The role of multiple global change factors in driving soil functions and microbial biodiversity

Warming leads to more closed nitrogen cycling in nitrogen-rich tropical forests

Warming may have profound effects on nitrogen (N) cycling by changing plant N demand and underground N supply. However, large uncertainty exists regarding how warming affects the integrated N dynamic in tropical forests. We translocated model plant-soil ecosystems from a high-altitude site (600 m) to low-altitude sites at 300 and 30 m to simulate warming by 1.0°C and 2.1°C, respectively, in tropical China. The effects of experimental warming on N components in plant, soil, leaching, and gas were studied over 6 years. Our results showed that foliar δ¹⁵ N values and inorganic N (NH₄ -N and NO₃ -N) leaching were decreased under warming, with greater decreases under 2.1°C of warming than under 1.0°C of warming. The 2.1°C of warming enhanced plant growth, plant N uptake, N resorption, and fine root biomass, suggesting higher plant N demand. Soil total N concentrations, NO₃ -N concentrations, microbial biomass N and arbuscular mycorrhizal fungal abundance were decreased under 2.1°C of warming, which probably restricted bioavailable N supply and arbuscular mycorrhizal contribution of N supply to plants. These changes in plants, soils and leaching indicated more closed N cycling under warming, the magnitude of which varied over time. The closed N cycling became pronounced during the first 3 years of warming where the sustained reductions in soil inorganic N could not meet plant N demand. Subsequently, the closed N cycling gradually mitigated, as observed by attenuated positive responses of plant growth and less negative responses of microbial biomass N to warming during the last 3 years. Overall, the more closed N cycling under warming could facilitate ecosystem N retention and affect production in these tropical forests, but these effects would be eventually mitigated with long-term warming probably due to the restricted plant growth and microbial acclimation.

Potential Effects of Microplastic on Arbuscular Mycorrhizal Fungi

Microplastics (MPs) are ubiquitously found in terrestrial ecosystems and are increasingly recognized as a factor of global change (GCF). Current research shows that MP can alter plant growth, soil inherent properties, and the composition and activity of microbial communities. However, knowledge about how microplastic affects arbuscular mycorrhizal fungi (AMF) is scarce. For plants it has been shown that microplastic can both increase and decrease the aboveground biomass and reduce the root diameter, which could indirectly cause a change in AMF abundance and activity. One of the main direct effects of microplastic is the reduction of the soil bulk density, which translates to an altered soil pore structure and water transport. Moreover, especially fibers can have considerable impacts on soil structure, namely the size distribution and stability of soil aggregates. Therefore, microplastic alters a number of soil parameters that determine habitat space and conditions for AMF. We expect that this will influence functions mediated by AMF, such as soil aggregation, water and nutrient transport. We discuss how the impacts of microplastic on AMF could alter how plants deal with other GCFs in the context of sustainable food production. The co-occurrence of several GCFs, e.g., elevated temperature, drought, pesticides, and microplastic could modify the impact of microplastic on AMF. Furthermore, the ubiquitous presence of microplastic also relates to earth system processes, e.g., net primary production (NPP), carbon and nitrogen cycling, which involve AMF as key soil organisms. For future research, we outline which experiments should be prioritized.

Changes in soil fungal community composition depend on functional group and forest disturbance type

Disturbances have altered community dynamics in boreal forests with unknown consequences for belowground ecological processes. Soil fungi are particularly sensitive to such disturbances; however, the individual response of fungal guilds to different disturbance types is poorly understood. Here, we profiled soil fungal communities in lodgepole pine forests following a bark beetle outbreak, wildfire, clear-cut logging, and salvage-logging. Using Illumina MiSeq to sequence ITS1 and SSU rDNA, we characterized communities of ectomycorrhizal, arbuscular mycorrhizal, saprotrophic, and pathogenic fungi in sites representing each disturbance type paired with intact forests. We also quantified soil fungal biomass by measuring ergosterol. Abiotic disturbances changed the community composition of ectomycorrhizal fungi and shifted the dominance from ectomycorrhizal to saprotrophic fungi compared to intact forests. The disruption of the soil organic layer with disturbances correlated with the decline of ectomycorrhizal and the increase of arbuscular mycorrhizal fungi. Wildfire changed the community composition of pathogenic fungi but did not affect their proportion and diversity. Fungal biomass declined with disturbances that disrupted the forest floor. Our results suggest that the disruption of the forest floor with disturbances, and the changes in C and nutrient dynamics it may promote, structure the fungal community with implications for fungal biomass-C.

Microbiome Research: Open Communication Today, Microbiome Applications in the Future

Microbiome research has recently gained centre-stage in both basic science and translational applications, yet researchers often feel that public communication about its potential overpromises. This manuscript aims to share a perspective on how scientists can engage in more open, ethical and transparent communication using an ongoing research project on food systems microbiomes as a case study. Concrete examples of strategically planned communication efforts are outlined, which aim to inspire and empower other researchers. Finally, we conclude with a discussion on the benefits of open and transparent communication from early-on in innovation pathways, mainly increasing trust in scientific processes and thus paving the way to achieving societal milestones such as the UN Sustainable Development Goals and the EU Green Deal.

Microplastics could be a threat to plants in terrestrial systems directly or indirectly

Microplastics (MPs) are an emerging threat to ecosystem functioning and biota. The major sources of MPs are terrestrial and agricultural lands. But their fate, concentration in the terrestrial environment, and effects on soil and biota are poorly understood. There is a growing body of concern about the adverse effects of MPs on soil-dwelling organisms such as microbes in mycorrhizae and earthworms that mediate essential ecosystem services. Environmental concentrations and effects of MPs are considered to increase with increasing trend of its global production. MPs in the soil could directly impact plants through blocking the seed pore, limiting the uptake of water and nutrient through roots, aggregation, and accumulation in the root, shoot, and leaves. However, MPs can also indirectly impact plants by affecting soil physicochemical characteristics, soil-dwelling microbes, and fauna. An affected soil could impact plant community structure and perhaps primary production. In this article, we have assessed the potential direct and indirect impacts of MPs on plants. We have discussed both the positive and negative impacts of MPs on plants in terrestrial systems based on currently available limited literature on this topic and our hypothetical understandings. We have summarized the most current progress in this regard highlighting the future directions on microplastic research in terrestrial systems.

Plant invasion impacts on fungal community structure and function depend on soil warming and nitrogen enrichment

The impacts of invasive species on biodiversity may be mitigated or exacerbated by abiotic environmental changes. Invasive plants can restructure soil fungal communities with important implications for native biodiversity and nutrient cycling, yet fungal responses to invasion may depend on numerous anthropogenic stressors. In this study, we experimentally invaded a long-term soil warming and simulated nitrogen deposition experiment with the widespread invasive plant Alliaria petiolata (garlic mustard) and tested the responses of soil fungal communities to invasion, abiotic factors, and their interaction. We focused on the phytotoxic garlic mustard because it suppresses native mycorrhizae across forests of North America. We found that invasion in combination with warming, but not under ambient conditions or elevated nitrogen, significantly reduced soil fungal biomass and ectomycorrhizal relative abundances and increased relative abundances of general soil saprotrophs and fungal genes encoding for hydrolytic enzymes. These results suggest that warming potentially exacerbates fungal responses to plant invasion. Soils collected from uninvaded and invaded plots across eight forests spanning a 4 °C temperature gradient further demonstrated that the magnitude of fungal responses to invasion was positively correlated with mean annual temperature. Our study is one of the first empirical tests to show that the impacts of invasion on fungal communities depends on additional anthropogenic pressures and were greater in concert with warming than under elevated nitrogen or ambient conditions.

Climate Disruption of Plant-Microbe Interactions

Interactions between plants and microbes have important influences on evolutionary processes, population dynamics, community structure, and ecosystem function. We review the literature to document how climate change may disrupt these ecological interactions and develop a conceptual framework to integrate the pathways of plant-microbe responses to climate over different scales in space and time. We then create a blueprint to aid generalization that categorizes climate effects into changes in the context dependency of plant-microbe pairs, temporal mismatches and altered feedbacks over time, or spatial mismatches that accompany species range shifts. We pair a new graphical model of how plant-microbe interactions influence resistance to climate change with a statistical approach to predictthe consequences of increasing variability in climate. Finally, we suggest pathways through which plant-microbe interactions can affect resilience during recovery from climate disruption. Throughout, we take a forward-looking perspective, highlighting knowledge gaps and directions for future research.

Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities

The use of synthetic pesticides in agriculture is increasingly debated. However, few studies have compared the impact of synthetic pesticides and alternative biopesticides on non-target soil microorganisms playing a central role in soil functioning. We conducted a mesocosm experiment and used high-throughput amplicon sequencing to test the impact of a fungal biopesticide and a synthetic fungicide on the diversity, the taxonomic and functional compositions, and co-occurrence patterns of soil bacterial, fungal and protist communities. Neither the synthetic pesticide nor the biopesticide had a significant effect on microbial α-diversity. However, both types of pesticides decreased the complexity of the soil microbial network. The two pesticides had contrasting impacts on the composition of microbial communities and the identity of key taxa as revealed by microbial network analyses. The biopesticide impacted keystone taxa that structured the soil microbial network. The synthetic pesticide modified biotic interactions favouring taxa that are less efficient at degrading organic compounds. This suggests that the biopesticides and the synthetic pesticide have different impact on soil functioning. Altogether, our study shows that pest management products may have functionally significant impacts on the soil microbiome even if microbial α-diversity is unaffected. It also illustrates the potential of high-throughput sequencing analyses to improve the ecotoxicological risk assessment of pesticides on non-target soil microorganisms.

Climate-driven benthic invertebrate activity and biogeochemical functioning across the Barents Sea polar front

Arctic marine ecosystems are undergoing rapid correction in response to multiple expressions of climate change, but the consequences of altered biodiversity for the sequestration, transformation and storage of nutrients are poorly constrained. Here, we determine the bioturbation activity of sediment-dwelling invertebrate communities over two consecutive summers that contrasted in sea-ice extent along a transect intersecting the polar front. We find a clear separation in community composition at the polar front that marks a transition in the type and amount of bioturbation activity, and associated nutrient concentrations, sufficient to distinguish a southern high from a northern low. While patterns in community structure reflect proximity to arctic versus boreal conditions, our observations strongly suggest that faunal activity is moderated by seasonal variations in sea ice extent that influence food supply to the benthos. Our observations help visualize how a climate-driven reorganization of the Barents Sea benthic ecosystem may be expressed, and emphasize the rapidity with which an entire region could experience a functional transformation. As strong benthic-pelagic coupling is typical across most parts of the Arctic shelf, the response of these ecosystems to a changing climate will have important ramifications for ecosystem functioning and the trophic structure of the entire food web. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment

Microplastics are recognized as an emerging contaminant worldwide. Although microplastics have been shown to strongly affect organisms in aquatic environments, less is known about whether and how microplastics can affect different taxa within a soil community, and it is unclear whether these effects can cascade through soil food webs. By conducting a microplastic manipulation experiment, i.e. adding low-density polyethylene fragments in the field, we found that microplastic addition significantly affected the composition and abundance of microarthropod and nematode communities. Contrary to soil fauna, we found only small effects of microplastics on the biomass and structure of soil microbial communities. Nevertheless, structural equation modelling revealed that the effects of microplastics strongly cascade through the soil food webs, leading to the modification of microbial functioning with further potential consequences on soil carbon and nutrient cycling. Our results highlight that taking into account the effects of microplastics at different trophic levels is important to elucidate the mechanisms underlying the ecological impacts of microplastic pollution on soil functioning.

Interactive global change factors mitigate soil aggregation and carbon change in a semi-arid grassland

The ongoing global change is multi-faceted, but the interactive effects of multiple drivers on the persistence of soil carbon (C) are poorly understood. We examined the effects of warming, reactive nitrogen (N) inputs (12 g N m^-2  year^-1 ) and altered precipitation (+ or - 30% ambient) on soil aggregates and mineral-associated C in a 4 year manipulation experiment with a semi-arid grassland on China's Loess Plateau. Our results showed that in the absence of N inputs, precipitation additions significantly enhanced soil aggregation and promoted the coupling between aggregation and both soil fungal biomass and exchangeable Mg²⁺ . However, N inputs negated the promotional effects of increased precipitation, mainly through suppressing fungal growth and altering soil pH and clay-Mg²⁺ -OC bridging. Warming increased C content in the mineral-associated fraction, likely by increasing inputs of root-derived C, and reducing turnover of existing mineral-associated C due to suppression of fungal growth and soil respiration. Together, our results provide new insights into the potential mechanisms through which multiple global change factors control soil C persistence in arid and semi-arid grasslands. These findings suggest that the interactive effects among global change factors should be incorporated to predict the soil C dynamics under future global change scenarios.

Soil functional biodiversity and biological quality under threat: intensive land use outweighs climate change

Climate change and land use intensification are the two most common global change drivers of biodiversity loss. Like other organisms, the soil meso-fauna are expected to modify their functional diversity and composition in response to climate and land use changes. Here, we investigated the functional responses of Collembola, one of the most abundant and ecologically important groups of soil invertebrates. This study was conducted at the Global Change Experimental Facility (GCEF) in central Germany, where we tested the effects of climate (ambient vs. 'future' as projected for this region for the years between 2070 and 2100), land use (conventional farming, organic farming, intensively-used meadow, extensively-used meadow, and extensively-used pasture), and their interactions on the functional diversity (FD), community-weighted mean (CWM) traits (life-history, morphology), and functional composition of Collembola, as well as the Soil Biological Quality-Collembola (QBS-c) index. We found that land use was overwhelmingly the dominant driver of shifts in functional diversity, functional traits, and functional composition of Collembola, and of shifts in soil biological quality. These significant land use effects were mainly due to the differences between the two main land use types, i.e. cropland vs. grasslands. Specifically, Collembola functional biodiversity and soil biological quality were significantly lower in croplands than grasslands. However, no interactive effect of climate × land use was found in this study, suggesting that land use effects on Collembola were independent of the climate change scenario. Overall, our study shows that functional responses of Collembola are highly vulnerable to land use intensification under both climate scenarios. We conclude that land use changes reduce functional biodiversity and biological quality of soil.

Biodiversity mediates the effects of stressors but not nutrients on litter decomposition

Understanding the consequences of ongoing biodiversity changes for ecosystems is a pressing challenge. Controlled biodiversity-ecosystem function experiments with random biodiversity loss scenarios have demonstrated that more diverse communities usually provide higher levels of ecosystem functioning. However, it is not clear if these results predict the ecosystem consequences of environmental changes that cause non-random alterations in biodiversity and community composition. We synthesized 69 independent studies reporting 660 observations of the impacts of two pervasive drivers of global change (chemical stressors and nutrient enrichment) on animal and microbial decomposer diversity and litter decomposition. Using meta-analysis and structural equation modeling, we show that declines in decomposer diversity and abundance explain reduced litter decomposition in response to stressors but not to nutrients. While chemical stressors generally reduced biodiversity and ecosystem functioning, detrimental effects of nutrients occurred only at high levels of nutrient inputs. Thus, more intense environmental change does not always result in stronger responses, illustrating the complexity of ecosystem consequences of biodiversity change. Overall, these findings provide strong evidence that the consequences of observed biodiversity change for ecosystems depend on the kind of environmental change, and are especially significant when human activities decrease biodiversity.

Diversity of Growth Responses of Soil Saprobic Fungi to Recurring Heat Events

As a consequence of ongoing climate change, the frequency of extreme heat events is expected to increase. Recurring heat pulses may disrupt functions supported by soil microorganisms, thus affecting the entire ecosystem. However, most perturbation experiments only test effects of single heat events, and therefore it remains largely unknown how soil microorganisms react to repeated pulse events. Here we present data from a lab experiment exposing 32 filamentous fungi, originally isolated from the same soil, to sequential heat perturbations. Soil saprobic fungi isolates were exposed to one or two heat pulses: mild (35°C/2 h), strong (45°C/1 h), or both in sequence (35°C/2 h+45°C/1 h), and we assessed growth rate. Out of the 32 isolates 13 isolates showed an antagonistic response, 3 isolates a synergistic response and 16 isolates responded in an additive manner. Thus the 32 filamentous fungal isolates used here showed the full range of possible responses to an identical heat perturbation sequence. This diversity of responses could have consequences for soil-borne ecosystem services, highlighting the potential importance of fungal biodiversity in maintaining such services, particularly in the context of climate change.

Soil Microbial Community Response Differently to the Frequency and Strength of Freeze-Thaw Events in a Larix gmelinii Forest in the Daxing'an Mountains, China

Sustained climate warming increases the frequency and strength of soil freeze-thaw (FT) events, which strongly affect the properties of soil microbial communities. To explore the responses and mechanisms of the frequency and strength of freeze-thaw events on soil microbial communities, a lab-scale FT test was conducted on forest soil in permafrost region from the Daxing'an Mountains, China. The number of FT cycles (FTN) had a greater effect on microbial communities than FT temperature fluctuation (FTF). The FTN and FTF explained 20.9 and 10.8% of the variation in microbial community structure, respectively, and 22.9 and 11.6% of the variation in enzyme activities, respectively. The total and subgroup microbial biomass, the ratio of fungi to bacteria (F/B), and C- and N-hydrolyzing enzyme activities all decreased with an increase in FTN. Among microbial groups, arbuscular mycorrhizal fungi (AMF) were the most sensitive to FT events. Based on the changes of F/B and AMF, the reduction in soil carbon sequestration caused by frequent FT events can be explained from a perspective of microorganisms. Based on redundancy analysis and Mental Test, soil moisture, total organic carbon, and total nitrogen were the major factors affecting microorganisms in FT events. In the forest ecosystem, soil water and fertilizer were important factors to resist the damage of FT to microorganism, and sufficient water and fertilizer can lighten the damage of FT events to microorganisms. As a result of this study, the understanding of the responses of soil microorganisms to the variation in FT patterns caused by climate changes has increased, which will lead to better predictions of the effects of likely climate change on soil microorganisms.

Towards a unified study of multiple stressors: divisions and common goals across research disciplines

Anthropogenic environmental changes, or 'stressors', increasingly threaten biodiversity and ecosystem functioning worldwide. Multiple-stressor research is a rapidly expanding field of science that seeks to understand and ultimately predict the interactions between stressors. Reviews and meta-analyses of the primary scientific literature have largely been specific to either freshwater, marine or terrestrial ecology, or ecotoxicology. In this cross-disciplinary study, we review the state of knowledge within and among these disciplines to highlight commonality and division in multiple-stressor research. Our review goes beyond a description of previous research by using quantitative bibliometric analysis to identify the division between disciplines and link previously disconnected research communities. Towards a unified research framework, we discuss the shared goal of increased realism through both ecological and temporal complexity, with the overarching aim of improving predictive power. In a rapidly changing world, advancing our understanding of the cumulative ecological impacts of multiple stressors is critical for biodiversity conservation and ecosystem management. Identifying and overcoming the barriers to interdisciplinary knowledge exchange is necessary in rising to this challenge. Division between ecosystem types and disciplines is largely a human creation. Species and stressors cross these borders and so should the scientists who study them.

How Plants Sense and Respond to Stressful Environments

Plants are exposed to an ever-changing environment to which they have to adjust accordingly. Their response is tightly regulated by complex signaling pathways that all start with stimulus perception. Here, we give an overview of the latest developments in the perception of various abiotic stresses, including drought, salinity, flooding, and temperature stress. We discuss whether proposed perception mechanisms are true sensors, which is well established for some abiotic factors but not yet fully elucidated for others. In addition, we review the downstream cellular responses, many of which are shared by various stresses but result in stress-specific physiological and developmental output. New sensing mechanisms have been identified, including heat sensing by the photoreceptor phytochrome B, salt sensing by glycosylinositol phosphorylceramide sphingolipids, and drought sensing by the specific calcium influx channel OSCA1. The simultaneous occurrence of multiple stress conditions shows characteristic downstream signaling signatures that were previously considered general signaling responses. The integration of sensing of multiple stress conditions and subsequent signaling responses is a promising venue for future research to improve the understanding of plant abiotic stress perception.

Putting soil invertebrate diversity on the map

Ecologists have had a very good foundational knowledge of the global distribution of plants and aboveground animals for many decades. But despite the immense diversity of soil organisms, our knowledge of the global distribution, drivers and threats to soil biodiversity is very limited. In this issue of Molecular Ecology, Bastida et al. (2020) produce the first global maps of soil invertebrate diversity that have been sampled at 83 locations, across six continents, using standardised methods and DNA sequencing. Using data from nematodes, arachnids and rotifers, and structural equation models, they find that diversity of these taxa is primarily driven by vegetation and climate. Given the anthropogenic changes that are occurring, and are projected to continue, this study provides important baseline information for future soil biodiversity and function monitoring, as well as exciting working hypotheses for targeted experiments.