Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions

Soil microbiota are important components of healthy ecosystems. Greater consideration of soil microbiota in the restoration of biodiverse, functional, and resilient ecosystems is required to address the twin global crises of biodiversity decline and climate change. In this review, we discuss available and emerging practical applications of soil microbiota into (i) restoration planning, (ii) direct interventions for shaping soil biodiversity, and (iii) strategies for monitoring and predicting restoration trajectories. We show how better planning of restoration activities to account for soil microbiota can help improve progress towards restoration targets. We show how planning to embed soil microbiota experiments into restoration projects will permit a more rigorous assessment of the effectiveness of different restoration methods, especially when complemented by statistical modelling approaches that capitalise on existing data sets to improve causal understandings and prioritise research strategies where appropriate. In addition to recovering belowground microbiota, restoration strategies that include soil microbiota can improve the resilience of whole ecosystems. Fundamentally, restoration planning should identify appropriate reference target ecosystem attributes and - from the perspective of soil microbiota - comprehensibly consider potential physical, chemical and biological influences on recovery. We identify that inoculating ecologically appropriate soil microbiota into degraded environments can support a range of restoration interventions (e.g. targeted, broad-spectrum and cultured inoculations) with promising results. Such inoculations however are currently underutilised and knowledge gaps persist surrounding successful establishment in light of community dynamics, including priority effects and community coalescence. We show how the ecological trajectories of restoration sites can be assessed by characterising microbial diversity, composition, and functions in the soil. Ultimately, we highlight practical ways to apply the soil microbiota toolbox across the planning, intervention, and monitoring stages of ecosystem restoration and address persistent open questions at each stage. With continued collaborations between researchers and practitioners to address knowledge gaps, these approaches can improve current restoration practices and ecological outcomes.

Quantifying soil microbial effects on plant species coexistence: A conceptual synthesis

Soil microorganisms play a critical role in shaping the biodiversity dynamics of plant communities. These microbial effects can arise through direct mediation of plant fitness by pathogens and mutualists, and over the past two decades, numerous studies have shined a spotlight on the role of dynamic feedbacks between plants and soil microorganisms as key determinants of plant species coexistence. Such feedbacks occur when plants modify the composition of the soil community, which in turn affects plant performance. Stimulated by a theoretical model developed in the 1990s, a bulk of the empirical evidence for microbial controls over plant coexistence comes from experiments that quantify plant growth in soil communities that were previously conditioned by conspecific or heterospecific plants. These studies have revealed that soil microbes can generate strong negative to positive frequency-dependent dynamics among plants. Even as soil microbes have become recognized as a key player in determining plant coexistence outcomes, the past few years have seen a renewed interest in expanding the conceptual foundations of this field. New results include re-interpretations of key metrics from classic two-species models, extensions of plant-soil feedback theory to multispecies communities, and frameworks to integrate plant-soil feedbacks with processes like intra- and interspecific competition. Here, I review the implications of theoretical developments for interpreting existing empirical results and highlight proposed analyses and designs for future experiments that can enable a more complete understanding of microbial regulation of plant community dynamics.

Synergistic effects of arbuscular mycorrhizal fungi and biochar are highly beneficial to Ligustrum lucidum seedlings in Cd-contaminated soil

Cadmium (Cd) contamination is a widespread environmental issue. There is a lack of knowledge about the impacts of applying arbuscular mycorrhizal fungi (AMF) and biochar, either alone or in their combination, on alleviating Cd phytotoxicity in Ligustrum lucidum. Therefore, a pot experiment was conducted in a greenhouse, where L. lucidum seedlings were randomly subjected to four regimes of AMF treatments (inoculation with sterilized AMF, with Rhizophagus irregularis, Diversispora versiformis, alone or a mixture of these two fungi), and two regimes of biochar treatments (with or without rice-husk biochar), as well as three regimes of Cd treatments (0, 15, and 150 mg kg-1), to examine the responses of growth, photosynthetic capabilities, soil enzymatic activities, nutritional concentrations, and Cd absorption of L. lucidum plants to the interactive effects of AMF, biochar, and Cd. The results demonstrated that under Cd contaminations, AMF alone significantly increased plant total dry weight, soil pH, and plant nitrogen (N) concentration by 84%, 3.2%, and 13.2%, respectively, and inhibited soil Cd transferring to plant shoot by 42.2%; biochar alone significantly enhanced net photosynthetic rate, soil pH, and soil catalase of non-mycorrhizal plants by 16.4%, 9%, and 11.9%, respectively, and reduced the soil Cd transferring to plant shoot by 44.7%; the additive effect between AMF and biochar greatly enhanced plant total dry weight by 101.9%, and reduced the soil Cd transferring to plant shoot by 51.6%. Furthermore, dual inoculation with D. versiformis and R. irregularis conferred more benefits on plants than the single fungal species did. Accordingly, amending Cd-contaminated soil with the combination of mixed-fungi inoculation and biochar application performed the best than either AMF or biochar alone. These responses may have been attributed to higher mycorrhizal colonization, soil pH, biomass accumulation, and biomass allocation to the roots, as well as photosynthetic capabilities. In conclusion, the combined use of mixed-fungi involving D. versiformis and R. irregularis and biochar addition had significant synergistic effects on enhancing plant performance and reducing Cd uptake of L. lucidum plants in Cd-contaminated soil.

No evidence that modification of soil microbiota by woody invader facilitates subsequent invasion by herbaceous species

Many terrestrial ecosystems are co-invaded by multiple exotic species. The "invasional meltdown" hypothesis predicts that an initial invasive species will facilitate secondary invasions. In the plant kingdom, the potential underlying mechanisms of this hypothesis may be that modification of the soil properties by the initial invaders benefits for the subsequent exotic species invasion. In this study, we analyzed the composition of soil microbial communities and soil chemical properties from sites invaded by woody Rhus typhina, as well as uninvaded sites, to assess the impact of R. typhina invasion. Furthermore, we conducted a greenhouse experiment with multiple native-invasive pairs of herbaceous species to test whether R. typhina invasion facilitates subsequent exotic herb invasion. Our results showed that R. typhina invasion significantly altered the composition of soil fungal communities, especially pathogenic, endophytic, and arbuscular mycorrhizal fungi. However, this change in microbial composition led to neither direction nor magnitude changes in negative plant-soil feedback effects on both native and invasive species. This indicates that initial R. typhina invasion does not facilitate subsequent herb invasion, which does not support the "invasional meltdown" hypothesis. Additionally, R. typhina invasion significantly decreased soil total nitrogen and organic carbon contents, which may explain the significantly lower biomass of herbaceous roots grown in invaded soils compared with uninvaded soils. Alternately, although invasive herb growth was significantly more inhibited by soil microbiota compared with native herb growth, such inhibition cannot completely eliminate the risk of exotic herb invasion because of their innate growth advantages. Therefore, microbial biocontrol agents for plant invasion management should be combined with another approach to suppress the innate growth advantages of exotic species.

Introducing desirable patches to initiate ecosystem transitions and accelerate ecosystem restoration

Meeting restoration targets may require active strategies to accelerate natural regeneration rates or overcome the resilience associated with degraded ecosystem states. Introducing desired ecosystem patches in degraded landscapes constitutes a promising active restoration strategy, with various mechanisms potentially causing these patches to become foci from which desired species can re-establish throughout the landscape. This study considers three mechanisms previously identified as potential drivers of introduced patch dynamics: autocatalytic nucleation, directed dispersal, and resource concentration. These mechanisms reflect qualitatively different positive feedbacks. We developed an ecological model framework that compared how the occurrence of each mechanism was reflected in spatio-temporal patch dynamics. We then analyzed the implications of these relationships for optimal restoration design. We found that patch expansion accelerated over time when driven by the autocatalytic nucleation mechanism, while patch expansion driven by the directed dispersal or resource concentration mechanisms decelerated over time. Additionally, when driven by autocatalytic nucleation, patch expansion was independent of patch position in the landscape. However, the proximity of other patches affected patch expansion either positively or negatively when driven by directed dispersal or resource concentration. For autocatalytic nucleation, introducing many small patches was a favorable strategy, provided that each individual patch exceeded a critical patch size. Introducing a single patch or a few large patches was the most effective restoration strategy to initiate the directed dispersal mechanism. Introducing many small patches was the most effective strategy for reaching restored ecosystem states driven by a resource concentration mechanism. Our model results suggest that introducing desirable patches can substantially accelerate ecosystem restoration, or even induce a critical transition from an otherwise stable degraded state toward a desired ecosystem state. However, the potential of this type of restoration strategy for a particular ecosystem may strongly depend on the mechanism driving patch dynamics. In turn, which mechanism drives patch dynamics may affect the optimal spatial design of an active restoration strategy. Each of the three mechanisms considered reflects distinct spatio-temporal patch dynamics, providing novel opportunities for empirically identifying key mechanisms, and restoration designs that introduce desired patches in degraded landscapes according to these patch dynamics.

Rapid differentiation of soil and root microbiomes in response to plant composition and biodiversity in the field

Research suggests that microbiomes play a major role in structuring plant communities and influencing ecosystem processes, however, the relative roles and strength of change of microbial components have not been identified. We measured the response of fungal, arbuscular mycorrhizal fungal (AMF), bacteria, and oomycete composition 4 months after planting of field plots that varied in plant composition and diversity. Plots were planted using 18 prairie plant species from three plant families (Poaceae, Fabaceae, and Asteraceae) in monoculture, 2, 3, or 6 species richness mixtures and either species within multiple families or one family. Soil cores were collected and homogenized per plot and DNA were extracted from soil and roots of each plot. We found that all microbial groups responded to the planting design, indicating rapid microbiome response to plant composition. Fungal pathogen communities were strongly affected by plant diversity. We identified OTUs from genera of putatively pathogenic fungi that increased with plant family, indicating likely pathogen specificity. Bacteria were strongly differentiated by plant family in roots but not soil. Fungal pathogen diversity increased with planted species richness, while oomycete diversity, as well as bacterial diversity in roots, decreased. AMF differentiation in roots was detected with individual plant species, but not plant family or richness. Fungal saprotroph composition differentiated between plant family composition in plots, providing evidence for decomposer home-field advantage. The observed patterns are consistent with rapid microbiome differentiation with plant composition, which could generate rapid feedbacks on plant growth in the field, thereby potentially influencing plant community structure, and influence ecosystem processes. These findings highlight the importance of native microbial inoculation in restoration.

The temporal and spatial dimensions of plant-soil feedbacks

Feedbacks between plants and soil microbes form a keystone to terrestrial community and ecosystem dynamics. Recent advances in dissecting the spatial and temporal dynamics of plant-soil feedbacks (PSFs) have challenged longstanding assumptions of spatially well-mixed microbial communities and exceedingly fast microbial assembly dynamics relative to plant lifespans. Instead, PSFs emerge from interactions that are inherently mismatched in spatial and temporal scales, and explicitly considering these spatial and temporal dynamics is crucial to understanding the contribution of PSFs to foundational ecological patterns. I propose a synthetic spatiotemporal framework for future research that pairs experimental and modeling approaches grounded in mechanism to improve predictability and generalizability of PSFs.

Functional shifts in soil fungal communities regulate differential tree species establishment during subalpine forest succession

Soil fungi can differentially affect plant performance and community dynamics. While fungi play key roles in driving the plant-soil feedbacks (PSFs) that promote grassland succession, it remains unclear how the fungi-mediated PSFs affect tree species establishment during forest succession. We inoculated pioneer broadleaf (Betula platyphylla and Betula albosinensis) and nonpioneer coniferous tree seedlings (Picea asperata and Abies faxoniana) with fungal-dominated rooting zone soils collected from dominant plant species of early-, mid- and late-successional stages in a subalpine forest, and compared their biomass and fungal communities. All tree species accumulated abundant pathogenic fungi in early-successional inoculated soil, which generated negative biotic feedbacks and lowered seedling biomass. High levels of soil ectomycorrhizal fungi from mid- and late-successional stages resulted in positive biotic PSFs and strongly facilitated slow-growing coniferous seedling performance to favour successional development. B. albosinensis also grew better in mid- and late-successional soils with fewer pathogenic fungi than in early-successional soil, indicating its large susceptibility to pathogen attack. In contrast, the growth of another pioneer tree, B. platyphylla, was significantly suppressed in late-successional soil and was mostly driven by saprotrophic fungi, despite the unchanged pathogenic fungal community traits between the two fast-growing species. This unexpected result suggested a host specificity-dependent mechanism involved in the different impacts of fungal pathogens on host trees. Our findings reveal a critical role of functional shifts in soil fungal communities in mediating differential PSFs of tree species across successional stages, which should be considered to improve the prediction and management of community development following forest disturbances.

Variations of arbuscular mycorrhizal fungi following succession stages in a tropical lowland rainforest ecosystem of South China

Introduction

The grasslands in the Nature Reserve of Ganshenling, in the south of Hainan Island, were first formed after deforestation disturbance before a natural restoration of shrubs and secondary forests. However, the stages of grassland and shrubs in some parts of Ganshenling regions could not be naturally restored to secondary forests. In addition, the forest form of the secondary forest after 40 years (40a) of succession was similar to that of the secondary forest of 60 years (60a). However, it was not known whether the microorganisms recovered to the level of the secondary forest of 60a. Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that can improve the nitrogen and phosphorus absorption of plants and play a key role in secondary forest succession. An understanding of the essential role of soil AMF in secondary forest succession of tropical rainforest in Ganshenling regions is still limited.

Methods

Therefore, the soil of 0–10 cm was collected with the help of a 5-point sampling method in grassland, shrubs, and second tropical lowland rainforest of 40a and 60a. We studied community changes in AMF with the succession and explored the impacts of soil physicochemical properties on soil AMF.

Results

Our findings were as follows: (1) Different successional stages showed divergent effects on soil AMF communities. (2) After 40a recovery, the alpha-diversity indices of AMF recovered to the level of secondary forest of 60a, but the similarity of soil AMF communities only recovered to 25.3%. (3) Species richness of common species, rare species, and all the species of AMF showed a significantly positive correlation with soil nitrogen. (4) OTU10; OTU6, OTU9, and OTU141; OTU3 and OTU38; and OTU2, OTU15, OTU23, and OTU197 were significantly unique AMF for grasslands, shrubs, and secondary forests of 40a and 60a, respectively. (5) The phylogenetic tree and the heatmap of AMF showed that the OTUs in grasslands and shrubs were in contrast to the OTUs in secondary forests of 40a and 60a.

Discussion

We concluded that the succession of a secondary forest after deforestation disturbance was probably limited by its AMF community.

Arbuscular Mycorrhizal Fungi Taxa Show Variable Patterns of Micro-Scale Dispersal in Prairie Restorations

Human land use disturbance is a major contributor to the loss of natural plant communities, and this is particularly true in areas used for agriculture, such as the Midwestern tallgrass prairies of the United States. Previous work has shown that arbuscular mycorrhizal fungi (AMF) additions can increase native plant survival and success in plant community restorations, but the dispersal of AMF in these systems is poorly understood. In this study, we examined the dispersal of AMF taxa inoculated into four tallgrass prairie restorations. At each site, we inoculated native plant species with greenhouse-cultured native AMF taxa or whole soil collected from a nearby unplowed prairie. We monitored AMF dispersal, AMF biomass, plant growth, and plant community composition, at different distances from inoculation. In two sites, we assessed the role of plant hosts in dispersal, by placing known AMF hosts in a “bridge” and “island” pattern on either side of the inoculation points. We found that AMF taxa differ in their dispersal ability, with some taxa spreading to 2-m in the first year and others remaining closer to the inoculation point. We also found evidence that AMF spread altered non-inoculated neighboring plant growth and community composition in certain sites. These results represent the most comprehensive attempt to date to evaluate AMF spread.

A quantitative synthesis of soil microbial effects on plant species coexistence

SignificanceUnderstanding the processes that maintain plant diversity is a key goal in ecology. Many previous studies have shown that soil microbes can generate stabilizing or destabilizing feedback loops that drive either plant species coexistence or monodominance. However, theory shows that microbial controls over plant coexistence also arise through microbially mediated competitive imbalances, which have been largely neglected. Using data from 50 studies, we found that soil microbes affect plant dynamics primarily by generating competitive fitness differences rather than stabilizing or destabilizing feedbacks. Consequently, in the absence of other competitive asymmetries among plants, soil microbes are predicted to drive species exclusion more than coexistence. These results underscore the need for measuring competitive fitness differences when evaluating microbial controls over plant coexistence.

Changes in precipitation patterns can destabilize plant species coexistence via changes in plant-soil feedback

Climate change can alter species coexistence through changes in biotic interactions. By describing reciprocal interactions between plants and soil microbes, plant-soil feedback (PSF) has emerged as a powerful framework for predicting plant species coexistence and community dynamics, but little is known about how PSF will respond to changing climate conditions. Hence, the context dependency of PSF has recently gained attention. Water availability is a major driver of all biotic interactions, and it is expected that precipitation patterns will change with ongoing climate change. We tested how soil water content affects PSF by conducting a full factorial pairwise PSF experiment using eight plant species common to southeastern United States coastal prairies under three watering treatments. We found coexistence-stabilizing negative PSF at drier-than-average conditions shifted to coexistence-destabilizing positive PSF under wetter-than-average conditions. A simulation model parameterized with the experimental results supports the prediction that more positive PSF accelerates the erosion of diversity within communities while decreasing the predictability in plant community composition. Our results underline the importance of considering environmental context dependency of PSF in light of a rapidly changing climate.

Pine savanna restoration on agricultural landscapes: The path back to native savanna ecosystem services

Restoration of savanna ecosystems within their historic range is expected to increase provision of ecosystem services to resident human populations. However, the benefits of restoration depend on the degree to which ecosystems and their services can be restored, the rate of restoration of particular services, and tradeoffs in services between restored ecosystems and other common land uses. We use a chronosequence approach to infer multi-decadal changes in ecosystem services under management aimed at restoring fire-dependent pine savannas, including the use of frequent prescribed fire, following abandonment of row-crop agriculture in the southeastern U.S. We compare ecosystem services between restored pine savannas of different ages and reference pine savannas as well as other common land uses (row-crop agriculture, improved pasture, pine plantation, unmanaged forest). Our results suggest that restoring pine savannas results in many improvements to ecosystem services, including increases in plant species richness, perennial grass cover, tree biomass, total ecosystem carbon, soil carbon and C:N, reductions in soil bulk density and predicted erosion and sedimentation, shifts from soil fungal pathogens to fungal symbionts, and changes in soil chemistry toward reference pine savanna conditions. However, the rate of improvement varies widely among services from a few years to decades. Compared to row-crop agriculture and improved pasture, restored savannas have lower erosion, soil bulk density, and soil pathogens and a higher percentage of mycorrhizal fungi and ecosystem carbon storage. Compared to pine plantations and unmanaged forests, restored pine savannas have lower fire-prone fuel loads and higher water yield and bee pollinator abundance. Our results indicate that restoration of pine savanna using frequent fire provides a broad suite of ecosystem services that increase the landscape's overall resilience to climate change. These results are likely relevant to other savannas dominated by perennial vegetation and maintained with frequent fire.

Microbial mediators of plant community response to long-term N and P fertilization: Evidence of a role of plant responsiveness to mycorrhizal fungi

Climate changes and anthropogenic nutrient enrichment widely threaten plant diversity and ecosystem functions. Understanding the mechanisms governing plant species turnover across nutrient gradients is crucial to developing successful management and restoration strategies. We tested whether and how soil microbes, particularly arbuscular mycorrhizal fungi (AMF), could mediate plant community response to a 15 years long-term N (0, 4, 8, and 16 g N m^-2  year^-1 ) and P (0 and 8 g N m^-2  year^-1 ) enrichment in a grassland system. We found N and P enrichment resulted in plant community diversity decrease and composition change, in which perennial C₄  graminoids were dramatically reduced while annuals and perennial forbs increased. Metabarcoding analysis of soil fungal community showed that N and P changed fungal diversity and composition, of which only a cluster of AMF identified by the co-occurrence networks analysis was highly sensitive to P treatments and was negatively correlated with shifts in percentage cover of perennial C₄  graminoids. Moreover, by estimating the mycorrhizal responsiveness (MR) of 41 plant species in the field experiment from 264 independent tests, we found that the community weighted mean MR of the plant community was substantially reduced with nutrient enrichment and was positively correlated with C₄  graminoids percentage cover. Both analyses of covariance and structural equation modeling indicated that the shift in MR rather than AMF composition change was the primary predictor of the decline in perennial C₄  graminoids, suggesting that the energy cost invested by C₄ plants on those sensitive AMF might drive the inferior competitive abilities compared with other groups. Our results suggest that shifts in the competitive ability of mycorrhizal responsive plants can drive plant community change to anthropogenic eutrophication, suggesting a functional benefit of mycorrhizal mutualism in ecological restoration following climatic or anthropogenic degradation of soil communities.

Conspecific leaf litter induces negative feedbacks in Asteraceae seedlings

The plant soil feedback (PSF) framework has been instrumental in understanding the impacts of soil microbes on plant fitness and species coexistence. PSFs develop when soil microbial communities are altered due to the identity and density of a particular plant species, which can then enhance or inhibit the local survival and growth of that plant species as well as different plant species. The recent extension of the PSF framework to aboveground microbiota, termed here as plant phyllosphere feedbacks (PPFs), can also help to determine the impact of aboveground microbes on plant fitness and species interactions. However, experimental tests of PPFs during early plant growth are nascent and the prevalence of PPFs across diverse plant species remains unknown. Additionally, it is unclear whether plant host characteristics, such as functional traits or phylogenetic distance, may help to predict the strength and direction of PPFs. To test for the prevalence of litter-mediated PPFs, recently senesced plant litter from 10 native Asteraceae species spanning a range of life history strategies was used to inoculate seedlings of both conspecific and heterospecific species. We found that exposure to conspecific litter significantly reduced the growth of four species relative to exposure to heterospecific litter (i.e., significant negative PPFs), three species experienced marginally significant negative PPFs, and the PPF estimates for all 10 species were negative. However, neither plant functional traits, nor phylogenetic distance were predictive of litter feedbacks across plant species pairs, suggesting that other mechanisms or traits not measured may be driving conspecific negative PPFs. Our results indicate that negative, litter-mediated PPFs are common among native Asteraceae species and that they may have substantial impacts on plant growth and plant species interactions, particularly during early plant growth.

Dynamic plant-soil microbe interactions: the neglected effect of soil conditioning time

Plant-soil feedback (PSF) may change in strength over the life of plant individuals as plants continue to modify the soil microbial community. However, the temporal variation in PSF is rarely quantified and its impacts on plant communities remain unknown. Using a chronosequence reconstructed from annual aerial photographs of a coastal dune ecosystem, we characterized > 20-yr changes in soil microbial communities associated with individuals of the four dominant perennial species, one legume and three nonlegume. We also quantified the effects of soil biota on conspecific and heterospecific seedling performance in a glasshouse experiment that preserved soil properties of these individual plants. Additionally, we used a general individual-based model to explore the potential consequences of temporally varying PSF on plant community assembly. In all plant species, microbial communities changed with plant age. However, responses of plants to the turnover in microbial composition depended on the identity of the seedling species: only the soil biota effect experienced by the nonlegume species became increasingly negative with longer soil conditioning. Model simulation suggested that temporal changes in PSF could affect the transient dynamics of plant community assembly. These results suggest that temporal variation in PSF over the life of individual plants should be considered to understand how PSF structures plant communities.

Short-lived legacies of Prunus serotina plant-soil feedbacks

Plant-soil feedbacks (PSFs) are often involved in fundamental ecological processes such as plant succession and species coexistence. After a plant initiating PSFs dies, legacies of PSFs occurring as soil signatures that influence subsequent plants could persist for an unknown duration. Altered resource environments following plant death (especially light availability) could affect whether legacy effects manifest and persist. To evaluate PSFs and their legacies, we obtained soils from a chronosequence of Prunus serotina harvests. In a greenhouse experiment, we planted conspecific seedlings under two light levels in these soils of varying time since the influence of live Prunus serotina, and compared seed/seedling survival in soils from live trees, stumps, and surrounding forest matrix within each site and across the chronosequence. PSF legacies were measured as the difference between seedling performance in live tree and stump soils within a site. Negative PSF legacies of P. serotina were short-lived, lasting up to 0.5 years after tree removal. These effects occurred under 5% but not 30% full sun. PSFs and their legacies manifested in seed/seedling survival, but not biomass. Though restricted to low light, short-lived legacies of P. serotina PSFs could have lasting impacts on plant community dynamics during post-disturbance regeneration by disfavoring P. serotina regeneration in small tree-fall gaps.

Globally, plant-soil feedbacks are weak predictors of plant abundance

Plant-soil feedbacks (PSFs) have been shown to strongly affect plant performance under controlled conditions, and PSFs are thought to have far reaching consequences for plant population dynamics and the structuring of plant communities. However, thus far the relationship between PSF and plant species abundance in the field is not consistent. Here, we synthesize PSF experiments from tropical forests to semiarid grasslands, and test for a positive relationship between plant abundance in the field and PSFs estimated from controlled bioassays. We meta-analyzed results from 22 PSF experiments and found an overall positive correlation (0.12 ≤  r ¯  ≤ 0.32) between plant abundance in the field and PSFs across plant functional types (herbaceous and woody plants) but also variation by plant functional type. Thus, our analysis provides quantitative support that plant abundance has a general albeit weak positive relationship with PSFs across ecosystems. Overall, our results suggest that harmful soil biota tend to accumulate around and disproportionately impact species that are rare. However, data for the herbaceous species, which are most common in the literature, had no significant abundance-PSFs relationship. Therefore, we conclude that further work is needed within and across biomes, succession stages and plant types, both under controlled and field conditions, while separating PSF effects from other drivers (e.g., herbivory, competition, disturbance) of plant abundance to tease apart the role of soil biota in causing patterns of plant rarity versus commonness.

Plants mitigate restrictions to phosphatase activity in metal contaminated soils

Soil anthropogenic contaminants can limit enzymatic nutrient mineralization, either by direct regulation or via impacts on the microbial community, thus affecting plant growth in agricultural and non-agricultural soils. The impact on phosphatase activity of mixing two contaminated, post-industrial rail yard soils was investigated; one was vegetated and had high phosphatase function, the other was barren and had low enzymatic function. The two soils had different abiotic properties, including contaminant load, vegetation cover, soil aggregate size distribution, and phosphatase potential. An experimental gradient was established between the two soils to systematically vary the abiotic properties and microbial community composition of the two soils, creating a gradient of novel ecosystems. The time dependence of extracellular phosphatase activity, soil moisture, and organic matter content was assessed along this gradient in the presence and absence of plants. Initially, mixtures with higher percentages of functional, vegetated soil had higher phosphatase activities. Phosphatase activity remained unchanged through time (65 days) in all soil mixtures in unplanted pots, but it increased in planted pots. For example, in the presence of plants, phosphatase activity increased from 0.6 ± 0.1 to 2.4 ± 0.3 μmol•h^-1•g_{dry soil}^-1 from day one to day 65 in the 1:1 functional:barren soil mixture. The presence of plants also promoted moisture retention. Inoculation of poorly functioning soil with 10% of the functional soil with its microbial community did not, over 65 days, revitalize the poorly functioning soil. The findings showed that abiotic limitations to enzymatic activity in barren brownfield soils could be mitigated by establishing primary production but not by the addition of enzymatically active microbial communities alone.

Soil biota increase the likelihood for coexistence among competing plant species

Theory predicts that stable species coexistence will occur when population growth rates of competitively dominant species are suppressed when at high conspecific density. Although there is now compelling evidence that plant communities exhibit negative density dependence, the relative importance of the underlying processes leading to these patterns is rarely tested. We coupled reciprocal greenhouse and field experiments with community dynamics modeling to untangle the relative importance of soil biota from competition as stabilizing forces to coexistence. We found that (1) plant-soil biotic interactions compared to competitive interactions were stronger stabilizing forces, (2) only the strength of plant-soil biotic interactions was dependent on plant evolutionary history, and (3) the variation in the strength of plant-soil biotic interactions was correlated with relative abundance patterns in an opposite way than was the variation in the strength of competitive interactions. Collectively, our results demonstrate the fundamental role soil biota have in maintaining plant community diversity.

Resistance Genes Affect How Pathogens Maintain Plant Abundance and Diversity

AbstractSpecialized pathogens are thought to maintain plant community diversity; however, most ecological studies treat pathogens as a black box. Here we develop a theoretical model to test how the impact of specialized pathogens changes when plant resistance genes (R-genes) mediate susceptibility. This work synthesizes two major hypotheses: the gene-for-gene model of pathogen resistance and the Janzen-Connell hypothesis of pathogen-mediated coexistence. We examine three scenarios. First, R-genes do not affect seedling survival; in this case, pathogens promote diversity. Second, seedlings are protected from pathogens when their R-gene alleles and susceptibility differ from those of nearby conspecific adults, thereby reducing transmission. If resistance is not costly, pathogens are less able to promote diversity because populations with low R-gene diversity suffer higher mortality, putting those populations at a disadvantage and potentially causing their exclusion. R-gene diversity may also be reduced during population bottlenecks, creating a priority effect. Third, when R-genes affect survival but resistance is costly, populations can avoid extinction by losing resistance alleles, as they cease paying a cost that is unneeded. Thus, the impact pathogens can have on tree diversity depends on the mechanism of plant-pathogen interactions. Future empirical studies should examine which of these scenarios most closely reflects the real world.

Effects of the soil microbiome on the demography of two annual prairie plants

Both mutualistic and pathogenic soil microbes are known to play important roles in shaping the fitness of plants, likely affecting plants at different life cycle stages.In order to investigate the differential effects of native soil mutualists and pathogens on plant fitness, we compared survival and reproduction of two annual tallgrass prairie plant species (Chamaecrista fasciculata and Coreopsis tinctoria) in a field study using 3 soil inocula treatments containing different compositions of microbes. The soil inocula types included fresh native whole soil taken from a remnant prairie containing both native mutualists and pathogens, soil enhanced with arbuscular mycorrhizal (AM) fungi derived from remnant prairies, and uninoculated controls.For both species, plants inoculated with native prairie AM fungi performed much better than those in uninoculated soil for all parts of the life cycle. Plants in the native whole prairie soil were either generally similar to plants in the uninoculated soil or had slightly higher survival or reproduction.Overall, these results suggest that native prairie AM fungi can have important positive effects on the fitness of early successional plants. As inclusion of prairie AM fungi and pathogens decreased plant fitness relative to prairie AM fungi alone, we expect that native pathogens also can have large effects on fitness of these annuals. Our findings support the use of AM fungi to enhance plant establishment in prairie restorations.

Abiotic and biotic context dependency of perennial crop yield

Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass-Thinopyrum intermedium-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (Silphium intregrifolium), and alfalfa (Medicago sativa). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both Silphium and alfalfa strongly benefited from AM fungi. The presence of native prairie AM fungi had a greater benefit to Silphium in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of Silphium and alfalfa. This study identifies the importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.

Community context for mechanisms of disease dilution: insights from linking epidemiology and plant-soil feedback theory

In many natural systems, diverse host communities can reduce disease risk, though less is known about the mechanisms driving this "dilution effect." We relate feedback theory, which focuses on pathogen-mediated coexistence, to mechanisms of dilution derived from epidemiological models, with the central goal of gaining insights into host-pathogen interactions in a community context. We first compare the origin, structure, and application of epidemiological and feedback models. We then explore the mechanisms of dilution, which are grounded in single-pathogen, single-host epidemiological models, from the perspective of feedback theory. We also draw on feedback theory to examine how coinfecting pathogens, and pathogens that vary along a host specialist-generalist continuum, apply to dilution theory. By identifying synergies among the feedback and epidemiological approaches, we reveal ways in which organisms occupying different trophic levels contribute to diversity-disease relationships. Additionally, using feedbacks to distinguish dilution in disease incidence from dilution in the net effect of disease on host fitness allows us to articulate conditions under which definitions of dilution may not align. After ascribing dilution mechanisms to macro- or microorganisms, we propose ways in which each contributes to diversity-disease and productivity-diversity relationships. Our analyses lead to predictions that can guide future research efforts.

A nucleation framework for transition between alternate states: short-circuiting barriers to ecosystem recovery

The theory of alternate stable states provides an explanation for rapid ecosystem degradation, yielding important implications for ecosystem conservation and restoration. However, utilizing this theory to initiate transitions from degraded to desired ecosystem states remains a significant challenge. Applications of the alternative stable states framework may currently be impeded by a mismatch between local‐scale driving processes and landscape‐scale emergent system transitions. We show how nucleation theory provides an elegant bridge between local‐scale positive feedback mechanisms and landscape‐scale transitions between alternate stable ecosystem states. Geometrical principles can be used to derive a critical patch radius: a spatially explicit, local description of an unstable equilibrium point. This insight can be used to derive an optimal patch size that minimizes the cost of restoration, and to provide a framework to measure the resilience of desired ecosystem states to the synergistic effects of disturbance and environmental change.

Plant-soil feedback effects altered by aboveground herbivory explain plant species abundance in the landscape

Relatively little is known about how plant-soil feedbacks (PSFs) may affect plant growth in field conditions where factors such as herbivory may be important. Using a potted experiment in a grassland, we measured PSFs with and without aboveground insect herbivory for 20 plant species. We then compared PSF values to plant landscape abundance. Aboveground herbivory had a large negative effect on PSF values. For 15 of 20 species, PSFs were more negative with herbivory than without. This occurred because plant biomass on "home" soils was smaller with herbivory than without. PSF values with herbivory were correlated with plant landscape abundance, whereas PSF values without herbivory were not. Shoot nitrogen concentrations suggested that plants create soils that increase nitrogen uptake, but that greater shoot nitrogen values increase herbivory and that the net effect of positive PSF and greater aboveground herbivory is less aboveground biomass. Results provided clear evidence that PSFs alone have limited power in explaining species abundances and that herbivory has stronger effects on plant biomass and growth on the landscape. Our results provide a potential explanation for observed differences between greenhouse and field PSF experiments and suggest that PSF experiments need to consider important biotic interactions, like aboveground herbivory, particularly when the goal of PSF research is to understand plant growth in field conditions.

Initial soil community drives heathland fungal community trajectory over multiple years through altered plant-soil interactions

Dispersal limitation, biotic interactions, and environmental filters interact to drive plant and fungal community assembly, but their combined effects are rarely investigated. This study examines how different heathland plant and fungal colonization scenarios realized via three biotic treatments - addition of mature heathland-derived sod, addition of hay, and no additions - affect soil fungal community development over 6 yr along a manipulated pH gradient in a large-scale experiment starting from an agricultural, topsoil removed state. Our results show that both biotic and abiotic (pH) treatments had a persistent influence on the development of fungal communities, but that sod additions diminished the effect of abiotic treatments through time. Analysis of correlation networks between soil fungi and plants suggests that the reduced effect of pH in the sod treatment, where both soil and plant propagules were added, might be due to plant-fungal interactions since the sod additions caused stronger, more specific, and more consistent connections compared with the no addition treatment. Based on these results, we suggest that the initial availability of heathland fungal and plant taxa, which reinforce each other, can significantly steer further fungal community development to an alternative configuration, overriding the otherwise prominent effect of abiotic (pH) conditions.

Multi-scale analysis of hydrological connectivity and plant response in the Yellow River Delta

The Yellow River Delta is one of the International Important Wetlands on the west coastline of the Pacific Ocean in China. Despite its importance for regional and global ecological security, it is vulnerable because of human activities and climate change. Local government is trying to identify a more efficient way to conserve the delta thereby reducing a potential environmental crisis. The framework of hydrological connectivity provides a new perspective to study hydrological related ecological processes, while the method is highly exclusive because of environment and scale heterogeneity. This study collaborated with managers to develop a new algorithm to parameterize the hydrological connectivity on plot, point and landscape scales. Then the interspecific and conspecific structures of two dominate species (Phragmites communis and Suaeda salsa) are linked to these indices. The results show: (1) According to the point and plot scale results, AP (semi-artificial pond) and IF (intertidal flat) has the strongest hydrological connectivity followed by TM (tidal marsh). The average positive point-scale index values in AP, IF RS (river side wetland) and TM are 0.610, 0.495, 1.162 and 1.217 and the average plot-scale index values in AP, IF RS and TM are 1.53, 0.87, 0.48 0.55. At the landscape scale, index values show high collinearity with plot density and lack of hydrological significance because of low data resolution and scale effects. (2) At the individual level, P. communis and S. salsa showed a higher interspecific and conspecific competitive strength to respond to environmental stress in the weak hydrological connectivity area. (3) At the community level, in higher salinity wetland classes, biomass, plant coverage and biodiversity showed a positive linear correlation with plot-scale indices. Future study will improve the current parametrization method at the landscape scale and reveal the response of other important plant species to hydrological connectivity in this area.

Climate change effects on plant-soil feedbacks and consequences for biodiversity and functioning of terrestrial ecosystems

Plant-soil feedbacks (PSFs) are interactions among plants, soil organisms, and abiotic soil conditions that influence plant performance, plant species diversity, and community structure, ultimately driving ecosystem processes. We review how climate change will alter PSFs and their potential consequences for ecosystem functioning. Climate change influences PSFs through the performance of interacting species and altered community composition resulting from changes in species distributions. Climate change thus affects plant inputs into the soil subsystem via litter and rhizodeposits and alters the composition of the living plant roots with which mutualistic symbionts, decomposers, and their natural enemies interact. Many of these plant-soil interactions are species-specific and are greatly affected by temperature, moisture, and other climate-related factors. We make a number of predictions concerning climate change effects on PSFs and consequences for vegetation-soil-climate feedbacks while acknowledging that they may be context-dependent, spatially heterogeneous, and temporally variable.

When and where plant-soil feedback may promote plant coexistence: a meta-analysis

Plant-soil feedback (PSF) theory provides a powerful framework for understanding plant dynamics by integrating growth assays into predictions of whether soil communities stabilise plant-plant interactions. However, we lack a comprehensive view of the likelihood of feedback-driven coexistence, partly because of a failure to analyse pairwise PSF, the metric directly linked to plant species coexistence. Here, we determine the relative importance of plant evolutionary history, traits, and environmental factors for coexistence through PSF using a meta-analysis of 1038 pairwise PSF measures. Consistent with eco-evolutionary predictions, feedback is more likely to mediate coexistence for pairs of plant species (1) associating with similar guilds of mycorrhizal fungi, (2) of increasing phylogenetic distance, and (3) interacting with native microbes. We also found evidence for a primary role of pathogens in feedback-mediated coexistence. By combining results over several independent studies, our results confirm that PSF may play a key role in plant species coexistence, species invasion, and the phylogenetic diversification of plant communities.

Soil microbiome mediates positive plant diversity-productivity relationships in late successional grassland species

Which processes drive the productivity benefits of biodiversity remain a critical, but unanswered question in ecology. We tested whether the soil microbiome mediates the diversity-productivity relationships among late successional plant species. We found that productivity increased with plant richness in diverse soil communities, but not with low-diversity mixtures of arbuscular mycorrhizal fungi or in pasteurised soils. Diversity-interaction modelling revealed that pairwise interactions among species best explained the positive diversity-productivity relationships, and that transgressive overyielding resulting from positive complementarity was only observed with the late successional soil microbiome, which was both the most diverse and exhibited the strongest community differentiation among plant species. We found evidence that both dilution/suppression from host-specific pathogens and microbiome-mediated resource partitioning contributed to positive diversity-productivity relationships and overyielding. Our results suggest that re-establishment of a diverse, late successional soil microbiome may be critical to the restoration of the functional benefits of plant diversity following anthropogenic disturbance.

Single introductions of soil biota and plants generate long-term legacies in soil and plant community assembly

Recent demonstrations of the role of plant–soil biota interactions have challenged the conventional view that vegetation changes are mainly driven by changing abiotic conditions. However, while this concept has been validated under natural conditions, our understanding of the long‐term consequences of plant–soil interactions for above‐belowground community assembly is restricted to mathematical and conceptual model projections. Here, we demonstrate experimentally that one‐time additions of soil biota and plant seeds alter soil‐borne nematode and plant community composition in semi‐natural grassland for 20 years. Over time, aboveground and belowground community composition became increasingly correlated, suggesting an increasing connectedness of soil biota and plants. We conclude that the initial composition of not only plant communities, but also soil communities has a long‐lasting impact on the trajectory of community assembly.

Glyphosate decreases mycorrhizal colonization and affects plant-soil feedback

Our aim was to study the effects of glyphosate, tilling practice and cultivation history on mycorrhizal colonization and growth of target (weeds) and non-target (crops) plants. Glyphosate, the world's most widely used pesticide, inhibits an enzyme found in plants but also in microbes. We examined the effects of glyphosate treatment applied in the preceding fall on growth of a perennial weed, Elymus repens (target plant) and a forage grass, Festuca pratensis (non-target plant) and their arbuscular mycorrhizal fungal (AMF) root colonization in a field pot experiment. Non-target plants were sown in the following spring. Furthermore, we tested if glyphosate effects depend on tillage or soil properties modulated by long cultivation history of endophyte symbiotic grass (E+ grass). AMF root colonization, plant establishment and growth, glyphosate residues in plants, and soil chemistry were measured. Glyphosate reduced the mycorrhizal colonization and growth of both target and non-target grasses. The magnitude of reduction depended on tillage and soil properties due to cultivation history of E+ grass. We detected glyphosate residues in weeds and crop plants in the growing season following the glyphosate treatment. Residues were higher in plants growing in no-till pots compared to conspecifics in tilled pots. These results demonstrate negative effects of glyphosate on non-target organisms in agricultural environments and grassland ecosystems.

Live long and prosper: plant-soil feedback, lifespan, and landscape abundance covary

Plant soil feedbacks (PSFs) are thought to be important to plant growth and species coexistence, but most support for these hypotheses is derived from short-term greenhouse experiments. Here we use a seven-year, common garden experiment to measure PSFs for seven native and six nonnative species common to the western United States. We use these long-term, field-based estimates to test correlations between PSF and plant landscape abundance, species origin, functional type, and lifespan. To assess potential PSF mechanisms, we also measured soil microbial community composition, root biomass, nitrogen cycling, bulk density, penetration resistance, and shear strength. Plant abundance on the landscape and plant lifespan were positively correlated with PSFs, though this effect was due to the relationships for native plants. PSFs were correlated with indices of soil microbial community composition. Soil nutrient and physical traits and root biomass differed among species but were not correlated with PSF. While results must be taken with caution because only 13 species were examined, these species represent most of the dominant plant species in the system. Results suggest that native plant abundance is associated with the ability of long-lived plants to create positive plant-soil microbe interactions, while short-lived nonnative plants maintain dominance by avoiding soil-borne antagonists, increasing nitrogen cycling and dedicating resources to aboveground growth and reproduction rather than to belowground growth. Broadly, results suggest that PSFs are correlated with a suite of traits that determine plant abundance.

Potential for synergy in soil inoculation for nature restoration by mixing inocula from different successional stages

BACKGROUND AND AIMS

Soil inoculation is a powerful tool for the restoration of terrestrial ecosystems. However, the origin of the donor material may differentially influence early- and late-successional plant species. Donor soil from late-succession stages may benefit target plant species due to a higher abundance of soil-borne mutualists. Arable soils, on the other hand, may suppress ruderals as they support more root herbivores that preferentially attack ruderal plant species, while mid-succession soils may be intermediate in their effects on ruderals and target species performance. We hypothesized that a mixture of arable and late-succession inocula may outperform pure late-successional inocula for restoration, by promoting late-successional target plants, while simultaneously reducing ruderal species' performance.

METHODS

We conducted a glasshouse experiment and tested the growth of ruderal and target plant species on pure and mixed inocula. The inocula were derived from arable fields, mid-succession grasslands and late-succession heathlands and we created a replacement series testing different pairwise mixitures for each of these inocula types (ratios: 100:0, 75:25, 50:50, 25:75, 0:100 of inoculum A and B respectively).

RESULTS

In general, we found that a higher proportion of heathland material led to a higher aboveground biomass of target plant species, while responses of ruderal species were variable. We found synergistic effects when specific inocula were mixed. In particular, a 50:50 mixture of heathland and arable soil in the inoculum led to a significant reduction in ruderal species biomass relative to the two respective pure inocula. The overall response was driven by Myosotis arvensis, since the other two ruderal species were not significantly affected.

CONCLUSIONS

Mixing inocula from different successional stages can lead to synergistic effects on restoration, but this highly depends on the specific combination of inocula, the mixing ratio and plant species. This suggest that specific inocula may need to be developed in order to rapidly restore different plant communities.

Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence

Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition vs. plant-soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter- to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbour identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low-resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure.

Heterospecific plant-soil feedback and its relationship to plant traits, species relatedness, and co-occurrence in natural communities

Plant-soil feedback is one of the mechanisms affecting co-existence of species, ecological succession, and species invasiveness. However, in contrast to conspecific plant-soil feedback, general patterns in heterospecific feedback are mostly unknown. We used a meta-analysis to search for correlations between heterospecific feedback and species relatedness, functional traits, and field co-occurrence patterns. We searched published literature and compiled a data set of 618 PSF interactions. We gathered data on species traits reflecting plant size and growth rate (height, specific leaf area, and life span), co-occurrence in habitats and phylogenetic distance between species pairs. We found that species grew better in soil conditioned by (i) close relatives than in conspecific soil, whereas there was no relationship with phylogeny for distantly related species, (ii) species of greater plant height (but there was no relationship with species SLA or life span), and (iii) species more frequently co-occurring in the field. The results show that heterospecific plant-soil feedback can be explained by plant traits (height) and is reflected in co-occurrence patterns. Phylogeny was a significant predictor of feedbacks over short phylogenetic distance, suggesting fast evolution of traits related to feedback. The low variability explained by the models, however, indicates that other factors such as environmental conditions possibly alter plant-soil feedback responses.