Wim H. van der Putten

Extensifying land use practices – i.e. decreasing management intensity – is pivotal to facilitate the transition towards sustainable agriculture in productive grasslands, as it promotes the enhancement of soil biotic communities that support important ecosystem services. To monitor these transitions effectively, improved inventories are needed to track changes in microbial communities. Microbial Volatile Organic Compounds (mVOCs) are potential biomarkers that can link soil community change to land use extensification (i.e. reducing land use intensity) and may provide important information on changes in soil processes in transitional productive grasslands. We investigated how land use extensification affects mVOC profiles in grassland soils through both abiotic and biotic factors and whether mVOCs can be linked to bacterial (16S) and fungal (ITS2) community composition. We measured mVOCs (GC-MS), microbial communities, and abiotic soil parameters (SOM, SOC, pH, bulk density, and nutrients) across eighteen grasslands with varying land use intensity. A total of 75 mVOCs were identified using the mVOC 4.0 library. Furthermore, we show that mVOC profiles and chemical classes differ across land use types – conventional, extensive, and semi-natural grasslands. Within these grasslands, only fungi showed distinct community compositions between land use intensity types, whereas there were no compositional differences of bacteria. Using Taxon Indicator Threshold Analysis (TITAN), we identified sixteen mVOC compounds that varied significantly along a land use intensification gradient. These findings suggest that mVOCs can serve as biomarkers linking changes in land use intensity and soil microbial communities, although these relationships are complex in field conditions. We identified a set of mVOCs tied to changes in land-use extensification and highlighted their potential as indicators of soil microbial community turnover. mVOCs offer a valuable tool for monitoring land use transitions, and our results emphasize their role in integrating microbial community metrics and soil health indicators into land management strategies.

Overgrazing by sheep causes degradation of grasslands in the Inner Mongolian steppe, yet our understanding of its impact on grassland plant communities is limited by lack of observations at high spatial resolution. Employing a nested experimental design in a long-term grazing experiment provides insights into effects of increasing sheep grazing intensity on community composition, diversity, and spatial patterns in the grassland vegetation. Effects of observed changes in the plant community are discussed based on monthly weight gain of sheep during grazing. The design of the long-term experiment included four triplicated grazing intensities applied during an 8-year period. At the end of that period, we evaluated vegetation coverage, categorized plant species by functional groups, and analyzed the data using a mixed linear model. Moreover, spatial autocorrelation methods were employed to investigate spatial patterns, visualized via a kriging model. We found that the plant community composition differed among grazing treatments, with high grazing intensity showing higher plant species richness and stronger clustering of plants at our fine scale of observation. These fine-grained spatial scale observations are usually not recorded in larger spatial scale analyses of grassland responses to overgrazing. While the grazing intensities used in our study did not influence individual sheep weight gain, total sheep weight gain per hectare increased with an increase in grazing intensity. Our study shows that in a sheep grazing intensity experiment in Inner Mongolia grasslands total sheep weight gain may increase at the expense of fine-scale species composition and spatial dynamics of the grassland vegetation. These insights may be used for determining trade-offs of sheep meat production with original composition and structure of grassland plant communities. Effects on other ecosystem properties and functions, such as on belowground biodiversity, remain to be assessed.

The aim of the European Union is to have all soils healthy by 2050. This requires efficient and effective soil health indicators and references that enable comparing soil-health-related measurements to target conditions. We propose to adopt the practice of quality control by benchmarking to set targets for soil health.

There is an increasing interest in developing agricultural management practices that support a more nature-based, sustainable food production system. In organic systems, extracellular enzymes released by soil microorganisms are important regulators of the cycling and bioavailability of plant nutrients due to the lack of synthetical inputs. We used a chronosequence coupled with a paired field approach to evaluate how potential activity of hydrolytic soil extracellular enzymes changed over time (0–69 years) during the transition from conventional to organic agriculture in two types of soils, marine clay and sandy soils. Organic management generally enhanced the activity of enzymes related to the C cycle, particularly in sandy soils, and increased the proportion of C-related enzymes relative to N- and P-related enzymes. Differences in soil extracellular enzyme activity between organic and conventional farming increased with time since conversion to organic farming for α-β-glucosidase, xylosidase, phosphomonoesterase, 4-N-acetylglucosaminidase, arylsulphatase, and the ratio of C:N enzymes. In some cases, the divergence in enzyme activity was driven by enhanced activity with time in organic fields, but in others by reduced activity over time in conventional fields. Our findings suggest that organically managed soils with higher enzyme activity may have a greater potential for organic matter breakdown, residue decomposition, and higher rates of cycling of C and nutrients. However, these positive effects may take time to become apparent due to legacy effects of conventional management.

DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. ‘Italica’ clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses.

Agricultural intensification and expansion are regarded as main drivers of biodiversity loss. This conclusion is mainly based on observed declines of local diversity (α-diversity), while effects on community composition homogenization (decrease of β-diversity) at a larger spatial scale are less well understood. Carabid beetles and spiders represent two widespread guilds and are important predators of pest species. Here we surveyed carabid beetles and spiders in 66 winter wheat fields in four northwestern European countries (Germany, the Netherlands, Sweden and UK) and analyzed how their community composition was related to geographic distance (separation distance between any pairwise fields) and three environmental variables: crop yield (proxy for land-use intensity), percentage cropland (proxy for landscape complexity) and soil organic carbon content (proxy for local soil conditions). We further analyzed whether the relationship between carabid beetle and spider community composition and geographic distance was influenced by environmental variables. We found that, 55 % and 75 % of all observed carabid and spider individuals, respectively, belonged to species that occurred in all four countries. However, individuals of species that were unique to a particular country only accounted for 3 % of all collected individuals for both taxa. Furthermore, we found a negative relationship between distance and similarity of spider communities but not for carabid beetle communities. None of the environmental variables were related to similarity of carabid beetle and spider communities, nor moderated the effects of distance. Our study indicates that across a great part of the European continent, arthropod communities (especially carabid beetles) in agricultural landscapes are composed of very similar species that are robust to current variations in environment and land-use.

Monitoring agriculture by remote sensing enables large-scale evaluation of biomass production across space and time. The normalized difference vegetation index (NDVI) is used as a proxy for green biomass. Here, we used satellite-derived NDVI of arable farms in the Netherlands to evaluate changes in biomass following conversion from conventional to organic farming. We compared NDVI and the stability of NDVI across 72 fields on sand and marine clay soils. Thirty-six of these fields had been converted into organic agriculture between 0 and 50 years ago (with 2017 as reference year), while the other 36 were paired control fields where conventional farming continued. We used high-resolution images from the Sentinel-2 satellite to obtain NDVI estimates across 5 years (January 2016–October 2020). Overall, NDVI did not differ between conventional and organic management during the time series, but NDVI stability was significantly higher under organic management. NDVI was lower under organic management in sandy, but not in clay, soils. Organic farms that had been converted less than ~19 years ago had lower NDVI than conventional farms. However, the difference diminished over time and eventually turned positive after ~19 years since the conversion. NDVI, averaged across the 5 years of study, was positively correlated to soil Olsen-P measured from soil samples collected in 2017. We conclude that NDVI in organic fields was more stable than in conventional fields, and that the lower biomass in the early years since the transition to organic agriculture can be overcome with time. Our study also indicates the role of soil P bioavailability for plant biomass production across the examined fields, and the benefit of combining remote sensing with on-site soil measurements to develop a more mechanistic understanding that may help us navigate the transition to a more sustainable type of agriculture.

Range expansions, whether they are biological invasions or climate change-mediated range shifts, may have profound ecological and evolutionary consequences for plant–soil interactions. Range-expanding plants encounter soil biota with which they have a limited coevolutionary history, especially when introduced to a new continent. Past studies have found mixed results on whether plants experience positive or negative soil feedback interactions in their novel range, and these effects often change over time. One important theoretical explanation is that plants locally adapt to the soil pathogens and mutualists in their novel range. We tested this hypothesis in Dittrichia graveolens, an annual plant that is both expanding its European native range, initially coinciding with climate warming, and rapidly invading California after human introduction. In parallel greenhouse experiments on both continents, we used plant genotypes and soils from 5 locations at the core and edge of each range to compare plant growth in soil inhabited by D. graveolens and nearby control microsites as a measure of plant–soil feedback. Plant–soil interactions were highly idiosyncratic across each range. On average, plant–soil feedbacks were more positive in the native range than in the exotic range. In line with the strongly heterogeneous pattern of soil responses along our biogeographic gradients, we found no evidence for evolutionary differentiation between plant genotypes from the core to the edge of either range. Our results suggest that the evolution of plant–soil interactions during range expansion may be more strongly driven by local evolutionary dynamics varying across the range than by large-scale biogeographic shifts.

Forest restoration mitigates climate change by removing CO₂ and storing C in terrestrial ecosystems. However, incomplete information on C storage in restored tropical forests often fails to capture the ecosystem's holistic C dynamics. This study provides an integrated assessment of C storage in above to belowground subsystems, its consequences for greenhouse gas (GHG) fluxes, and the quantity, quality, and origin of soil organic matter (SOM) in restored Atlantic forests in Brazil. Relations between SOM properties and soil health indicators were also explored. We examined two restorations using tree planting (‘active restoration’): an 8-year-old forest with green manure and native trees planted in two rounds, and a 15-year-old forest with native-planted trees in one round without green manure. Restorations were compared to reformed pasture and primary forest sites. We measured C storage in soil layers (0–10, 10–20, and 20–30 cm), litter, and plants. GHG emissions were assessed using CH₄ and CO₂ fluxes. SOM quantity was evaluated using C and N, quality using humification index (H_LIFS), and origin using δ¹³C and δ¹⁵N. Nine soil health indicators were interrelated with SOM attributes. The primary forest presented the highest C stocks (107.7 Mg C ha⁻¹), followed by 15- and 8-year-old restorations and pasture with 69.8, 55.5, and 41.8 Mg C ha⁻¹, respectively. Soil C stocks from restorations and pasture were 20% lower than primary forest. However, 8- and 15-year-old restorations stored 12.3 and 28.3 Mg ha⁻¹ more aboveground C than pasture. The younger forest had δ¹³C and δ¹⁵N values of 2.1 and 1.7‰, respectively, lower than the 15-year-old forest, indicating more C derived from C₃ plants and biological N fixation. Both restorations and pasture had at least 34% higher H_LIFS in deeper soil layers (10–30 cm) than primary forest, indicating a lack of labile SOM. Native and 15-year-old forests exhibited higher soil methane influx (141.1 and 61.9 μg m⁻² h⁻¹). Forests outperformed pasture in most soil health indicators, with 69% of their variance explained by SOM properties. However, SOM quantity and quality regeneration in both restorations approached the pristine forest state only in the top 10 cm layer, while deeper soil retained agricultural degradation legacies. In conclusion, active restoration of the Atlantic Forest is a superior approach compared to pasture reform for GHG mitigation. Nonetheless, the development of restoration techniques to facilitate labile C input into deeper soil layers (>10 cm) is needed to further improve soil multifunctionality and long-term C storage.

Brazilian sugarcane plays a vital role in the production of both sugar and renewable energy. However, land use change and long-term conventional sugarcane cultivation have degraded entire watersheds, including a substantial loss of soil multifunctionality. In our study, riparian zones have been reforested to mitigate these impacts, protect aquatic ecosystems, and restore ecological corridors within the sugarcane production landscapes. We examined (i) how forest restoration enables rehabilitation of the soil's multifunctionality after long-term sugarcane cultivation and (ii) how long it takes to regain ecosystem functions comparable to those of a primary forest. We investigated a time series of riparian forests at 6, 15, and 30 years after starting restoration by planting trees (named ‘active restoration’) and determined soil C stocks, δ¹³C (indicative of C origin), as well as measures indicative of soil health. A primary forest and a long-term sugarcane field were used as references. Eleven soil physical, chemical, and biological indicators were used for a structured soil health assessment, calculating index scores based on soil functions. Forest-to-cane conversion reduced 30.6 Mg ha⁻¹ of soil C stocks, causing soil compaction and loss of cation exchange capacity, thus degrading soil's physical, chemical, and biological functions. Forest restoration for 6–30 years recovered 16–20 Mg C ha⁻¹ stored in soils. In all restored sites, soil functions such as supporting root growth, aerating the soil, nutrient storage capacity, and providing C energy for microbial activity were gradually recovered. Thirty years of active restoration was sufficient to reach the primary forest state in overall soil health index, multifunctional performance, and C sequestration. We conclude that active forest restoration in sugarcane-dominated landscapes is an effective way to restore soil multifunctionality approaching the level of the native forest in approximately three decades. Moreover, the C sequestration in the restored forest soils will help to mediate global warming.

BACKGROUND: Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome.

RESULTS: We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in.

CONCLUSIONS: Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.

Reconciling biodiversity conservation with agricultural production requires a better understanding of how key ecosystem service providing species respond to agricultural intensification. Carabid beetles and spiders represent two widespread guilds providing biocontrol services. Here we surveyed carabid beetles and spiders in 66 winter wheat fields in four northwestern European countries and analyzed how the activity density and diversity of carabid beetles and spiders were related to crop yield (proxy for land-use intensity), percentage cropland (proxy for landscape complexity) and soil organic carbon content, and whether these patterns differed between dominant and non-dominant species. <17 % of carabid or spider species were classified as dominant, which accounted for >90 % of individuals respectively. We found that carabids and spiders were generally related to different aspects of agricultural intensification. Carabid species richness was positively related with crop yield and evenness was negatively related to crop cover. The activity density of non-dominant carabids was positively related with soil organic carbon content. Meanwhile, spider species richness and non-dominant spider species richness and activity density were all negatively related to percentage cropland. Our results show that practices targeted to enhance one functionally important guild may not promote another key guild, which helps explain why conservation measures to enhance natural enemies generally do not ultimately enhance pest regulation. Dominant and non-dominant species of both guilds showed mostly similar responses suggesting that management practices to enhance service provisioning by a certain guild can also enhance the overall diversity of that particular guild.

Background and aims: Plants continuously interact with soil microbiota. These plant-soil feedbacks (PSFs) are considered a driving force in plant community dynamics. However, most PSF information comes from inter-family studies, with limited information on possible causes. We studied the variation of PSFs between and within grass species and identified the soil microbes that are associated with the observed PSFs effects. Methods: We grew monocultures of ten cultivars of three grass species (Lolium perenne, Poa pratensis, Schedonorus arundinaceus) using a two-phase PSF experiment. We measured plant total biomass to determine PSFs between and within species and correlated it with sequenced rhizosphere bacteria and fungi. Results: In the soil conditioning phase, grass species developed microbial legacies that affected the performance of other grass species in the feedback phase. We detected overall negative interspecific PSFs. While we show that L. perenne and P. pratensis increased their performance respectively in conspecific and heterospecific soils, S. arundinaceus was not strongly affected by the legacies of the previous plant species. Contrary to our expectation, we found no evidence for intraspecific variation in PSFs. Bacterial taxa associated with PSFs included members of Proteobacteria, Firmicutes, Verrucomicrobia and Planctomycetes whereas fungal taxa included members of Ascomycota. Conclusion: Our results suggest differences in PSF effects between grass species, but not between cultivars within species. Thus, in the studied grass species, there might be limited potential for breeding on plant traits mediated by PSFs. Furthermore, we point out potential microbial candidates that might be driving the observed PSF effects that could be further explored.

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.

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

Beneficial soil microbes can enhance plant growth and defense, but the extent to which this occurs depends on the availability of resources, such as water and nutrients. However, relatively little is known about the role of light quality, which is altered during shading, resulting a low red: far-red ratio (R:FR) of light. We examined how low R:FR light influences arbuscular mycorrhizal fungus (AMF)-mediated changes in plant growth and defense using Solanum lycopersicum (tomato) and the insect herbivore Chrysodeixis chalcites. We also examined effects on third trophic level interactions with the parasitoid Cotesia marginiventris. Under low R:FR light, non-mycorrhizal plants activated the shade avoidance syndrome (SAS), resulting in enhanced biomass production. However, mycorrhizal inoculation decreased stem elongation in shaded plants, thus counteracting the plant’s SAS response to shading. Unexpectedly, activation of SAS under low R:FR light did not increase plant susceptibility to the herbivore in either non-mycorrhizal or mycorrhizal plants. AMF did not significantly affect survival or growth of caterpillars and parasitoids but suppressed herbivore-induced expression of jasmonic acid-signaled defenses genes under low R:FR light. These results highlight the context-dependency of AMF effects on plant growth and defense and the potentially adverse effects of AMF under shading.

Plant and soil microbial community composition play a central role in maintaining ecosystem functioning. Most studies have focused on soil microbes in the bulk soil, the rhizosphere and inside plant roots, however, less is known about the soil community that exists within soil aggregates, and how these soil communities influence plant biomass production. Here, using field-conditioned soil collected from experimental ungrazed and grazed grasslands in Inner Mongolia, China, we examined the composition of microbiomes inside soil aggregates of various size classes, and determined their roles in plant-soil feedbacks (PSFs), diversity-productivity relationships, and diversity-dependent overyielding. We found that grazing induced significantly positive PSF effects, which appeared to be mediated by mycorrhizal fungi, particularly under plant monocultures. Despite this, non-additive effects of microbiomes within different soil aggregates enhanced the strength of PSF under ungrazed grassland, but decreased PSF strength under intensively grazed grassland. Plant mixture-related increases in PSF effects markedly enhanced diversity-dependent overyielding, primarily due to complementary effects. Selection effects played far less of a role. Our work suggests that PSF contributes to diversity-dependent overyielding in grasslands via non-additive effects of microbiomes within different soil aggregates. The implication of our work is that assessing the effectiveness of sustainable grassland restoration and management on soil properties requires inspection of soil aggregate size-specific microbiomes, as these are relevant determinants of the feedback interactions between soil and plant performance.

Evaluation of restoration activities is indispensable to assess the extent to which targets have been reached. Usually, the main goal of ecological restoration is to restore biodiversity and ecosystem functioning, but validation is often based on a single indicator, which may or may not cope with whole-ecosystem dynamics. Network analyses are, however, powerful tools, allowing to examine both the recovery of various biotic and abiotic properties and the integrated response at community and ecosystem level. We used restoration sites where topsoil was removed from former intensively managed grassland and seeds were added. These sites were between 3 and 32 years old. We assessed how plants, soil biota, soil properties and correlation-based interactions between biotic communities and their abiotic environment developed over time and compared the results with (i) intensively managed (not restored), and (ii) well-preserved targeted semi-natural grasslands. Plant, nematode, fungal and prokaryotic diversity and community structures of the restored grasslands revealed clear successional patterns and followed similar trajectories towards targeted semi-natural grasslands. All biotic communities reached targeted diversity levels no later than 18 years post-restoration. Ecological networks of intensively managed and short-term (~4 years) restored grasslands were less tightly connected compared to those found in mid- and long-term (~18–30 years) restored and target grasslands. Restoration specifically enhanced interactions among biotic communities, but reduced interactions between biotic communities and their abiotic environment as well as interactions among abiotic properties in the short- and mid-term. Synthesis and applications: Overall, our study demonstrated that topsoil removal and seed addition were successful in restoring diverse, tightly coupled and well-connected biotic communities above- and below-ground similar to those found in the semi-natural grasslands that were restoration targets. Network analyses proved to be powerful in examining the long-term re-establishment of functionally connected biotic communities in restored ecosystems. Thus, we provide an approach to holistically assess restoration activities by notably considering the complexity of ecosystems, much in contrast to most traditional approaches.

Aviation biofuels are promising to reduce carbon emissions in the aviation sector. However, emerging concerns over biofuels indicate a need for sustainability analyses that take into consideration the context around biofuel production. Here, we present a novel ex-ante sustainability analysis of production alternatives for aviation biofuel in Southeast Brazil. Considering local stakeholders’ concerns, the analysis is focused on climate change, commercial acceptability, efficiency, energy security, investment security, profitability, social development, and soil sustainability. By identifying tensions between production alternatives and these sustainability aspects, we discuss opportunities for further developments, such as sugarcane ethanol-to-jet production in the short term, and in-house production of hydrogen and power with renewable energy. Additionally, producer–operator partnerships and opening the decision-making to stakeholder participation are suggested to stimulate social cohesion, and reconcile diverging interests with biobased production. Analyzing sustainability with consideration of the local context can contribute to identify opportunities for more sustainable decarbonization alternatives.

Global change frequently disrupts the connections among species, as well as among species and their environment, before the most obvious impacts can be detected. Therefore, we need to develop a unified conceptual framework that allows us to predict early ecological impacts under changing environments. The concept of coupling, defined as the multiple ways in which the biotic and abiotic components of ecosystems are orderly connected across space and/or time, may provide such a framework. Here, we operationally define the coupling of ecosystems based on a combination of correlational matrices and a null modeling approach. Compared with null models, ecosystems can be (1) coupled; (2) decoupled; and (3) anticoupled. Given that more tightly coupled ecosystems displaying higher levels of internal order may be characterized by a more efficient capture, transfer, and storage of energy and matter (i.e., of functioning), understanding the links between coupling and functioning may help us to accelerate the transition to planetary-scale sustainability. This may be achieved by promoting self-organized order.

Embedded in longer term warming are extreme climatic events such as heatwaves and droughts that are increasing in frequency, duration and intensity. Changes in climate attributes such as temperature are often measured over larger spatial scales, whereas environmental conditions to which many small ectothermic arthropods are exposed are largely determined by small-scale local conditions. Exposed edges of plant patches often exhibit significant short-term (daily) variation to abiotic factors due to wind exposure and sun radiation. By contrast, within plant patches, abiotic conditions are generally much more stable and thus less variable. Over an eight-week period in the summer of 2020, including an actual heatwave, we measured small-scale (1 m²) temperature variation in patches of forbs in experimental mesocosms. We found that soil surface temperatures at the edge of the mesocosms were more variable than those within mesocosms. Drought treatment two years earlier, amplified this effect but only at the edges of the mesocosms. Within a plant patch both at the soil surface and within the canopy, the temperature was always lower than the ambient air temperature. The temperature of the soil surface at the edge of a patch may exceed the ambient air temperature when ambient air temperatures rise above 23 °C. This effect progressively increased with ambient temperature. We discuss how microscale-variation in temperature may affect small ectotherms such as insects that have limited ability to thermoregulate, in particular under conditions of extreme heat.

It is generally assumed that restoring biodiversity will enhance diversity and ecosystem functioning. However, to date, it has rarely been evaluated whether and how restoration efforts manage to rebuild biodiversity and multiple ecosystem functions (ecosystem multifunctionality) simultaneously. Here, we quantified how three restoration methods of increasing intervention intensity (harvest only < topsoil removal < topsoil removal + propagule addition) affected grassland ecosystem multifunctionality 22 yr after the restoration event. We compared restored with intensively managed and targeted seminatural grasslands based on 13 biotic and abiotic, above- and belowground properties. We found that all three restoration methods improved ecosystem multifunctionality compared to intensively managed grasslands and developed toward the targeted seminatural grasslands. However, whereas higher levels of intervention intensity reached ecosystem multifunctionality of targeted seminatural grasslands after 22 yr, lower intervention missed this target. Moreover, we found that topsoil removal with and without seed addition accelerated the recovery of biotic and aboveground properties, and we found no negative long-term effects on abiotic or belowground properties despite removing the top layer of the soil. We also evaluated which ecosystem properties were the best indicators for restoration success in terms of accuracy and cost efficiency. Overall, we demonstrated that low-cost measures explained relatively more variation of ecosystem multifunctionality compared to high-cost measures. Plant species richness was the most accurate individual property in describing ecosystem multifunctionality, as it accounted for 54% of ecosystem multifunctionality at only 4% of the costs of our comprehensive multifunctionality approach. Plant species richness is the property that typically is used in restoration monitoring by conservation agencies. Vegetation structure, soil carbon storage and water-holding capacity together explained 70% of ecosystem multifunctionality at only twice the costs (8%) of plant species richness, which is, in our opinion, worth considering in future restoration monitoring projects. Hence, our findings provide a guideline for land managers how they could obtain an accurate estimate of aboveground-belowground ecosystem multifunctionality and restoration success in a highly cost-efficient way.

1. Climate change is known to disrupt above-ground food chains when the various trophic layers respond differently to warming. However, little is known about below-ground food chains involving microbial preys and their predators. Here, we study how climate warming-induced heat shocks influence resistance (change immediately after a disturbance) and resilience (ability to recover back to pre-disturbance levels) in rhizosphere microbial communities.

2. We used three species of rhizosphere protists as microbial predators and six different rhizosphere bacterial communities as their prey. Protist species and bacterial communities were extracted from Centaurea stoebe—a range-expanding plant species in the Northern Europe. We then examined the temporal dynamics of protists and bacterial communities after an extreme heat event for several generations with sufficient recovery periods. We hypothesized that bacterial community resistance and resilience after the extreme heat event would be higher particularly when extreme heat effects would negatively affect their predators.

3. Our results show that prey community biomass was strongly reduced after the extreme heat event and persisted with lower biomass throughout the recovery period. Opposite to what was expected, predators showed negligible changes in their active density after the same heat event. However, abundances of the three predators varied markedly in their temporal dynamics independent of the extreme heat event. Extreme heat event further increased the inactive density of predators, whereas one of the predators showed a decline in its body size owing to extreme heat event. Bacterial community resistance and resilience after the extreme heat event were independent of predator presence, although species-specific effects of predators on bacterial community resilience were different in the last week of recovery. Predator resilience (based on active predator density) also varied among the three predators but converged over time.

4. Our results highlight that extreme heat events can be more detrimental to microbial prey communities than microbial predators when microbial predators can exhibit thermal acclimation (e.g. change in body size or become inactive) to overcome heat stress. Such thermal acclimation may promote predator resilience after extreme heat events.

The restoration of Nardus grasslands is often hampered by high bioavailability of soil phosphorus and disturbed soil communities. In order to better understand these bottlenecks, we studied Nardus grassland species grown together in communities with fast-growing species in 50-liter pots along a gradient of bioavailable phosphorus with or without inoculated soil biota. These mesocosms allowed the plants to freely interact, including competition for light and nutrients. We investigated changes in the plant community composition along the phosphorus gradient using Threshold Indicator Taxa Analysis (TITAN). We found a negative threshold of 11.5 mg P_Olsen kg⁻¹ with six significant indicator plant species. Above the threshold, a small increase in phosphorus resulted in a disproportionally large drop in biomass for the indicator species, including four typical Nardus grassland species. The decline in these ‘oligotrophic indicator species’ was also linked to increasing plant community biomass, so we suggest the oligotrophic indicator species to be outcompeted for light by fast-growing plant species. We did not find an effect of the soil biota treatment on the biomass of the oligotrophic indicator species, but did observe a positive effect of inoculation with soil biota on the total biomass of the plant community. Interestingly, the threshold for the plant communities in the mesocosm experiment was comparable to the upper bioavailable phosphorus concentrations in remnant Nardus grasslands in northern Belgium. For the restoration of Nardus grasslands, such phosphorus-poor soil conditions appear to be essential, because the plant species that typically occur in these grasslands are able to handle nutrient limitation, but not light limitation.

The mycobiome (fungal microbiome) influences plants—from seed germination to full maturation. While many studies on fungal-plant interaction studies have focused on known mutualistic and pathogenic fungi, the functional role of ubiquitous endophytic fungi remains little explored. We examined how root-inhabiting fungi (endophytes) influence range-expanding plant species. We isolated endophytes from three European intra-continental range-expanders and three congenerics that are native both in the range expander's original (southern Europe) and new (northern Europe) range. To standardize our collection, endophytes were obtained from all six plant species growing under controlled conditions in northern (new range of the range expander) and southern (native range of the range expander) soils. We cultivated, molecularly identified and tested the effects of all isolates on seed germination, and growth of seedlings and older plants. Most of the 34 isolates could not be functionally characterized based on their taxonomic identity and literature information on functions. Endophytes affected plant growth in a plant species–endophyte-specific manner, but overall differed between range-expanders and natives. While endophytes reduced germination and growth of range-expanders compared to natives, they reduced seedling growth of natives more than of range-expanders. Synthesis. We conclude that endophytic fungi have a direct effect on plant growth in a plant growth stage-dependent manner. While these effects differed between range expanders and natives, the effect strength and significance varied among the plant genera included in the present study. Nevertheless, endophytes likely influence the establishment of newly arriving plants and influence vegetation dynamics.

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.

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.

Establishment and growth of grassland plant species is generally promoted by arbuscular mycorrhizal fungi (AMF) when grown in isolation. However, in grassland communities AMF form networks that may connect individual plants of different ages within and between species. Here, we use an ingrowth core approach to examine how mycorrhizal networks influences performance of seedlings in grasslands. We selected four grass and four forb species with known negative or neutral-positive plant–soil feedback and grew them individually in steel mesh cores filled with living field soil. Cores were placed in six restored grasslands, three grasslands were of relatively young and three were of older successional age. Ingrowing mycorrhizal fungal hyphae were severed twice a week in half of all cores, which resulted into reduced AMF colonization and increased seedling biomass, irrespective of the fields' succession stage, and the plants' grass/forb group, or plant–soil feedback type. In the control cores, root colonization by AMF was negatively correlated to seedling biomass, whereas there was no such relationships in the cores that had been lifted. We conclude that connections to arbuscular mycorrhizal networks of surrounding plants had a negative impact on biomass of establishing forb and grass seedlings.

Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.

Biobased production has been promoted as an alternative to fossil-based production to mitigate climate change. However, emerging concerns over the sustainability of biobased products have shown that tensions can emerge between different objectives and concerns, like emission reduction targets and food security, and that these are dependent on local contexts. Here we present the Open Sustainability-in-Design (OSiD) framework, the aim of which is to integrate a context-sensitive sustainability analysis in the conceptual design of biobased processes. The framework is illustrated, taking as an example the production of sustainable aviation fuel in southeast Brazil. The OSiD framework is a novel concept that brings the perspectives of stakeholders and considerations of the regional context to an ex ante sustainability analysis of biobased production. This work also illustrates a way to integrate methods from different scientific disciplines supporting the analysis of sustainability and the identification of tensions between different sustainability aspects. Making these tensions explicit early in the development of biobased production can make them more responsive to emerging sustainability concerns. Considering the global pressure to reduce carbon emissions, situating sustainability analyses in their socio-technical contexts as presented here can help to explain and improve the impacts of biobased production in the transition away from fossil resources.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios.

We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria. This article is protected by copyright. All rights reserved.

Interactions between aboveground and belowground organisms are important drivers of plant growth and performance in natural ecosystems. Making practical use of such above-belowground biotic interactions offers important opportunities for enhancing the sustainability of agriculture, as it could favor crop growth, nutrient supply, and defense against biotic and abiotic stresses. However, the operation of above-and belowground organisms at different spatial and temporal scales provides important challenges for application in agriculture. Aboveground organisms, such as herbivores and pollinators, operate at spatial scales that exceed individual fields and are highly variable in abundance within growing seasons. In contrast, pathogenic, symbiotic, and decomposer soil biota operate at more localized spatial scales from individual plants to patches of square meters, however, they generate legacy effects on plant performance that may last from single to multiple years. The challenge is to promote pollinators and suppress pests at the landscape and field scale, while creating positive legacy effects of local plant-soil interactions for next generations of plants. Here, we explore the possibilities to improve utilization of above-belowground interactions in agro-ecosystems by considering spatio-temporal scales at which aboveground and belowground organisms operate. We identified that successful integration of above-belowground biotic interactions initially requires developing crop rotations and intercropping systems that create positive local soil legacy effects for neighboring as well subsequent crops. These configurations may then be used as building blocks to design landscapes that accommodate beneficial aboveground communities with respect to their required resources. For successful adoption of above-belowground interactions in agriculture there is a need for context-specific solutions, as well as sound socio-economic embedding.

DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.

Established theory addresses the idea that herbivory can have positive feedbacks on nutrient flow to plants. Positive feedbacks likely emerge from a greater availability of organic carbon that primes the soil by supporting nutrient turnover through consumer and especially microbially-mediated metabolism in the detrital pool. We developed an entirely novel stoichiometric model that demonstrates the mechanism of a positive feedback. In particular, we show that sloppy or partial feeding by herbivores increases detrital carbon and nitrogen allowing for greater nitrogen mineralization and nutritive feedback to plants. The model consists of differential equations coupling flows among pools of: plants, herbivores, detrital carbon and nitrogen, and inorganic nitrogen. We test the effects of different levels of herbivore grazing completion and of the stoichiometric quality (carbon to nitrogen ratio, C:N) of the host plant. Our model analyses show that partial feeding and plant C:N interact because when herbivores are sloppy and plant biomass is diverted to the detrital pool, more mineral nitrogen is available to plants because of the stoichiometric difference between the organisms in the detrital pool and the herbivore. This model helps to identify how herbivory may feedback positively on primary production, and it mechanistically connects direct and indirect feedbacks from soil to plant production.