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Brame JE, Liddicoat C, Abbott CA, Cando‐Dumancela C, Fickling NW, Robinson JM, Breed MF. Urban sports fields support higher levels of soil butyrate and butyrate-producing bacteria than urban nature parks. Ecol Evol 2024; 14:e70057. [PMID: 39041015 PMCID: PMC11262829 DOI: 10.1002/ece3.70057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024] Open
Abstract
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 reservoirs of butyrate-producing bacteria as they supplement the human microbiome, but soil butyrate producer communities have rarely been examined in detail. Here, we studied soil metagenome taxonomic and functional profiles and soil physicochemical data from two urban greenspace types: sports fields (n = 11) and nature parks (n = 22). We also developed a novel method to quantify soil butyrate and characterised the in situ activity of butyrate-producing bacteria. We show that soil butyrate was higher in sports fields than nature parks and that sports fields also had significantly higher relative abundances of the terminal butyrate production genes buk and butCoAT than nature parks. Soil butyrate positively correlated with buk gene abundance (but not butCoAT). Soil moisture (r = .50), calcium (r = -.62), iron (ρ = .54), ammonium nitrogen (ρ = .58) and organic carbon (r = .45) had the strongest soil abiotic effects on soil butyrate concentrations and iron (ρ = .56) and calcium (ρ = -.57) had the strongest soil abiotic effects on buk read abundances. Overall, our findings contribute important new insights into the role of sports fields as key exposure reservoirs of butyrate producing bacteria, with important implications for the provision of microbiome-mediated human health benefits via butyrate.
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Affiliation(s)
- Joel E. Brame
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
- The Aerobiome Innovation and Research Hub (The AIR Hub), College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Craig Liddicoat
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
- The Aerobiome Innovation and Research Hub (The AIR Hub), College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Catherine A. Abbott
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Christian Cando‐Dumancela
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
- The Aerobiome Innovation and Research Hub (The AIR Hub), College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Nicole W. Fickling
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
- The Aerobiome Innovation and Research Hub (The AIR Hub), College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Jake M. Robinson
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
- The Aerobiome Innovation and Research Hub (The AIR Hub), College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Martin F. Breed
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
- The Aerobiome Innovation and Research Hub (The AIR Hub), College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
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2
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Qiao H, Wu L, Li C, Yuan T, Gao J. Microbial perspective on restoration of degraded urban soil using ornamental plants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120920. [PMID: 38688130 DOI: 10.1016/j.jenvman.2024.120920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024]
Abstract
The urban soil where abandoned buildings are demolished is barren and structurally poor, and this degraded soil requires restoration. Ornamental plants enhance the urban environment, increase biodiversity, and affect soil physicochemical properties, microbial diversity; however, their effects remain unclear. Thus, in this study, a mixed-planting meadow consisting of 14 perennial ornamental flower species, including Iris tectorum, Iris lacteal, and Patrinia scabiosaefolia, etc. Was planted at a demolition site with sewage-contaminated soil in Beijing. Simultaneously, a single-planting lawn of I. tectorum was established in a nearby park. We aimed to examine soil physicochemical properties, sequence soil bacterial 16S rRNA and fungal ITS amplicons, and analyze soil microbial diversity and community structure at both sites at five time points in the year after planting, To explore the effect of herbaceous ornamental plants on degraded urban soil, we used FAPROTAX and FUNGuild to predict bacterial and fungal functions, the bin-based null model to evaluate the soil microbial community, and random matrix theory to construct soil microbial molecular networks. The mixed-planting meadow produced a visually appealing landscape and dynamic seasonal enrichment, significantly increasing soil total nitrogen (TN) and organic matter (SOM) contents by 1.99 and 1.21 times, respectively. TN had a positive correlation with soil microbial α diversity and community structure. Dominant phyla at both sites included Proteobacteria, Actinobacteria, and Ascomycota. Although soil microorganisms were primarily influenced by stochastic processes, stochasticity was notably higher in the mixed-planting meadow than in the single-planting lawn. The mixed-planting meadow significantly increased the relative abundance of beneficial microorganisms, improving nitrification and aerobic ammonium oxidation of soil bacteria, as well as symbiotroph of fungi. No significant changes were observed in the single-planting lawn. The mixed-planting meadow established a complex soil microbial molecular network, enhancing the correlation between bacteria and fungi and increasing the number of key microorganisms. Our findings suggest the potential of mixed-planting meadow in restoring degraded urban soils by influencing the soil microbial community and enhancing the ecological service function. Our study provides theoretical support for applying mixed-planting meadow communities to improve the soil environment of urban green spaces.
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Affiliation(s)
- Hongyong Qiao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China
| | - Luyao Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China; Zhejiang Provincial Institute of Cultural Relice and Archaeology, Zhejiang Province, PR China
| | - Chaonan Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China
| | - Tao Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China.
| | - Jianzhou Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing, PR China; National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, PR China; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing, PR China; School of Landscape Architecture, Beijing Forestry University, Beijing, PR China
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3
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Sanchez-Tello JD, Corrales A. Ectomycorrhizal fungal communities in natural and urban ecosystems: Quercus humboldtii as a study case in the tropical Andes. MYCORRHIZA 2024; 34:45-55. [PMID: 38483629 PMCID: PMC10998789 DOI: 10.1007/s00572-024-01140-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/22/2024] [Indexed: 04/07/2024]
Abstract
Worldwide urban landscapes are expanding because of the growing human population. Urban ecosystems serve as habitats to highly diverse communities. However, studies focusing on the diversity and structure of ectomycorrhizal communities are uncommon in this habitat. In Colombia, Quercus humboldtii Bonpl. is an ectomycorrhizal tree thriving in tropical montane forests hosting a high diversity of ectomycorrhizal fungi. Q. humboldtii is planted as an urban tree in Bogotá (Colombia). We studied how root-associated fungal communities of this tree change between natural and urban areas. Using Illumina sequencing, we amplified the ITS1 region and analyzed the resulting data using both OTUs and Amplicon Sequence Variants (ASVs) bioinformatics pipelines. The results obtained using both pipelines showed no substantial differences between OTUs and ASVs for the community patterns of root-associated fungi, and only differences in species richness were observed. We found no significant differences in the species richness between urban and rural sites based on Fisher's alpha or species-accumulation curves. However, we found significant differences in the community composition of fungi present in the roots of rural and urban trees with rural communities being dominated by Russula and Lactarius and urban communities by Scleroderma, Hydnangium, and Trechispora, suggesting a high impact of urban disturbances on ectomycorrhizal fungal communities. Our results highlight the importance of urban trees as reservoirs of fungal diversity and the potential impact of urban conditions on favoring fungal species adapted to more disturbed ecosystems.
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Affiliation(s)
- Juan David Sanchez-Tello
- Center for Research in Microbiology and Biotechnology-UR (CIMBIUR), Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia.
| | - Adriana Corrales
- Center for Research in Microbiology and Biotechnology-UR (CIMBIUR), Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Society for the Protection of Underground Networks, SPUN, 3500 South DuPont Highway, Dover, DE, 19901, USA
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4
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Yao H, Li Z, Geisen S, Qiao Z, Breed MF, Sun X. Degree of urbanization and vegetation type shape soil biodiversity in city parks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:166437. [PMID: 37604369 DOI: 10.1016/j.scitotenv.2023.166437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
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.
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Affiliation(s)
- Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Zhipeng Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Stefan Geisen
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, 6700 ES Wageningen, the Netherlands.
| | - Zhihong Qiao
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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5
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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6
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Grierson J, Flies EJ, Bissett A, Ammitzboll H, Jones P. Which soil microbiome? Bacteria, fungi, and protozoa communities show different relationships with urban green space type and use-intensity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160468. [PMID: 36464041 DOI: 10.1016/j.scitotenv.2022.160468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Exposure to diverse microbial communities early in life can help support healthy human immune function. Soil microbiomes in public and private urban green spaces are potentially important sources of contact with diverse microbiomes for much of the global population. However, we lack understanding of how soil microbial communities vary across and within urban green spaces, and whether these patterns vary across microbial kingdoms; closing this knowledge gap may help us optimise green spaces' capacities to provide this ecosystem service. Here we explore the diversity and community compositions of soil microbiomes across urban green space types in Tasmania, Australia. Specifically, we analysed soil bacterial, fungal, and protozoan diversity and composition across private backyards and public parks. Within parks, we conducted separate sampling for areas of high and low intensity use. We found that: (i) bacteria, fungi, and protozoa showed different patterns of variation, (ii) bacterial alpha-diversity was lowest in low-intensity use areas of parks, (iii) there was relatively little variation in the community composition across backyards, and high and low intensity-use park areas and (iv) neither human-associated bacteria, nor potential microbial community function of bacteria and fungi differed significantly across green space types. To our knowledge, this is the first urban soil microbiome analysis which analyses these three soil microbial kingdoms simultaneously across public and private green space types and within public spaces according to intensity of use. These findings demonstrate how green space type and use intensity may impact on soil microbial diversity and composition, and thus may influence our opportunity to gain healthy exposure to diverse environmental microbiomes.
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Affiliation(s)
- Jessica Grierson
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia.
| | - Emily J Flies
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Hobart, TAS 7000, Australia
| | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia
| | - Penelope Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
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7
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Scholier T, Lavrinienko A, Brila I, Tukalenko E, Hindström R, Vasylenko A, Cayol C, Ecke F, Singh NJ, Forsman JT, Tolvanen A, Matala J, Huitu O, Kallio ER, Koskela E, Mappes T, Watts PC. Urban forest soils harbour distinct and more diverse communities of bacteria and fungi compared to less disturbed forest soils. Mol Ecol 2023; 32:504-517. [PMID: 36318600 DOI: 10.1111/mec.16754] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/27/2022]
Abstract
Anthropogenic changes to land use drive concomitant changes in biodiversity, including that of the soil microbiota. However, it is not clear how increasing intensity of human disturbance is reflected in the soil microbial communities. To address this issue, we used amplicon sequencing to quantify the microbiota (bacteria and fungi) in the soil of forests (n = 312) experiencing four different land uses, national parks (set aside for nature conservation), managed (for forestry purposes), suburban (on the border of an urban area) and urban (fully within a town or city), which broadly represent a gradient of anthropogenic disturbance. Alpha diversity of bacteria and fungi increased with increasing levels of anthropogenic disturbance, and was thus highest in urban forest soils and lowest in the national parks. The forest soil microbial communities were structured according to the level of anthropogenic disturbance, with a clear urban signature evident in both bacteria and fungi. Despite notable differences in community composition, there was little change in the predicted functional traits of urban bacteria. By contrast, urban soils exhibited a marked loss of ectomycorrhizal fungi. Soil pH was positively correlated with the level of disturbance, and thus was the strongest predictor of variation in alpha and beta diversity of forest soil communities, indicating a role of soil alkalinity in structuring urban soil microbial communities. Hence, our study shows how the properties of urban forest soils promote an increase in microbial diversity and a change in forest soil microbiota composition.
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Affiliation(s)
- Tiffany Scholier
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Ilze Brila
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Ecology and Genetics Unit, University of Oulu, Oulu, Finland
| | - Eugene Tukalenko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Rasmus Hindström
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Ecology and Genetics Unit, University of Oulu, Oulu, Finland
| | - Andrii Vasylenko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Claire Cayol
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.,The Pirbright Institute, Pirbright, UK
| | - Frauke Ecke
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Navinder J Singh
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jukka T Forsman
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Anne Tolvanen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Juho Matala
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Otso Huitu
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eva R Kallio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Esa Koskela
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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8
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Okrasińska A, Decewicz P, Majchrowska M, Dziewit L, Muszewska A, Dolatabadi S, Kruszewski Ł, Błocka Z, Pawłowska J. Marginal lands and fungi - linking the type of soil contamination with fungal community composition. Environ Microbiol 2022; 24:3809-3825. [PMID: 35415861 PMCID: PMC9544152 DOI: 10.1111/1462-2920.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
Fungi can be found in almost all ecosystems. Some of them can even survive in harsh, anthropogenically transformed environments, such as post-industrial soils. In order to verify how the soil fungal diversity may be changed by pollution, two soil samples from each of the 28 post-industrial sites were collected. Each soil sample was characterized in terms of concentration of heavy metals and petroleum derivatives. To identify soil fungal communities, fungal ITS2 amplicon was sequenced for each sample using Illumina MiSeq platform. There were significant differences in the community structure and taxonomic diversity among the analyzed samples. The highest taxon richness and evenness were observed in the non-polluted sites, and lower numbers of taxa were identified in multi-polluted soils. The presence of monocyclic aromatic hydrocarbons, gasoline, and mineral oil were determined as the factors driving the differences in the mycobiome. Further, in the culture-based selection experiment, two main groups of fungi growing on polluted media were identified - generalists able to live in the presence of pollution, and specialists adapted to the usage of BTEX as a sole source of energy. Our selection experiment proved that it is long-term soil contamination that shapes the community, rather than temporary addition of pollutant. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alicja Okrasińska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maria Majchrowska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Łukasz Kruszewski
- Institute of Geological Sciences, Polish Academy of Sciences, Warsaw, Poland
| | - Zuzanna Błocka
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
| | - Julia Pawłowska
- Institute of Evolutionary Biology, Centre of Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw
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9
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Mills JG, Selway CA, Weyrich LS, Skelly C, Weinstein P, Thomas T, Young JM, Marczylo E, Yadav S, Yadav V, Lowe AJ, Breed MF. Rare genera differentiate urban green space soil bacterial communities in three cities across the world. Access Microbiol 2022; 4:000320. [PMID: 35252756 PMCID: PMC8895604 DOI: 10.1099/acmi.0.000320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Jacob G. Mills
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Caitlin A. Selway
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Laura S. Weyrich
- Department of Anthropology and Huck Institutes of the Life Sciences, Pennsylvania State University, Pennsylvania, USA
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Chris Skelly
- Research & Intelligence, Public Health Dorset, Dorset County Council, Dorset, UK
- Healthy Urban Microbiome Initiative
| | - Philip Weinstein
- School of Public Health, The University of Adelaide, Adelaide, Australia
- Environment Institute, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Environmental and Earth Sciences, University of New South Wales, Sydney, Australia
| | - Jennifer M. Young
- College of Science and Engineering, Flinders University, Bedford Park, South Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Emma Marczylo
- Toxicology Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Oxfordshire, UK
| | - Sudesh Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Andrew J. Lowe
- Environment Institute, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Martin F. Breed
- Environment Institute, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- College of Science and Engineering, Flinders University, Bedford Park, South Australia
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10
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Mata L, Andersen AN, Morán-Ordóñez A, Hahs AK, Backstrom A, Ives CD, Bickel D, Duncan D, Palma E, Thomas F, Cranney K, Walker K, Shears I, Semeraro L, Malipatil M, Moir ML, Plein M, Porch N, Vesk PA, Smith TR, Lynch Y. Indigenous plants promote insect biodiversity in urban greenspaces. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02309. [PMID: 33605502 DOI: 10.1002/eap.2309] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/26/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
The contribution of urban greenspaces to support biodiversity and provide benefits for people is increasingly recognized. However, ongoing management practices favor vegetation oversimplification, often limiting greenspaces to lawns and tree canopy rather than multi-layered vegetation that includes under- and midstorey, and the use of nonnative species. These practices hinder the potential of greenspaces to sustain indigenous biodiversity, particularly for taxa like insects that rely on plants for food and habitat. Yet, little is known about which plant species may maximize positive outcomes for taxonomically and functionally diverse insect communities in greenspaces. Additionally, while cities are expected to experience high rates of introductions, quantitative assessments of the relative occupancy of indigenous vs. introduced insect species in greenspace are rare, hindering understanding of how management may promote indigenous biodiversity while limiting the establishment of introduced insects. Using a hierarchically replicated study design across 15 public parks, we recorded occurrence data from 552 insect species on 133 plant species, differing in planting design element (lawn, midstorey, and tree canopy), midstorey growth form (forbs, lilioids, graminoids, and shrubs) and origin (nonnative, native, and indigenous), to assess (1) the relative contributions of indigenous and introduced insect species and (2) which plant species sustained the highest number of indigenous insects. We found that the insect community was overwhelmingly composed of indigenous rather than introduced species. Our findings further highlight the core role of multi-layered vegetation in sustaining high insect biodiversity in urban areas, with indigenous midstorey and canopy representing key elements to maintain rich and functionally diverse indigenous insect communities. Intriguingly, graminoids supported the highest indigenous insect richness across all studied growth forms by plant origin groups. Our work highlights the opportunity presented by indigenous understory and midstorey plants, particularly indigenous graminoids, in our study area to promote indigenous insect biodiversity in urban greenspaces. Our study provides a blueprint and stimulus for architects, engineers, developers, designers, and planners to incorporate into their practice plant species palettes that foster a larger presence of indigenous over regionally native or nonnative plant species, while incorporating a broader mixture of midstorey growth forms.
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Affiliation(s)
- Luis Mata
- School of Ecosystem and Forest Sciences, University of Melbourne, Parkville, Victoria, 3010, Australia
- Centre for Urban Research, School of Global, Urban and Social Studies, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Alan N Andersen
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
| | | | - Amy K Hahs
- School of Ecosystem and Forest Sciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Anna Backstrom
- Centre for Urban Research, School of Global, Urban and Social Studies, RMIT University, Melbourne, Victoria, 3000, Australia
| | | | - Daniel Bickel
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, 2010, Australia
| | - David Duncan
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Estibaliz Palma
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Freya Thomas
- Centre for Urban Research, School of Global, Urban and Social Studies, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Kate Cranney
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland, 4102, Australia
| | - Ken Walker
- Science Department, Museum Victoria, Carlton, Victoria, 3053, Australia
| | - Ian Shears
- City of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Linda Semeraro
- Department of Jobs, Precincts and Regions, Agriculture Victoria Research, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
| | - Mallik Malipatil
- Department of Jobs, Precincts and Regions, Agriculture Victoria Research, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3083, Australia
| | - Melinda L Moir
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Michaela Plein
- Administration de la Nature et des Forêts, Diekirch, 9233, Luxembourg
| | - Nick Porch
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, 3216, Australia
| | - Peter A Vesk
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Tessa R Smith
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Yvonne Lynch
- City of Melbourne, Melbourne, Victoria, 3000, Australia
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11
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Stanhope J, Liddicoat C, Weinstein P. Outdoor artificial light at night: A forgotten factor in green space and health research. ENVIRONMENTAL RESEARCH 2021; 197:111012. [PMID: 33716029 DOI: 10.1016/j.envres.2021.111012] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Exposure to green space has been associated with a range of human health benefits, largely in spatial epidemiological studies. Green space and artificial light at night are both associated with breast and prostate cancer, depressive symptoms, obesity, and sleep problems, and are both influenced by the built environment and urbanisation. We identified a negative correlation between green space diversity and outdoor artificial light at night for Australian major cities. Outdoor artificial light at night is therefore a potential, but overlooked, confounder in spatial epidemiological studies of green space exposure and human health, and should be incorporated into future models.
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Affiliation(s)
- Jessica Stanhope
- School of Allied Health Science and Practice, The University of Adelaide, Australia.
| | - Craig Liddicoat
- School of Public Health, The University of Adelaide, Australia; College of Science and Engineering, Flinders University, Australia
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12
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Robinson JM, Cando-Dumancela C, Antwis RE, Cameron R, Liddicoat C, Poudel R, Weinstein P, Breed MF. Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity. Sci Rep 2021; 11:9516. [PMID: 33947905 PMCID: PMC8096821 DOI: 10.1038/s41598-021-89065-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/20/2021] [Indexed: 02/02/2023] Open
Abstract
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.
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Affiliation(s)
- Jake M Robinson
- Department of Landscape Architecture, The University of Sheffield, Sheffield, S10 2TN, UK.
- inVIVO Planetary Health of the Worldwide Universities Network, NJ, 10704, USA.
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia.
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia.
| | - Christian Cando-Dumancela
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, M5 4WX, UK
| | - Ross Cameron
- Department of Landscape Architecture, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
- School of Public Health and the Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ravin Poudel
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA
| | - Philip Weinstein
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
- School of Public Health and the Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
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13
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Baruch Z, Liddicoat C, Cando-Dumancela C, Laws M, Morelli H, Weinstein P, Young JM, Breed MF. Increased plant species richness associates with greater soil bacterial diversity in urban green spaces. ENVIRONMENTAL RESEARCH 2021; 196:110425. [PMID: 33157108 DOI: 10.1016/j.envres.2020.110425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- Zdravko Baruch
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Craig Liddicoat
- School of Public Health, University of Adelaide, Adelaide, SA, 5005, Australia; College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia
| | | | - Mark Laws
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Hamish Morelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Philip Weinstein
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia; School of Public Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia.
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14
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Bradby K, Wallace KJ, Cross AT, Flies EJ, Witehira C, Keesing A, Dudley T, Breed MF, Howling G, Weinstein P, Aronson J. Four Islands
EcoHealth
Network: an Australasian initiative building synergies between the restoration of ecosystems and human health. Restor Ecol 2021. [DOI: 10.1111/rec.13382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Kiri J. Wallace
- People, Cities and Nature University of Waikato Hillcrest Hamilton 3216 New Zealand
| | - Adam T. Cross
- EcoHealth Network 1330 Beacon Street, Suite 355a Brookline MA 02446 U.S.A
- School of Molecular and Life Sciences Curtin University GPO Box U1987 Bentley WA 6102 Australia
| | - Emily J. Flies
- Healthy Landscapes Group, School of Natural Sciences University of Tasmania Churchill Avenue Hobart TAS 7005 Australia
| | - Celia Witehira
- Reconnecting Northland PO Box 5019 Whangārei Aotearoa New Zealand
| | | | - Todd Dudley
- North East Bioregional Network 24751 Tasman Highway St. Marys TAS 7215 Australia
| | - Martin F. Breed
- College of Science and Engineering Flinders University Bedford Park SA 5042 Australia
| | - Gary Howling
- Great Eastern Ranges Initiative P.O. Box 528 Pyrmont NSW 2009 Australia
| | - Philip Weinstein
- School of Public Health University of Adelaide Adelaide SA 5001 Australia
| | - James Aronson
- EcoHealth Network 1330 Beacon Street, Suite 355a Brookline MA 02446 U.S.A
- Center for Conservation and Sustainable Development Missouri Botanical Garden 4344 Shaw Boulevard St. Louis MO 63166‐0299 U.S.A
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15
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Cando‐Dumancela C, Liddicoat C, McLeod D, Young JM, Breed MF. A guide to minimize contamination issues in microbiome restoration studies. Restor Ecol 2021. [DOI: 10.1111/rec.13358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Craig Liddicoat
- College of Science and Engineering Flinders University Bedford Park SA 5042 Australia
- School of Public Health, University of Adelaide Adelaide SA 5001 Australia
| | - Daphne McLeod
- College of Science and Engineering Flinders University Bedford Park SA 5042 Australia
| | - Jennifer M. Young
- College of Science and Engineering Flinders University Bedford Park SA 5042 Australia
| | - Martin F. Breed
- College of Science and Engineering Flinders University Bedford Park SA 5042 Australia
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