Global patterns and drivers of plant-soil microbe interactions

Plant-soil feedback (PSF) is an important mechanism determining plant community dynamics and structure. Understanding the geographic patterns and drivers of PSF is essential for understanding the mechanisms underlying geographic plant diversity patterns. We compiled a large dataset containing 5969 observations of PSF from 202 studies to demonstrate the global patterns and drivers of PSF for woody and non-woody species. Overall, PSF was negative on average and was influenced by plant attributes and environmental settings. Woody species PSFs did not vary with latitude, but non-woody PSFs were more negative at higher latitudes. PSF was consistently more positive with increasing aridity for both woody and non-woody species, likely due to increased mutualistic microbes relative to soil-borne pathogens. These findings were consistent between field and greenhouse experiments, suggesting that PSF variation can be driven by soil legacies from climates. Our findings call for caution to use PSF as an explanation of the latitudinal diversity gradient and highlight that aridity can influence plant community dynamics and structure across broad scales through mediating plant-soil microbe interactions.

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.

Negative plant-soil feedbacks are stronger in agricultural habitats than in forest fragments in the tropical Andes

There is now strong evidence suggesting that interactions between plants and their species-specific antagonistic microbes can maintain native plant community diversity. In contrast, the decay in diversity in plant communities invaded by nonnative plant species might be caused by weakening negative feedback strengths, perhaps because of the increased relative importance of plant mutualists such as arbuscular mycorrhizal fungi (AMF). Although the vast majority of studies examining plant-soil feedbacks have been conducted in a single habitat type, there are fewer studies that have tested how the strength and direction of these feedbacks change across habitats with differing dominating plants. In a fragmented montane agricultural system in Colombia, we experimentally teased apart the relative importance of AMF and non-AMF microbes (a microbial filtrate) to the strength and direction of feedbacks in both native and nonnative plant species. We hypothesized that native tree species of forest fragments would exhibit stronger negative feedbacks with a microbial filtrate that likely contained pathogens than with AMF alone, whereas nonnative plant species, especially a highly invasive dominant grass, would exhibit overall weaker negative feedbacks or even positive feedbacks regardless of the microbial type. We reciprocally inoculated each of 10 plant species separately with either the AMF community or the microbial filtrate originating from their own conspecifics, or with the AMF or microbial filtrate originating from each of the other nine heterospecific plant species. Overall, we found that the strength of negative feedback mediated by the filtrate was much stronger than feedbacks mediated by AMF. Surprisingly, we found that the two nonnative species, Urochloa brizantha and Coffea arabica, experienced stronger negative feedbacks with microbial filtrate than did the native forest tree species, suggesting that species-specific antagonistic microbes accumulate when a single host species dominates, as is the case in agricultural habitats. However, negative feedback between forest trees and agricultural species suggests that soil community dynamics may contribute to the re-establishment of native species into abandoned agricultural lands. Furthermore, our finding of no negative feedbacks among trees in forest fragments may be due to a loss in diversity of those microbes that drive diversity-maintaining processes in intact tropical forests.

Divergence in Diversity and Composition of Root-Associated Fungi Between Greenhouse and Field Studies in a Semiarid Grassland

Investigations of plant-soil feedbacks (PSF) and plant-microbe interactions often rely exclusively on greenhouse experiments, yet we have little understanding of how, and when, results can be extrapolated to explain phenomena in nature. A systematic comparison of microbial communities using the same host species across study environments can inform the generalizability of such experiments. We used Illumina MiSeq sequencing to characterize the root-associated fungi of two foundation grasses from a greenhouse PSF experiment, a field PSF experiment, field monoculture stands, and naturally occurring resident plants in the field. A core community consisting < 10% of total fungal OTU richness but > 50% of total sequence abundance occurred in plants from all study types, demonstrating the ability of field and greenhouse experiments to capture the dominant component of natural communities. Fungal communities were plant species-specific across the study types, with the core community showing stronger host specificity than peripheral taxa. Roots from the greenhouse and field PSF experiments had lower among sample variability in community composition and higher diversity than those from naturally occurring, or planted monoculture plants from the field. Core and total fungal composition differed substantially across study types, and dissimilarity between fungal communities did not predict plant-soil feedbacks measured in experiments. These results suggest that rhizobiome assembly mechanisms in nature differ from the dynamics of short-term, inoculation studies. Our results validate the efficacy of common PSF experiment designs to test soil inoculum effects, and highlight the challenges of scaling the underlying microbial mechanisms of plant responses from whole-community inoculation experiments to natural ecosystems.

Using plant-soil feedbacks to predict plant biomass in diverse communities

It has become clear that plants can create soils that affect subsequent plant growth. However, because plant-soil feedbacks (PSFs) are typically measured in monoculture experiments, it remains unclear to what extent PSFs affect plant growth in communities. Here we used data from a factorial PSF experiment to predict the biomass of 12 species grown in 162 plant community combinations. Five different plant growth models were parameterized with either monoculture biomass data (Null) or with PSF data (PSF) and model predictions were compared to plant growth observed in communities. For each of the five models, PSF model predictions were closer to observed species biomass in communities than Null model predictions. PSFs, which were associated with a 28% difference in plant biomass across soil types, explained 10% more variance than Null models. Results provided strong support for a small role for PSFs in predicting plant growth in communities and suggest several reasons that PSFs, as traditionally measured in monoculture experiments, may overestimate PSF effects in communities. First, monoculture data used in Null models inherently includes "self " PSF effects. Second, PSFs must be large relative to differences in intrinsic growth rates among species to change competitive outcomes. Third, PSFs must vary among species to change species relative abundances.

Framework for assessment and phytoremediation of asbestos-contaminated sites

We examine the feasibility of phytoremediation as an alternative strategy to limit the exposure of asbestos in site with asbestos-containing materials. We collected soils from four locations from two sites-one with naturally occurring asbestos, and another, a superfund site, where asbestos-containing materials were disposed over decades-and performed ecotoxicology tests. We also performed two experiments with crop cultivar and two grasses from serpentine ecotype and cultivar to determined best choice for phytoremediation. Asbestos concentrations in different size fractions of soils varied by orders of magnitude. However, different asbestos concentrations had little effect on germination and root growth. Presence of co-contaminants such as heavy metals and lack of nutrients affected plant growth to different extents, indicating that several of these limiting factors should be considered instead of the primary contaminant of concern. Crop cultivar survived on asbestos-contaminated soil. Grasses from serpentine ecotype did not show higher biomass than the cultivar. Overall, these results showed that soil conditions play a critical role in screening different crop species for phytoremediation and that asbestos concentration has limited to no effect on plant growth. Our study provided a framework for phytoremediation of asbestos-contaminated sites to limit long-term asbestos exposure.

Dissecting Solidago canadensis-soil feedback in its real invasion

The importance of plant-soil feedback (PSF) has long been recognized, but the current knowledge on PSF patterns and the related mechanisms mainly stems from laboratory experiments. We aimed at addressing PSF effects on community performance and their determinants using an invasive forb Solidago canadensis. To do so, we surveyed 81 pairs of invaded versus uninvaded plots, collected soil samples from these pairwise plots, and performed an experiment with microcosm plant communities. The magnitudes of conditioning soil abiotic properties and soil biotic properties by S. canadensis were similar, but the direction was opposite; altered abiotic and biotic properties influenced the production of subsequent S. canadensis communities and its abundance similarly. These processes shaped neutral S. canadensis-soil feedback effects at the community level. Additionally, the relative dominance of S. canadensis increased with its ability of competitive suppression in the absence and presence of S. canadensis-soil feedbacks, and S. canadensis-induced decreases in native plant species did not alter soil properties directly. These findings provide a basis for understanding PSF effects and the related mechanisms in the field conditions and also highlight the importance of considering PSFs holistically.

Co-occurring nonnative woody shrubs have additive and non-additive soil legacies

To maximize limited conservation funds and prioritize management projects that are likely to succeed, accurate assessment of invasive nonnative species impacts is essential. A common challenge to prioritization is a limited knowledge of the difference between the impacts of a single nonnative species compared to the impacts of nonnative species when they co-occur, and in particular predicting when impacts of co-occurring nonnative species will be non-additive. Understanding non-additivity is important for management decisions because the management of only one co-occurring invader will not necessarily lead to a predictable reduction in the impact or growth of the other nonnative plant. Nonnative plants are frequently associated with changes in soil biotic and abiotic characteristics, which lead to plant-soil interactions that influence the performance of other species grown in those soils. Whether co-occurring nonnative plants alter soil properties additively or non-additively relative to their effects on soils when they grow in monoculture is rarely addressed. We use a greenhouse plant-soil feedback experiment to test for non-additive soil impacts of two common invasive nonnative woody shrubs, Lonicera maackii and Ligustrum sinense, in deciduous forests of the southeastern United States. We measured the performance of each nonnative shrub, a native herbaceous community, and a nonnative woody vine in soils conditioned by each shrub singly or together in polyculture. Soils conditioned by both nonnative shrubs had non-additive impacts on native and nonnative performance. Root mass of the native herbaceous community was 1.5 times lower and the root mass of the nonnative L. sinense was 1.8 times higher in soils conditioned by both L. maackii and L. sinense than expected based upon growth in soils conditioned by either shrub singly. This result indicates that when these two nonnative shrubs co-occur, their influence on soils disproportionally favors persistence of the nonnative L. sinense relative to this native herbaceous community, and could provide an explanation of why native species abundance is frequently depressed in these communities. Additionally, the difference between native and nonnative performance demonstrates that invasive impact studies focusing on the impact only of single species can be insufficient for determining the impact of co-occurring invasive plant species.

Plant–microbe interactions along a gradient of soil fertility in tropical dry forest

Theoretical models predict that plant interactions with free-living soil microbes, pathogens and fungal symbionts are regulated by nutrient availability. Working along a steep natural gradient of soil fertility in a Costa Rican tropical dry forest, we examined how soil nutrients affect plant–microbe interactions using two complementary approaches. First, we measured mycorrhizal colonization of roots and soil P availability in 18 permanent plots spanning the soil fertility gradient. We measured root production, root colonization by mycorrhizal fungi, phosphatase activity and Bray P in each of 144 soil cores. Next, in a full-factorial manipulation of soil type and microbial community origin, tree seedlings of Albizia guachapele and Swietenia macrophylla were grown in sterilized high-, intermediate- and low-fertility soils paired with microbial inoculum from each soil type. Seedling growth, biomass allocation and root colonization by mycorrhizas were quantified after 2 mo. In the field, root colonization by mycorrhizal fungi was unrelated to soil phosphorus across a five-fold gradient of P availability. In the shadehouse, inoculation with soil microbes had either neutral or positive effects on plant growth, suggesting that positive effects of mycorrhizal symbionts outweighed negative effects of soil pathogens. The presence of soil microbes had a greater effect on plant biomass than variation in soil nutrient concentrations (although both effects were modest), and plant responses to mycorrhizal inoculation were not dependent on soil nutrients. Taken together, our results emphasize that soil microbial communities can influence plant growth and morphology independently of soil fertility.

Response of AM fungi spore population to elevated temperature and nitrogen addition and their influence on the plant community composition and productivity

To examine the influence of elevated temperature and nitrogen (N) addition on species composition and development of arbuscular mycorrhizal fungi (AMF) and the effect of AMF on plant community structure and aboveground productivity, we conducted a 5-year field experiment in a temperate meadow in northeast China and a subsequent greenhouse experiment. In the field experiment, N addition reduced spore population diversity and richness of AMF and suppressed the spore density and the hyphal length density (HLD). Elevated temperature decreased spore density and diameter and increased the HLD, but did not affect AMF spore population composition. In the greenhouse experiment, AMF altered plant community composition and increased total aboveground biomass in both elevated temperature and N addition treatments; additionally, AMF also increased the relative abundance and aboveground biomass of the grasses Leymus chinensis (Poaceae) and Setaria viridis (Gramineae) and significantly reduced the relative abundance and aboveground biomass of the Suaeda corniculata (Chenopodiaceae). Although elevated temperature and N addition can affect species composition or suppress the development of AMF, AMF are likely to play a vital role in increasing plant diversity and productivity. Notably, AMF might reduce the threat of climate change induced degradation of temperate meadow ecosystems.

An affinity-effect relationship for microbial communities in plant-soil feedback loops

Feedback loops involving soil microorganisms can regulate plant populations. Here, we hypothesize that microorganisms are most likely to play a role in plant-soil feedback loops when they possess an affinity for a particular plant and the capacity to consistently affect the growth of that plant for good or ill. We characterized microbial communities using whole-community DNA fingerprinting from multiple "home-and-away" experiments involving giant ragweed (Ambrosia trifida L.) and common sunflower (Helianthus annuus L.), and we looked for affinity-effect relationships in these microbial communities. Using canonical ordination and partial least squares regression, we developed indices expressing each microorganism's affinity for ragweed or sunflower and its putative effect on plant biomass, and we used linear regression to analyze the relationship between microbial affinity and effect. Significant linear affinity-effect relationships were found in 75 % of cases. Affinity-effect relationships were stronger for ragweed than for sunflower, and ragweed affinity-effect relationships showed consistent potential for negative feedback loops. The ragweed feedback relationships indicated the potential involvement of multiple microbial taxa, resulting in strong, consistent affinity-effect relationships in spite of large-scale microbial variability between trials. In contrast, sunflower plant-soil feedback may involve just a few key players, making it more sensitive to underlying microbial variation. We propose that affinity-effect relationship can be used to determine key microbial players in plant-soil feedback against a low "signal-to-noise" background of complex microbial datasets.

Soil and geography are more important determinants of indigenous arbuscular mycorrhizal communities than management practices in Swiss agricultural soils

Arbuscular mycorrhizal fungi (AMF) are ubiquitous soil fungi, forming mutualistic symbiosis with a majority of terrestrial plant species. They are abundant in nearly all soils, less diverse than soil prokaryotes and other intensively studied soil organisms and thus are promising candidates for universal indicators of land management legacies and soil quality degradation. However, insufficient data on how the composition of indigenous AMF varies along soil and landscape gradients have hampered the definition of baselines and effect thresholds to date. Here, indigenous AMF communities in 154 agricultural soils collected across Switzerland were profiled by quantitative real-time PCR with taxon-specific markers for six widespread AMF species. To identify the key determinants of AMF community composition, the profiles were related to soil properties, land management and site geography. Our results indicate a number of well-supported dependencies between abundances of certain AMF taxa and soil properties such as pH, soil fertility and texture, and a surprising lack of effect of available soil phosphorus on the AMF community profiles. Site geography, especially the altitude and large geographical distance, strongly affected AMF communities. Unexpected was the apparent lack of a strong land management effect on the AMF communities as compared to the other predictors, which could be due to the rarity of highly intensive and unsustainable land management in Swiss agriculture. In spite of the extensive coverage of large geographical and soil gradients, we did not identify any taxon suitable as an indicator of land use among the six taxa we studied.

Belowground biotic complexity drives aboveground dynamics: a test of the soil community feedback model

Feedbacks between soil communities and plants may determine abundance and diversity in plant communities by influencing fitness and competitive outcomes. We tested the core hypotheses of soil community feedback theory: plant species culture distinct soil communities that alter plant performance and the outcome of interspecific competition. We applied this framework to inform the repeated dominance of Solidago canadensis in old-field communities. In glasshouse experiments, we examined the effects of soil communities on four plant species' performance in monoculture and outcomes of interspecific competition. We used terminal restriction fragment length polymorphism (TRFLP) analysis to infer differences in the soil communities associated with these plant species. Soil community origin had strong effects on plant performance, changed the intensity of interspecific competition and even reversed whether plant species were limited by conspecifics or heterospecifics. These plant-soil feedbacks are strong enough to upend winners and losers in classic competition models. Plant species cultured significantly different mycorrhizal fungal and bacterial soil communities, indicating that these feedbacks are likely microbiotic in nature. In old-fields and other plant communities, these soil feedbacks appear common, fundamentally alter the intensity and nature of plant competition and potentially maintain diversity while facilitating the dominance of So. canadensis.

The role of plant-soil feedbacks in driving native-species recovery

The impacts of exotic plants on soil nutrient cycling are often hypothesized to reinforce their dominance, but this mechanism is rarely tested, especially in relation to other ecological factors. In this manuscript we evaluate the influence of biogeochemically mediated plant-soil feedbacks on native shrub recovery in an invaded island ecosystem. The introduction of exotic grasses and grazing to Santa Cruz Island, California, USA, converted native shrublands (dominated by Artemisia californica and Eriogonum arborescens) into exotic-dominated grasslands (dominated by Avena barbata) over a century ago, altering nutrient-cycling regimes. To test the hypothesis that exotic grass impacts on soils alter reestablishment of native plants, we implemented a field-based soil transplant experiment in three years that varied widely in rainfall. Our results showed that growth of Avena and Artemisia seedlings was greater on soils influenced by their heterospecific competitor. Theory suggests that the resulting plant-soil feedback should facilitate the recovery of Artemisia in grasslands, although four years of monitoring showed no such recovery, despite ample seed rain. By contrast, we found that species effects on soils lead to weak to negligible feedbacks for Eriogonum arborescens, yet this shrub readily colonized the grasslands. Thus, plant-soil feedbacks quantified under natural climate and competitive conditions did not match native-plant recovery patterns. We also found that feedbacks changed with climate and competition regimes, and that these latter factors generally had stronger effects on seedling growth than species effects on soils. We conclude that even when plant-soil feedbacks influence the balance between native and exotic species, their influence may be small relative to other ecological processes.

The importance of soil microorganisms for maintaining diverse plant communities in tallgrass prairie

PREMISE OF THE STUDY

According to the "Janzen-Connell hypothesis," soil microorganisms have the potential to increase plant community diversity by mediating negative feedback on plant growth. Evidence for such microbe-driven negative feedback has been found in a variety of terrestrial systems. However, it is currently unknown how general this phenomenon is within most plant communities. Also unknown is the role of mutualists in generating such feedback: do they decrease the influence of soil-mediated negative feedback on plant fitness or do they increase its effect by proliferating with plant hosts to which they give the least benefit? •

METHODS

We investigated soil-microbe-mediated feedback via a series of reciprocal transplant experiments in the greenhouse using soil from a restored tallgrass prairie and native tallgrass prairie plant species. •

KEY RESULTS

We found that negative feedback was very common but that mutualists (arbuscular mycorrhizal fungi) influence plant growth in opposition to the overall negative feedback trend. •

CONCLUSIONS

Widespread microbially mediated negative feedback indicates that plant community diversity and composition in tallgrass prairie are dependent on soil microorganisms. Native soil microorganisms should be considered in restoration efforts of tallgrass prairie and, potentially, other native plant communities.

Native shrub reestablishment in exotic annual grasslands: do ecosystem processes recover?

The impacts of exotic plant species on ecosystem processes are well established, motivating numerous efforts to facilitate native-species recovery. Nonetheless, how the return of native species influences ecosystem processes and how these changes feed back to influence the recovery process are poorly understood. We examined these questions in exotic annual grasslands on Santa Cruz Island, California, USA, where the removal of nonnative herbivores has led to the recovery of the native shrubs Artemisia californica and Eriogonum arborescens. To examine the influence of shrub colonization on nutrient cycling, and the mechanisms by which these changes arise, we measured available nitrogen and phosphorus, and quantified nitrogen mineralization and litterfall rates under shrubs and grasses in the field and in experimental monoculture plots. Both native shrubs altered nitrogen cycling as they colonized the grassland, but they did so in opposite directions. Eriogonum depressed nitrogen pools and mineralization rates via large inputs of nitrogen-poor litter. In contrast Artemisia increased nitrogen and phosphorus pools and nitrogen mineralization rates. Last, to determine if shrub effects on soils favor shrubs or grasses, we conducted a nitrogen and phosphorus fertilization experiment in the field. Only the exotic grass was significantly limited by nitrogen. Thus the depressed nitrogen availability associated with Eriogonum colonization is more harmful to exotic grasses than to the native shrub. By contrast, the elevated nitrogen associated with recovering Artemisia favors grasses over the shrub, possibly hindering recovery of the native. Mechanistic studies of the ecosystem ,impacts of native-plant recovery are useful for managers wishing to predict which native species return ecosystem function, and whether such changes feed back to influence native recovery.