Root traits and belowground herbivores relate to plant-soil feedback variation among congeners

Enhancing intercropping sustainability: Manipulating soybean rhizosphere microbiome through cropping patterns

Understanding the responses of soybean rhizosphere and functional microbiomes in intercropping scenarios holds promise for optimizing nitrogen utilization in legume-based intercropping systems. This study investigated three cropping layouts under film mulching: sole soybean (S), soybean-maize intercropping in one row (IS), and soybean-maize intercropping in two rows (IIS), each subjected to two nitrogen levels: 110 kg N ha-1 (N110) and 180 kg N ha-1 (N180). Our findings reveal that cropping patterns alter bacterial and nifh communities, with approximately 5 % of soybean rhizosphere bacterial amplicon sequence variants (ASVs) and 42 % of rhizosphere nifh ASVs exhibiting altered abundances (termed sensitive ASVs). Root traits and soil properties shape these communities, with root traits exerting greater influence. Sensitive ASVs drive microbial co-occurrence networks and deterministic processes, predicting 85 % of yield variance and 78 % of partial factor productivity of nitrogen, respectively. These alterations impact bacterial and nifh diversity, complexity, stability, and deterministic processes in legume-based intercropping systems, enhancing performance in terms of yield, nitrogen utilization efficiency, land equivalent ratio, root nodule count, and nodule dry weight under IIS patterns with N110 compared to other treatments. Our findings underscore the importance of field management practices in shaping rhizosphere-sensitive ASVs, thereby altering microbial functions and ultimately impacting the productivity of legume-based intercropping systems. This mechanistic understanding of soybean rhizosphere microbial responses to intercropping patterns offers insights for sustainable intercropping enhancements through microbial manipulation.

Multifunctionality promotes the prosperity of riverine planktonic diatoms in plateau

Interpreting the biogeographic distribution and underlying mechanisms of functional traits not only contributes to revealing the spatiotemporal dynamics of species biodiversity but also helps to maintain ecological stability during environmental variations. However, little is known about the functional profiles of diatom communities over large river systems. Herein, we provided the first blueprints about the spatiotemporal distributions and driving forces of functional traits for both planktonic and sedimentary diatoms over the 6030 km continuum of the Yangtze River, with the help of the high-throughput sequencing and functional identification. By investigating the 28 functional traits affiliated into five categories, we found that planktonic diatom functions showed clearer landform-heterogeneity patterns (ANOSIM R = 0.336) than sedimentary functions (ANOSIM R = 0.172) along the river, represented by life-forms and ecological-guilds prominent in water-plateau as well as cell-sizes and life-forms particularly in sediment-plateau. Planktonic diatom functions also displayed higher richness and network complexity in plateau (richness: 58.70 ± 9.30, network edges: 65) than in non-plateau regions (23.82 ± 13.16, 16), promoting the stability and robustness of diatom functions against the high-radiation and low-temperature plateau environment. Environmental selection (mainly exerted by PAR, UV, and Tw) played crucial roles in determining the functional variations of planktonic diatoms (explaining 80.5%) rather than sedimentary diatoms (14.5%) between plateau and non-plateau regions. Meanwhile, planktonic diatom traits within life-forms were identified to be well responsive to the ecological environment quality (r = 0.56-0.60, P < 0.001) in the Yangtze. This study provided comprehensive insights into the multifunctionality of diatoms and their responses to environmental disturbance and environment quality, which helps to develop effective strategies for maintaining ecological stability in changing river environments.

Fungal complexity and stability across afforestation areas in changing desert environments

The great achievements in combating desertification are attributed to large-scale afforestation, yet we lack verification of how the stability of the fungal community changes in afforestation areas in desert environments. Here, we present the fungal network structure from different niches (root and bulk soil) of plantations of Mongolian pine, a crucial species for afforestation introduced widely in desertification regions. We assessed changes in community complexity and stability of root-associated fungi (RAF) and soil fungi (SF) among different introduction sites: the Hulunbuir Desert (HB), the Horqin Desert (HQ) and the Mu Us Desert (MU). To illuminate the complexity and stability of the fungal network, the differences in topological properties, fungal function, and vegetation and environmental factors between introduction sites were fully considered. We showed that (1) the SF networks had more nodes and edges than the RAF networks. There was a lower ratio of negative:positive cohesion of RAF networks in HB and MU. For SF but not for RAF, across the three introduction sites, a higher modularity and ratio of negative:positive cohesion indicated higher stability. (2) Ectomycorrhizal (EcM) fungi were the dominant functional group in the RAF network (especially in HQ), and were only significantly correlated with vegetation factor. There was a higher relative abundance and number of OTUs of saprophytic fungi in the SF network and they showed positive correlations with soil nutrients. (3) RAF and SF network complexity and stability showed different responses to environmental and vegetation variables. The key determinant of the complexity and stability of the SF networks in Mongolian pine plantations was soil nutrients, followed by climate conditions. The composition and structure of the RAF community was closely related to host plants. Therefore, clarifying the complexity and stability of fungal communities in afforestation areas in changing desert environments is helpful for understanding the interactions between the environment, plants and fungi.

Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest

Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw ) and mean nearest neighbor distance (Dnn ) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.

Responses of Soil Microbial Survival Strategies and Functional Changes to Wet-Dry Cycle Events

Soil microbial taxa have different functional ecological characteristics that influence the direction and intensity of plant-soil feedback responses to changes in the soil environment. However, the responses of soil microbial survival strategies to wet and dry events are poorly understood. In this study, soil physicochemical properties, enzyme activity, and high-throughput sequencing results were comprehensively anal0079zed in the irrigated cropland ecological zone of the northern plains of the Yellow River floodplain of China, where Oryza sativa was grown for a long period of time, converted to Zea mays after a year, and then Glycine max was planted. The results showed that different plant cultivations in a paddy-dryland rotation system affected soil physicochemical properties and enzyme activity, and G. max field cultivation resulted in higher total carbon, total nitrogen, soil total organic carbon, and available nitrogen content while significantly increasing α-glucosidase, β-glucosidase, and alkaline phosphatase activities in the soil. In addition, crop rotation altered the r/K-strategist bacteria, and the soil environment was the main factor affecting the community structure of r/K-strategist bacteria. The co-occurrence network revealed the inter-relationship between r/K-strategist bacteria and fungi, and with the succession of land rotation, the G. max sample plot exhibited more stable network relationships. Random forest analysis further indicated the importance of soil electrical conductivity, total carbon, total nitrogen, soil total organic carbon, available nitrogen, and α-glucosidase in the composition of soil microbial communities under wet-dry events and revealed significant correlations with r/K-strategist bacteria. Based on the functional predictions of microorganisms, wet-dry conversion altered the functions of bacteria and fungi and led to a more significant correlation between soil nutrient cycling taxa and environmental changes. This study contributes to a deeper understanding of microbial functional groups while helping to further our understanding of the potential functions of soil microbial functional groups in soil ecosystems.

Plant-soil feedback effects on conspecific and heterospecific successors of annual and perennial Central European grassland plants are correlated

Plant-soil feedbacks (PSFs), soil-mediated plant effects on conspecific or heterospecific successors, are a major driver of vegetation development. It has been proposed that specialist plant antagonists drive differences in PSF responses between conspecific and heterospecific plants, whereas contributions of generalist plant antagonists to PSFs remain understudied. Here we examined PSFs among nine annual and nine perennial grassland species to test whether poorly defended annuals accumulate generalist-dominated plant antagonist communities, causing equally negative PSFs on conspecific and heterospecific annuals, whereas well-defended perennial species accumulate specialist-dominated antagonist communities, predominantly causing negative conspecific PSFs. Annuals exhibited more negative PSFs than perennials, corresponding to differences in root-tissue investments, but this was independent of conditioning plant group. Overall, conspecific and heterospecific PSFs did not differ. Instead, conspecific and heterospecific PSF responses in individual species' soils were correlated. Soil fungal communities were generalist dominated but could not robustly explain PSF variation. Our study nevertheless suggests an important role for host generalists as drivers of PSFs.

Light availability and plant shade tolerance modify plant-microbial interactions and feedbacks in subtropical trees

Plant-soil feedbacks (PSFs) are an important mechanism of species coexistence in forest communities. However, evidence remains limited for how light availability regulates PSFs in species with different shade tolerance via changes in plant-microbial interactions. Here we tested in a glasshouse experiment how PSFs changed as a function of light availability and tree shade tolerance. Soil bacterial and fungal communities were profiled using the 16S rRNA and ITS2 gene sequencing, respectively. Under low light, individual PSFs were positively related to shade tolerance, while the least shade-tolerant species produced the most positive PSFs under high light. Pairwise PSFs between species with contrasting shade tolerance were strongly positive under high light but negative under low light, thereby promoting the dominance of less shade-tolerant species in forest gaps and species coexistence under closed canopy, respectively. Under high light, PSFs were related to soil microbial composition and diversity, with the relative abundance of arbuscular mycorrhizal fungi being the primary driver of PSFs. Under low light, none of soil microbial properties were significantly related to PSFs. These findings indicate PSFs and plant shade tolerance interact to promote species coexistence and improve our understanding of how soil microbes contribute to variation in PSFs.

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.

Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities

Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant-insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil 'memories' that influence aboveground plant community interactions in the next growing season. These soil-borne 'memories' can be altered by climate warming-induced plant range shifts and extreme drought.

The pervasive impact of global climate change on plant-nematode interaction continuum

Pest profiles in today's global food production system are continually affected by climate change and extreme weather. Under varying climatic conditions, plant-parasitic nematodes (PPNs) cause substantial economic damage to a wide variety of agricultural and horticultural commodities. In parallel, their herbivory also accredit to diverse ecosystem services such as nutrient cycling, allocation and turnover of plant biomass, shaping of vegetation community, and alteration of rhizospheric microorganism consortium by modifying the root exudation pattern. Thus PPNs, together with the vast majority of free-living nematodes, act as ecological drivers. Because of direct exposure to the open environment, PPN biology and physiology are largely governed by environmental factors including temperature, precipitation, humidity, atmospheric and soil carbon dioxide level, and weather extremes. The negative effects of climate change such as global warming, elevated CO₂, altered precipitation and the weather extremes including heat waves, droughts, floods, wildfires and storms greatly influence the biogeographic range, distribution, abundance, survival, fitness, reproduction, and parasitic potential of the PPNs. Changes in these biological and ecological parameters associated to the PPNs exert huge impact on agriculture. Yet, depending on how adaptable the species are according to their geo-spatial distribution, the consequences of climate change include both positive and negative effects on the PPN communities. While assorting the effects of climate change as a whole, it can be estimated that the changing environmental factors, on one hand, will aggravate the PPN damage by aiding to abundance, distribution, reproduction, generation, plant growth and reduced plant defense, but the phenomena like sex reversal, entering cryptobiosis, and reduced survival should act in counter direction. This seemingly creates a contraposition effect, where assessing any confluent trend is difficult. However, as the climate change effects will differ according to space and time it is apprehensible that the PPNs will react and adapt according to their location and species specificity. Nevertheless, the bio-ecological shifts in the PPNs will necessitate tweaking their management practices from the agri-horticultural perspective. In this regard, we must aim for a 'climate-smart' package that will take care of the food production, pest prevention and environment protection. Integrated nematode management involving precise monitoring and modeling-based studies of population dynamics in relation to climatic fluctuations with escalated reliance on biocontrol, host resistance, and other safer approaches like crop rotation, crop scheduling, cover cropping, biofumigation, use of farmyard manure (FYM) would surely prove to be viable options. Although the novel nematicidal molecules are target-specific and relatively less harmful to the environment, their application should not be promoted following the global aim to reduce pesticide usage in future agriculture. Thus, having a reliable risk assessment with scenario planning, the adaptive management strategies must be designed to cope with the impending situation and satisfy the farmers' need.

Foliar Pathogen Infection Manipulates Soil Health through Root Exudate-Modified Rhizosphere Microbiome

Negative plant-soil feedback (NPSF) due to the buildup of soilborne pathogens in soil is a major obstacle in sustainable agricultural systems. Beneficial rhizosphere microfloras are recruited by plants, and mediating this has become a strategic priority to manipulate plant health. Here, we found that foliar infection of Panax notoginseng by Alternaria panax changed plant-soil feedback from negative to positive. Foliar infection modified the rhizosphere soil microbial community and reversed the direction of the buildup of the soilborne pathogen Ilyonectria destructans and beneficial microbes, including Trichoderma, Bacillus, and Streptomyces, in rhizosphere soil. These beneficial microbes not only showed antagonistic ability against the pathogen I. destructans but also enhanced the resistance of plants to A. panax. Foliar infection enhanced the exudation of short- and long-chain organic acids, sugars, and amino acids from roots. In vitro and in vivo experiments validated that short- and long-chain organic acids and sugars play dual roles in simultaneously suppressing pathogens but enriching beneficial microbes. In summary, foliar infection could change root secretion to drive shifts in the rhizosphere microbial community to enhance soil health, providing a new strategy to alleviate belowground disease in plants through aboveground inducement. IMPORTANCE Belowground soilborne disease is the main factor limiting sustainable agricultural production and is difficult to manage due to the complexity of the soil environment. Here, we found that aboveground parts of plants infected by foliar pathogens could enhance the secretion of organic acids, sugars, and amino acids in root exudates to suppress soilborne pathogens and enrich beneficial microbes, eventually changing the plant and soil feedback from negative to positive and alleviating belowground soilborne disease. This is an exciting strategy by which to achieve belowground soilborne disease management by manipulating the aboveground state through aboveground stimulation.

Arbuscular mycorrhizal colonization increases plant above-belowground feedback in a northwest Chinese coal mining-degraded soil by increasing photosynthetic carbon assimilation and allocation to maize

A three-compartment culture system was used to study the mechanism by which the AM fungus Funneliformis mosseae influences host plant growth and soil organic carbon (SOC) content in a northwest China coal mining area. A ¹³CO₂ pulse tracing technique was used to trace the allocation of maize photosynthetic C in shoots, roots, AM fungus, and soil. Carbon accumulation and allocation in mycorrhizal (inoculated with Funneliformis mosseae) and non-mycorrhizal treatments were detected. AM fungal inoculation significantly increased the ¹³C concentration and content in both above- and below-ground plant parts and also significantly enhanced anti-aging ability by increasing soluble sugars and catalase activity (CAT) in maize leaves while reducing foliar malondialdehyde content (MDA) and leaf temperature and promoted plant growth. AM fungi also increased P uptake to promote maize growth. Soil organic carbon (SOC), glomalin, microbial biomass carbon (MBC), and nitrogen (MBN) contents increased significantly after inoculation. A mutually beneficial system was established involving maize, the AM fungus and the microbiome, and the AM fungus became an important regulator of C flux between the above- and below-ground parts of the system. Inoculation with the AM fungus promoted plant growth, C fixation and allocation belowground to enhance soil quality. A positive above-belowground feedback appeared to be established.

Drought legacy effects on root morphological traits and plant biomass via soil biota feedback

Drought causes soil feedback effects on plant performance. However, how the linkages between conditioned soil biota and root traits contribute to explain plant-soil feedback (PSF) as a function of drought is unknown. We utilized soil inoculum from a conditioning experiment where grassland species grew under well-watered and drought conditions, and their soil fungi were analyzed. Under well-watered conditions, we grew 21 grassland species with those inocula from either conspecific or heterospecific soils. At harvest, plant biomass and root traits were measured. Negative PSF (higher biomass in heterospecific than in conspecific soils) was predominant, and favored in drought-conditioned soils. Previous drought affected the relationship between root traits and fungal groups. Specific root surface area (SRSA) was higher in heterospecific than in conspecific droughted soils and was linked to an increase in saprotroph richness. Overall, root diameter was higher in conspecific soils and was linked to mutualist and pathogen composition, whereas the decrease of root : shoot in heterospecific soils was linked to pathogenic fungi. Drought legacy affects biomass and root morphological traits via conditioned soil biota, even after the drought conditions have disappeared. This provides new insights into the role that soil biota have modulating PSF responses to drought.

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

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

Towards revealing the global diversity and community assembly of soil eukaryotes

Soil fungi, protists, and animals (i.e., the eukaryome) play a critical role in key ecosystem functions in terrestrial ecosystems. Yet, we lack a holistic understanding of the processes shaping the global distribution of the eukaryome. We conducted a molecular analysis of 193 composite soil samples spanning the world's major biomes. Our analysis showed that the importance of selection processes was higher in the community assemblage of smaller-bodied and wider niche breadth organisms. Soil pH and mean annual precipitation were the primary determinants of the community structure of eukaryotic microbes and animals, respectively. We further found contrasting latitudinal diversity patterns and strengths for soil eukaryotic microbes and animals. Our results point to a potential link between body size and niche breadth of soil eukaryotes and the relative effect of ecological processes and environmental factors in driving their biogeographic patterns.

Effects of arbuscular mycorrhizal fungi on the nitrogen distribution in endangered Torreya jackii under nitrogen limitation

Arbuscular mycorrhizal fungi regulated the distribution of nitrogen in the leaves, thereby facilitating the adaptation of the endangered plant Torreya jackii to a low-nitrogen environment. Rhizophagus irregularis was inoculated into sterilized soil to investigate its impact on the distribution ratio of leaf nitrogen in cell wall proteins, cell membrane proteins, water-soluble proteins, and photosynthetic systems which includes the carboxylation system (P_C), energy metabolism (P_B), and light-harvesting system in the endangered species Torreya jackii. The results showed that R. irregularis reduced the specific leaf weight and the distribution ratio of nitrogen in cell wall proteins in the leaves of T. jackii, whereas it enhanced the distribution ratio of nitrogen in cell membrane proteins and water-soluble proteins. R. irregularis enabled more nitrogen uptake for growth by decreasing the distribution of nitrogen to the structural substances. At low-nitrogen levels, inoculation with R. irregularis improved the plant height (18.78 ~ 36.04%), shoot dry weight (50.53 ~ 64.33%), total dry weight (42.86 ~ 52.82%), maximal net photosynthetic rate (P_max) (16.83 ~ 20.11%), photosynthetic nitrogen use efficiency (PNUE) (40.01 ~ 43.14%), P_C (33.56 ~ 38.59%) and P_B (29.08 ~ 34.02%). However, it did not substantially affect the leaf nitrogen content per unit area or the leaf nitrogen content per unit mass. Moreover, P_max exhibited a significant positive correlation with P_C and P_B, and all three parameters showed a significant positive correlation with the PNUE, thereby revealing that R. irregularis increased the photosynthetic capacity and PNUE of T. jackii through boosting P_C and P_B.

A global overview of the trophic structure within microbiomes across ecosystems

The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.

Plant-Soil Feedbacks and Temporal Dynamics of Plant Diversity-Productivity Relationships

Plant-soil feedback (PSF) and diversity-productivity relationships are important research fields to study drivers and consequences of changes in plant biodiversity. While studies suggest that positive plant diversity-productivity relationships can be explained by variation in PSF in diverse plant communities, key questions on their temporal relationships remain. Here, we discuss three processes that change PSF over time in diverse plant communities, and their effects on temporal dynamics of diversity-productivity relationships: spatial redistribution and changes in dominance of plant species; phenotypic shifts in plant traits; and dilution of soil pathogens and increase in soil mutualists. Disentangling these processes in plant diversity experiments will yield new insights into how plant diversity-productivity relationships change over time.

Protists as main indicators and determinants of plant performance

BACKGROUND

Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes.

RESULTS

Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer.

CONCLUSIONS

We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers. Video abstract.

Nematodes as Drivers of Plant Performance in Natural Systems

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

An invasive plant rapidly increased the similarity of soil fungal pathogen communities

BACKGROUND AND AIMS

Plant invasions can change soil microbial communities and affect subsequent invasions directly or indirectly via foliar herbivory. It has been proposed that invaders promote uniform biotic communities that displace diverse, spatially variable communities (the biotic homogenization hypothesis), but this has not been experimentally tested for soil microbial communities, so the underlying mechanisms and dynamics are unclear. Here, we compared density-dependent impacts of the invasive plant Alternanthera philoxeroides and its native congener A. sessilis on soil fungal communities, and their feedback effects on plants and a foliar beetle.

METHODS

We conducted a plant-soil feedback (PSF) experiment and a laboratory bioassay to examine PSFs associated with the native and invasive plants and a beetle feeding on them. We also characterized the soil fungal community using high-throughput sequencing.

KEY RESULTS

We found locally differentiated soil fungal pathogen assemblages associated with high densities of the native plant A. sessilis but little variation in those associated with the invasive congener A. philoxeroides, regardless of plant density. In contrast, arbuscular mycorrhizal fungal assemblages associated with high densities of the invasive plant were more variable. Soil biota decreased plant shoot mass but their effect was weak for the invasive plant growing in native plant-conditioned soils. PSFs increased the larval biomass of a beetle reared on leaves of the native plant only. Moreover, PSFs on plant shoot and root mass and beetle mass were predicted by different pathogen taxa in a plant species-specific manner.

CONCLUSION

Our results suggest that plant invasions can rapidly increase the similarity of soil pathogen assemblages even at low plant densities, leading to taxonomically and functionally homogeneous soil communities that may limit negative soil effects on invasive plants.

Enemies mediate distance- and density-dependent mortality of tree seeds and seedlings: a meta-analysis of fungicide, insecticide and exclosure studies

Conspecific negative distance- and density-dependence is often assumed to be one of the most important mechanisms controlling forest community assembly and species diversity globally. Plant pathogens, and insect and mammalian herbivores, are the most common natural enemy types that have been implicated in this phenomenon, but their general effects at different plant life stages are still unclear. Here, we conduct a meta-analysis of studies that involved robust manipulative experiments, using fungicides, insecticides and exclosures, to assess the contributions of different natural enemy types to distance- and density-dependent effects at seed and seedling stages. We found that distance- and density-dependent mortality caused by natural enemies was most likely at the seedling stage and was greater at higher mean annual temperatures. Conspecific negative distance- and density-dependence at the seedling stage is significantly weakened when fungicides were applied. By contrast, negative conspecific distance- and density-dependence is not a general pattern at the seed stage. High seed mass reduced distance- and density-dependent mortality at the seed stage. Seed studies excluding only large mammals found significant negative conspecific distance-dependent mortality, but exclusion of all mammals resulted in a non-significant effect of conspecifics. Our study suggests that plant pathogens are a major cause of distance- and density-dependent mortality at the seedling stage, while the impacts of herbivores on seedlings have been understudied. At the seed stage, large and small mammals, respectively, weaken and enhance negative conspecific distance-dependent mortality. Future research should identify specific agents of mortality, investigate the interactions among different enemy types and assess how global change may affect natural enemies and thus influence the strength of conspecific distance- and density-dependence.

Plant genotypic diversity effects on soil nematodes vary with trophic level

At local spatial scales, loss of genetic diversity within species can lead to species loss. Few studies, however, have examined plant genotypic diversity effects across trophic levels. We investigated genotypic diversity effects of Phragmites australis on belowground biomass and soil nematode communities. Our results revealed that belowground plant biomass and nematode abundance responses to plant genotypic diversity were uncoupled. Decreasing plant genotypic diversity decreased the abundance of lower, but not higher trophic level nematodes. Low plant genotypic diversity also decreased the structural footprint and functional indices of nematodes, indicating lowered metabolic functioning of higher trophic level nematodes and decreased soil food web stability. Our study suggests that plant genotypic diversity effects differ across trophic levels, taxonomic groups and ecosystem functions and that decreasing plant genotypic diversity could destabilise belowground food webs. This highlights the importance of conserving intraspecific plant diversity.

Phylogenetic signals and predictability in plant-soil feedbacks

There is strong evidence for a phylogenetic signal in the degree to which species share co-evolved biotic partners and in the outcomes of biotic interactions. This implies there should be a phylogenetic signal in the outcome of feedbacks between plants and the soil microbiota they cultivate. However, attempts to identify a phylogenetic signal in plant-soil feedbacks have produced mixed results. Here we clarify how phylogenetic signals could arise in plant-soil feedbacks and use a recent compilation of data from feedback experiments to identify: whether there is a phylogenetic signal in the outcome of plant-soil feedbacks; and whether any signal arises through directional or divergent changes in feedback outcomes with evolutionary time. We find strong evidence for a divergent phylogenetic signal in feedback outcomes. Distantly related plant species show more divergent responses to each other's soil microbiota compared with closely related plant species. The pattern of divergence implies occasional co-evolutionary shifts in how plants interact with soil microbiota, with strongly contrasting feedback responses among some plant lineages. Our results highlight that it is difficult to predict feedback outcomes from phylogeny alone, other than to say that more closely related species tend to have more similar responses.

Plant population and soil origin effects on rhizosphere nematode community composition of a range-expanding plant species and a native congener

Climate change causes species range expansions to higher latitudes and altitudes. It is expected that, due to differences in dispersal abilities between plants and soil biota, range-expanding plant species will become associated with a partly new belowground community in their expanded range. Theory on biological invasions predicts that outside their native range, range-expanding plant species may be released from specialist natural enemies, leading to the evolution of enhanced defence against generalist enemies. Here we tested the hypothesis that expanded range populations of the range-expanding plant species Centaurea stoebe accumulate fewer root-feeding nematodes than populations from the original range. Moreover, we examined whether Centaurea stoebe accumulates fewer root-feeding nematodes in expanded range soil than in original range soil. We grew plants from three expanded range and three original range populations of C. stoebe in soil from the original and from the new range. We compared nematode communities of C. stoebe with those of C. jacea, a congeneric species native to both ranges. Our results show that expanded range populations of C. stoebe did not accumulate fewer root-feeding nematodes than populations from the original range, but that C. stoebe, unlike C. jacea, accumulated fewest root-feeding nematodes in expanded range soil. Moreover, when we examined other nematode feeding groups, we found intra-specific plant population effects on all these groups. We conclude that range-expanding plant populations from the expanded range were not better defended against root-feeding nematodes than populations from the original range, but that C. stoebe might experience partial belowground enemy release.

Wind intensity affects fine root morphological traits with consequences for plant-soil feedback effects

Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant-soil feedbacks-PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant-soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant-soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant-soil interactions under changing environmental conditions.

Soil origin corresponds with variation in growth of an invasive Centaurea, but not of non-invasive congeners

Why only a small proportion of exotic species become invasive is an unresolved question. Escape from the negative effects of soil biota in the native range can be important for the success of many invasives, but comparative effects of soil biota on less successful exotic species are poorly understood. Studies of other mechanisms suggest that such comparisons might be fruitful. Seeds of three closely related Centaurea species with overlapping distributions in both their native range of Spain and their nonnative range of California were grown to maturity in pots to obtain an F1 generation of full sibling seeds with reduced maternal effects. Full sibling F1 seeds from both ranges were subsequently grown in pots with inoculations of soil from either the native or nonnative ranges in a fully orthogonal factorial design. We then compared plant biomass among species, regions, and soil sources. Our results indicate that escape from soil pathogens may unleash the highly invasive Centaurea solstitialis, which was suppressed by native Spanish soils but not by soils from California. In contrast, the two non-invasive Centaurea species grew the same on all soils. These results add unprecedented phylogenetically controlled insight into why some species invade and others do not.

A non-invasive soil-based setup to study tomato root volatiles released by healthy and infected roots

The role of root exudates in mediating plant–microbe interactions has been well documented. However, the function of volatile organic compounds (VOCs) emitted by plant roots has only recently begun to attract attention. This newly recognized relevance of belowground VOCs has so far mostly been tested using systems limited to a two-compartment Petri-dish design. Furthermore, many of the plant–microbe interaction studies have only investigated the effects of microbial VOCs on plant growth. Here, we go two steps further. First we investigated the volatile profile of healthy and pathogen (Fusarium oxysporum) infected tomato roots grown in soil. We then used a unique soil-based olfactometer-choice assay to compare the migration pattern of four beneficial bacteria (Bacillus spp.) towards the roots of the tomato plants. We demonstrate that the blend of root-emitted VOCs differs between healthy and diseased plants. Our results show that VOCs are involved in attracting bacteria to plant roots.

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history

As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species' average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.

Plants and Associated Soil Microbiota Cooperatively Suppress Plant-Parasitic Nematodes

Disease suppressive soils with specific suppression of soil-borne pathogens and parasites have been long studied and are most often of microbiological origin. As for the plant-parasitic nematodes (PPN), which represent a huge threat to agricultural crops and which successfully defy many conventional control methods, soil progression from conducive to suppressive state is accompanied by the enrichment of specific antagonistic microbial consortia. However, a few microbial groups have come to the fore in diminishing PPN in disease suppressive soils using culture-dependent methods. Studies with cultured strains resulted in understanding the mechanisms by which nematodes are antagonized by microorganisms. Recent culture-independent studies on the microbiome associated with soil, plant roots, and PPN contributed to a better understanding of the functional potential of disease suppressive microbial cohort. Plant root exudation is an important pathway determining host-microbe communication and plays a key role in selection and enrichment of a specific set of microbial antagonists in the rhizosphere as first line of defense against crop pathogens or parasites. Root exudates comprising primary metabolites such as amino acids, sugars, organic acids, and secondary metabolites can also cause modifications in the nematode surface and subsequently affect microbial attachment. A positive interaction between hosts and their beneficial root microbiota is correlated with a low nematode performance on the host. In this review, we first summarized the historical records of nematode-suppressive soils and then focused on more recent studies in this aspect, emphasizing the advances in studying nematode-microbe interactions over time. We highlighted nematode biocontrol mechanisms, especially parasitism, induced systemic resistance, and volatile organic compounds using microbial consortia, or bacterial strains of the genera Pasteuria, Bacillus, Pseudomonas, Rhizobium, Streptomyces, Arthrobacter, and Variovorax, or fungal isolates of Pochonia, Dactylella, Nematophthora, Purpureocillium, Trichoderma, Hirsutella, Arthrobotrys, and Mortierella. We discussed the importance of root exudates in plant communication with PPN and soil microorganisms, emphasizing their role in microbial attachment to the nematode surface and subsequent events of nematode parasitism. Comprehensive understanding of the plant-beneficial microbial consortia and the mechanisms underlying disease suppression may help to develop synthetic microbial communities for biocontrol of PPN, thereby reducing nematicides and fertilizers inputs.