Plant range expansion is occurring at a rapid pace, largely in response to human-induced climate warming. Although the movement of plants along latitudinal and altitudinal gradients is well-documented, effects on belowground microbial communities remain largely unknown. Furthermore, for range expansion, not all plant species are equal: in a new range, the relatedness between range-expanding plant species and native flora can influence plant–microorganism interactions. Here we use a latitudinal gradient spanning 3,000 km across Europe to examine bacterial and fungal communities in the rhizosphere and surrounding soils of range-expanding plant species. We selected range-expanding plants with and without congeneric native species in the new range and, as a control, the congeneric native species, totalling 382 plant individuals collected across Europe. In general, the status of a plant as a range-expanding plant was a weak predictor of the composition of bacterial and fungal communities. However, microbial communities of range-expanding plant species became more similar to each other further from their original range. Range-expanding plants that were unrelated to the native community also experienced a decrease in the ratio of plant pathogens to symbionts, giving weak support to the enemy release hypothesis. Even at a continental scale, the effects of plant range expansion on the belowground microbiome are detectable, although changes to specific taxa remain difficult to decipher.
Species range expansion in response to climate change is recognized as a major uncertainty in predicting the consequences of global warming for biodiversity and ecosystem functions1,2. Initially, attention was given to the ability of species to keep up with their shifting climate envelope; now, research questions have expanded to include the consequences of range shifts for community interactions3. The disruption of plant range expansions on aboveground interactions have been well-documented4,5,6, including on aboveground herbivores and higher tropic levels7,8. Although evidence suggests that introduced invasive species can alter soil communities9,10,11, the effects of plant range expansion on belowground microbial communities remain ambiguous.
The relationships between plants and their associated microorganisms can influence plant establishment, fitness and community assembly12,13,14. It has been proposed that range-expanding plants will be successful in their new range, because they lose their specialized soil pathogens5,15,16. At the same time, range-expanding plants may also lose specialized mutualistic microorganisms17,18,19. Results of these studies lead to the similar expectation that the plant-associated microbial community in the rhizosphere and surrounding soil (here called the belowground plant microbiome) of range-expanding plant species will associate less with the belowground microbiome in their new range compared to their native range, and compared to native plant species. However, few studies have characterized or compared the structure and diversity of the microbiome communities associated with range-expanding plant species (although see a previous study20), nor has a direct comparison been made with related native plant species at a continental scale.
The soil and rhizosphere microbiome, made up largely of bacteria and fungi, is taxonomically and functionally diverse21. The community composition of the belowground microbiome is broadly structured by abiotic factors, yet effects differ between bacteria and fungi22,23. For example, whereas at large spatial scales bacterial communities are strongly influenced by soil pH24,25, the composition of fungal communities are simultaneously affected by climate and nutrients26,27,28. At the same time, both the soil and rhizosphere microbiomes are strongly controlled by biotic factors, including the composition of root exudates, plant species identities and plant traits29,30,31. Through these properties, plant species can assemble species-specific microbiomes in which microbial taxa are enriched or suppressed under some plants and not under others14,32,33,34,35. At the same time, phylogenetic relatedness of range-expanding plants with native flora can represent another potential effect of range expansion on microbial communities—for which some research suggests that closely related plant species can contain similar microbial taxa, especially pathogens36,37. Finally, plant–microorganism interactions evolve over time, changing over years and even decades38,39; therefore, during range expansion, both the distance from the original range and the evolutionary history between plants and microorganisms40 have the potential to influence the belowground plant microbiome.
Here we analyse the microbiome of intra-continental range-expanding plant species along a latitudinal gradient to explore key hypotheses that have been previously proposed for exotic and invasive plants, but that may also apply to climate warming-induced range expansions. To test for the influence of plant phylogeny on the belowground microbiome during range expansion, we selected range-expanding plants that are either related or unrelated to the native flora (Fig. 1a). To test for the effects of range expansion on the belowground plant microbiome, we compared changes in community composition and the relative abundance of pathogens across the range-expansion gradient (Fig. 1b). We hypothesize that if plant range expansion influences the belowground plant microbiome, observed patterns will be stronger in the rhizosphere41 than in bulk soil. Furthermore, if range-expanding plants that are further from their original range either lose the ability to interact with certain microbial taxa or preferentially promote the growth of a beneficial community, the microbiome of the range-expanding plants will become more similar and alpha diversity of communities will decrease in the new range. However, because plants that are more closely related to the native community may share microorganisms, this change will be less pronounced for range-expanding plants that encounter congeneric native species in the new habitat. Finally, if the enemy release hypothesis common to invasive plant species is also applicable to range-expanding plants, we expect fewer belowground pathogens to be associated with range-expanding plants that are unrelated to the native flora compared to related expanding and native species.
In Europe, the range expansion of plants induced by climate change is well-documented; many plant species are expanding their range into higher latitudes and altitudes2,42. Here we use high-throughput Illumina sequencing to explore how the belowground microbiome of plant species changes when plants expand from their original range (in lower latitudes) to new ranges (in higher latitudes). We targeted the microbiome of three plant groups: unrelated range-expanding plants (species without native species from the same genus in their new range); related range-expanding plants (species that have native species from the same genus in their new range) (Supplementary Table 1 and Supplementary Fig. 1); and native plant species, which are congeneric to the related range-expanding plant species and native throughout the entire gradient. All range-expanding plants had either arrived or greatly expanded within the Netherlands in the late twentieth and early twenty-first centuries43. In an effort to minimize variation in abiotic factors, we selected 11 plant species grown on similar parent soil (see Methods). For each species, we sampled the microbiome in the rhizosphere and surrounding (bulk) soil of up to 9 plant individuals collected from up to 6 countries, spanning from Greece to the Netherlands, totalling 382 plant individuals (Supplementary Table 1 and Supplementary Data 2). While some species were cosmopolitan44, others were quite rare and more difficult to find. Here we included replicates not only for individual plant species, but also for each plant type (native, and related and unrelated range-expanding plant species), and we collected 382 bulk-soil and rhizosphere samples to obtain a number that should be sufficient to capture large-scale patterns in the microbial communities25,27.
Results and discussion
Overall, rhizosphere and bulk-soil communities were significantly different from each other, both in community overlap—as visualized by principal component analysis (PCA) (P < 0.001 for both bacteria and fungi; Fig. 2a,b)—and in taxa overlap (Fig. 2c,d). We found 47,704 bacterial phylotypes and 9,374 fungal phylotypes in soils, and 33,939 bacterial phylotypes and 6,438 fungal phylotypes in the rhizosphere. Furthermore, there was little community overlap among plant individuals in both the soil (averaging 4,092 (8%) unique bacterial taxa and 523 (5.5%) unique fungal phylotypes per sample) and the rhizosphere (averaging 1,932 (5.6%) unique bacterial phylotypes and 257 (4%) unique fungal phylotypes per sample). High microbiome diversity among 11 plant species is not a surprise, especially because the selected plants represent a range of phylogenetically and ecologically distinct species35,45,46.
Across the gradient, plant species was the strongest predictor of the composition of the bacterial and fungal communities in both soil and rhizosphere environments, explaining 7 to 14% of the variation (Fig. 3 and Supplementary Table 2) and plant genus as a proxy of phylogenetic relatedness (Supplementary Fig. 1) provided no additional predictive power. Conversely, the effects of plant grouping (unrelated range-expanding, related range-expanding and native plant species) and latitude had a much smaller effect on microbial composition and explained a maximum of 2% of the variation in all cases. In general, soil abiotic factors also had a minor influence on variation, accounting for less than 1% of the variation for all factors (for example pH, nitrogen and carbon), except for soil bacterial communities, for which pH explained approximately 5% of the variation. The relatively minor effect of soil abiotic factors on microbial communities—compared to previous studies24—can be explained by the small variation in soil factors across the gradient and between plants (Supplementary Fig. 2), as was the goal of choosing plant species that grow on the same parent soil material. In comparison, other studies have been more focused on elucidating patterns in the composition of the microbial community relative to changes in abiotic factors25,27,47. Thus, the observed differences are more likely to be due to the effects of the plant species themselves46, such as plant ecology, relatedness with native flora and life-history traits44,48,49.
In support of our hypothesis, we found that range-expanding plants that were further from their original range had microbial communities that were more similar to other plant individuals. Put another way, the variation in community composition decreased among individuals in the new range. Furthermore, there were negative correlations between ‘range’ (the country samples were collected from) and community dissimilarity for all plant groups (Fig. 4 and Supplementary Table 3); when analysed using latitude and distance, equivalent results were obtained. This pattern was significant for bacterial communities in the soil and rhizosphere of all plant types (ρ varied between −0.08 and −0.32 and P < 0.05 for all). However, for fungal communities, correlations were only observed in soils (ρ varied from −0.10 to −0.13, P < 0.05 for all) and not in the rhizosphere. The negative correlation between range and community dissimilarity was strongest in unrelated range-expanding species (Supplementary Table 3). We also found a significant difference in the degree of microbial community similarity by plant group, although there was an interaction of country in two scenarios (soil fungi and rhizosphere bacteria) (P < 0.0001 in all cases) (Supplementary Table 4). This suggests that controls on the composition of microbiome communities of native and range-expanding plants differs across the gradient. For instance, the microbiomes of native plants (and to a lesser extent related range-expanding species) may be more influenced by a long-term co-evolutionary history that would be consistent across this latitudinal gradient50,51, whereas microbiome patterns of unrelated range-expanding plants might be more determined by more recent spatial effects and the native (neighbour) plant community52. Because we used a survey to explore changes to the belowground microbiome across a natural range expansion transect, we were unable to test for co-evolutionary history between microorganisms and plants. Still, our results suggest that future studies should be designed with this process in mind, particularly to identify the role of the microbial community for plant adaptions during climate change38,53.
Whereas community structure became more similar across the gradient, changes in bacterial richness and fungal richness was much more variable (Fig. 5 and Supplementary Table 5). Under unrelated range-expanding species, fungal alpha diversity in the rhizosphere significantly increased with distance from the original range (ρ = 0.36, P < 0.001 in the rhizosphere, P > 0.05 in soil). However, related range-expanding plants showed no relationship between fungal diversity and distance from original range (P > 0.05 for both soil and rhizosphere) in comparison to native plants, for which fungal alpha diversity increased with latitude in both the rhizosphere (ρ = 0.20, P < 0.05) and the bulk soil (ρ = 0.23, P < 0.05). The mechanisms behind increased fungal diversity in the rhizosphere of unrelated range-expanding remain unclear. It could be that if range-expanding plants do not need to invest in belowground defence54,55, the rhizosphere becomes accessible for a larger proportion of microorganisms, although this varies by plant species56. Alternatively, it has been proposed that exotic species and range-expanding plants promote high microbial diversity as part of a defence mechanism52,56. The latter proposition, that range-expanding plants enrich their rhizosphere, is congruent with our findings that community composition becomes more similar among individuals in the northern part of the range (Fig. 4), and that unrelated range-expanding plants had higher fungal and bacterial diversities in their rhizosphere and lower diversities in the associated soils (P < 0.0001 in all cases) (Supplementary Table 6). Overall, the inconsistency between the responses of the two types of range-expanding plant species suggests that related and unrelated range-expanding plants have different controls on microbial diversity. Furthermore, the variability in alpha diversity patterns indicates that alpha diversity and community similarity are affected by different mechanisms.
It has been proposed that in novel ecosystems, the success or failure of a plant species is based on reduced exposure to soil-borne pathogens combined with continued association with symbionts57,58. We applied this concept here and used FunGuild59 to test how the abundance of potential fungal functional groups changes as range-expanding plants move further from their original range. Specifically, we examined potential plant pathogens and arbuscular mycorrhizal fungi, as these are the relevant mutualistic symbionts for most of our plant species, except for the crucifers. However, we could not detect any significant changes in the relative abundance in either of these groups under range-expanding plant species (Supplementary Fig. 3). However, there was a significant positive correlation in the ratio of plant pathogens to symbionts across the transect (ρ = 0.31, P < 0.001) (Supplementary Table 7). By contrast, under native plants the relative abundance of plant pathogens increased in both the soil and rhizosphere from south to north (ρ = 0.23 for both). In contrast to previous studies, these results do not directly verify that range-expanding plants lose their specialist microorganisms57 or are released from specialist enemies55. Instead, the results suggest that compared to native species, range-expanding plants are exposed to fewer potential pathogens and symbionts in the new range, which has been predicted for range-expanding plant species60 and demonstrated for introduced exotic species in their new range61,62. At the same time, recent studies of plant succession63,64 clearly demonstrate that plant success and nutrient cycling is tied to the microbial communities. However, it remains unclear whether the mechanisms that underlie plant range expansion are the same as those observed elsewhere.
Still, these results are not without caveats. Notably, the molecular methods used are not infallible—the DNA community analysis does not assess the active microbial community nor the true functional capabilities of the detected microorganisms. Thus, potential functional groupings and relative abundances of taxa cannot indicate the expected pathogenicity of these fungi in the rhizospheres of the host plant. Equally important is that, for all plant groups, the relative abundance of these functional groupings make up approximately 5% of the fungal community. This indicates that any changes in composition or diversity may overinflate or obscure true changes in these low-abundance groups65 and specific primers or culture work is necessary to explore the functional changes more thoroughly. Our study exemplifies that high-throughput sequence data can be used to assess large-scale patterns in plant–soil associations; however, future functional analyses (for example, metagenomics and metatranscriptomics approaches) and experimental studies must be designed to take the low abundance of pathogen sequences into account.
Our study contributes initial steps for the identification of the patterns of the changes in the plant microbiome that occur during plant range expansion. Although we show that microbial community and diversity dynamics change across a range-expansion gradient, clarifying the mechanisms behind the observed changes would require further experimental study. In the present study, we attempted to link the concepts from plant ecology to the microbiome by assuming that plant establishment outside the native range results in altered exposure to soil microorganisms. Our results suggest that although terms such as ‘exotic species’, ‘range-expanding species’ and ‘native species’ are helpful descriptors in plant ecology, it should not be assumed that these labels are equally relevant to describe the belowground microbial community of such plant species. Future research will require consideration of the ecological roles of both plants and microorganisms25,35; however, the ecological roles of many microbial taxa currently remain unknown. At the same time, we think that this large-scale biogeographical study of plant–soil–microorganism associations of native, related and unrelated range-expanding plant species along a latitudinal gradient is an essential step to understand how climate warming-induced range-expanding plant species may assemble a new microbiome in their novel range. This approach may also stand as a model for processes that take place belowground after introduction of exotic plant species in a new continent. Subsequent experimental work is needed to understand the functional consequences of invasiveness and naturalization.
Almost 4% of extant global vascular flora have established outside their native range66, and range expansion induced by climate change is not expected to slow down67. Although soil microorganisms exert strong selective pressures on plant species and communities68,69, our understanding of microbial community dynamics during range expansion remains limited. Range expansion offers an opportunity to explore not only how global change may alter the relationship between plants and their microbiome, but also how the belowground microbiome changes across large geographical scales. Understanding the effect of range expansion on the belowground plant microbiome can provide baseline knowledge for predicting ecological consequences of current rapid climate warming, and it may also be used to enhance our understanding of community responses to invasion scenarios for introduced exotic species.
Plant species and soil collection
In central Europe, rivers flow to the south and north away from the Alps, resulting in habitats with sediments from similar parent materials and soils that spread across a latitudinal gradient. Within these well-connected river habitats, and in response to climate change, many plant species are expanding their range with much more movement expected in the coming decades1,70,71. Within this latitudinal gradient, spanning almost 3,000 km from Greece in the south to the Netherlands in the north, we identified 7 range-expanding species for which the range has expanded north into Austria, Germany and the Netherlands over the last 50 years, approximately72. Range-expanding plants without native congeneric species in the northern sites (that is, unrelated range-expanding plants) include Dittrichia graveolens, Lactuca serriola and Rapistrum rugosum. Range-expanders with native congenerics (that is, related range-expanding plants) include Centaurea stoebe, Geranium pyrenaicum, Tragopogon pratensis and Rorippa austriaca. As a control, we also included 4 native plant species that are congeneric with the related range-expanding species, Centaurea jacea, Geranium molle, Tragopogon dubious and Rorippa sylvestris. C. stoebe and R. austriaca originated from central and eastern Europe, while all other range-expanding species originated from southern Europe (www.gbif.org). Plant populations were sampled from 6 countries in Europe—Greece, Montenegro, Slovenia, Austria, Germany and the Netherlands—in the summer growing seasons of 2013 and 2014. All plants were flowering at the time of sampling. At each sampling site, environmental parameters, including weather conditions at sampling dates, were recorded (Supplementary Data 2). For each sampling location of a single species, 3 individuals of 3 distinct populations (in most cases, with a separation of at least 400 m) were chosen, totalling 9 plant individuals for each location (see Supplementary Table 1 for sample numbers). For collection of all samples, permissions were obtained from both the nature reserves and government agencies that are responsible for the land.
To assess the soil and rhizosphere microbiomes of native and range-expanding plant species, soil and roots plus rhizosphere were collected from under individual plants. In brief, the entire plant was dug up within a 10-cm radius around the plant and bulk soil was shaken off the plant roots. Bulk soil was homogenized and 10 g was collected for microbial and chemical analyses. Separately from the bulk soil, the fine plant root and rhizosphere soil was then collected separately, which is referred to as the rhizosphere community. All rhizosphere and soil samples were stored at 4 °C until shipped, within 1 week, to the Netherlands Institute of Ecology (NIOO). At the NIOO, soil and rhizosphere samples for DNA extraction were frozen at −80 °C. A subset of soil was stored in the fridge at 4 °C for chemical analyses.
Soil chemical analyses
For all soil samples collected in 2014, nutrients and pH were measured on fresh soil stored at 4 °C (Supplementary Data and Supplementary Fig. 2). Gravimetric moisture (percentage of water) was determined on soil samples that were oven-dried at 105 °C. Total soil carbon and nitrogen content was determined from these dried soils on an elemental analyser (LECO). Extractable NO3 and NH4 were measured using the KCl extraction protocol. In brief, soils were dried at 4 °C, 10 g dry soil was then mixed with 1 M KCl solution and shaken, after which the supernatant was used for analyses of NO3 and NH4. Soil pH was measured in an H2O slurry solution using a bench-top pH meter following the ISO 10309 standard procedure.
Community level sequence analysis
To identify the bulk-soil and rhizosphere microbiomes of native and range-expanding plants, DNA was extracted from 0.25 g of ground bulk soil and 0.35 g of ground rhizosphere material using the PowerSoil-htp 96-well soil DNA isolation kit (MO BIO Laboratories) according to the manufacturer’s instructions. Bacterial community composition was determined by targeting 16S rRNA amplicons using 515F/806R primers73 and the fungal community composition was determined by targeting the ITS region using primers ITS4/fITS974. To prevent the amplification of plant material75, PNA Clamps (PCR Blockers) (CGACACTGACACTGA-KK) were added at the PCR step for rhizosphere bacterial DNA. For all samples, DNA was amplified by PCR in duplicate using barcoded primers73. PCR products were purified using the Agencourt AMPure XP magnetic bead system (Beckman Coulter Life Sciences) and analysed using the Standard Sensitivity NGS Fragment Analysis kit (1–6,000 bp). Pooled PCR amplicons were sequenced with the Illumina MiSeq platform at BGI Tech Solutions.
MiSeq paired-end reads targeting the 16S rRNA amplicon were merged and only reads that had a minimum overlap of 150 bp and a PHRED score of 25 (estimated using the RDP extension of PANDASeq76). Primer sequences were stripped using Flexbar version 2.577. Sequences were then clustered to OTUs with VSEARCH version 1.0.1078, using the UPARSE strategy of dereplication, sorting by abundance and clustering using the UCLUST smallmem algorithm79. All singletons were removed and potential chimeric sequences were removed using the UCHIME algorithm80. Taxonomic classification for each OTU was obtained using the RDP classifier version 2.1081.
Similarly, MiSeq paired-end reads targeting the ITS region were treated as described above with the following adjustments: ITS primer sequences were stripped using ITSx version 1.0.1182 before clustering, and sequences were classified using the UNITE database83. All bioinformatics steps were implemented with a publicly available workflow made with Snakemake84. After samples were removed due to sampling error or falling below the rarified threshhold, 382 samples were included in downstream analyses of plant soil and rhizosphere microbiomes.
Community similarity was visualized with a PCA of the dissimilarity matrix based on Bray–Curtis distances. Plotted in Fig. 3 is the centroid of each plant species community with lines representing connections to all other samples of that species. We quantified phylogenetic distances between all plant species used, but did not make a full analysis of these distances with differences in microbiome composition, as plant genus or family-specific issues might interfere with pure phylogenetic distances (Supplementary Fig. 1). To investigate how distance from the original range influences the microbiome for each plant species, we tested within country dissimilarity of bacterial and fungal communities in both the rhizosphere and the soil. In brief, pairwise Bray–Curtis dissimilarity was estimated between samples of each plant species within each country. Diversity of soil communities were analysed using the ‘vegan’ package85 using the PERMANOVA test and visualized with the ‘ggplot2’ package. Correlation patterns were visualized with the LOESS smoothing function86. Because within-country distance was much smaller than between-country distance, diversity patterns were the same whether plotted by latitude, country or geographical distance, which here we refer to as ‘range’. Spearman rank correlations were run on latitude and plots show country name for clarity. FunGuild analyses were generated using the web interface and only taxa that received a ‘highly probable’ classification were included. When all taxa were included results remained the same. All other analyses were performed using the R programming language (R Development Core Team).
Further information on research design is available in the Nature Research Reporting Summary linked to this article.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Pecl, G. T. et al. Biodiversity redistribution under climate change: impacts on ecosystems and human well-being. Science 355, eaai9214 (2017).
Parmesan, C. & Yohe, G. A globally coherent fingerprint of climate change impacts across natural systems. Nature 421, 37–42 (2003).
Classen, A. T. et al. Direct and indirect effects of climate change on soil microbial and soil microbial–plant interactions: what lies ahead? Ecosphere 6, art130 (2015).
Meisner, A., De Deyn, G. B., de Boer, W. & van der Putten, W. H. Soil biotic legacy effects of extreme weather events influence plant invasiveness. Proc. Natl Acad. Sci. USA 110, 9835–9838 (2013).
Engelkes, T. et al. Successful range-expanding plants experience less above-ground and below-ground enemy impact. Nature 456, 946–948 (2008).
van der Putten, W. H., Bradford, M. A., Brinkman, E. P., van de Voorde, T. F. J. & Veen, G. F. Where, when and how plant–soil feedback matters in a changing world. Funct. Ecol. 30, 1109–1121 (2016).
Gonzalez-Megias, A. & Menendez, R. Climate change effects on above- and below-ground interactions in a dryland ecosystem. Phil. Trans. R. Soc. B 367, 3115–3124 (2012).
Tylianakis, J. M., Didham, R. K., Bascompte, J. & Wardle, D. A. Global change and species interactions in terrestrial ecosystems. Ecol. Lett. 11, 1351–1363 (2008).
Kourtev, P. S., Ehrenfeld, J. G. & Häggblom, M. Exotic plant species alter the microbial community structure and function in the soil. Ecology 83, 3152–3166 (2002).
McLeod, M. L. et al. Exotic invasive plants increase productivity, abundance of ammonia-oxidizing bacteria and nitrogen availability in intermountain grasslands. J. Ecol. 104, 994–1002 (2016).
Coats, V. C. & Rumpho, M. E. The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants. Front. Microbiol. 5, 368 (2014).
Klironomos, J. N. Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417, 67–70 (2002).
Kardol, P. & Wardle, D. A. How understanding aboveground–belowground linkages can assist restoration ecology. Trends Ecol. Evol. 25, 670–679 (2010).
Van Nuland, M. E., Bailey, J. K. & Schweitzer, J. A. Divergent plant–soil feedbacks could alter future elevation ranges and ecosystem dynamics. Nat. Ecol. Evol. 1, 0150 (2017).
van Grunsven, R. H. A. et al. Reduced plant–soil feedback of plant species expanding their range as compared to natives. J. Ecol. 95, 1050–1057 (2007).
Dostálek, T., Münzbergová, Z., Kladivová, A. & Macel, M. Plant–soil feedback in native vs. invasive populations of a range expanding plant. Plant Soil 399, 209–220 (2015).
Berg, G. & Smalla, K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol. Ecol. 68, 1–13 (2009).
De Frenne, P. et al. Plant movements and climate warming: intraspecific variation in growth responses to nonlocal soils. New Phytol. 202, 431–441 (2014).
Van Grunsven, R. H. A., van der Putten, W. H., Bezemer, T., Berendse, F. & Veenendaal, E. M. Plant–soil interactions in the expansion and native range of a poleward shifting plant species. Glob. Change Biol. 16, 380–385 (2010).
Collins, C. G., Carey, C. J., Aronson, E. L., Kopp, C. W. & Diez, J. M. Direct and indirect effects of native range expansion on soil microbial community structure and function. J. Ecol. 104, 1271–1283 (2016).
Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).
Kuramae, E., Gamper, H., van Veen, J. & Kowalchuk, G. Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH. FEMS Microbiol. Ecol. 77, 285–294 (2011).
Tecon, R. & Or, D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol. Rev. 41, 599–623 (2017).
Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111–5120 (2009).
Delgado-Baquerizo, M. et al. A global atlas of the dominant bacteria found in soil. Science 359, 320–325 (2018).
Talbot, J. M. et al. Endemism and functional convergence across the North American soil mycobiome. Proc. Natl Acad. Sci. USA 111, 6341–6346 (2014).
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
Barberán, A. et al. Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria. Ecol. Lett. 17, 794–802 (2014).
Lekberg, Y., Rosendahl, S. & Olsson, P. A. The fungal perspective of arbuscular mycorrhizal colonization in ‘nonmycorrhizal’ plants. New Phytol. 205, 1399–1403 (2015).
Lau, J. A. & Lennon, J. T. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc. Natl Acad. Sci. USA 109, 14058–14062 (2012).
de Vries, F. T. et al. Land use alters the resistance and resilience of soil food webs to drought. Nat. Clim. Change 2, 276–280 2012).
Peay, K. G. Back to the future: natural history and the way forward in modern fungal ecology. Fungal Ecol. 12, 4–9 (2014).
Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl Acad. Sci. USA 112, E911–E920 (2015).
Pieterse, C. M. J., de Jonge, R. & Berendsen, R. L. The soil-borne supremacy. Trends Plant Sci. 21, 171–173 (2016).
Prober, S. M. et al. Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. Ecol. Lett. 18, 85–95 (2015).
Gilbert, G. S. & Webb, C. O. Phylogenetic signal in plant pathogen–host range. Proc. Natl Acad. Sci. USA 104, 4979–4983 (2007).
Parker, I. M. et al. Phylogenetic structure and host abundance drive disease pressure in communities. Nature 520, 542–544 (2015).
Lankau, R. A. Coevolution between invasive and native plants driven by chemical competition and soil biota. Proc. Natl Acad. Sci. USA 109, 11240–11245 (2012).
Morriën, E. et al. Soil networks become more connected and take up more carbon as nature restoration progresses. Nat. Commun. 8, 14349 (2017).
Keymer, D. P. & Lankau, R. A. Disruption of plant–soil–microbial relationships influences plant growth. J. Ecol. 105, 816–827 (2017).
Leach, J. E., Triplett, L. R., Argueso, C. T. & Trivedi, P. Communication in the phytobiome. Cell 169, 587–596 (2017).
Bakkenes, M., Alkemade, J. R. M., Ihle, F., Leemans, R. & Latour, J. B. Assessing effects of forecasted climate change on the diversity and distribution of European higher plants for 2050. Glob. Change Biol. 8, 390–407 (2002).
Wilschut, R. A., Kostenko, O., Koorem, K. & van der Putten, W. H. Nematode community responses to range-expanding and native plant communities in original and new range soils. Ecol. Evol. 8, 10288–10297 (2018).
Koorem, K. et al. Relatedness with plant species in native community influences ecological consequences of range expansions. Oikos 127, 981–990 (2018).
van der Heijden, M. G. A. & Hartmann, M. Networking in the plant microbiome. PLoS Biol. 14, e1002378 (2016).
Leff, J. W. et al. Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits. ISME J. 12, 1794–1805 (2018).
Fierer, N. et al. Reconstructing the Microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342, 621–624 (2013).
Emmett, B. D., Youngblut, N. D., Buckley, D. H. & Drinkwater, L. E. Plant phylogeny and life history shape rhizosphere bacterial microbiome of summer annuals in an agricultural field. Front. Microbiol. 8, 2414 (2017).
Goberna, M., Navarro-Cano, J. A. & Verdú, M. Opposing phylogenetic diversity gradients of plant and soil bacterial communities. Proc. R. Soc. B 283, 20153003 (2016).
Reynolds, H. L., Packer, A., Bever, J. D. & Clay, K. Grassroots ecology: plant–microbe–soil interactions as drivers of plant community structure and dynamics. Ecology 84, 2281–2291 (2003).
Bennett, J. A. et al. Plant–soil feedbacks and mycorrhizal type influence temperate forest population dynamics. Science 355, 181–184 (2017).
Golivets, M. & Wallin, K. F. Neighbour tolerance, not suppression, provides competitive advantage to non-native plants. Ecol. Lett. 21, 745–759 (2018).
Geml, J. & Wagner, M. R. Out of sight, but no longer out of mind — towards an increased recognition of the role of soil microbes in plant speciation. New Phytol. 217, 965–967 (2018).
Dawson, W. Release from belowground enemies and shifts in root traits as interrelated drivers of alien plant invasion success: a hypothesis. Ecol. Evol. 5, 4505–4516 (2015).
Blumenthal, D., Mitchell, C. E., Pysek, P. & Jarosík, V. Synergy between pathogen release and resource availability in plant invasion. Proc. Natl Acad. Sci. USA 106, 7899–7904 (2009).
Wilschut, R. A., Silva, J. C. P., Garbeva, P. & van der Putten, W. H. Belowground plant–herbivore interactions vary among climate-driven range-expanding plant species with different degrees of novel chemistry. Front. Plant Sci. 8, 1861 (2017).
Inderjit & van der Putten, W. H. Impacts of soil microbial communities on exotic plant invasions. Trends Ecol. Evol. 25, 512–519 (2010).
Rout, M. E. & Callaway, R. M. Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that ‘everything is not everywhere’. Ann. Bot 110, 213–222 (2012).
Nguyen, N. H. et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).
van der Putten, W. H. Climate change, aboveground–belowground interactions, and species’ range shifts. Annu. Rev. Ecol. Evol. Syst. 43, 365–383 (2012).
Mitchell, C. E. & Power, A. G. Release of invasive plants from fungal and viral pathogens. Nature 421, 625–627 (2003).
Bever, J. D., Mangan, S. A. & Alexander, H. M. Maintenance of plant species diversity by pathogens. Annu. Rev. Ecol. Evol. Syst. 46, 305–325 (2015).
Morriën, E. et al. Soil networks become more connected and take up more carbon as nature restoration progresses. Nat. Commun. 8, 14349 (2017).
Hannula, S. E. et al. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J. 11, 2294–2304 (2017).
Jousset, A. et al. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J. 11, 853–862 (2017).
van Kleunen, M., Dawson, W. & Maurel, N. Characteristics of successful alien plants. Mol. Ecol. 24, 1954–1968 (2015).
Chen, I.-C., Hill, J. K., Ohlemuller, R., Roy, D. B. & Thomas, C. D. Rapid range shifts of species associated with high levels of climate warming. Science 333, 1024–1026 (2011).
Bever, J., Platt, T. & Morton, E. Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu. Rev. Microbiol. 66, 265–283 (2012).
Wubs, E. R. J., van der Putten, W. H., Bosch, M. & Bezemer, T. M. Soil inoculation steers restoration of terrestrial ecosystems. Nat. Plants 2, 16107 (2016).
Alexander, J. M., Diez, J. M. & Levine, J. M. Novel competitors shape species’ responses to climate change. Nature 525, 515–518 (2015).
Fordham, D. A. et al. Plant extinction risk under climate change: are forecast range shifts alone a good indicator of species vulnerability to global warming? Glob. Change Biol. 18, 1357–1371 (2012).
Tamis, W. L. M., van’t Zelfde, M., van der Meijden, R. & de Haes, H. A. U. Changes in vascular plant biodiversity in the Netherlands in the 20th century explained by their climatic and other environmental characteristics. Climatic Change 72, 37–56 (2005).
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).
Ihrmark, K. et al. New primers to amplify the fungal ITS2 region—evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol. Ecol. 82, 666–677 (2012).
Lundberg, D. S., Yourstone, S., Mieczkowski, P., Jones, C. D. & Dangl, J. L. Practical innovations for high-throughput amplicon sequencing. Nat. Methods 10, 999–1002 (2013).
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G. & Neufeld, J. D. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics 13, 31 (2012).
Dodt, M., Roehr, J., Ahmed, R. & Dieterich, C. FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms. Biology (Basel) 1, 895–905 (2012).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).
Cole, J. R. et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633–D642 (2014).
Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol. Evol. 4, 914–919 (2013).
Kõljalg, U. et al. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22, 5271–5277 (2013).
Koster, J. & Rahmann, S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics 28, 2520–2522 (2012).
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.0-10 https://cran.r-project.org/web/packages/vegan/index.html (2013).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).
We are grateful for the support of Ž. Modrić-Surina, S. Dragićević, I. Starke and M. Hohla, who all helped with sampling. This work was supported in large part by the European Research Council (ERC advanced grant ERC-Adv 323020 (SPECIALS) to W.H.v.d.P. Additional support came from the Estonian Research Council (grant PUTJD78) (K.K.) and the Slovenian Research Agency (research core funding no. P1-0236) (B.V. and T.Č.).