Rooting theories of plant community ecology in microbial interactions

Accumulation of pathogens in soil microbiome can explain long-term fluctuations of legumes in a grassland community

All plant populations fluctuate in time. Apart from the dynamics imposed by external forces such as climate, these fluctuations can be driven by endogenous processes taking place within the community. In this study, we aimed to identify potential role of soil-borne microbial communities in driving endogenous fluctuations of plant populations. We combined a unique, 35-yr long abundance data of 11 common plant species from a species-rich mountain meadow with development of their soil microbiome (pathogenic fungi, arbuscular mycorrhizal fungi and oomycetes) observed during 4 yr of experimental cultivation in monocultures. Plant species which abundance fluctuated highly in the field (particularly legumes) accumulated plant pathogens in their soil mycobiome. We also identified increasing proportion of mycoparasitic fungi under highly fluctuating legume species, which may indicate an adaptation of these species to mitigate the detrimental effects of pathogens. Our study documented that long-term fluctuations in the abundance of plant species in grassland communities can be explained by the accumulation of plant pathogens in plant-soil microbiome. By contrast, we found little evidence of the role of mutualists in plant population fluctuations. These findings offer new insights for understanding mechanisms driving both long-term vegetation dynamics and patterns of species coexistence and richness.

Kiwifruit-Agaricus blazei intercropping effectively improved yield productivity, nutrient uptake, and rhizospheric bacterial community

Intercropping systems have garnered attention as a sustainable agricultural approach for efficient land use, increased ecological diversity in farmland, and enhanced crop yields. This study examined the effect of intercropping on the kiwifruit rhizosphere to gain a deeper understanding of the relationships between cover plants and kiwifruit in this sustainable agricultural system. Soil physicochemical properties and bacterial communities were analyzed using the Kiwifruit-Agaricus blazei intercropping System. Moreover, a combined analysis of 16S rRNA gene sequencing and metabolomic sequencing was used to identify differential microbes and metabolites in the rhizosphere. Intercropping led to an increase in soil physicochemical and enzyme activity, as well as re-shaping the bacterial community and increasing microbial diversity. Proteobacteria, Bacteroidota, Myxococcota, and Patescibacteria were the most abundant and diverse phyla in the intercropping system. Expression analysis further revealed that the bacterial genera BIrii41, Acidibacter, and Altererythrobacter were significantly upregulated in the intercropping system. Moreover, 358 differential metabolites (DMs) were identified between the monocropping and intercropping cultivation patterns, with fatty acyls, carboxylic acids and derivatives, and organooxygen compounds being significantly upregulated in the intercropping system. The KEGG metabolic pathways further revealed considerable enrichment of DMs in ABC transporters, histidine metabolism, and pyrimidine metabolism. This study identified a significant correlation between 95 bacterial genera and 79 soil metabolites, and an interactive network was constructed to explore the relationships between these differential microbes and metabolites in the rhizosphere. This study demonstrated that Kiwifruit-Agaricus blazei intercropping can be an effective, labor-saving, economic, and sustainable practice for reshaping bacterial communities and promoting the accumulation and metabolism of beneficial microorganisms in the rhizosphere.

Arbuscular Mycorrhizal inoculants and its regulatory landscape

One of the most prominent means for sustainable agriculture and ecosystem management are Arbuscular Mycorrhizal (AM) inoculants. These inoculants establish beneficial symbiotic relationships with land plant roots, offering a wide range of benefits, from enhanced nutrient absorption to improved resilience against environmental stressors. However, several currently available commercial AM inoculants face challenges such as inconsistency in field applications, ecological risks associated with non-native strains, and the absence of universal regulations. Currently, regulations for AM inoculants vary globally, with some regions leading efforts to standardize and ensure quality control. Proposed regulatory frameworks aim to establish parameters for composition, safety, and efficacy. Nevertheless, challenges persist in terms of scientific data, standardization, testing under real conditions, and the ecological impact of these inoculants. To address these challenges and unlock the full potential of AM inoculants, increased research funding, public-private partnerships, monitoring, awareness, and ecosystem impact studies are recommended. Future regulations have the potential to improve product quality, soil health, and crop productivity while reducing reliance on chemical inputs and benefiting the environment. However, addressing issues related to compliance, standardization, education, certification, monitoring, and cost is essential for realizing these benefits. Global harmonization and collaborative efforts are vital to maximize their impact on agriculture and ecosystem management, leading to healthier soils, increased crop yields, and a more sustainable agricultural industry.

The Heterogeneous Habitat of Taiga Forests Changes the Soil Microbial Functional Diversity

The soil contains abundant and diverse microorganisms, which interrelate closely with the aboveground vegetation and impact the structure and function of the forest ecosystem. To explore the effect of vegetation diversity on soil microbial functional diversity in taiga forests, we selected significantly different important values of Larix gmelinii as experimental grouping treatments based on plant investigation from fixed plots in Da Xing'anling Mountains. Following that, we collected soil samples and applied the Biolog-ECO microplate method to investigate differences in carbon source utilization, features of functional diversity in soil microorganisms, and factors influencing them in taiga forests. The AWCD decreased as the important value of Larix gmelinii grew, and soil microorganisms preferred carboxylic acids, amino acids, and carbohydrates over polymers, phenolic acids, and amines. The Shannon and McIntosh indexes decreased significantly with the increase of the important value of Larix gmelinii (p < 0.05) and were positively correlated with soil SOC, MBC, C/N, and pH, but negatively with TN, AP, and AN. Redundancy analysis revealed significant effects on soil microbial functional diversity from soil C/N, SOC, AP, MBC, TN, pH, AN, and WC. To sum up, heterogeneous habitats of taiga forests with different important values altered soil microbial functional diversity.

Restoration age affects microbial-herbaceous plant interactions in an oak woodland

In degraded ecosystems, soil microbial communities (SMCs) may influence the outcomes of ecological restoration. Restoration practices can affect SMCs, though it is unclear how variation in the onset of restoration activities in woodlands affects SMCs, how those SMCs influence the performance of hard-to-establish woodland forbs, and how different woodland forbs shape SMCs. In this study, we quantified soil properties and species abundances in an oak woodland restoration chronosequence (young, intermediate, and old restorations). We measured the growth of three woodland forb species when inoculated with live whole-soil from young, intermediate, or old restorations. We used DNA metabarcoding to characterize SMCs of each inoculum treatment and the soil after conditioning by each plant species. Our goals were to (1) understand how time since the onset of restoration affected soil abiotic properties, plant communities, and SMCs in a restoration chronosequence, (2) test growth responses of three forb species to whole-soil inoculum from restoration sites, and (3) characterize changes in SMCs before and after conditioning by each forb species. Younger restored woodlands had greater fire-sensitive tree species and lower concentrations of soil phosphorous than intermediate or older restored woodlands. Bacterial and fungal soil communities varied significantly among sites. Forbs exhibited the greatest growth in soil from the young restoration. Each forb species developed a unique soil microbial community. Our results highlight how restoration practices affect SMCs, which can in turn affect the growth of hard-to-establish forb species. Our results also highlight that the choice of forb species can alter SMCs, which could have long-term potential consequences for restoration success.

Mycoheterotrophy in the wood-wide web

The prevalence and potential functions of common mycorrhizal networks, or the 'wood-wide web', resulting from the simultaneous interaction of mycorrhizal fungi and roots of different neighbouring plants have been increasingly capturing the interest of science and society, sometimes leading to hyperbole and misinterpretation. Several recent reviews conclude that popular claims regarding the widespread nature of these networks in forests and their role in the transfer of resources and information between plants lack evidence. Here we argue that mycoheterotrophic plants associated with ectomycorrhizal or arbuscular mycorrhizal fungi require resource transfer through common mycorrhizal networks and thus are natural evidence for the occurrence and function of these networks, offering a largely overlooked window into this methodologically challenging underground phenomenon. The wide evolutionary and geographic distribution of mycoheterotrophs and their interactions with a broad phylogenetic range of mycorrhizal fungi indicate that common mycorrhizal networks are prevalent, particularly in forests, and result in net carbon transfer among diverse plants through shared mycorrhizal fungi. On the basis of the available scientific evidence, we propose a continuum of carbon transfer options within common mycorrhizal networks, and we discuss how knowledge on the biology of mycoheterotrophic plants can be instrumental for the study of mycorrhizal-mediated transfers between plants.

Genetic relatedness can alter the strength of plant-soil interactions

PREMISE

Intraspecific variation may play a key role in shaping the relationships between plants and their interactions with soil microbial communities. The soil microbes of individual plants can generate intraspecific variation in the responsiveness of the plant offspring, yet have been much less studied. To address this need, we explored how the relatedness of seedlings from established clones of Solidago altissima altered the plant-soil interactions of the seedlings.

METHODS

Seedlings of known parentage were generated from a series of 24 clones grown in a common garden. Seedlings from these crosses were inoculated with soils from maternal, paternal, or unrelated clones and their performance compared to sterilized control inocula.

RESULTS

We found that soil inocula influenced by S. altissima clones had an overall negative effect on seedling biomass. Furthermore, seedlings inoculated with maternal or paternal soils tended to experience larger negative effects than seedlings inoculated with unrelated soils. However, there was much variation among individual crosses, with not all responding to relatedness.

CONCLUSIONS

Our data argue that genetic relatedness to the plant from which the soil microbial inoculum was obtained may cause differential impacts on establishing seedlings, encouraging the regeneration of non-kin adjacent to established clones. Such intraspecific variation represents a potentially important source of heterogeneity in plant-soil microbe interactions with implications for maintaining population genetic diversity.

Chemically Mediated Plant-Plant Interactions: Allelopathy and Allelobiosis

Plant-plant interactions are a central driver for plant coexistence and community assembly. Chemically mediated plant-plant interactions are represented by allelopathy and allelobiosis. Both allelopathy and allelobiosis are achieved through specialized metabolites (allelochemicals or signaling chemicals) produced and released from neighboring plants. Allelopathy exerts mostly negative effects on the establishment and growth of neighboring plants by allelochemicals, while allelobiosis provides plant neighbor detection and identity recognition mediated by signaling chemicals. Therefore, plants can chemically affect the performance of neighboring plants through the allelopathy and allelobiosis that frequently occur in plant-plant intra-specific and inter-specific interactions. Allelopathy and allelobiosis are two probably inseparable processes that occur together in plant-plant chemical interactions. Here, we comprehensively review allelopathy and allelobiosis in plant-plant interactions, including allelopathy and allelochemicals and their application for sustainable agriculture and forestry, allelobiosis and plant identity recognition, chemically mediated root-soil interactions and plant-soil feedback, and biosynthesis and the molecular mechanisms of allelochemicals and signaling chemicals. Altogether, these efforts provide the recent advancements in the wide field of allelopathy and allelobiosis, and new insights into the chemically mediated plant-plant interactions.

An Overview of Mycorrhiza in Pines: Research, Species, and Applications

In the latest literature, climate models show that the conditions for pines, spruces, larches, and birches will deteriorate significantly. In Poland, as well as in other European countries, there are already signs of the decline of these species. This review article deals with the symbiotic relationships between fungi and plants, which can hardly be overestimated, using the example of pine trees. These are the oldest known symbiotic relationships, which are of great benefit to both components and can help plants, in particular, survive periods of severe drought and the attack of pathogens on the roots. This article describes symbioses and their causal conditions, as well as the mycorrhizal components of pine trees and their properties; characterizes ectomycorrhizal fungi and their mushroom-forming properties; and provides examples of the cultivation of pure fungal cultures, with particular attention to the specificity of the mycorrhizal structure and its effects on the growth and development of Pinus species. Finally, the role of mycorrhiza in plant protection and pathogen control is described.

Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages?

Soil history has been shown to condition future rhizosphere microbial communities. However, previous experiments have also illustrated that mature, adult plants can "re-write," or mask, different soil histories through host plant-soil community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Thus, here we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere, and roots of the B. napus hosts at different growth stages-the initial seeding conditions, seedling, rosette, bolting, and flower-from all three soil history plots. We compared composition and diversity of the B. napus soil bacterial communities, as estimated using 16S rRNA gene metabarcoding, to identify any changes associated with soil history and growth stages. We found that soil history remained significant across each growth stage in structuring the bacterial bulk soil and rhizosphere communities, but not the bacterial root communities. This suggests that the host plant's capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil history's identity remain present, such that the previously established soil history continues to impact the bacterial rhizosphere communities, but not the root communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.

Tree seedling functional traits mediate plant-soil feedback survival responses across a gradient of light availability

1. Though not often examined together, both plant-soil feedbacks (PSFs) and functional traits have important influences on plant community dynamics and could interact. For example, seedling functional traits could impact seedling survivorship responses to soils cultured by conspecific versus heterospecific adults. Furthermore, levels of functional traits could vary with soil culturing source. In addition, these relationships might shift with light availability, which can affect trait values, microbe abundance, and whether mycorrhizal colonization is mutualistic or parasitic to seedlings. 2. To determine the extent to which functional traits mediate PSFs via seedling survival, we conducted a field experiment. We planted seedlings of four temperate tree species across a gradient of light availability and into soil cores collected beneath conspecific (sterilized and live) and heterospecific adults. We monitored seedling survival twice per week over one growing season, and we randomly selected subsets of seedlings to measure mycorrhizal colonization and phenolics, lignin, and NSC levels at three weeks. 3. Though evidence for PSFs was limited, Acer saccharum seedlings exhibited positive PSFs (i.e., higher survival in conspecific than heterospecific soils). In addition, soil microbes had a negative effect on A. saccharum and Prunus serotina seedling survival, with reduced survival in live versus sterilized conspecific soil. In general, we found higher trait values (measured amounts of a given trait) in conspecific than heterospecific soils and higher light availability. Additionally, A. saccharum survival increased with higher levels of phenolics, which were higher in conspecific soils and high light. Quercus alba survival decreased with higher AMF colonization. 4. We demonstrate that functional trait values in seedlings as young as three weeks vary in response to soil source and light availability. Moreover, seedling survivorship was associated with trait values for two species, despite both drought and heavy rainfall during the growing season that may have obscured survivorship-trait relationships. These results suggest that seedling traits could have an important role in mediating the effects of local soil source and light levels on seedling survivorship and thus plant traits could have an important role in PSFs.

Modelling how negative plant-soil feedbacks across life stages affect the spatial patterning of trees

In this work, we theoretically explore how litter decomposition processes and soil-borne pathogens contribute to negative plant-soil feedbacks, in particular in transient and stable spatial organisation of tropical forest trees and seedlings known as Janzen-Connell distributions. By considering soil-borne pathogens and autotoxicity both separately and in combination in a phenomenological model, we can study how both factors may affect transient dynamics and emerging Janzen-Connell distributions. We also identify parameter regimes associated with different long-term behaviours. Moreover, we compare how the strength of negative plant-soil feedbacks was mediated by tree germination and growth strategies, using a combination of analytical approaches and numerical simulations. Our interdisciplinary investigation, motivated by an ecological question, allows us to construct important links between local feedbacks, spatial self-organisation, and community assembly. Our model analyses contribute to understanding the drivers of biodiversity in tropical ecosystems, by disentangling the abilities of two potential mechanisms to generate Janzen-Connell distributions. Furthermore, our theoretical results may help guiding future field data analyses by identifying spatial signatures in adult tree and seedling distribution data that may reflect the presence of particular plant-soil feedback mechanisms.

Impacts of 10 Years of Elevated CO2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field

Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.

Mycorrhizal feedbacks influence global forest structure and diversity

One mechanism proposed to explain high species diversity in tropical systems is strong negative conspecific density dependence (CDD), which reduces recruitment of juveniles in proximity to conspecific adult plants. Although evidence shows that plant-specific soil pathogens can drive negative CDD, trees also form key mutualisms with mycorrhizal fungi, which may counteract these effects. Across 43 large-scale forest plots worldwide, we tested whether ectomycorrhizal tree species exhibit weaker negative CDD than arbuscular mycorrhizal tree species. We further tested for conmycorrhizal density dependence (CMDD) to test for benefit from shared mutualists. We found that the strength of CDD varies systematically with mycorrhizal type, with ectomycorrhizal tree species exhibiting higher sapling densities with increasing adult densities than arbuscular mycorrhizal tree species. Moreover, we found evidence of positive CMDD for tree species of both mycorrhizal types. Collectively, these findings indicate that mycorrhizal interactions likely play a foundational role in global forest diversity patterns and structure.

Plant productivity response to inter- and intra-symbiont diversity: Mechanisms, manifestations and meta-analyses

Symbiont diversity can have large effects on plant growth but the mechanisms generating this relationship remain opaque. We identify three potential mechanisms underlying symbiont diversity-plant productivity relationships: provisioning with complementary resources, differential impact of symbionts of varying quality and interference between symbionts. We connect these mechanisms to descriptive representations of plant responses to symbiont diversity, develop analytical tests differentiating these patterns and test them using meta-analysis. We find generally positive symbiont diversity-plant productivity relationships, with relationship strength varying with symbiont type. Inoculation with symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia) yields strongly positive relationships, consistent with complementary benefits from functionally distinct symbionts. In contrast, inoculation with symbionts from the same guild yields weak relationships, with co-inoculation not consistently generating greater growth than the best individual symbiont, consistent with sampling effects. The statistical approaches we outline, along with our conceptual framework, can be used to further explore plant productivity and community responses to symbiont diversity, and we identify critical needs for additional research to explore context dependency in these relationships.

Phosphorus availability and planting patterns regulate soil microbial effects on plant performance in a semiarid steppe

BACKGROUND AND AIMS

Growing evidence has suggested that plant responses to model soil microorganisms are context dependent; however, few studies have investigated the effects of whole soil microbial communities on plant performance in different abiotic and biotic conditions. To address this, we examined how soil phosphorus (P) availability and different planting patterns regulate soil microbial effects on the growth of two native plant species in a semiarid steppe.

METHODS

We carried out a glasshouse experiment to explore the effects of the whole indigenous soil microbiota on the growth and performance of Leymus chinensis and Cleistogenes squarrosa using soil sterilization with different soil P availabilities and planting patterns (monoculture and mixture). Transcriptome sequencing (RNA-seq) was used to explain the potential molecular mechanisms of the soil microbial effects on C. squarrosa.

KEY RESULTS

The soil sterilization treatment significantly increased the biomass of L. chinensis and C. squarrosa in both monoculture and mixture conditions, which indicated that the soil microbiota had negative growth effects on both plants. The addition of P neutralized the negative microbial effects for both L. chinensis and C. squarrosa, whereas the mixture treatment amplified the negative microbial effects on L. chinensis but alleviated them on C. squarrosa. Transcriptomic analysis from C. squarrosa roots underscored that the negative soil microbial effects were induced by the upregulation of defence genes. The P addition treatment resulted in significant decreases in the number of differentially expressed genes attributable to the soil microbiota, and some defence genes were downregulated.

CONCLUSIONS

Our results underline that indigenous soil microbiota have negative effects on the growth of two dominant plant species from a semiarid steppe, but their effects are highly dependent on the soil P availability and planting patterns. They also indicate that defence genes might play a key role in controlling plant growth responses to the soil microbiota.

Interplant carbon and nitrogen transfers mediated by common arbuscular mycorrhizal networks: beneficial pathways for system functionality

Arbuscular mycorrhizal fungi (AMF) are ubiquitous in soil and form nutritional symbioses with ~80% of vascular plant species, which significantly impact global carbon (C) and nitrogen (N) biogeochemical cycles. Roots of plant individuals are interconnected by AMF hyphae to form common AM networks (CAMNs), which provide pathways for the transfer of C and N from one plant to another, promoting plant coexistence and biodiversity. Despite that stable isotope methodologies (¹³C, ¹⁴C and ¹⁵N tracer techniques) have demonstrated CAMNs are an important pathway for the translocation of both C and N, the functioning of CAMNs in ecosystem C and N dynamics remains equivocal. This review systematically synthesizes both laboratory and field evidence in interplant C and N transfer through CAMNs generated through stable isotope methodologies and highlights perspectives on the system functionality of CAMNs with implications for plant coexistence, species diversity and community stability. One-way transfers from donor to recipient plants of 0.02-41% C and 0.04-80% N of recipient C and N have been observed, with the reverse fluxes generally less than 15% of donor C and N. Interplant C and N transfers have practical implications for plant performance, coexistence and biodiversity in both resource-limited and resource-unlimited habitats. Resource competition among coexisting individuals of the same or different species is undoubtedly modified by such C and N transfers. Studying interplant variability in these transfers with ¹³C and ¹⁵N tracer application and natural abundance measurements could address the eco physiological significance of such CAMNs in sustainable agricultural and natural ecosystems.

Effects of scale and contrast of spatial heterogeneity in plant-soil feedbacks on plant growth

Spatial heterogeneity in plant-soil feedbacks (PSFs) has been evidenced to influence plant growth. However, it is unclear whether patch size and contrast of PSF heterogeneity influence plant growth. We first conditioned a background soil by seven species separately and then grew each of them in a homogeneous soil and three heterogeneous soils. The first heterogeneous soil (large patch and high contrast; LP-HC) consisted of two large patches, of which one was filled with the sterilized background soil and the other with the conditioned soil. The second heterogeneous soil (small patch and high contrast; SP-HC) consisted of four small patches, of which two were filled the sterilized background soil and the other two with the conditioned soil. The third heterogeneous soil (small patch and low contrast; SP-LC) also consisted of four patches, of which two were filled with a 1:3 (w:w) mixture and the other two with a 3:1 mixture of the sterilized background soil and the conditioned soil. In the homogeneous soil, all patches were filled with a 1:1 mixture of the two soils. Both shoot biomass and root biomass were equal in the homogeneous and heterogeneous soils. No significant growth difference was observed between the SP-HC and LP-HC heterogeneous soil. However, shoot biomass and root biomass of the legume Medicago sativa, and root biomass of the grass Lymus dahuricus were greater in the SP-HC heterogeneous soil than in the SP-LC heterogeneous soil, probably due to enhanced root growth in the conditioned soil. Moreover, plant growth in the heterogeneous soils was associated with plant growth but not soil nutrient availability at the end of the conditioning phase. Our results show for the first time that patch contrast of PSF heterogeneity can influence plant growth via changing root placement and highlight the importance of fundamentally different facets of PSF variability.

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.

Co-occurring epiphytic orchids have specialized mycorrhizal fungal niches that are also linked to ontogeny

Mycorrhizal symbiosis has been related to the coexistence and community assembly of coexisting orchids in few studies despite their obligate dependence on mycorrhizal partners to establish and survive. In hyper-diverse environments like tropical rain forests, coexistence of epiphytic orchids may be facilitated through mycorrhizal fungal specialization (i.e., sets of unique and dominant mycorrhizal fungi associated with a particular host species). However, information on the role of orchid mycorrhizal fungi (OMF) in niche differentiation and coexistence of epiphytic orchids is still scarce. In this study, we sought to identify the variation in fungal preferences of four co-occurring epiphytic orchids in a tropical rainforest in Costa Rica by addressing the identity and composition of their endophytic fungal and OMF communities across species and life stages. We show that the endophytic fungal communities are formed mainly of previously recognized OMF taxa, and that the four coexisting orchid species have both a set of shared mycorrhizal fungi and a group of fungi unique to an orchid species. We also found that adult plants keep the OMF of the juvenile stage while adding new mycobionts over time. This study provides evidence for the utilization of specific OMF that may be involved in niche segregation, and for an aggregation mechanism where adult orchids keep initial fungal mycobionts of the juvenile stage while adding others.

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.

Short-term plant-soil feedback experiment fails to predict outcome of competition observed in long-term field experiment

Mounting evidence suggests that plant-soil feedbacks (PSF) may determine plant community structure. However, we still have a poor understanding of how predictions from short-term PSF experiments compare with outcomes of long-term field experiments involving competing plants. We conducted a reciprocal greenhouse experiment to examine how the growth of prairie grass species depended on the soil communities cultured by conspecific or heterospecific plant species in the field. The source soil came from monocultures in a long-term competition experiment (LTCE; Cedar Creek Ecosystem Science Reserve, MN, USA). Within the LTCE, six species of perennial prairie grasses were grown in monocultures or in eight pairwise competition plots for 12 years under conditions of low or high soil nitrogen availability. In six cases, one species clearly excluded the other; in two cases, the pair appeared to coexist. In year 15, we gathered soil from all 12 soil types (monocultures of six species by two nitrogen levels) and grew seedlings of all six species in each soil type for 7 weeks. Using biomass estimates from this greenhouse experiment, we predicted coexistence or competitive exclusion using pairwise PSFs, as derived by Bever and colleagues, and compared model predictions to observed outcomes within the LTCE. Pairwise PSFs among the species pairs ranged from negative, which is predicted to promote coexistence, to positive, which is predicted to promote competitive exclusion. However, these short-term PSF predictions bore no systematic resemblance to the actual outcomes of competition observed in the LTCE. Other forces may have more strongly influenced the competitive interactions or critical assumptions that underlie the PSF predictions may not have been met. Importantly, the pairwise PSF score derived by Bever et al. is only valid when the two species exhibit an internal equilibrium, corresponding to the Lotka-Volterra competition outcomes of stable coexistence and founder control. Predicting the other two scenarios, competitive exclusion by either species irrespective of initial conditions, requires measuring biomass in uncultured soil, which is methodologically challenging. Subject to several caveats that we discuss, our results call into question whether long-term competitive outcomes in the field can be predicted from the results of short-term PSF experiments.

Role of plant relatedness in plant-soil feedback dynamics of sympatric Asclepias species

Plants affect associated biotic and abiotic edaphic factors, with reciprocal feedbacks from soil characteristics affecting plants. These two-way interactions between plants and soils are collectively known as plant-soil feedbacks (PSFs). The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of PSFs, although the strength and direction of feedbacks among sympatric congeners are not well-understood. We examined plant-soil feedback responses of Asclepias syriaca, a common clonal milkweed species, with several sympatric congeners across a gradient of increasing phylogenetic distances (A. tuberosa, A. viridis, A. sullivantii, and A. verticillata, respectively). Plant-soil feedbacks were measured through productivity and colonization by arbuscular mycorrhizal (AM) fungi. Asclepias syriaca produced less biomass in soils conditioned by the most phylogenetically distant species (A. verticillata), relative to conspecific-conditioned soils. Similarly, arbuscular mycorrhizal (AM) fungal colonization of A. syriaca roots was reduced when grown in soils conditioned by A. verticillata, compared with colonization in plants grown in soil conditioned by any of the other three Asclepias species, indicating mycorrhizal associations are a potential mechanism of observed positive PSFs. This display of differences between the most phylogenetically distant, but not close or intermediate, paring(s) suggests a potential phylogenetic threshold, although other exogenous factors cannot be ruled out. Overall, these results highlight the potential role of phylogenetic distance in influencing positive PSFs through mutualists. The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of plant-soil feedbacks (PSFs), although the strength and direction of feedbacks among sympatric congeners are not well-understood. Congeneric, sympatric milkweeds typically generated positive PSFs in terms of productivity and AM fungal colonization, suggesting the low likelihood of coexistence among tested pairs, with a strength of feedback increasing as the phylogenetic distance increases.

Vertical-scale spatial influence of radial oxygen loss on rhizosphere microbial community in constructed wetland

Complex interactions between plants and microorganisms form the basis of constructed wetlands (CWs) for pollutant removal. In the rhizosphere, radial oxygen loss (ROL) plays a key role in the activity and abundance of functional microorganisms. However, little has been done to explore how ROL would influence the niche differentiation of microbial communities at different vertical spatial scales. We demonstrate that ROL decreases with depth, promoting an oxidation-reduction rhizosphere microecosystem in CWs. The high level of ROL in the upper layer could support the oxygen supply for aerobic bacteria (Haliangium), facilitating the COD (60%) and NH₄⁺-N (50%) removal, whereas the enrichment of denitrifiers (e.g., Hydrogenophaga and Ralstonia) and methanotrophs (Methanobaterium) in the lower layer could stimulate denitrification. The function prediction results further certified that the abundance of genes catalyzing nitrifying and denitrification processes were significantly enhanced in the upper and bottom layers, respectively, which was attributed to the oxygen concentration gradient in the rhizosphere. This study contributes to further unraveling the rhizosphere effect and enables an improved understanding of the decontamination mechanisms of CWs.

Impacts of an invasive filter-feeder on bacterial biodiversity are context dependent

Bacteria represent most of the biodiversity and play key roles in virtually every ecosystem. In doing so, bacteria act as part of complex communities shaped by interactions across all domains of life. Here, we report on direct interactions between bacteria and dreissenid mussels, a group of invasive filter-feeders threatening global aquatic systems due to high filtration rates. Previous studies showed that dreissenids can impact bacterial community structure by changing trait distributions and abundances of specific taxa. However, studies on bacterial community effects were conducted using water from Lake Michigan (an oligotrophic lake) only, and it is unknown whether similar patterns are observed in systems with differing nutrient regimes. We conducted ten short-term dreissenid grazing experiments in 2019 using water from two eutrophic lake regions-the western basin of Lake Erie and Saginaw Bay in Lake Huron. Predation by dreissenids led to decline in overall bacterial abundance and diversity in both lakes. However, feeding on bacteria was not observed during every experiment. We also found that traits related to feeding resistance are less phylogenetically conserved than previously thought. Our results highlight the role of temporal, spatial, and genomic heterogeneity in bacterial response dynamics to a globally important invasive filter feeder.

Identifying and Remediating Soil Microbial Legacy Effects of Invasive Grasses for Restoring California Coastal Sage Scrub Ecosystems

As invasive grasses encroach upon native ecosystems, they have the potential to transform intact California coastal sage scrub (CSS) into non-native grasslands. This occurs—in part—due to legacy effects: changes in soil microbial composition elicited by grass invasions with long-term impacts on soil and native vegetation. Along with direct effects on CSS vegetation, legacy effects may alter microbial communities which may in turn impact native plant growth. To tease apart these factors, we monitored growth in three CSS species inoculated with either uninvaded soil or sterilized uninvaded soil that were subsequently planted into a site characterized by observed microbial legacy effects. Our findings indicate native plant growth can be explained by changes in soil microorganisms. Specifically, native Artemisia californica and Baccharis pilularis grew larger in plots with unsterilized uninvaded soil inoculum, which contained a larger abundance of Gemmatimonadetes and Glomus, compared to the sterilized soil inoculum plots. Therefore, microbial augmentation may not only improve restoration in post-invasive sites but long-term changes in soil microbial communities may be linked to native plant growth. Furthermore, adding uninvaded soil replete with native microbes has the potential to support restoration of invaded sites by promoting native plant survival and establishment in these restored ecosystems.

Plant-microbe symbiosis widens the habitability range of the Daisyworld

Plant-microbe symbiosis is pervasive in the Earth's ecosystems and dates back to the early land colonisation by plants. Mutualistic partnership with rhizobia bacteria and mycorrhizal fungi promotes plant nutrition, growth and diversity, impacting important ecosystem functions. However, how the global behaviour and dynamical properties of an ecosystem are modified by plant-microbe symbiosis is still unclear. To tackle this theoretical question, we resorted to the Daisyworld as a toy model of the global ecosystem. We redesigned the original model to allow accounting for seed production, spreading, germination, and seedling development to mature seed-producing plants to describe how symbiotic and non-symbiotic daisy species differ in these key processes. Using the steady-state and bifurcation analysis of this model, we demonstrate that symbiosis with microbes broadens the habitability range of the Daisyworld by enhancing plant growth and/or facilitating plant access to otherwise uninhabitable nutrient-poor regions.

The culturable seed mycobiome of two Banksia species is dominated by latent saprotrophic and multi-trophic fungi

Seed fungal endophytes play an important beneficial role in the formation of the seedling mycobiome and contribute to plant establishment, but can also occur as latent pathogens and saprotrophs. Current knowledge on the function and diversity of seed fungal endophytes has been gained through studies in agricultural systems whilst knowledge from natural systems is relatively less. We used two co-occurring species from the genus Banksia from four sites in Australia's Sydney Basin Bioregion to investigate the abundance and diversity of seed fungal endophyte communities present in natural ecosystem hosts. Based on results from culturing and DNA sequence analysis of multiple loci, we found that Banksia seeds house a diverse range of fungal endophyte species, that when assigned to functional guilds belonged to multiple trophic modes. Thirty-one of the fungal taxa identified had not been previously reported as endophytes. Amongst the 58 Operational Taxonomic Units identified, Leotiomycetes and Sordariomycetes were the dominant classes and Banksiamyces (Leotiomycetes) and Penicillium (Sordariomycetes) the dominant genera, with many of the species isolated recorded in the literature as having a limited distribution. The two Banksias shared few fungal endophyte species, which were not always present across all study sites. We revealed a 'hidden diversity' within seeds of Banksia from natural ecosystems and provided insights into the influence host species can have on the seed mycobiome.

Biochar amendment reduces cadmium uptake by stimulating cadmium-resistant PGPR in tomato rhizosphere

Biochar amendment in the soil can exert a positive effect in reducing heavy metal toxicity in plants. However, it remains unclear the extent to which this effect is associated with the modulation of plant growth-promoting rhizobacteria (PGPR). Here, we initially conducted a pot experiment using tomato (Solanum lycopersicum L.) as a model plant grown in soil spiked with cadmium. First, we found biochar amendment to result in reduced cadmium uptake in tomato plants and trackable changes in the tomato rhizosphere microbiome. Then, a rhizosphere transplant experiment validated the importance of this microbiome modulation for cadmium-toxicity amelioration. Sequence-based analyses targeted the isolation of representative isolates of PGPR, including Bacillus and Flavisolibacter spp. that displayed in vitro cadmium tolerance and biosorption capabilities (in addition to abilities to solubilize phosphate and produce indole acetic acid). Last, we performed a soil inoculation experiment and confirmed the effectiveness of these isolates in reducing cadmium toxicity in tomato plants. Besides, we found the inoculation of these taxa as single inoculant and in combination to result in increased activities of specific antioxidant enzymes in tomato tissues. Taken together, this study revealed the ecological and physiological mechanisms by which biochar amendment indirectly alleviate cadmium toxicity in tomato plants, in this case, via the modulation and activity of specific PGPR populations. This study provides new insights into strategies able to promote beneficial PGPR in the rhizosphere with potential application to ameliorate heavy metal toxicity in plants.

Evidence for the evolution of native plant response to mycorrhizal fungi in post-agricultural grasslands

Plant-microbe interactions play an important role in structuring plant communities. Arbuscular mycorrhizal fungi (AMF) are particularly important. Nonetheless, increasing anthropogenic disturbance will lead to novel plant-AMF interactions, altering longstanding co-evolutionary trajectories between plants and their associated AMF. Although emerging work shows that plant-AMF response can evolve over relatively short time scales due to anthropogenic change, little work has evaluated how plant AMF response specificity may evolve due to novel plant-mycorrhizal interactions. Here, we examine changes in plant-AMF interactions in novel grassland systems by comparing the mycorrhizal response of plant populations from unplowed native prairies with populations from post-agricultural grasslands to inoculation with both native prairie AMF and non-native novel AMF. Across four plant species, we find support for evolution of differential responses to mycorrhizal inocula types, that is, mycorrhizal response specificity, consistent with expectations of local adaptation, with plants from native populations responding most to native AMF and plants from post-agricultural populations responding most to non-native AMF. We also find evidence of evolution of mycorrhizal response in two of the four plant species, as overall responsiveness to AMF changed from native to post-agricultural populations. Finally, across all four plant species, roots from native prairie populations had lower levels of mycorrhizal colonization than those of post-agricultural populations. Our results report on one of the first multispecies assessment of local adaptation to AMF. The consistency of the responses in our experiment among four species provides evidence that anthropogenic disturbance may have unintended impacts on native plant species' association with AMF, causing evolutionary change in the benefit native plant species gain from native symbioses.

Ectomycorrhizal Networks in the Anthropocene: From Natural Ecosystems to Urban Planning

Trees acquire hydric and mineral soil resources through root mutualistic associations. In most boreal, temperate and Mediterranean forests, these functions are realized by a chimeric structure called ectomycorrhizae. Ectomycorrhizal (ECM) fungi are highly diversified and vary widely in their specificity toward plant hosts. Reciprocally, association patterns of ECM plants range from highly specialist to generalist. As a consequence, ECM symbiosis creates interaction networks, which also mediate plant-plant nutrient interactions among different individuals and drive plant community dynamics. Our knowledge of ECM networks essentially relies on a corpus acquired in temperate ecosystems, whereas the below-ground facets of both anthropogenic ECM forests and inter-tropical forests remain poorly investigated. Here, we successively (1) review the current knowledge of ECM networks, (2) examine the content of early literature produced in ECM cultivated forests, (3) analyze the recent progress that has been made in understanding the place of ECM networks in urban soils, and (4) provide directions for future research based on the identification of knowledge gaps. From the examined corpus of knowledge, we reach three main conclusions. First, the emergence of metabarcoding tools has propelled a resurgence of interest in applying network theory to ECM symbiosis. These methods revealed an unexpected interconnection between mutualistic plants with arbuscular mycorrhizal (AM) herbaceous plants, embedding ECM mycelia through root-endophytic interactions. This affinity of ECM fungi to bind VA and ECM plants, raises questions on the nature of the associated functions. Second, despite the central place of ECM trees in cultivated forests, little attention has been paid to these man-made landscapes and in-depth research on this topic is lacking. Third, we report a lag in applying the ECM network theory to urban soils, despite management initiatives striving to interconnect motile organisms through ecological corridors, and the highly challenging task of interconnecting fixed organisms in urban greenspaces is discussed. In particular, we observe a pauperized nature of resident ECM inoculum and a spatial conflict between belowground human pipelines and ECM networks. Finally, we identify the main directions of future research to make the needed link between the current picture of plant functioning and the understanding of belowground ECM networks.

Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California

Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.

Biotic Interactions as Mediators of Context-Dependent Biodiversity-Ecosystem Functioning Relationships

Biodiversity drives the maintenance and stability of ecosystem functioning as well as many of nature’s benefits to people, yet people cause substantial biodiversity change. Despite broad consensus about a positive relationship between biodiversity and ecosystem functioning (BEF), the underlying mechanisms and their context-dependencies are not well understood. This proposal, submitted to the European Research Council (ERC), aims at filling this knowledge gap by providing a novel conceptual framework for integrating biotic interactions across guilds of organisms, i.e. plants and mycorrhizal fungi, to explain the ecosystem consequences of biodiversity change. The overarching hypothesis is that EF increases when more tree species associate with functionally dissimilar mycorrhizal fungi. Taking a whole-ecosystem perspective, we propose to explore the role of tree-mycorrhiza interactions in driving BEF across environmental contexts and how this relates to nutrient dynamics. Given the significant role that mycorrhizae play in soil nutrient and water uptake, BEF relationships will be investigated under normal and drought conditions. Resulting ecosystem consequences will be explored by studying main energy channels and ecosystem multifunctionality using food web energy fluxes and by assessing carbon storage. Synthesising drivers of biotic interactions will allow us to understand context-dependent BEF relationships. This interdisciplinary and integrative project spans the whole gradient from local-scale process assessments to global relationships by building on unique experimental infrastructures like the MyDiv Experiment, iDiv Ecotron and the global network TreeDivNet, to link ecological mechanisms to reforestation initiatives. This innovative combination of basic scientific research with real-world interventions links trait-based community ecology, global change research and ecosystem ecology, pioneering a new generation of BEF research and represents a significant step towards implementing BEF theory for human needs.

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.

No robust multispecies coexistence in a canonical model of plant-soil feedbacks

Plant–soil feedbacks (PSFs) are considered a key mechanism generating frequency‐dependent dynamics in plant communities. Negative feedbacks, in particular, are often invoked to explain coexistence and the maintenance of diversity in species‐rich communities. However, the primary modelling framework used to study PSFs considers only two plant species, and we lack clear theoretical expectations for how these complex interactions play out in communities with natural levels of diversity. Here, we extend this canonical model of PSFs to include an arbitrary number of plant species and analyse the dynamics. Surprisingly, we find that coexistence of more than two species is virtually impossible, suggesting that alternative theoretical frameworks are needed to describe feedbacks observed in diverse natural communities. Drawing on our analysis, we discuss future directions for PSF models and implications for experimental study of PSF‐mediated coexistence in the field.

Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought

Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems. This article is protected by copyright. All rights reserved.

Inorganic phosphorus nutrition in green-leaved terrestrial orchid seedlings

BACKGROUND AND AIMS

Many terrestrial orchids have an obligate dependence on their mycorrhizal associations for nutrient acquisition, particularly during germination and early seedling growth. Though important in plant growth and development, phosphorus (P) nutrition studies in mixotrophic orchids have been limited to only a few orchid species and their fungal symbionts. For the first time, we demonstrate the role of a range of fungi in the acquisition and transport of inorganic P to four phylogenetically distinct green-leaved terrestrial orchid species (Diuris magnifica, Disa bracteata, Pterostylis sanguinea and Microtis media subsp. media) that naturally grow in P-impoverished soils.

METHODS

Mycorrhizal P uptake and transfer to orchids was determined and visualized using agar microcosms with a diffusion barrier between P source (33P orthophosphate) and orchid seedlings, allowing extramatrical hyphae to reach the source.

KEY RESULTS

Extramatrical hyphae of the studied orchid species were effective in capturing and transporting inorganic P into the plant. Following 7 d of exposure, between 0.5 % (D. bracteata) and 47 % (D. magnifica) of the P supplied was transported to the plants (at rates between 0.001 and 0.097 fmol h-1). This experimental approach was capable of distinguishing species based on their P-foraging efficiency, and highlighted the role that fungi play in P nutrition during early seedling development.

CONCLUSIONS

Our study shows that orchids occurring naturally on P-impoverished soils can obtain significant amounts of inorganic P from their mycorrhizal partners, and significantly more uptake of P supplied than previously shown in other green-leaved orchids. These results provide support for differences in mycorrhiza-mediated P acquisition between orchid species and fungal symbionts in green-leaved orchids at the seedling stage. The plant-fungus combinations of this study also provide evidence for plant-mediated niche differentiation occurring, with ecological implications in P-limited systems.

Ectomycorrhizal fungi mediate belowground carbon transfer between pines and oaks

Inter-kingdom belowground carbon (C) transfer is a significant, yet hidden, biological phenomenon, due to the complexity and highly dynamic nature of soil ecology. Among key biotic agents influencing C allocation belowground are ectomycorrhizal fungi (EMF). EMF symbiosis can extend beyond the single tree-fungus partnership to form common mycorrhizal networks (CMNs). Despite the high prevalence of CMNs in forests, little is known about the identity of the EMF transferring the C and how these in turn affect the dynamics of C transfer. Here, Pinus halepensis and Quercus calliprinos saplings growing in forest soil were labeled using a ¹³CO₂ labeling system. Repeated samplings were applied during 36 days to trace how ¹³C was distributed along the tree-fungus-tree pathway. To identify the fungal species active in the transfer, mycorrhizal fine root tips were used for DNA-stable isotope probing (SIP) with ¹³CO₂ followed by sequencing of labeled DNA. Assimilated ¹³CO₂ reached tree roots within four days and was then transferred to various EMF species. C was transferred across all four tree species combinations. While Tomentella ellisii was the primary fungal mediator between pines and oaks, Terfezia pini, Pustularia spp., and Tuber oligospermum controlled C transfer among pines. We demonstrate at a high temporal, quantitative, and taxonomic resolution, that C from EMF host trees moved into EMF and that C was transferred further to neighboring trees of similar and distinct phylogenies.

Nutrients Regulate the Effects of Arbuscular Mycorrhizal Fungi on the Growth and Reproduction of Cherry Tomato

Arbuscular mycorrhizal fungi (AMF) colonize the rhizosphere of plants and form a symbiotic association with plants. Mycorrhizal symbionts have diversified ecological roles and functions which are affected by soil conditions. Understanding the effects of different AMF inoculation on plants under varied nutritional conditions is of great significance for further understanding the effects of the external environment regulating mycorrhizal symbiosis on plant phenotypic traits. In this study, the effects of four AMF inoculation treatments on the growth and reproductive performance of cherry tomato (Solanum lycopersicum var. cerasiforme) were investigated under three nutrient levels by pot experiment. It was found that the growth-promoting effect of AMF on cherry tomato decreased with nutrient reduction, and the effects of the same AMF inoculation treatment on cherry tomato were different at different nutrient levels. Nutrient levels and AMF had interactive effects on flower characteristics, fruit yield, resource allocation, and seed germination of the cherry tomato. In addition, AMF could promote sexual reproductive investment. Nutrient levels and AMF also affected the accumulation of nitrogen and phosphorus in cherry tomato, and there were significant differences among different AMF inoculation treatments. The results indicated that nutrient differences could affect the symbiosis between AMF and plants, and confirmed that there were differences in the effects of the four AMF inoculation treatments on the growth and reproductive traits of plants. The differences in growth and reproduction characteristics of cherry tomato between different AMF inoculation treatments at different nutrient levels indicated that the effects of AMF mycorrhizal on the traits of cherry tomato were regulated by nutrients.

Niche expansion via acquired metabolism facilitates competitive dominance in planktonic communities

Acquired phototrophs, organisms that obtain their photosynthetic abilities by hosting endosymbionts or stealing plastids from their prey, are omnipresent in aquatic ecosystems. This acquisition of photosynthetic metabolism allows for niche expansion, and can therefore influence competition outcomes by alleviating competition for shared resources. Here, we test how acquired metabolism alters competitive outcomes by manipulating light availability to control the energetic contribution of photosynthesis to acquired phototrophs. Using freshwater protists that compete for bacterial prey, we demonstrate light-dependent competition outcomes of acquired phototrophs (Paramecium bursaria) and strict heterotrophs (Colpidium sp.) in laboratory model experiments. We then synthesize these findings using a series of mathematical models, and show that explicitly accounting for resource competition improves model fits. Both empirical and mathematical models predict that the acquired phototroph should increase in competitive dominance with increasing light availability. Our results highlight the importance of acquired metabolism to community dynamics, highlighting the need for more empirical and theoretical studies of this mechanism for niche expansion.

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.

Responses of AM fungal abundance to the drivers of global climate change: A meta-analysis

Arbuscular mycorrhizal fungi (AMF), playing critical roles in carbon cycling, are vulnerable to climate change. However, the responses of AM fungal abundance to climate change are unclear. A global-scale meta-analysis was conducted to investigate the response patterns of AM fungal abundance to warming, elevated CO₂ concentration (eCO₂), and N addition. Both warming and eCO₂ significantly stimulated AM fungal abundance by 18.6% (95%CI: 5.9%-32.8%) and 21.4% (15.1%-28.1%) on a global scale, respectively. However, the response ratios (RR) of AM fungal abundance decreased with the degree of warming while increased with the degree of eCO₂. Furthermore, in warming experiments, as long as the warming exceeded 4 °C, its effects on AM fungal abundance changed from positive to negative regardless of the experimental durations, methods, periods, and ecosystem types. The effects of N addition on AM fungal abundance are -5.4% (-10.6%-0.2%), and related to the nitrogen fertilizer input rate and ecosystem type. The RR of AM fungal abundance is negative in grasslands and farmlands when the degree of N addition exceeds 33.85 and 67.64 kg N ha^-1 yr^-1, respectively; however, N addition decreases AM fungal abundance in forests only when the degree of N addition exceeds 871.31 kg N ha^-1 yr^-1. The above results provide an insight into predicting ecological functions of AM fungal abundance under global changes.

Mycorrhiza governs plant-plant interactions through preferential allocation of shared nutritional resources: A triple (13C, 15N and 33P) labeling study

Plant-plant interactions and coexistence can be directly mediated by symbiotic arbuscular mycorrhizal (AM) fungi through asymmetric resource exchange between the plant and fungal partners. However, little is known about the effects of AM fungal presence on resource allocation in mixed plant stands. Here, we examined how phosphorus (P), nitrogen (N) and carbon (C) resources were distributed between coexisting con- and heterospecific plant individuals in the presence or absence of AM fungus, using radio- and stable isotopes. Congeneric plant species, Panicum bisulcatum and P. maximum, inoculated or not with Rhizophagus irregularis, were grown in two different culture systems, mono- and mixed-species stands. Pots were subjected to different shading regimes to manipulate C sink-source strengths. In monocultures, P. maximum gained more mycorrhizal phosphorus uptake benefits than P.bisulcatum. However, in the mixed culture, the AM fungus appeared to preferentially transfer nutrients (³³P and ¹⁵N) to P.bisulcatum compared to P. maximum. Further, we observed higher ¹³C allocation to mycorrhiza by P.bisulcatum in mixed- compared to the mono-systems, which likely contributed to improved competitiveness in the mixed cultures of P.bisulcatum vs. P. maximum regardless of the shading regime. Our results suggest that the presence of mycorrhiza influenced competitiveness of the two Panicum species in mixed stands in favor of those with high quality partner, P. bisulcatum, which provided more C to the mycorrhizal networks. However, in mono-species systems where the AM fungus had no partner choice, even the lower quality partner (i.e., P.maximum) could also have benefitted from the symbiosis. Future research should separate the various contributors (roots vs. common mycorrhizal network) and mechanisms of resource exchange in such a multifaceted interaction.

Interaction between bacterial endophytes and host plants

Endophytic bacteria are mainly present in the plant's root systems. Endophytic bacteria improve plant health and are sometimes necessary to fight against adverse conditions. There is an increasing trend for the use of bacterial endophytes as bio-fertilizers. However, new challenges are also arising regarding the management of these newly discovered bacterial endophytes. Plant growth-promoting bacterial endophytes exist in a wide host range as part of their microbiome, and are proven to exhibit positive effects on plant growth. Endophytic bacterial communities within plant hosts are dynamic and affected by abiotic/biotic factors such as soil conditions, geographical distribution, climate, plant species, and plant-microbe interaction at a large scale. Therefore, there is a need to evaluate the mechanism of bacterial endophytes' interaction with plants under field conditions before their application. Bacterial endophytes have both beneficial and harmful impacts on plants but the exact mechanism of interaction is poorly understood. A basic approach to exploit the potential genetic elements involved in an endophytic lifestyle is to compare the genomes of rhizospheric plant growth-promoting bacteria with endophytic bacteria. In this mini-review, we will be focused to characterize the genetic diversity and dynamics of endophyte interaction in different host plants.