Biology subjects

Breed, M. F.

Publications and source records attributed to Breed, M. F..

9 recordsLinked to original sources

bioRxiv2025

Overlapping soil and gut microbiome compound processing potential in a gradient of ecosystem quality and subjects with type 2 diabetes

Global change profoundly impacts microbial systems but cascading effects on human metabolic health remain largely unexplored. Type 2 diabetes (T2D) is shaped by nutrition, host and environmental factors, with rapidly increasing global prevalence. Soil microbiomes shift with ecosystem degradation and influence metabolism through shaping food quality and gut microbiomes, including metabolite exposures without requiring colonization. Here, we explored functional overlaps between degraded soil microbiomes from five ecosystem quality gradients and gut microbiomes in T2D. We developed a method to translate metagenomic functional pathways to potential metabolism of biochemical compounds. In silico trend analyses revealed consistent shifts relevant to energy harvesting and management. Degraded soil microbiomes and T2D gut microbiomes exhibited increased potential metabolism for sugars and decreased potential metabolism for lignin and monomethyl branched-chain fatty acids. Our results advance the hypothesis that soil-ecosystem degradation may contribute to T2D pathogenesis through nutrient-depleted food and/or adverse shaping of gut microbiome functional capacities.

genomics↗

bioRxiv2024

Sounds of the underground reflect soil biodiversity dynamics across a grassy woodland restoration chronosequence

Fifty-nine percent of the worlds species inhabit the soil. However, soils are degrading at unprecedented rates, necessitating efficient, cost-effective, and minimally intrusive biodiversity monitoring methods to aid in their restoration. Ecoacoustics is emerging as a promising tool for detecting and monitoring soil biodiversity, recently proving effective in a temperate forest restoration context. However, understanding the efficacy of soil ecoacoustics in other ecosystems and bioregions is essential. Here, we applied ecoacoustics tools and indices (Acoustic Complexity Index, Bioacoustic Index, Normalised Difference Soundscape Index) to measure soil biodiversity in an Australian grassy woodland restoration chronosequence. We collected 240 soil acoustic samples from two cleared plots (continuously cleared through active management), two woodland restoration plots (revegetated 14-15 years ago), and two remnant vegetation plots over 5 days at Mount Bold, South Australia. We used a below-ground sampling device and sound attenuation chamber to record soil invertebrate communities, which were also manually counted. We show that acoustic complexity and diversity were significantly higher in revegetated and remnant plots than in cleared plots, both in-situ and in sound attenuation chambers. Acoustic complexity and diversity were also strongly positively associated with soil invertebrate abundance and richness, and each chronosequence age class supported distinct invertebrate communities. Our results provide support that soil ecoacoustics can effectively measure soil biodiversity in woodland restoration contexts. This technology holds promise in addressing the global need for effective soil biodiversity monitoring methods and protecting our planets most diverse ecosystems.

ecology↗

bioRxiv2024

Sonic restoration: Acoustic stimulation enhances soil fungal biomass and activity of plant growth-promoting fungi

Ecosystem restoration interventions often utilise visible elements to restore an ecosystem (e.g., replanting native plant communities and reintroducing lost species). However, using acoustic stimulation to restore ecosystems has received little attention. Our study aimed to (a) investigate the potential effects of acoustic stimulation on fungal biomass and organic matter decomposition, which are both crucial components of ecosystem functioning and (b) assess the effect of acoustic stimulation on the growth rate and sporulation of the plant growth-promoting fungus Trichoderma harzianum. We played 70 dB and 90 dB soundscape treatments (@ 8 kHz) to green and rooibos teabags in compost in experimental mesocosms for 8 hours per day for 14 days to test whether acoustic stimulation affected fungal biomass and organic matter decomposition (a control mesocosm received only ambient sound stimulation <30 dB). We played a monotone soundscape (80 dB @ 8 kHz) over five days to Trichoderma harzianum to assess whether this stimulation affected the growth rate and sporulation of this fungus (control samples received only ambient sound stimulation <30 dB). We show that the acoustic stimulation treatments resulted in increased fungal biomass, greater decomposition, and enhanced T. harzianum conidia (spore) activity compared to controls. These results indicate that acoustic stimulation influences soil fungal growth and potentially facilitates their functioning. A piezoelectric effect and/or fungal mechanoreceptor stimulation are possible mechanisms. Our study highlights the potential of acoustic stimulation to alter important functional soil components, which could, with further development, be harnessed to aid ecosystem restoration.

ecology↗

bioRxiv2024

Urban greenspace aerobiomes are shaped by soil conditions and land cover type

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 on aerobiomes in urban greenspaces. Here, we utilised 16S rRNA amplicon sequence data to analyse the effects of land cover, soil abiotic characteristics, surrounding vegetation diversity, and rainfall on aerobiome diversity and composition from 33 urban greenspace sites in Adelaide, South Australia. We sampled air and soil from two urban greenspace land cover types: highly-managed sports fields (n = 11) and minimally-managed nature parks (n = 22). Sports field aerobiomes had a distinct aerobiome community composition and higher alpha diversity than nature parks. Aerobiome alpha diversity was shaped more by soil abiotic characteristics, particularly soil pH and iron levels, than woody plant species diversity. Rainfall prior to sampling also had strong effects on the aerobiome community composition and associated with decreased alpha diversity. These findings point toward soil iron and pH management as pathways to increase aerobiome bacterial diversity. Our study shows that, with additional research, there is potential for greenspace managers and urban planners to target specific soil abiotic characteristics in urban greenspaces to improve microbiome-mediated urban health.

ecology↗

bioRxiv2023

Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes

Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of healthy microbiomes remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, there exists an intriguing opportunity to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of the potential for human gut and environmental soil metagenomes to process major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping landscape based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of compound processing potential associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92% of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role and linkages of microbiota in environmental- and human-health.

bioinformatics↗

bioRxiv2022

Biogeography of human-health associated butyrate-producing bacteria

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 continent Time period2005-2020 Major taxa studiedButyrate-producing bacteria MethodsWe 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.

ecology↗

bioRxiv2021

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 in harnessing genomics. For example, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasised the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to biodiverse and functional ecosystems.

scientific communication and education↗

bioRxiv2021

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.

ecology↗

bioRxiv2020

Exposure to Airborne Bacteria Depends upon Vertical Stratification and Vegetation Complexity

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 of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial 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 new insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace.

ecology↗