Martijn Bezemer

Janzen-Connell effects state that the accumulation of host-specific natural enemies near parent plants can negatively affect their offspring. Negative plant-soil feedbacks can produce patterns of seedling performance predicted by Janzen-Connell effects and influence plant populations, but their relevance in field conditions remains unclear. Here, using spatial point-pattern analysis, we examine the spatial distribution of Jacobaea vulgaris to assess whether distance- and density-dependent predictions of Janzen-Connell effects are evident in the field. We established 27 replicated 64 m² plots at two grassland sites and mapped positions of rosette-bearing and flowering J. vulgaris plants within each plot. To investigate temporal distribution patterns, we tracked plant positions repeatedly in three plots during a single season. Additionally, we tested whether these patterns are soil-mediated. Soil samples were collected underneath flowering plants and at a distance of 0.5 meter, and used to compare seed germination, seedling survival, and growth under controlled conditions. Furthermore, we measured J. vulgaris growth in soil from patches with high J. vulgaris densities and in soil from areas outside these patches. The density of rosette-bearing plants was lower at close distances from flowering plants than expected from null models, suggesting negative distance-dependent plant recruitment. The degree of clustering decreased over time from rosette-bearing to flowering plants, indicating density-dependent self-thinning. Seed germination was higher in soil further away from flowering J. vulgaris plants than in soil underneath plants at one site, but soil distance was not an overall significant factor in explaining seed germination. However, seedling mortality and biomass did not differ between soils collected at the two distances, and plants produced similar biomass in soil collected from inside and outside J. vulgaris patches. Our study demonstrates conspecific distance- and density-dependent plant recruitment in J. vulgaris in the field, but we found no evidence this depends on belowground natural enemies.

Despite increasing evidence that intercropping systems may increase crop productivity, little is known about whether and how soil biota change under interspecific competition among plants. A field experiment with maize/soybean intercropping and the corresponding monoculture systems was conducted under four nitrogen fertilization regimes to investigate the effects of interspecific plant interactions on grain yield, soil properties (β-glucosidase and water-soluble carbohydrates), and biotic communities (bacteria, fungi, and nematodes). The soils under maize and soybean in the intercropping system were sampled separately to represent intercropped maize and intercropped soybean, respectively. Compared to monocultures, the complexity and robustness of soil networks comprising bacterial, fungal, and nematode communities increased in intercropped maize soils, but densities of plant parasitic nematodes and β-glucosidase activity were reduced. Intercropped soybean soils had lower C availability due to chronic shading by maize, but a significant increase was found in saprophytic fungi, and plant parasitic nematodes compared to soybean monoculture soils. Although intercropped soybean suffered from interspecific competition with maize, the interactions within the fungal community increased for both crop species in the intercropping system. Our study demonstrates that increased carbon uptake in maize due to increased light capture in the intercropping system can facilitate nutrient cycling by altering the abundance of functional groups of soil organisms, such as saprophytic fungi, and enhancing network complexity and stability. We detected a trade-off between productivity and soil nematode diversity in the intercropping system under nitrogen fertilization, the yield of maize increased but soil nematode richness decreased at low nitrogen level, while the yield of soybean decreased but the nematode richness increased at high nitrogen level. These findings show that both trade-offs and benefits occur in intercropping systems and highlight the role of plant-soil biota interactions in such systems.

The application of organic amendments (OAs) obtained from biological treatment technologies is a common agricultural practice to increase soil functionality and fertility. OAs and their respective pretreatment processes have been extensively studied. However, comparing the properties of OAs obtained from different pretreatment processes remains challenging. In most cases, the organic residues used to produce OAs exhibit intrinsic variability and differ in origin and composition. In addition, few studies have focused on comparing OAs from different pretreatment processes in the soil microbiome, and the extent to which OAs affect the soil microbial community remains unclear. This limits the design and implementation of effective pretreatments aimed at reusing organic residues and facilitating sustainable agricultural practices. In this study, we used the same model residues to produce OAs to enable meaningful comparisons among compost, digestate, and ferment. These three OAs contained different microbial communities. Compost had higher bacterial but lower fungal alpha diversity than ferment and digestate. Compost-associated microbes were more prevalent in the soil than ferment- and digestate-associated microbes. More than 80% of the bacterial ASVs and fungal OTUs from the compost were detected 3 months after incorporation into the soil. However, the addition of compost had less influence on the resulting soil microbial biomass and community composition than the addition of ferment or digestate. Specific native soil microbes, members from Chloroflexi, Acidobacteria, and Mortierellomycota, were absent after ferment and digestate application. The addition of OAs increased the soil pH, particularly in the compost-amended soil, whereas the addition of digestate enhanced the concentrations of dissolved organic carbon (DOC) and available nutrients (such as ammonium and potassium). These physicochemical variables were key factors that influenced soil microbial communities. This study furthers our understanding of the effective recycling of organic resources for the development of sustainable soils.

Soil addition is now widely used in the restoration of degraded ecosystems, but how soil addition influences multiple ecological functions of degraded grasslands, and whether these effects depend on the amount and type of soil inoculum, are still not clear. We performed two parallel experiments to examine how two different donor soil types and two amounts of donor soil addition affect the restoration of degraded grassland. In a field experiment at a degraded grassland site where the top layer of the soil was removed (5 cm), we assessed the effect of addition of soil collected from two different ecosystems (upland meadow and meadow steppe) and addition of different amounts of soil (0 cm, 1 cm and 3 cm) on ecosystem multifunctionality. In a microcosm experiment, we examined the effects of soil biotic and abiotic factors on ecosystem functions by inoculating sterilized and non-sterilized soil. Soil addition promoted the restoration of degraded grassland, particularly when higher amounts of soil were added. Both biotic and abiotic factors increased ecosystem multifunctionality. Biotic factors, especially fungal richness and network complexity, had the strongest positive effects on ecosystem multifunctionality. Our study reveals the importance of fungal communities in soil for improving ecosystem multifunctionality in restoration of degraded grassland. Future studies should explore the effects of joint addition of arbuscular mycorrhizal fungi and saprophytic fungi on the ecosystem functions of degraded grasslands.

Current and legacy effects can greatly affect the growth of a focal plant and its interactions with herbivores and such effects can be mediated by above- and belowground effects. However, determining the relative importance of current and legacy above- and belowground effects in natural conditions is a major challenge. In a long-term grassland experiment, we examined the relative importance of the current and legacy above- and belowground effects of plant communities on the growth and aboveground herbivore damage on a focal plant, Leucanthemum vulgare. Focal plants were planted into tubes with soil collected from different plant communities and placed back into the plant communities. Weekly, plant growth and damage were recorded and after 12 weeks plant biomass was measured. We analyzed how well aboveground and belowground characteristics of the current and legacy plots explained plant growth and herbivory. We found both current plant communities and legacy plant communities significantly affected plant growth (shoot biomass and the number of leaves) and herbivory. Root biomass of the focal plants was influenced by current plant communities only. Current and legacy above- and belowground characteristics explained 12% and 11% of the variation in shoot biomass. Root biomass was mainly explained by current above- and belowground characteristics with a total explained variation of 10%, while legacy effects explained 3%. Legacy effects explained most variation in the number of leaves during the first two weeks of measurements, and the effect remained present during the growth season. In contrast, characteristics of the current community explained most of the variation in herbivory throughout the growth period, with on average 6% explained variance aboveground vs. 5% belowground. Our grassland field study highlights that both current and legacy effects influence plant growth, but herbivory on focal plants is caused by current neighborhood effects only and not by legacy effects.

Green roofs provide ecosystem services and can promote biodiversity in urban areas. Blue-green roofs have an additional water storage compartment under the substrate to reduce roof water runoff, thereby also reducing drought stress which is beneficial for green roof vegetation. In order to study which blue-green roof design supports the highest plant diversity, we assessed the effect of different substrates and seed mixtures on vegetation development in a short-term greenhouse experiment and long-term blue-green roof experiment. A ten-week full-factorial greenhouse experiment was performed for six substrate composition and four seed mixture treatments. On an experimental blue-green roof, we annually surveyed plants from 2013 to 2021 in nine different treatments (five replicates each), that varied in substrate composition, substrate depth and seed mixture that was initially applied. Two treatments resembled conventional non-green roofs (100% gravel) and conventional extensive Sedum green roofs. The results of the greenhouse experiment showed that seed mixture is more important than substrate composition in shaping the initial species richness and species composition. However, on the experimental roof the substrate composition was an important determinant of species richness and species composition long-term. Plant species richness on the experimental roof was lowest in the gravel treatment (resembling conventional non-green roofs), and highest in treatments where locally collected soil was used, likely due to additional species that appeared from the seed bank present in the transplanted soil. Soil was never completely covered with vegetation on unfertilized substrates that contained 20% or less dense and organic materials. Plant species richness on conventional Sedum roof substrate was higher on the experimental blue-green roof compared to an adjacent non-blue roof, highlighting that blue-green roofs can promote biodiversity more than conventional green roofs. For future construction of blue-green roofs in our region, we recommend the addition of 30% locally collected soil to a 6 cm deep lightweight substrate to maximize long-term plant cover and plant species richness.

The gut microbiome of plant-eaters is affected by the food they eat, but it is currently unclear how the plant metabolome and microbiome are influenced by the substrate the plant grows in and how this subsequently impacts the feeding behavior and gut microbiomes of insect herbivores. Here, we use Plutella xylostella caterpillars and show that the larvae prefer leaves of cabbage plants growing in a vermiculite substrate to those from plants growing in conventional soil systems. From a plant metabolomics analysis, we identified 20 plant metabolites that were related to caterpillar feeding performance. In a bioassay, the effects of these plant metabolites on insects’ feeding were tested. Nitrate and compounds enriched with leaves of soilless cultivation promoted the feeding of insects, while compounds enriched with leaves of plants growing in natural soil decreased feeding. Several microbial groups (e.g., Sporolactobacillus, Haliangium) detected inside the plant correlated with caterpillar feeding performance and other microbial groups, such as Ramlibacter and Methylophilus, correlated with the gut microbiome. Our results highlight the role of growth substrates on the food metabolome and microbiome and on the feeding performance and the gut microbiome of plant feeders. It illustrates how belowground factors can influence the aboveground properties of plant-animal systems, which has important implications for plant growth and pest control.

Biochar is proposed as an option to sequester carbon (C) in soils and promote other soil-based ecosystem services. However, its impact on soil biota from micro to macroscale remains poorly understood. We investigated biochar effects on the soil biota across the soil food web, on plant community composition and on biomass production. We conducted a field experiment in a nature restoration grassland testing four treatments: two biochar types (herbaceous feedstock pyrolyzed at 400 °C or 600 °C – hereafter B400 and B600), and a positive (i.e. unpyrolysed biochar feedstock, hereafter Hay) and negative (no addition) control. Responses of plants and soil biota were evaluated one and three years after establishing the treatments. Soil pH and K concentrations increased significantly in the B600 treatment. Mite abundances were significantly higher in B400 whereas nematode abundances were highest in Hay (1st year) and lowest in B400 (3rd year). Other soil fauna groups (enchytraeids and earthworms) varied more between years than between treatments. Legume cover increased significantly in the biochar treatments but this effect was transient. Legumes, grasses and primary productivity also showed a statistically significant Treatment x Year interaction due to transitory effects that were no longer present by the 3rd year. Our results suggest that biochar produced from meadow cuttings and applied at the 10 t/ha rate cause transitory impacts on soil biota abundance and plant communities over the 3-year timeframe used for this experiment. Therefore, this type of biochar could potentially be used for soil carbon sequestration, with minimal impacts on soil biota abundance or diversity, within the groups studied here, or plant biodiversity and productivity. Further research is required to investigate the longer-term impacts of this potential soil C storage sink.

Environmental conditions experienced by parent plants can influence offspring performance through parental effects induced by DNA methylation. The offspring can also be influenced by environmental conditions experienced by their parents via soil legacy effects due to plant-mediated changes in the composition of soil microbes. These two effects are likely to act simultaneously, but empirical evidence for combined effects is limited. We conducted a two-phase experiment with five genotypes of a clonal plant Hydrocotyle vulgaris. In the first phase, we grew parent plants of each genotype under two light conditions (ambient vs. shade) and two DNA demethylation treatments [treated with water vs. 5-azacytidine (5-azaC)]. We then collected soils and clonal offspring for each genotype from each of these four treatments and measured soil (a)biotic properties. In the second phase, we grew the offspring from each of the four treatments in the four different soils, under the two light conditions. When grown under ambient light condition and in soil from ambient parents, offspring produced by ambient parents grew larger than offspring produced by shaded parents when the parents were treated with water. This difference was smaller when the parents were treated with 5-azaC, and disappeared when the offspring were grown in soil from shaded parents. The growth difference was also observed when the offspring were grown under shaded condition and in soil from shaded parents. However, this difference was greater when the parents were treated with 5-azaC, and disappeared when the offspring were grown in soil from ambient parents. Moreover, offspring growth was associated with fungal composition and total phosphorus of the soil in which the parents had grown. Our results show, for the first time, that light condition experienced by parents can influence offspring responses to light through both parental effects and soil legacies. The parental effects were mediated by changes in DNA methylation and the soil legacies were due to plant-mediated changes in a combination of soil biotic and abiotic properties. These impacts may eventually influence the ecological and evolutionary trajectories of clonal plant populations. Read the free Plain Language Summary for this article on the Journal blog.

Plants leave legacy effects in the soil they grow in, which can drive important vegetation processes, including productivity, community dynamics and species turnover. Plants at the same time also face continuous pressure posed by insect herbivores. Given the intimate interactions between plants and herbivores in ecosystems, plant identity and herbivory are likely to interactively shape soil legacies. However, the mechanisms that drive such legacy effects on future generations of plants and associated herbivores are little known. In a greenhouse study, we exposed 10 common grasses and non-leguminous forbs individually to insect herbivory by two closely related noctuid caterpillars, Mamestra brassicae and Trichoplusia ni (Lepidoptera: Noctuidae) or kept them free of herbivores. We then used the soil legacies created by these plant individuals to grow a plant community composed of all 10 plant species in each soil and exposed these plant communities to M. brassicae. We measured conditioning plant biomass, soil respiration and chemistry of the conditioned soils, as well as individual plant, plant community and herbivore biomass responses. At the end of the conditioning phase, soils with herbivore legacies had higher soil respiration, but only significantly so for M. brassicae. Herbivore legacies had minimal impacts on community productivity. However, path models reveal that herbivore-induced soil legacies affected responding herbivores through changes in plant community shoot: root ratios. Soil legacy effect patterns differed between functional groups. We found strong plant species and functional group-specific effects on soil respiration parameters, which in turn led to plant community shifts in grass: forb biomass ratios. Soil legacies were negative for the growth of plants of the same functional group. Synthesis. We show that insect herbivory, plant species and their functional groups, all incur soil microbial responses that lead to subtle (herbivory) or strong (plants and their functional group) effects in response plant communities and associated polyphagous herbivores. Hence, even though typically ignored, our study emphasizes that legacies of previous insect herbivory in the soil can influence current soil–plant–insect community interactions. A free Plain Language Summary can be found within the Supporting Information of this article.

The living soil harbors a significant number and diversity of bacteria and fungi, which are essential in sustaining soil ecosystem functions. Most studies focus on soil bacteria or fungi, ignoring potential interrelationships between kingdoms that coevolve and synergistically provide ecosystem functions. In a seven-year agricultural field, we explored the effects of organic amendments (OAs; i.e., compost and bokashi) on intra- and inter-kingdom co-occurrence networks of soil bacterial and fungal communities. We observed that OAs changed the co-occurrence patterns of bacteria and fungi. Distinct network modules were observed in the unamended and amended soils, and the physicochemical properties of the soil could partially explain the formation of these modules. We also found that compost and bokashi increased the proportion of positive correlations, and this could reduce competition among microorganisms for soil resources. Our study reveals that soil management with OAs affects relationships between bacterial and fungal subpopulations that physically co-exist, cooperate, and compete in non-random structured networks. It highlights that ecosystem functions may depend on inter-kingdom interactions shaped by different amendments and their applied dose.

Background and aims: Jacobaea vulgaris plants grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on plant growth. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the soil.

Methods: We studied the composition of the microbial community over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. We initiated the experiment with an inoculum of live soil collected from the field, and at the start of each subsequent plant cycle, we inoculated a small part of the soil from the previous plant cycle into sterile bulk soil.

Results: Application of SA did not significantly increase or decrease the Shannon diversity at genus level within each generation, but several specific genera were enriched or depleted after foliar SA application. The composition of bacterial communities in the rhizosphere significantly differed between plant cycles (generations), but application of SA did not alter this pattern. In the first generation no genera were significantly affected by the SA treatment, but in the second, third and fourth generations, specific genera were significantly affected. 89 species out of the total 270 (32.4%) were present as the “core” microbiome in all treatments over four plant cycles.

Conclusions: Overall, our study shows that the composition of bacterial genera in the rhizosphere significantly differed between plant cycles, but that it was not strongly affected by foliar application of SA on J. vulgaris leaves. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere bacterial community.

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

Purpose: Insect herbivory affects plant growth, nutrient and secondary metabolite concentrations and litter quality. Changes to litter quality due to insect herbivory can alter decomposition, with knock on effects for plant growth mediated through the plant-litter-soil feedback pathway. Methods: Using a multi-phase glasshouse experiment, we tested how changes in shoot and root litter quality of fast- and slow-growing grass caused by insect herbivores affect the performance of response plants in the soil in which the litter decomposed. Results: We found that insect herbivory resulted in marginal changes to litter quality and did not affect growth when plants were grown with fast- versus slow-growing litter. Overall, presence of litter resulted in reduced root and shoot growth and this effect was significantly more negative in shoots versus roots. However, this effect was minimal, with a loss of c. 1.4% and 3.1% dry weight biomass in roots versus shoots, respectively. Further, shoot litter exposed to insect herbivory interacted with response plant identity to affect root growth. Conclusions: Our results suggest that whether litter originates from plant tissues exposed to insect herbivory or not and its interaction with fast- versus slow-growing grasses is of little importance, but species-specific responses to herbivory-conditioned litter can occur. Taken collectively, the overall role of the plant-litter-soil feedback pathway, as well as its interaction with insect herbivory, is unlikely to affect broader ecosystem processes in this system.

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

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.