Global homogenization of the structure and function in the soil microbiome of urban greenspaces

Delgado‐Baquerizo, Manuel; Eldridge, David J.; Liu, Yurong; Sokoya, Blessing; Wang, Juntao; Hu, Hang‐Wei; Bastida, Felipe; Moreno, J.L.; Bamigboye, Adebola R.; Blanco‐Pastor, José Luis; Cano‐Díaz, Concha; Illán, Javier Gutiérrez; Makhalanyane, Thulani P.; Siebe, Christina; Trivedi, Pankaj; Zaady, Eli; Verma, Jay Prakash; Wang, Ling; Wang, Jianyong; Grebenc, Tine; Peñaloza-Bojacá, Gabriel F.; Nahberger, Tina Unuk; Teixido, Alberto L.; Zhou, Xinquan; Berdugo, Miguel; Durán, Jorge; Rodríguez, Alexandra; Zhou, Xiaobing; Alfaro, Fernando D.; Abades, Sebastián; Plaza, César; Rey, Ana; Singh, Brajesh K.; Tedersoo, Leho; Fierer, Noah

doi:10.1126/sciadv.abg5809

Cited by 103 publications

(73 citation statements)

References 44 publications

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“…To study fungal endemicity and vulnerability to global change, we combined data from the Global Soil Mycobiome consortium (GSMc) open dataset (Tedersoo et al 2021b) with materials from five other global soil biological surveys ( Fig. 1 ) – BIODESERT (Maestre et al 2022), MUSGONET (including the natural sites in Delgado-Baquerizo et al 2021), CLIMIFUN (Bastida et al 2021), GlobalAM (Davison et al 2021), GlobalWetlands (Bahram et al 2022) as well as Sanger sequence data from soil-inhabiting fungi obtained from the UNITE database (Nilsson et al 2019) covering GenBank. We obtained the DNA from all five surveys and performed new DNA metabarcoding analyses following the protocols outlined for the GSMc dataset (Tedersoo et al 2021b).…”

Section: Methodsmentioning

confidence: 99%

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

Tedersoo

Mikryukov

Zizka

et al. 2022

Preprint

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Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unknown fungal taxa. We used a Global Soil Mycobiome consortium dataset to test relative performance of various sequencing depth standardization methods (calculation of residuals, exclusion of singletons, traditional and SRS rarefaction, use of Shannon index of diversity) to find optimal protocols for statistical analyses. Altogether, we used six global surveys to infer these patterns for soil-inhabiting fungi and their functional groups. We found that residuals of log-transformed richness (including singletons) against log-transformed sequencing depth yields significantly better model estimates compared with most other standardization methods. With respect to global patterns, fungal functional groups differed in the patterns of diversity, endemicity and vulnerability to main global change predictors. Unlike α-diversity, endemicity and global-change vulnerability of fungi and most functional groups were greatest in the tropics. Fungi are vulnerable mostly to drought, heat, and land cover change. Fungal conservation areas of highest priority include wetlands and moist tropical ecosystems.

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Section: Methodsmentioning

confidence: 99%

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

Tedersoo

Mikryukov

Zizka

et al. 2022

Preprint

Self Cite

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“…Some studies have found evidence for this trend with biological, geochemical, soil, and microclimate variables, as well as in urban streams and waterways (Booth et al, 2016; Groffman et al, 2017; Hall et al, 2016; Herrmann et al, 2020; Kaye et al, 2006; McKinney, 2006; Pearse et al, 2016; Polsky et al, 2014). Recently, Delgado‐Baquerizo et al (2021) found evidence for the homogenization of soil microbial taxa and functional genes in urban green spaces across the globe. Homogenization of soil communities was related to economic metrics, climate, and land management practices.…”

Section: Heterogeneitymentioning

confidence: 99%

A framework for soil microbial ecology in urban ecosystems

Nugent

Allison

2022

Ecosphere

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Nearly all ecosystems host diverse microbiomes that support vital ecosystem processes. At the same time, these ecosystems and their microbiomes are increasingly altered by human activities, particularly in highly managed urban environments. While microbial ecologists are beginning to understand the drivers of microbial assembly and the link between community structure and function in many ecosystems, few of these advances have been applied to urban ecosystems. In this synthesis, we review research on the urban soil microbiome and develop a framework to integrate soil microbial communities with urban ecosystem function. We identify disturbance, altered resources, and heterogeneity as key drivers through which human activities including urban development affect soils and their resident microorganisms. Steep environmental gradients in many urban systems present a unique opportunity to address fundamental questions in microbial ecology, such as how microbes respond to stress and how biogeochemical rates relate to microbial diversity and composition. Soil microbiomes in cities also provide ecosystem services and harms, making it crucial to understand how human activity drives those functions and the consequences for environmental and human health. We argue that much-needed integration across disturbance ecology, urban ecology, and microbial ecology will help generate practical and equitable strategies for managing ecosystem benefits in cities where most humans now live.

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“…The composition of soil fungal communities in urban soils remains largely unexplored ( Delgado-Baquerizo et al, 2021 ). Published research consistently shows eroded patterns of ECM diversity in cities, as compared to forest ecosystems ( Bainard et al, 2011 ; Karpati et al, 2011 ; Martinová et al, 2016 ).…”

Section: Ecm Common Mycorrhizal Network In Urban Soils: Headache In A...mentioning

confidence: 99%

Ectomycorrhizal Networks in the Anthropocene: From Natural Ecosystems to Urban Planning

Authier

Violle²,

Richard³

2022

Front. Plant Sci.

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Trees acquire hydric and mineral soil resources through root mutualistic associations. In most boreal, temperate and Mediterranean forests, these functions are realized by a chimeric structure called ectomycorrhizae. Ectomycorrhizal (ECM) fungi are highly diversified and vary widely in their specificity toward plant hosts. Reciprocally, association patterns of ECM plants range from highly specialist to generalist. As a consequence, ECM symbiosis creates interaction networks, which also mediate plant–plant nutrient interactions among different individuals and drive plant community dynamics. Our knowledge of ECM networks essentially relies on a corpus acquired in temperate ecosystems, whereas the below-ground facets of both anthropogenic ECM forests and inter-tropical forests remain poorly investigated. Here, we successively (1) review the current knowledge of ECM networks, (2) examine the content of early literature produced in ECM cultivated forests, (3) analyze the recent progress that has been made in understanding the place of ECM networks in urban soils, and (4) provide directions for future research based on the identification of knowledge gaps. From the examined corpus of knowledge, we reach three main conclusions. First, the emergence of metabarcoding tools has propelled a resurgence of interest in applying network theory to ECM symbiosis. These methods revealed an unexpected interconnection between mutualistic plants with arbuscular mycorrhizal (AM) herbaceous plants, embedding ECM mycelia through root-endophytic interactions. This affinity of ECM fungi to bind VA and ECM plants, raises questions on the nature of the associated functions. Second, despite the central place of ECM trees in cultivated forests, little attention has been paid to these man-made landscapes and in-depth research on this topic is lacking. Third, we report a lag in applying the ECM network theory to urban soils, despite management initiatives striving to interconnect motile organisms through ecological corridors, and the highly challenging task of interconnecting fixed organisms in urban greenspaces is discussed. In particular, we observe a pauperized nature of resident ECM inoculum and a spatial conflict between belowground human pipelines and ECM networks. Finally, we identify the main directions of future research to make the needed link between the current picture of plant functioning and the understanding of belowground ECM networks.

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Global homogenization of the structure and function in the soil microbiome of urban greenspaces

Cited by 103 publications

References 44 publications

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

A framework for soil microbial ecology in urban ecosystems

Ectomycorrhizal Networks in the Anthropocene: From Natural Ecosystems to Urban Planning

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