmental microbiomes) provide vital ecosystem services and affect human health. Despite their importance, public awareness of environmental microbiomes has lagged behind that of human microbiomes. A key problem has been a scarcity of research demonstrating the microbial connections across environmental biomes (e.g., marine, soil) and between environmental and human microbiomes. We show in the present article, through analyses of almost 10,000 microbiome papers and three global data sets, that there are significant taxonomic similarities in microbial communities across biomes, but very little cross-biome research exists. This disconnect may be hindering advances in microbiome knowledge and translation. In this article, we highlight current and potential applications of environmental microbiome research and the benefits of an interdisciplinary, cross-biome approach. Microbiome scientists need to engage with each other, government, industry, and the public to ensure that research and applications proceed ethically, maximizing the potential benefits to society.

The Lovebug Effect: Is the human biophilic drive influenced by interactions between the host, the environment, and the microbiome?

Psychological frameworks are often used to investigate the mechanisms involved with our affinity towards, and connection with nature--such as the Biophilia Hypothesis and Nature Connectedness. Recent revelations from microbiome science suggest that animal behaviour can be strongly influenced by the host's microbiome--for example, via the bidirectional communication properties of the gut-brain axis. Here, we build on this theory to hypothesise that a microbially-influenced mechanism could also contribute to the human biophilic drive - the tendency for humans to affiliate and connect with nature. Humans may be at an evolutionary advantage through health-regulating exchange of environmental microbiota, which in turn could influence our nature affinity. We present a conceptual model for microbially-influenced nature affinity, calling it the Lovebug Effect. We present an overview of the potential mechanistic pathways involved in the Lovebug Effect, and consider its dependence on the hologenome concept of evolution, direct behavioural manipulation, and host-microbiota associated phenotypes independent of these concepts. We also discuss its implications for human health and ecological resilience. Finally, we highlight several possible approaches to scrutinise the hypothesis. The Lovebug Effect could have important implications for our understanding of exposure to natural environments for health and wellbeing, and could contribute to an ecologically resilient future.

Microbiome-Inspired Green Infrastructure: A Toolkit for Multidisciplinary Landscape Design

Incorporating recent advances in environmental microbiome research and policy is a major challenge for urban design. We set out a framework for managing construction projects so that multidisciplinary teams of researchers and practitioners can explicitly consider environmental microbiota in design and construction contexts, thereby increasing ecosystem functionality and public health.

Naturally-diverse airborne environmental microbial exposures modulate the gut microbiome and may provide anxiolytic benefits in mice

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.

How well do revegetation plantings capture genetic diversity?

Revegetation plantings are a key management tool for ecological restoration. Revegetation success is usually measured using ecological traits, however, genetic diversity should also be considered as it can influence fitness, adaptive capacity and long-term viability of revegetation plantings and ecosystem functioning. Here we review the global literature comparing genetic diversity in revegetation plantings to natural stands. Findings from 48 studies suggest variable genetic outcomes of revegetation, with 46% demonstrating higher genetic diversity in revegetation than natural stands and 52% demonstrating lower diversity. Levels of genetic diversity were most strongly associated with the number of source sites used-where information was available, 69% of studies showing higher genetic diversity in revegetation reported using multiple provenances, compared with only 33% for those with lower diversity. However, with a few exceptions, it was unclear whether differences in genetic diversity between revegetation and natural stands were statistically significant. This reflected insufficient reporting of statistical error and metadata within the published studies, which limited conclusions about factors contributing to patterns. Nonetheless, our findings indicate that mixed seed sourcing can contribute to higher genetic diversity in revegetation. Finally, we emphasize the type of metadata needed to determine factors influencing genetic diversity in revegetation and inform restoration efforts.