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A systematic scoping review reveals that geographic and taxonomic patterns influence the scientific and societal interest in urban soil microbial diversity

Environmental Microbiome volume 20, Article number: 17 (2025) Cite this article

Abstract

Urban green areas provide multiple ecosystem services in cities, mitigating environmental risks and providing a healthier environment for humans. Even if urban ecology has become popular in the last decade, the soil environment with its microbiota, which sustains many other biodiversity layers, remains overlooked. Here, a comprehensive database of scientific papers published in the last 30 years investigating different aspects of soil microbial diversity was built and systematically reviewed. The aim was to identify the taxa, experimental methods and geographical areas that have been investigated, and to highlight gaps in knowledge and research prospects. Our results show that current knowledge on urban soil microbiota remains incomplete, mainly due to the lack of publications on functional aspects, and is biased, in terms of investigated taxa, with most studies focused on Prokaryotes, and geographic representativeness, with the interest focused on a few large cities in the Northern hemisphere. By coupling bibliometrics with statistical modelling we found that soil microbial traits such as biomass and respiration and omics techniques attract the interest of the scientific community while multi-taxa and time-course studies appeal more to the general public.

Introduction

According to recent estimates, nearly 70% of the world’s population will live in urban environments by 2050 [1]. A current challenge is therefore to develop urban planning attentive to the needs of citizens and in line with sustainability principles. Urban green areas represent crucial components of modern cities as they can provide many ecosystem services, e.g. contributing to lower heat-island effect [2]. These services largely depend on the microbial life in soil which is one of the planet’s greatest reservoirs of biological diversity [3]. Indeed, soil microbial communities contribute to crucial functions such as nutrient cycling, disease suppression and root symbioses, with an impact on plant growth and health [4,5,6]. Moreover, urban soil microbiota can directly influence human health by suppressing pathogens, stimulating the immune system or decreasing the exposure to pollutants in case of bioremediation [7, 8], revealing its central role in a One Health perspective [9].

Urban environments are often exposed to abiotic stresses (e.g. pollution) that can have a negative impact on biological diversity [10]. However, recent surveys showed that urban soils are hotspots of microbial diversity [4, 11, 12], not only from a taxonomic but also from a functional point of view [4, 13], possibly due to intense human driven management practices. Delgado-Baquerizo et al. [13], in a global-scale survey of soil microbiome, found an enrichment of microorganisms involved in denitrification and methanogenesis, human/plant pathogens, and strains carrying antibiotic-resistance genes in urban sites compared to nearby undisturbed ecosystems.

Notwithstanding increasing attention on the importance of soils raised by public awareness campaigns and outreach and educational activities in schools [14], several studies highlighted that social awareness of crucial ecosystem services and potential risks provided by soil remains very low for both citizens [15] and professional workers as gardeners [16]. This is even more true when considering the non-visible biotic components of the soil such as the microbiota [17]. In addition, the limited engagement between soil scientists, stakeholders, and the population often results in the misalignment between research agendas and population needs. As a consequence most of the hidden soil diversity is not yet sufficiently addressed in nature conservation or urban-related policies [18,19,20]. This phenomenon is coupled to a poor microbiological literacy that is often found in our societies and highlights that microbiota-related topics should be added to school curricula as early as primary school [21, 22].

In this framework, there is a clear need for an improved knowledge of urban soils which also considers their microbial diversity and a more effective way to communicate scientific results to the specialised public as well as citizens and policymakers. However, how the scientific community develops research on urban soil microbiota and communicates research outputs has not been addressed so far. A quick survey through the scientific literature revealed several knowledge gaps: some geographical areas seem to be poorly studied and very few studies applied metagenomics or metatranscriptomics that are the most informative tools to describe the functional biodiversity [23, 24]. Rega-Brodsky et al. [24] advocate that future research in urban environments encompasses a greater diversity of taxonomic groups, including less studied taxa such as microbes that are closely associated with ecosystem functions. To provide an overview of how microbial communities have been studied in urban environments we systematically reviewed the scientific literature on urban soil microbial biodiversity over the last 30 years. In particular, we assessed which taxa, experimental methods, and geographical areas have been investigated and whether there were any biases and we highlighted how these aspects influence scientific and societal attention.

Results & discussion

To identify the parameters investigated in urban soil microbiota studies (i.e. taxa, experimental methods, geographical areas), and to show how these parameters could drive the attention of scientists and the general public, we performed a bibliometric analysis.

Through an automated extensive search on the Web of Sciences database using specific keywords (see methods), we retrieved research publications focusing on urban soil microbiota published from 1987 to 2023, obtaining an initial database of 354 entries. The list was further manually refined by excluding studies out of the scope and a total of 237 studies were kept for further analyses. Our choice was validated by double-checking study eligibility for 50 studies, with a resulting Cohen’s k value [25] of 0.83.

Globally, our search revealed that in the last 30 years, a rather limited amount of scientific works aimed to investigate urban soils considering microbiological issues compared to other related research fields such as the study of the plant microbiota (e.g. 343 studies on urban microbiota published over 37 years vs. 382 studies related to rhizosphere microbiota published in a single year, 2018 [26]). Despite early works (around the 2000s) already investigating some aspects of microbial soil diversity in urban environments (Fig. 1), we noticed that the increasing multi-disciplinary interest in urban ecology occurring over the last ten years has also brought to the fore urban microbial ecology (Figure S1).

Fig. 1
figure 1

Microbial domains of life investigated and experimental approaches adopted to unravel urban soil microbiota in the scientific literature over the last 30 years. (A) Trend of the scientific interest of the different microbial kingdoms over time using the cumulative numbers of citations of each study included in the dataset as a proxy; blue lines indicate the linear regression fitting the data; determination coefficient (R2), P-value and model equation are also showed. (B) Alluvial plot showing the number of studies for each taxa group and profiling approach adopted to investigate the urban soil microbial diversity. The “molecular” category includes all the profiling approaches based on biological macromolecules (nucleic acids, proteins, fatty acids) while “culturomics” includes all those where the isolation of microorganisms on growth media was performed. (C-G) Number of articles that considered (addressed) or not (not addressed) soil pollutants (C), soil physicochemical characteristics (D), microbial biomass (E), enzymatic activity (F), or soil respiration (G) parameters across the different microbial taxa investigated. We categorised as “whole community” all the studies which comprehensively profiled all the domains of microbial life or used respiration- or enzyme-based methods as a proxy for microbiota functionality. See also Table S1 for details on the variables collected

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For each of the selected papers, variables identifying scientific features, including groups of studied taxa and adopted experimental techniques, were manually retrieved (see Material and Methods for further details) and were then related to citation metrics and geographical distributions. This analysis revealed that several different approaches and different areas across the world have been the focus of urban soil microbiologists.

Interest in microbial life forms in urban soils

Soil is likely home to about 59% of the species on Earth and its biotic diversity is still considered largely unexplored [3, 27]. Several pieces of evidence suggest that urban soils host an increased microbial diversity compared to undisturbed ecosystems [4, 13, 28]. This, coupled with the few detailed studies on urban soil microbiota available in the literature, highlights that our current knowledge on urban soil biodiversity remains still overlooked. In the analysed publications we found that the interest within the scientific community (measured as the number of citations) towards microorganisms in urban soils is increasing with time (Fig. 1A), with different trends across the different taxonomic groups investigated.

Notably, interest in prokaryotes shows a strong positive trend with time, increasing from the 1990s to the present. This could be related to the observation that prokaryotes are generally more susceptible to environmental changes as pointed out by Grierson and colleagues who explored the diversity of three soil microbial kingdoms across urban green spaces in Tasmania [29]. The authors show that bacterial communities were more susceptible to changes in urban environments than fungal communities, suggesting that bacteria might be a more accurate bioindicator of urban soil quality [29].

Similarly, the interest in fungi is also increasing, although not as much as for prokaryotes. However, fungal communities have an important role sustaining plant growth and stress tolerance as in the case of mycorrhizal fungi [30,31,32], as bioremediation agents [33] or as human and plant pathogens [34, 35].

Despite the overall number of scientific articles published each year increasing exponentially, for other Microbial Eukaryotes the trend is unchanged [36]. This may be due to a general limited knowledge of the diversity and functions of eukaryotic microbes, with the exception of a few groups. For example, diatoms are used worldwide for water quality monitoring but their application as markers in other environments, such as sea, sediment, and soil quality, is rather recent [37].

Notwithstanding the relevance of Viruses for plant, animal, and human health [38, 39], their impacts on biogeochemical cycles [40], and their use as bioindicators in environmental samples, they are largely underlooked, (only 1 publication, Fig. 1B) and their occurrence in urban soils still remains largely unexplored. This is probably explained by the polyphyletic origin of the viruses, which has made it difficult to attempt to characterize entire viral communities on the basis of a single gene marker using meta-barcoding [41].

We also investigated which are the most frequently used experimental techniques to investigate microbial communities in urban soils. Molecular approaches, including all those techniques analysing biological molecules (nucleic acids, proteins, and fatty acids), are the most widely used, with 51.48% of studies on prokaryotes (87 out of 169) being carried out with these approaches, 40.7% for fungi (46 out of 113), and 47.37% for other microbial eukaryotes (18 out of 38) (Fig. 1B). This trend is fully in line with the increase in popularity of next-generation DNA sequencing techniques [42]. Culturomics approaches lag behind, although a number of papers applied both molecular and culturomics methods. Conversely, considering the studies investigating comprehensively the soil microbiota (all the taxa super-groups, indicated as “whole community”) we noticed that the use of indirect quantitative techniques, such those measuring microbial biomass, still overtakes the use of molecular tools (> 85% of the studies investigating the whole community). In particular, the microbial biomass is the most studied, followed by soil respiration and enzymatic activity (Fig. 1E-G). This evidence indicates that a large proportion of studies are based on soil biomass-related indicators rather than biota community profiling techniques highlighting that the common interest is still overlooking the relevance of microbial population composition.

Conversely, it has been recently demonstrated that human-driven perturbations, such as land-use changes, reduce not only microbial diversity but also functional potential of soils at a continental scale [43] opening the question of how microbiota functioning is altered in urban environments. Although functional aspects seem crucial in modulating the ecosystem services provided by the soil microbiota, only three publications [13, 44, 45] applied metagenomics and metatranscriptomics, potentially the most appropriate approaches to shed light on these issues. Indeed, Delgado-Baquerizo and colleagues, in their global metagenomic study, revealed that urban ecosystems harbour higher proportions of genes associated with human pathogens, greenhouse gas emissions and nutrient cycling [13]. Metatranscriptome was applied by Scharko et al. [44] to link nitrous acid emissions to ammonia oxidizing bacteria and archaea. Gill et al. [45] surveyed the abundance of seven specific genes that play a role in biogeochemical cycles or the degradation of pollutants (i.e. hydrocarbons, bisphenol and herbicides). The scarcity of this type of studies likely reflects the cost of analysis and the complexity of computational efforts required.

We also found that a vast majority of studies in our dataset consider physico-chemical features (total carbon, total nitrogen, organic/inorganic carbon, percentage of clay, silt or sand, etc.) regardless of the type of taxa investigated (Fig. 1D). It is well known that these soil characteristics contribute to shaping microbial biodiversity and, as a consequence, biogeochemical cycles, fertility, and soil “health” [46]. Soil pollutants were also often considered, regardless of the taxa being investigated (Fig. 1C). Urban soils are often contaminated with heavy metals, hydrocarbons, pesticides, or solvents [47, 48]. Pollutants affect the soil microbial community and interfere not only with the health and functionality of microbial communities and plants but also with animal and human health [49, 50]. In light of this, the large number of studies exploring both microbiota and pollutants in soil may reflect the recognition of microorganisms as relevant soil quality indicators. In our database, 29% of the studies also considered plant communities (data not shown), but vegetation parameters often simply accompany the characterization of the sampling site. Few studies considered the effect of selected plant species on urban soil microbiota in the context of afforestation [51] or food production [52]. Only a few works analysed the effect of management practices and socio-economic factors (see as examples Xie et al. [53] or Fang et al. [54]), which makes the data too fragmentary and uninformative. This may be explained by the difficulty to retrieve exhaustive information on management practices in urban environments [55].

Taken as a whole, our analysis shows that multiple soil microbiota-related characteristics are often monitored: general features such as microbial biomass and respiration or community diversity using molecular methods, which are low-cost and easily accessible techniques, are commonly measured while functional aspects remain unexplored. This leads to a fragmented view of urban soil biology, being limited to soil features and to a still partial microbial census, with a limited insight on functioning.

Influence of studies variables on scientific interest and popularity

It is known that scientific research across many disciplines, including ecology, suffers from cognitive biases introduced by the researchers [56]. We therefore investigated which are the factors that drive scientific and public interest in the urban soil microbial ecology field. By applying a bibliometric approach coupled with statistical modelling we searched for effects of the different aspects previously reviewed (general scientific variables, non scientific variables, techniques used and investigated taxa; Fig. 2) in predicting citations number (CrossRef database) and the Altmetric Attention Score considered as a proxy for scientific and societal interest, respectively. The Altmetric Attention Score is specifically an indicator of potential downstream impact of research. We included in the model one well-acknowledged non-scientific factor affecting citational metrics, i.e. open-access variable. Publishing in ‘gold’ open-access journals does not have an impact on societal attention while it significantly increases scientific interest, as already demonstrated [57]. It should be noted that these two metrics (citations and Altmetric Attention Score) show a very weak correlation (Figure S2), confirming what has been previously demonstrated [58].

Fig. 2
figure 2

Influence of urban soil studies variables on scientific interest (CrossRef citations, panel A) and web popularity (Altmetric Attention Score, panel B). Forest plots summarise the variable effects based on Gaussian linear mixed models (GLMMs). Positive residuals indicate higher effect of the variable compared with its baseline level (see Table S1). Colours indicate different categories of the independent variables. Error bars show 95% confidence intervals while asterisks (*) the significance of the effects (α = 0.05). Estimated regression parameters are provided in Table S2; see also Figure S3 and Figure S4 for model validation parameters

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Our results show that the two different modelled metrics are affected by different factors. Scientific attention seems to be mainly driven by the use of omics tools and classical microbial features such as biomass and respiration, while studies reporting microbial respiration or focusing on edaphic features negatively influenced the attention on the web (Fig. 2). Unexpectedly, multi taxa-focused studies (i.e. those which considered other layers of biodiversity, including animals and plants, besides microorganisms) do not meet the interest of the scientific community while increasing the attention score on the web. Popularity on the web can be explained by the fact that these publications often consider animals such as earthworms [59, 60], which are normally better known to any citizen. In addition, studies also focusing on plants may be more attractive due to their potential applications in afforestation [51, 61] or food production [52] programs.

In general, the specific microbial taxa investigated do not influence public attention. This evidence could be explained by the fact that a non-scientific public often has a general interest in biodiversity but is less interested in the details of the taxonomic group investigated and in the experimental techniques adopted. The lack of interest in experimental techniques is expected since it requires specialised knowledge, as pointed out by a systematic analysis of the literature in the field of omics techniques [62].

Considering the scientific community, studies investigating fungi were significantly less-cited compared to the Prokaryotes baseline and those including all the other microbial groups (Other microorganisms, Fig. 2) followed the same trend. The lesser scientific interest in fungi, and even with a weak effect on all the other microorganisms, compared to prokaryotes could be explained by the fact that these taxa may constitute a fairly specific field of study, for example yeasts [63], mycorrhizal fungi [30] or algae [64], limiting the interest to specific niches of the scientific community. In the case of fungi, we anticipate a change of route, given that recent large international initiatives, such as SPUN (https://www.spun.earth/), are having success in involving the public and giving impulse to scientific research. Moreover, the study of some groups of microbial eukaryotes (i.e. Excavata, Amoebozoa, Cercozoa, Ciliophora, Apicomplexa) is fairly recent [64] and more time is needed to include these domains of life in routine analyses.

Is the microbial diversity of urban soils being studied comprehensively worldwide?

We further reconstructed the spatial distribution of the study sites investigated and that of the corresponding author institutions from the collected papers (see methods). At first glance, we highlighted a fairly clear overlap between the studied cities and corresponding authors’ countries with the global population density (Fig. 3A, B). The most studied continents were Europe, Asia, and America (Fig. 3C). Notably, many low-income and densely populated countries are underrepresented in our dataset, including Central America, Africa, and South Asia (India, Indonesia, the Philippines), recalling citational biases already known for researchers working in the Southern hemisphere [65]. In these countries, scientific research in different disciplines is limited, possibly due to a scarcity of funding [66]. Also, the political instability of some of these countries can lead to a less efficient allocation of resources and a reduction in research and development efforts by companies and governments [67]. In addition, a systematic study of urban ecology in Africa [68] revealed that, beside the economic reasons, there may also be a lack of local experts in this field, a situation further aggravated by the brain drain phenomenon [69, 70]. Moreover, here we systematically reviewed only articles written in English; the inclusion of articles in other languages or from minor journals (referred to as “peripheral publishing” [71]) would have better represented these regions.

Fig. 3
figure 3

Geographic distribution of the studies and their main features. (A) Overall distribution of sites where soil samples were taken in the various studies. (B) Worldwide distribution of the corresponding authors of the articles included in the study. Both maps show the log-scaled population density (Gridded Population of the World, GPWv4). (C) Frequency of corresponding authors and study sites by continent. (D) Frequency of articles by geographical scale (local means that the sampling took place in the same town and its surroundings; regional means that the sampling took place in the same country or on the same continent; global means that the sampling took place on at least two continents). (E) Cumulative number of citations by continent (each point corresponds to a city)

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The scarcity of collaboration between Northern and Southern Hemisphere countries [72] should also be taken into account in explaining these results. It is indicative that the most comprehensive study among the few conducted on a global scale [13] looked at only a few cities in the Southern Hemisphere. In any case, these areas deserve further investigation since the knowledge obtained from researches in the North Globe will not be sufficient to implement effective urban developmental policies in these countries [73]. The extremely fast growth of some of these urban areas offers the opportunity to study the ongoing effect of urbanisation; moreover, these cases would represent a possible model for what happened in North America and Europe between the mid-19th and mid-20th century in terms of environmental and social impact. For the future, it is hoped that there may be more interactions and more fruitful collaborations between research groups of the two hemispheres [74]. Diversifying the academic publication space by authorising non-English versions of articles or encouraging the use of citations from studies carried out in Southern countries could be another way of ensuring that these countries are not left on the periphery [75].

The spatial distribution of the corresponding author’s institution indicates that scientists mostly investigate cities in which they work [76] (bias in favour of the ‘home’ university city) probably because of easy sampling and/or since several funding agencies mostly promote research in local territories. Considering the geographical scale of the investigation, we observed that the majority of studies (85%) explored the urban soil microbiota at the local scale (same city). These data may be not representative of the different urban areas of the same country limiting the implementation of soil biodiversity protection legislation or urban greening planning at a national scale. The large scale study of microbial community composition across Europe by Labouyrie et al. [43], although referring to natural forests and agricultural systems, is undoubtedly an example to follow. Within our dataset, only three studies were conducted on a global scale [13, 77, 78] (sites across different continents). It is likely that increasing the geographical scale makes search for funding, collaboration and sampling more difficult, limiting this type of approach, even if their contribution to knowledge is often more important [79] (Fig. 3D).

The interest of the scientific community is directed towards studies analysing the soil microbiota of a few and larger cities (Fig. 3E): among them, Beijing and Seoul emerged for Asia, New York, Washington, and Moscow (Idaho) in America, Naples, Belfast and two Finnish cities (Helsinki and Lahti) for Europe. This might be due to the fact that those cities have been investigated across different studies, as in the case of Beijing (n = 18), New York (n = 12). It is worth noting that only a few cases of single studies gathered a high scientific recognition (number of citations). For example, the work by Scharenbroch et al., investigating the city of Moscow [80] (Idaho, USA), was cited 222 times, probably because it describes different physical, chemical, and biological properties of urban soils that may be of interest to a wider audience. Similarly, a work carried out in Belfast [81] has gathered 136 citations, possibly because it investigates the hot topic of the occurrence of antibiotic resistance genes.

Overall we noticed that a small number of very large cities worldwide have attracted considerable attention from researchers, resulting in a city size-related bias that has been already described with large cities being much better represented in the literature than smaller ones [76] also when considering urban ecosystem services [82]. Focusing only on large cities can distort our understanding of urban microbial diversity, as many stressors reach extreme and harsh values in these areas (e.g. pollution, human and animal densities, soil sealing, temperature, etc.). This may skew the research only towards organisms with multi resistant traits. In addition it is worth noting that almost 50% of the world’s urban population lives in cities of less than 500,000 inhabitants [83]. This observation underlines the importance of the spatial scale when conducting urban ecology studies, and emphasises the need to investigate both large and small cities [84] to explore how eco-evolutionary processes scale to shape urban biodiversity [85, 86].

Conclusions

Concluding remarks

In this work we reviewed the scientific literature on urban soil microbial diversity encompassing the last 30 years of research which was dominated by a growing interest in urban ecology paralleled by the increasing availability of powerful molecular tools that allow an efficient description of the diversity of microscopic organisms. Our results highlighted that current knowledge and attention on urban soil microbiota remains incomplete, mainly due to the lack of studies on functional aspects, and is biased, in terms of investigated taxa and geographic representativeness. Prokaryotes are the most studied organisms while other taxa, such as microbial eukaryotes and viruses, seem to be neglected. Even considering fungi, which play an acknowledged ecological role, the collected bibliometric data clearly show that they still do not warrant enough attention by scientists also in urban environments, as already underlined in other contexts [19, 20]. We also envisage that viromes of urban environments will also be the focus of future investigations, due to their implications on human health and ecosystems [39].

By coupling bibliometrics with statistical modelling we defined factors driving the interest of scientists and general public: the scientific community gave more attention to general microbial traits such as biomass and respiration and omics techniques while multi-taxa and time-course studies attracted the interest of the general public.

Our analysis also revealed the occurrence of a geographic pattern in the study of urban soil microbial diversity. The interest of researchers focused on a few large cities in the Northern hemisphere. We highlight the need to extend investigations to poorly explored geographical locations, such as Central America and Africa. They could provide an unprecedented opportunity for delving into the impact of human activities on soil microbiota in the context of different models of urban development.

Our data suggest the urgent need to promote an integrated view of the urban soil environment, which simultaneously considers different soil traits, from microbial diversity and functioning to chemical-physical features, and, possibly, other layers of biological diversity [87] (e.g. including macroorganisms).

Limitations of the study

Our approach intentionally excluded the elaboration and interpretation of the data included in the retrieved publications, as a meta-analysis was out of the scope of this work and would have required a different methodological approach. Rather, we focused on the general breadth of the most relevant studies and systematically captured which factors, considered by authors when planning research and analysing results, influence the scientific impact and the society’s interest. We are aware that the metrics considered in this study may provide a distorted view, especially for the public interest that has been measured only using a web-based score (Altmetric Attention Score), that is however a quantitative score easy to retrieve at a global scale.

Methods

Data mining and variable selection

This study is based on studies retrieved through the Web of Science (WoS) advanced search including all the available databases (last access 03/21/2023) following the PRISMA Extension for Scoping Reviews (PRISMA-ScR) and using the following query:

QUERY = (((((TS=(“urban soil*” AND microb* )) OR TI=(“urban soil*” AND microb* )) OR AB=(“urban soil*” AND microb* )) OR AK=(“urban soil*” AND microb* )) NOT (DT==(“REVIEW”) OR DT==(“PROCEEDINGS PAPER” OR “BOOK CHAPTER” OR “EDITORIAL MATERIAL”))) AND ((LA==(“ENGLISH”)) NOT (SILOID==(“PPRN”) OR DT==(“OTHER” OR “MEETING” OR “DATA SET” OR “ABSTRACT” OR “PATENT” OR “UNSPECIFIED” OR “LETTER”))).

The query already excluded studies not focused on soil microbial diversity in urban environments, review papers, documents not written in English and data papers. The obtained list of papers was further manually refined by excluding studies not fitting the topic or not available/retrievable. We measured the degree of agreement between authors by means of the Cohen’s K approach [25], using the online cohen’s K free calculator resource (https://idostatistics.com/cohen-kappa-free-calculator/#calculator).

Data belonging to the categories described in Table S1 were manually extracted from each study. The data-entry operations were performed on a spreadsheet, while the subsequent data-analysis operations were done in the R v4.3.3 [88] The only exception concerns the data-entry of the dependent variables: we extracted the number of citations using the ‘rcrossref’ package (last update: 04/12/2023), and the Altmetric Attention Score was obtained directly from Altmetric using the Altmetric Explorer tool (https://www.altmetric.com/explorer/) with a custom API key. Two of the most important non-scientific factors potentially affecting the impact of a study on science and society were included in the analysis: the open access (OA) status and the name of the journal where the study was published [89].

The coordinates of the cities of the study sites and the corresponding authors were extracted with an automatic R script on openstreetmap (https://www.openstreetmap.org) by using the manually-collected locations names (see Table S1) and the ISO 3166 country code (to avoid homonyms and clarify the search) with the help of RJSONIO package v1.3-1.9 [90]. If the city was not specified in the article, the country coordinates were entered manually instead.

Visualisation

All the graphical elaborations were performed in R v4.3.3 [88] using ‘ggplot2’ v3.5.0 [91] and ‘ggalluvial’ v0.12.5 [92] libraries. Global distributions of the study sites and corresponding author institutions were visualised using ggplot2 package with extended functionality from the ‘tidyterra’ v0.5.1 [93] package and using the log(1 + x)-scaled Gridded Population of the World (GPWv4) global population density raster obtained from the ‘geodata’ v0.5-9 [94].

Modelling and statistical analysis

We used regression analyses [95] to assess relationships between scientific (number of citations in CrossRef database) and societal (Altmetric Attention Score) interest in urban soil microbial diversity. Collinearity between the independent variables (Figure S2) and regressions reported in Fig. 1A were obtained using a linear model and by calculating the R-squared, P-value and the Pearson’s correlation coefficient using the ‘ggpmisc’ v0.5.5 library in R [96].

We used the package ‘glmmTMB’ v1.1.1 for modelling [97] and ‘tidyverse’ version 2.0.0 [98] for data wrangling and visualisations.

We followed the approach described by Zuur et al. for data exploration, model fitting, and validations [95]. We visually inspected data distribution, checked the presence of outliers, and verified multicollinearity by using the VIF (Variance Inflation Factor) for independent factorial variables and pairwise Pearson’s correlations for the two dependent variables. We balanced factor levels, as much as possible [99] as described in Table S1. We created two separate models, one for citation number and a second for Altmetric Attention Score. In both models we included the same variables (see below formula).

We normalised the y variables (citations and Altmetric Attention Score) by the study publication year, hypothesising that older studies should be more cited than recent studies. To this aim, we first fitted a GAM (Generalised Additive Model) to predict the over- or the under-citation of each study and we used the residuals as a dependent variable [89] in the subsequent GLMM models according to the following formula (see Table S1 for variables IDs:

$$\begin{gathered}y \sim MolTech + Targets + MolStudied \hfill \\\,\,\,\,\,\,\,\,{\text{ }} + MBiomass + PhChCharact + Pollutants \hfill \\\,\,\,\,\,\,\,\,\,\,\, + TempSampling + OA. + \left( {1|SO} \right) \hfill \\ \end{gathered} $$

We introduced random factors to remove the journal prestige (1|SO), in view of the fact that its influence should smooth out most of the trends produced by the scientific approach itself. Model results were visualised in ‘sjPlot’ v2.8.15 [100]. To validate models we used the ‘performance’ package v 0.10.8 [101]. Results of model validation are reported in Figure S3 and Figure S4.

Data availability

Data and code generated in this study are publicly available in FigShare, (https://doiorg.publicaciones.saludcastillayleon.es/10.6084/m9.figshare.25360240).

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Acknowledgements

The Authors thank Stefano Mammola and Paola Bonfante for useful comments and discussions.

Funding

The work was supported by the project CN_00000033 funded under the National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4 - Call for tender No. 3138 of 16 December 2021, rectified by Decree n. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union– NextGenerationEU. Funders had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

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  1. Simon Masson and Matteo Chialva contributed equally to this work.

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  1. Department of Life Sciences and Systems Biology (DBIOS), University of Torino, Viale Mattioli, 25, Torino, I-10125, Italy

    Simon Masson, Matteo Chialva, Davide Bongiovanni, Martino Adamo, Irene Stefanini & Luisa Lanfranco

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Contributions

SM contributed to the methodology, investigation, data curation, writing of the original draft and writing - review and editing. MC contributed to the conceptualization, methodology, investigation, data curation, formal analysis, visualisation, writing of the original draft, and writing - review and editing. DB contributed to the investigation, data curation, and writing of the original draft. MA contributed to the conceptualization, methodology, investigation, data curation, formal analysis, visualisation, writing of the original draft, and writing - review and editing. IS was responsible for writing - review and editing, and funding acquisition. LL contributed to conceptualization, writing the original draft, writing - review and editing, and funding acquisition. All authors read and approved the final manuscript.

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Correspondence to Luisa Lanfranco.

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Masson, S., Chialva, M., Bongiovanni, D. et al. A systematic scoping review reveals that geographic and taxonomic patterns influence the scientific and societal interest in urban soil microbial diversity. Environmental Microbiome 20, 17 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s40793-025-00677-7

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Keywords

Environmental Microbiome

ISSN: 2524-6372