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

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.

Active restoration efforts drive community succession and assembly in a desert during the past 53 years

Regreening efforts in deserts have been implemented globally to combat land degradation and desert expansion, but how they affect above- and belowground community succession and assembly processes remains unknown. Here, we examined variations in plant and soil microbial community attributes along a 53-year restoration chronosequence following the establishment of straw checkerboard barriers (SCBs) in the Tengger Desert of China. This approach is a combination of fixing shifting sand and adding organic material (straw) simultaneously to expedite vegetation restoration by enhancing the success of plant establishment. Our findings revealed that the establishment of SCBs significantly triggered plant and soil microbial communities to gradually approximate those of the natural community along restoration duration. We observed positive and negative bidirectional shifts in plant and soil microbial community composition. Critical temporal threshold zones for relatively rapid changes in community composition were identified, with 2-15.5 years for plants, 0.5-8.5 years for bacteria, and 2-8.5 years for fungi. This suggests a delayed response of plant communities to restoration efforts compared with soil microbial communities. Both stochastic and deterministic processes regulated plant and soil microbial community assembly. Stochastic processes played a more important role in plant and fungal community succession, whereas deterministic processes primarily governed bacterial succession. In terms of deterministic processes, temporal variations in community composition mainly resulted from the intrinsic correlations among plant, bacterial, and fungal communities, as well as an increase in soil organic carbon (SOC) with restoration duration. Thus, temporal patterns and functional contributions of bacterial communities appear to be more predictable than those of plant and fungal communities during desert ecosystem restoration. This study emphasizes that plant-bacteria-fungi correlations and increasing SOC content are critical for accelerating community succession and promoting dryland restoration. Future studies should explore and integrate temporal variations and restoration effects of multiple ecosystem functions to better predict dryland development and resilience to global climate changes over a large temporal scale.

Central Taxa Are Keystone Microbes During Early Succession

Microorganisms underpin numerous ecosystem processes and support biodiversity globally. Yet, we understand surprisingly little about what structures environmental microbiomes, including how to efficiently identify key players. Microbiome network theory predicts that highly connected hubs act as keystones, but this has never been empirically tested in nature. Combining culturing, sequencing, networks and field experiments, we isolated 'central' (highly connected, hub taxa), 'intermediate' (moderately connected), and 'peripheral' (weakly/unconnected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession in nature. Central early colonisers significantly (1) enhanced biodiversity (35%-40% richer communities), (2) reshaped trajectories of microbiome assembly and (3) increased recruitment of additional influential microbes by > 60%. In contrast, peripheral microbes did not increase diversity and were transient taxa, minimally affected by the presence of other microbes. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central microbes act as keystone taxa.

Fungal communities are passengers in community development of dune ecosystems, while bacteria are not

An increasing number of studies of above-belowground interactions provide a fundamental basis for our understanding of the coexistence between plant and soil communities. However, we lack empirical evidence to understand the directionality of drivers of plant and soil communities under natural conditions: 'Are soil microorganisms driving plant community functioning or do they adapt to the plant community?' In a field experiment in an early successional dune ecosystem, we manipulated soil communities by adding living (i.e., natural microbial communities) and sterile soil inocula, originating from natural ecosystems, and examined the annual responses of soil and plant communities. The experimental manipulations had a persistent effect on the soil microbial community with divergent impacts for living and sterile soil inocula. The plant community was also affected by soil inoculation, but there was no difference between the impacts of living and sterile inocula. We also observed an increasing convergence of plant and soil microbial composition over time. Our results show that alterations in soil abiotic and biotic conditions have long-term effects on the composition of both plant and soil microbial communities. Importantly, our study provides direct evidence that soil microorganisms are not "drivers" of plant community dynamics. We found that soil fungi and bacteria manifest different community assemblies in response to treatments. Soil fungi act as "passengers," that is, soil microorganisms reflect plant community dynamics but do not alter it, whereas soil bacteria are neither "drivers" nor "passengers" of plant community dynamics in early successional ecosystems. These results are critical for understanding the community assembly of plant and soil microbial communities under natural conditions and are directly relevant for ecosystem management and restoration.

Biodiversity-production feedback effects lead to intensification traps in agricultural landscapes

Intensive agriculture with high reliance on pesticides and fertilizers constitutes a major strategy for 'feeding the world'. However, such conventional intensification is linked to diminishing returns and can result in 'intensification traps'-production declines triggered by the negative feedback of biodiversity loss at high input levels. Here we developed a novel framework that accounts for biodiversity feedback on crop yields to evaluate the risk and magnitude of intensification traps. Simulations grounded in systematic literature reviews showed that intensification traps emerge in most landscape types, but to a lesser extent in major cereal production systems. Furthermore, small reductions in maximal production (5-10%) could be frequently transmitted into substantial biodiversity gains, resulting in small-loss large-gain trade-offs prevailing across landscape types. However, sensitivity analyses revealed a strong context dependence of trap emergence, inducing substantial uncertainty in the identification of optimal management at the field scale. Hence, we recommend the development of case-specific safety margins for intensification preventing double losses in biodiversity and food security associated with intensification traps.

Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency

Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine (i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and (ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs. high). Our results revealed that bacteria were associated with particular soil properties (such as base saturation) and both bacteria and fungi were associated with plant community composition across sites and within the majority of sites. Moreover, a discernible microbial community signal emerged, clearly distinguishing high and low-productivity soils across different grasslands independent of their location in the world. Hence, regional productivity differences may be typified by characteristic soil microbial communities across the grassland biome. These results could encourage future research aiming to predict the general effects of global changes on soil microbial community composition in grasslands and to discriminate fertile from infertile systems using generally applicable microbial indicators.

Microbial consortium mediated acceleration of the defense response in potato against Alternaria solani through prodigious inflation in phenylpropanoid derivatives and redox homeostasis

The present study was carried out in a pot experiment to examine the bioefficacy of three biocontrol agents, viz., Trichoderma viride, Bacillus subtilis, and Pseudomonas fluorescens, either alone or in consortium, on plant growth promotion and activation of defense responses in potato against the early blight pathogen Alternaria solani. The results demonstrate significant enhancement in growth parameters in plants bioprimed with the triple-microbe consortium compared to other treatments. In potato, the disease incidence percentage was significantly reduced in plants treated with the triple-microbe consortium compared to untreated control plants challenged with A. solani. Potato tubers treated with the consortium and challenged with pathogen showed significant activation of defense-related enzymes such as peroxidase (PO) at 96 h after pathogen inoculation (hapi) while, both polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) at 72 hapi, compared to the individual and dual microbial consortia-treated plants. The expression of antioxidant enzymes like superoxide dismutase (SOD) and catalase (CAT) and the accumulation of pathogenesis-related proteins such as chitinase and β-1,3-glucanase were observed to be highest at 72 hapi in the triple microbe consortium as compared to other treatments. HPLC analysis revealed significant induction in polyphenolic compounds in triple-consortium bioprimed plants compared to the control at 72 hapi. Histochemical analysis of hydrogen peroxide (H2O2) clearly showed maximum accumulation of H2O2 in pathogen-inoculated control plants, while the lowest was observed in triple-microbe consortium at 72 hapi. The findings of this study suggest that biopriming with a microbial consortium improved plant growth and triggered defense responses against A. solani through the induction of systemic resistance via modulation of the phenylpropanoid pathway and antioxidative network.

Native Microbes Amplify Native Seedling Establishment and Diversity While Inhibiting a Non-Native Grass

Although several studies have shown increased native plant establishment with native microbe soil amendments, few studies have investigated how microbes can alter seedling recruitment and establishment in the presence of a non-native competitor. In this study, the effect of microbial communities on seedling biomass and diversity was assessed by seeding pots with both native prairie seeds and a non-native grass that commonly invades US grassland restorations, Setaria faberi. Soil in the pots was inoculated with whole soil collections from ex-arable land, late successional arbuscular mycorrhizal (AM) fungi isolated from a nearby tallgrass prairie, with both prairie AM fungi and ex-arable whole soil, or with a sterile soil (control). We hypothesized (1) late successional plants would benefit from native AM fungi, (2) that non-native plants would outcompete native plants in ex-arable soils, and (3) early successional plants would be unresponsive to microbes. Overall, native plant abundance, late successional plant abundance, and total diversity were greatest in the native AM fungi+ ex-arable soil treatment. These increases led to decreased abundance of the non-native grass S. faberi. These results highlight the importance of late successional native microbes on native seed establishment and demonstrate that microbes can be harnessed to improve both plant community diversity and resistance to invasion during the nascent stages of restoration.

Temporal dynamics of range expander and congeneric native plant responses during and after extreme drought events

Climate change is causing range shifts of many species to higher latitudes and altitudes and increasing their exposure to extreme weather events. It has been shown that range-shifting plant species may perform differently in new soil than related natives; however, little is known about how extreme weather events affect range-expanding plants compared to related natives. In this study we used outdoor mesocosms to study how range-expanding plant species responded to extreme drought in live soil from a habitat in a new range with and without live soil from a habitat in the original range (Hungary). During summer drought, the shoot biomass of the range-expanding plant community declined. In spite of this, in the mixed community, range expanders produced more shoot biomass than congeneric natives. In mesocosms with a history of range expanders in the previous year, native plants produced less biomass. Plant legacy or soil origin effects did not change the response of natives or range expanders to summer drought. During rewetting, range expanders had less biomass than congeneric natives but higher drought resilience (survival) in soils from the new range where in the previous year native plant species had grown. The biomass patterns of the mixed plant communities were dominated by Centaurea spp.; however, not all plant species within the groups of natives and of range expanders showed the general pattern. Drought reduced the litter decomposition, microbial biomass, and abundances of bacterivorous, fungivorous, and carnivorous nematodes. Their abundances recovered during rewetting. There was less microbial and fungal biomass, and there were fewer fungivorous nematodes in soils from the original range where range expanders had grown in the previous year. We concluded that in mixed plant communities of range expanders and congeneric natives, range expanders performed better, under both ambient and drought conditions, than congeneric natives. However, when considering the responses of individual species, we observed variations among pairs of congenerics, so that under the present mixed-community conditions there was no uniformity in responses to drought of range expanders versus congeneric natives. Range-expanding plant species reduced soil fungal biomass and the numbers of soil fungivorous nematodes, suggesting that the effects of range-expanding plant species can trickle up in the soil food web.

Soil microbial legacies influence plant survival and growth in mine reclamation

Plants alter soil biological communities, generating ecosystem legacies that affect the performance of successive plants, influencing plant community assembly and successional trajectories. Yet, our understanding of how microbe-mediated soil legacies influence plant establishment is limited for primary successional systems and forest ecosystems, particularly for ectomycorrhizal plants. In a two-phase greenhouse experiment using primary successional mine reclamation materials with or without forest soil additions, we conditioned soil with an early successional shrub with low mycorrhizal dependence (willow, Salix scouleriana) and a later-successional ectomycorrhizal conifer (spruce, Picea engelmannii × glauca). The same plant species and later-successional plants (spruce and/or redcedar, Thuja plicata, a mid- to late-successional arbuscular mycorrhizal conifer) were grown as legacy-phase seedlings in conditioned soils and unconditioned control soils. Legacy effects were evaluated based on seedling survival and biomass, and the abundance and diversity of root fungal symbionts and pathogens. We found negative intraspecific (same-species) soil legacies for willow associated with pathogen accumulation, but neutral to positive intraspecific legacies in spruce associated with increased mycorrhizal fungal colonization and diversity. Our findings support research showing that soil legacy effects vary with plant nutrient acquisition strategy, with plants with low mycorrhizal dependence experiencing negative feedbacks and ectomycorrhizal plants experiencing positive feedbacks. Soil legacy effects of willow on next-stage successional species (spruce and redcedar) were negative, potentially due to allelopathy, while ectomycorrhizal spruce had neutral to negative legacy effects on arbuscular mycorrhizal redcedar, likely due to the trees not associating with compatible mycorrhizae. Thus, positive biological legacies may be limited to scenarios where mycorrhizal-dependent plants grow in soil containing legacies of compatible mycorrhizae. We found that soil legacies influenced plant performance in mine reclamation materials with and without forest soil additions, indicating that initial restoration actions may potentially exert long-term effects on plant community composition, even in primary successional soils with low microbial activity.

Defending Earth's terrestrial microbiome

Microbial life represents the majority of Earth's biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth's microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet's breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth's microbiome.

Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere

Tree planting and natural regeneration contribute to the ongoing effort to restore Earth's forests. Our review addresses how the plant microbiome can enhance the survival of planted and naturally regenerating seedlings and serve in long-term forest carbon capture and the conservation of biodiversity. We focus on fungal leaf endophytes, ubiquitous defensive symbionts that protect against pathogens. We first show that fungal and oomycetous pathogen richness varies greatly for tree species native to the United States (n = 0-876 known pathogens per US tree species), with nearly half of tree species either without pathogens in these major groups or with unknown pathogens. Endophytes are insurance against the poorly known and changing threat of tree pathogens. Next, we review studies of plant phyllosphere feedback, but knowledge gaps prevent us from evaluating whether adding conspecific leaf litter to planted seedlings promotes defensive symbiosis, analogous to adding soil to promote positive feedback. Finally, we discuss research priorities for integrating the plant microbiome into efforts to expand Earth's forests.

Soil Biota Adversely Affect the Resistance and Recovery of Plant Communities Subjected to Drought

Climate change predictions indicate that summer droughts will become more severe and frequent. Yet, the impact of soil communities on the response of plant communities to drought remains unclear. Here, we report the results of a novel field experiment, in which we manipulated soil communities by adding soil inocula originating from different successional stages of coastal dune ecosystems to a plant community established from seeds on bare dune sand. We tested if and how the added soil biota from later-successional ecosystems influenced the sensitivity (resistance and recovery) of plant communities to drought. In contrast to our expectations, soil biota from later-successional soil inocula did not improve the resistance and recovery of plant communities subjected to drought. Instead, inoculation with soil biota from later successional stages reduced the post-drought recovery of plant communities, suggesting that competition for limited nutrients between plant community and soil biota may exacerbate the post-drought recovery of plant communities. Moreover, soil pathogens present in later-successional soil inocula may have impeded plant growth after drought. Soil inocula had differential impacts on the drought sensitivity of specific plant functional groups and individual species. However, the sensitivity of individual species and functional groups to drought was idiosyncratic and did not explain the overall composition of the plant community. Based on the field experimental evidence, our results highlight the adverse role soil biota can play on plant community responses to environmental stresses. These outcomes indicate that impacts of soil biota on the stability of plant communities subjected to drought are highly context-dependent and suggest that in some cases the soil biota activity can even destabilize plant community biomass responses to drought.

Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field

Inoculation with soil from different ecosystems can induce changes in plant and soil communities and promote the restoration of degraded ecosystems. However, it is unknown how such inoculations influence the plant and soil communities, how much inoculum is needed, and whether inocula collected from similar ecosystems will steer soil and plant communities in different directions. We conducted a three-year soil inoculation experiment at a degraded grassland and used two different soil inocula both from grasslands with three inoculation rates. We measured the development of the soil and plant communities over a period of three years. Our results show that soil inoculation steers the soil microbiome and plant communities at the inoculated site into different directions and these effects were stronger with higher amount of soil used to inoculate. Network analyses showed that inoculation with upland meadow soil introduced more genera occupying the central position in the biotic network and resulted in more complex networks in the soil than inoculation with meadow steppe soil. Our findings emphasize that there are specific effects of donor soil on soil microbiomes as well as plant communities and that the direction and speed of development depend on the origin and the amount of soil inoculum used. Our findings have important implications for the restoration of biodiversity and ecosystem functioning in degraded grassland ecosystems.

Integrating design and ecological theory to achieve adaptive diverse pastures

Increasing plant diversity is often suggested as a way of overcoming some of the challenges faced by managers of intensive pasture systems, but it is unclear how to design the most suitable plant mixtures. Using innovative design theory, we identify two conceptual shifts that foster potentially beneficial design approaches. Firstly, reframing the goal of mixture design to supporting ecological integrity, rather than delivering lists of desired outcomes, leads to flexible design approaches that support context-specific solutions that should operate within identifiable ecological limits. Secondly, embracing, rather than minimising uncertainty in performance leads to adaptive approaches that could enhance current and future benefits of diversifying pasture. These two fundamental shifts could therefore accelerate the successful redesign of intensive pastures.

Increase in rainfall intensity promotes soil nematode diversity but offset by nitrogen addition in a temperate grassland

Precipitation regime in arid and semi-arid regions is exhibiting a trend of increase in rainfall intensity but reduction in frequency under global climate change. In addition, nitrogen (N) deposition occurs simultaneously in the same regions. Nematodes are the dominant soil biota in terrestrial ecosystems and are involved in various underground processes. How the diversity of nematode communities responds to changing precipitation regime and how N deposition regulates the responses remain unclear. Here, we performed a field experiment initiated in 2012 to examine the effect of changes in the precipitation regime (2 mm precipitation intensity, 5 mm precipitation intensity, 10 mm precipitation intensity, 20 mm precipitation intensity, and 40 mm precipitation intensity) and N addition (10 g N m^-2 yr^-1) on soil nematode community in a semi-arid grassland in Inner Mongolia of China. We found that the abundance and diversity of nematodes increased under the treatments with fewer but stronger precipitation events (the largest abundance of total nematodes was 1458.37 individuals/100 g dry soil occurred under 40 mm intensity treatment). However, N addition reduced nematode diversity under these treatments, which largely offset the positive effects of increased rainfall intensity alone. Soil pH and plant belowground biomass were the main factors affecting nematode diversity. Our results imply that, as a consequence of global climate change, an increase in the intensity of rainfall events in the coming decades may favor the nematode communities within arid and semi-arid ecosystems. However, this positive effect may be largely offset by soil acidification in the regions experiencing heavy N deposition.

Soil Microbe-Mediated N:P Stoichiometric Effects on Solidago canadensis Performance Depend on Nutrient Levels

Both soil microbes and soil N:P ratios can affect plant growth, but it is unclear whether they can interact to alter plant growth and whether such an interactive effect depends on nutrient levels. Here, we tested the hypothesis that soil microbes can ameliorate the negative effects of nutrient imbalance caused by low or high N:P ratios on plant growth and that such an ameliorative effect of soil microbes depends on nutrient supply levels. We grew individuals of six populations of the clonal plant Solidago canadensis at three N:P ratios (low (1.7), intermediate (15), and high (135)), under two nutrient levels (low versus high) and in the presence versus absence of soil microbes. The presence of soil microbes significantly increased biomass of S. canadensis at all three N:P ratios and under both nutrient levels. Under the low-nutrient level, biomass, height, and leaf number of S. canadensis did not differ significantly among the three N:P ratio treatments in the absence of soil microbes, but they were higher at the high than at the low and the intermediate N:P ratio in the presence of soil microbes. Under the high-nutrient level, by contrast, biomass, height, and leaf number of S. canadensis were significantly higher at the low than at the high and the intermediate N:P ratio in the absence of soil microbes, but increased with increasing the N:P ratio in the presence of soil microbes. In the presence of soil microbes, number of ramets (asexual individuals) and the accumulation of N and P in plants were significantly higher at the high than at the low and the intermediate N:P ratio under both nutrient levels, whereas in the absence of soil microbes, they did not differ significantly among the three N:P ratio regardless of the nutrient levels. Our results provide empirical evidence that soil microbes can alter effects of N:P ratios on plant performance and that such an effect depends on nutrient availability. Soil microbes may, therefore, play a role in modulating ecosystem functions such as productivity and carbon and nutrient cycling via modulating nutrient imbalance caused by low and high N:P ratios.

Biocrusts Influence Vascular Plant Community Development, Promoting Native Plant Dominance

The soil and its biota can shape the development of colonizing vascular plant communities. Because they occupy soil surfaces where most seeds disperse to, biological soil crusts (biocrusts) are uniquely positioned to influence vascular plant communities established by direct seeding, e.g., for restoration. We created mesocosms of soil overtopped by intact biocrust transplants from the field, varying in key community attributes: total cover, species richness, and proportional cover of mosses relative to lichens. We seeded the same diverse mixture of vascular plants into all mesocosms, including desired native species and problematic exotic invasive species. We tracked plant community development for two full growing seasons, both under ambient outdoor conditions and with supplemental irrigation to remove the influence of water limitation. Under ambient conditions, we found that total biocrust cover suppressed exotic plant emergence and biocrust richness slightly promoted native emergence (r = −0.23 to −0.39) but had weaker and less consistent effects on cover of either native or exotic plants (r ≤ |0.25|). Early emergence events were generally strong drivers of vascular plant recruitment (r = 0.17–0.78) and continued to influence community composition after 2 years, suggesting a priority effect. Biocrust cover also promoted final plant biomass under ambient conditions (r = 0.17–0.33) but did not influence the total cumulative number of native species (r ≤ |0.07|) nor the fecundity of exotics (r ≤ |0.08|). Biocrusts’ influence on total vascular plant biomass was minor. When water was added, biocrust effects sometimes switched from positive or negative to neutral, or vice-versa, indicating that our detection probability of biocrust effects on plants changes with moisture availability. Our results demonstrate that the condition of pre-existing biocrust communities can influence—but not strongly dictate—the outcome of multi-species restoration seedings, mostly positively or neutrally under normal conditions, but switching to potentially negatively under irrigated conditions. Our study also suggests that locations with more intact and richer biocrust communities might be slightly more conducive to successful seeding outcomes, while also providing additional contributions to ecosystem functions. As such, biocrusts, alongside vascular plants, have a role in restoring damaged or degraded ecosystems.

Microbiome-mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance

Fire plays a major role in structuring plant communities across the globe. Interactions with soil microbes impact plant fitness, scaling up to influence plant populations and distributions. Here we present the first factorial manipulation of both fire and soil microbiome presence to investigate their interactive effects on plant performance across a suite of plant species with varying life history traits. We conducted fully factorial experiments on 11 species from the Florida scrub ecosystem to test plant performance responses to soils with varying fire histories (36 soil sources), the presence/absence of a microbiome, and exposure to an experimental burn. Results revealed interactive 'pulse' effects between fire and the soil microbiome on plant performance. On average, post-fire soil microbiomes strongly reduced plant productivity compared to unburned or sterilized soils. Interestingly, longer-term fire 'legacy' effects had minor impacts on plant performance and were unrelated to soil microbiomes. While pulse fire effects on plant-microbiome interactions are short-term, they could have long-term consequences for plant communities by establishing differential microbiome-mediated priority effects during post-disturbance succession. The prominence of pulse fire effects on plant-microbe interactions has even greater import due to expected increases in fire disturbances resulting from anthropogenic climate change.

Native soil amendments combined with commercial arbuscular mycorrhizal fungi increase biomass of Panicum amarum

Coastal dune restorations often fail because of poorly performing plants. The addition of beneficial microbes can improve plant performance, though it is unclear if the source of microbes matters. Here, we tested how native soil amendments and commercially available arbuscular mycorrhizal (AM) fungi influenced performance of Panicum amarum, a dominant grass on Texas coastal dunes. In a greenhouse experiment, we manipulated the identity of native soil amendments (from P. amarum, Uniola paniculata, or unvegetated areas), the presence of soil microbes in the native soil amendments (live or sterile), and the presence of the commercial AM fungi (present or absent). Native soils from vegetated areas contained 149% more AM fungal spores than unvegetated areas. The commercial AM fungi, when combined with previously vegetated native soils, increased aboveground biomass of P. amarum by 26%. Effects on belowground biomass were weaker, although the addition of any microbes decreased the root:shoot ratio. The origin of native soil amendments can influence restoration outcomes. In this case soil from areas with vegetation outperformed soil from areas without vegetation. Combining native soils with commercial AM fungi may provide a strategy for increasing plant performance while also maintaining other ecosystem functions provided by native microbes.

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.

Quantifying the effects of Robinia pseudoacacia afforestation on plant community structure from a functional perspective: New prospects for management practices on the hilly and gullied Loess Plateau, China

Robinia pseudoacacia is regarded as a valuable but problematic plant due to its positive and negative environmental effects. A comprehensive and mechanistic understanding of the effects of R. pseudoacacia afforestation on ecosystems and striking a balance between ecosystem safety and functioning and R. pseudoacacia naturalization are crucially important. To achieve these goals, studying the community functional structure of R. pseudoacacia plantations is an essential prerequisite that remains understudied. Through quantifying and comparing the functional structure of R. pseudoacacia plantations and naturally restored communities relating to soil erosion control and plant ecology strategies along a 10-40-year chronosequence on the hilly and gullied Loess Plateau, China, we assessed the effects of R. pseudoacacia afforestation on plant community structure from a functional perspective. We found significant differences among restoration strategies in all the functional composition indices but only functional divergence (FDiv) indices, suggesting that the afforestation practice had a great impact on functional composition but not on functional diversity. Specifically, the plantations had relatively high community-weighted means (CWMs) of specific leaf area (SLA), plant height (PH), seed production, seed mass, root mean diameter, clonality and resprouting capacity and high FDivs of the leaf-height-seed scheme and persistence traits, partially suggesting that the exotic tree could naturalize and coexist with native plants in the study area. Moreover, the relatively high CWMs of woodiness, PH and SLA and high FDiv of erosion-control-related traits found in the plantations indicate that the plantations might have superiority in soil erosion control. R. pseudoacacia also had a homogenization effect on understory functional composition and divergence. Furthermore, we proposed a trait-based effect-and-response framework to find the balance, thus achieving sustainable coexistence of the exotic species with ecosystems. This study may provide new prospects for management practices of R. pseudoacacia plantations and a robust scaffold to maintain safe, resilient and functioning ecosystems.

Nematodes as Drivers of Plant Performance in Natural Systems

Nematodes form an important part of soil biodiversity as the most abundant and functionally diverse animals affecting plant performance. Most studies on plant-nematode interactions are focused on agriculture, while plant-nematode interactions in nature are less known. Here we highlight that nematodes can contribute to vegetation dynamics through direct negative effects on plants, and indirect positive effects through top-down predation on plant-associated organisms. Global change alters these interactions, of which better understanding is rapidly needed to better predict functional consequences. By expanding the knowledge of plant-nematode interactions in natural systems, an increase in basic understanding of key ecological topics such as plant-soil interactions and plant invasion dynamics will be obtained, while also increasing the insights and potential biotic repertoire to be applicable in sustainable plant management.

Residence time determines invasiveness and performance of garlic mustard (Alliaria petiolata) in North America

While biological invasions have the potential for large negative impacts on local communities and ecological interactions, increasing evidence suggests that species once considered major problems can decline over time. Declines often appear driven by natural enemies, diseases or evolutionary adaptations that selectively reduce populations of naturalised species and their impacts. Using permanent long-term monitoring locations, we document declines of Alliaria petiolata (garlic mustard) in eastern North America with distinct local and regional dynamics as a function of patch residence time. Projected site-specific population growth rates initially indicated expanding populations, but projected population growth rates significantly decreased over time and at the majority of sites fell below 1, indicating declining populations. Negative soil feedback provides a potential mechanism for the reported disappearance of ecological dominance of A. petiolata in eastern North America.

Plant-soil interactions limit lifetime fitness outside a native plant's geographic range margin

Plant species' distributions are often thought to overwhelmingly reflect their climatic niches. However, climate represents only a fraction of the n-dimensional environment to which plant populations adapt, and studies are increasingly uncovering strong effects of nonclimatic factors on species' distributions. We used a manipulative, factorial field experiment to quantify the effects of soil environment and precipitation (the putatively overriding climatic factor) on plant lifetime fitness outside the geographic range boundary of a native California annual plant. We grew plants outside the range edge in large mesocosms filled with soil from either within or outside the range, and plants were subjected to either a low (ambient) or high (supplemental) spring precipitation treatment. Soil environment had large effects on plant lifetime fitness that were similar in magnitude to the effects of precipitation. Moreover, mean fitness of plants grown with within-range soil in the low precipitation treatment approximated that of plants grown with beyond-range soil in the high precipitation treatment. The positive effects of within-range soil persisted in the second, wetter year of the experiment, though the magnitude of the soil effect was smaller than in the first, drier year. These results are the first we know of to quantify the effects of edaphic variation on plant lifetime fitness outside a geographic range limit and highlight the need to include factors other than climate in models of species' distributions.

Soil precipitation legacies influence intraspecific plant-soil feedback

Feedbacks between plants and soil microbial communities can play an important role in structuring plant communities. However, little is known about how soil legacies caused by environmental disturbances such as drought and extreme precipitation events may affect plant-soil feedback or whether plant-soil feedback operates within species as it does between species. If soil legacies alter plant-soil feedback among genotypes within a plant species, then soil legacies may alter the diversity within plant populations. We conducted a fully factorial pairwise plant-soil feedback experiment to test how precipitation legacies influenced intraspecific plant-soil feedbacks among three genotypes of a dominant grass species, Panicum virgatum. Panicum virgatum experienced negative intraspecific plant-soil feedback, i.e., genotypes generally performed worse on soil from the same genotype than different genotypes. Soil precipitation legacies reversed the rank order of the strength of negative feedback among the genotypes. Feedback is often positively correlated with plant relative abundance. Therefore, our results suggest that soil precipitation legacies may alter the genotypic composition of P. virgatum populations, favoring genotypes that develop less negative feedback. Changes in intraspecific diversity will likely further affect community structure and ecosystem functioning, and may constrain the ability of populations to respond to future changes in climate.

Living Litter: Dynamic Trait Spectra Predict Fauna Composition

Understanding what drives soil fauna species composition through space and time is crucial because we should preserve soil fauna biodiversity and its key role in ecosystem functioning in this era of fast environmental change. As plant leaf litter provides both food and habitat for soil fauna, a focus on litter traits that relate to these two functions will help in understanding soil invertebrate community structure and dynamics comprehensively. To advance this agenda, we propose a conceptual framework to explicitly link the invertebrate community composition to the temporal dynamics of the litter trait space defined by two axes: a food-quality axis related to plant resource economics and chemistry and a habitat-quality axis related to litter particle size and shape.

Plant community composition steers grassland vegetation via soil legacy effects

Soil legacy effects are commonly highlighted as drivers of plant community dynamics and species co-existence. However, experimental evidence for soil legacy effects of conditioning plant communities on responding plant communities under natural conditions is lacking. We conditioned 192 grassland plots using six different plant communities with different ratios of grasses and forbs and for different durations. Soil microbial legacies were evident for soil fungi, but not for soil bacteria, while soil abiotic parameters did not significantly change in response to conditioning. The soil legacies affected the composition of the succeeding vegetation. Plant communities with different ratios of grasses and forbs left soil legacies that negatively affected succeeding plants of the same functional type. We conclude that fungal-mediated soil legacy effects play a significant role in vegetation assembly of natural plant communities.

Soil Biodiversity Integrates Solutions for a Sustainable Future

Soils are home to more than 25% of the earth’s total biodiversity and supports life on land and water, nutrient cycling and retention, food production, pollution remediation, and climate regulation. Accumulating evidence demonstrates that multiple sustainability goals can be simultaneously addressed when soil biota are put at the center of land management assessments; this is because the activity and interactions of soil organisms are intimately tied to multiple processes that ecosystems and society rely on. With soil biodiversity at the center of multiple globally relevant sustainability programs, we will be able to more efficiently and holistically achieve the Sustainable Development Goals and Aichi Biodiversity Targets. Here we review scenarios where soil biota can clearly support global sustainability targets, global changes and pressures that threaten soil biodiversity, and actions to conserve soil biodiversity and advance sustainability goals. This synthesis shows how the latest empirical evidence from soil biological research can shape tangible actions around the world for a sustainable future.

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.

Agricultural production systems can serve as reservoir for human pathogens

Food-borne diseases are a threat to human health and can cause severe economic losses. Nowadays, in a growing and increasingly interconnected world, food-borne diseases need to be dealt with in a global manner. In order to tackle this issue, it is essential to consider all possible entry routes of human pathogens into the production chain. Besides the post-harvest handling of the fresh produce itself, also the prevention of contamination in livestock and agricultural soils are of particular importance. While the monitoring of human pathogens and intervening measures are relatively easy to apply in livestock and post-harvest, the investigation of the prevention strategies in crop fields is a challenging task. Furthermore, crop fields are interconnected with livestock via fertilizers and feed; therefore, a poor hygiene management can cause cross-contamination. In this review, we highlight the possible contamination of crop plants by bacterial human pathogens via the rhizosphere, their interaction with the plant and possible intervention strategies. Furthermore, we discuss critical issues and questions that are still open.

A checklist for choosing between R packages in ecology and evolution

The open source and free programming language R is a phenomenal mechanism to address a multiplicity of challenges in ecology and evolution. It is also a complex ecosystem because of the diversity of solutions available to the analyst.Packages for R enhance and specialize the capacity to explore both niche data/experiments and more common needs. However, the paradox of choice or how we select between many seemingly similar options can be overwhelming and lead to different potential outcomes.There is extensive choice in ecology and evolution between packages for both fundamental statistics and for more specialized domain-level analyses.Here, we provide a checklist to inform these decisions based on the principles of resilience, need, and integration with scientific workflows for evidence.It is important to explore choices in any analytical coding environment-not just R-for solutions to challenges in ecology and evolution, and document this process because it advances reproducible science, promotes a deeper understand of the scientific evidence, and ensures that the outcomes are correct, representative, and robust.