David Johnson

The University of Manchester · School of Earth and Environmental Sciences

Subtropical and tropical forests in Asia often comprise canopy dominant trees that form symbioses with ectomycorrhizal fungi, and species-rich understorey trees that form symbioses with arbuscular mycorrhizal fungi. We propose a virtuous phosphorus acquisition hypothesis to explain this distinct structure. The hypothesis is based on (i) seedlings b...

Tropical forests are threatened by degradation and deforestation but the consequences for these ecosystems are poorly understood, particularly at the landscape scale. We present the most extensive ecosystem analysis to date of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing respo...

The supply of recent photosynthate from plants to soils is thought to be a critical mechanism regulating the activity and diversity of soil biota. In the Arctic, large‐scale vegetation transitions are underway in response to warming, and there is an urgent need to understand how these changes affect soil biodiversity and function. We investigated h...

While most studies yield positive relationships between biodiversity (B) and ecosystem functioning (EF), awareness is growing that BEF relationships can vary with ecological context. The awareness has led to increased efforts to understand how contemporary environmental context modifies BEF relationships, but the role of historical context, and the...

Modification of soil food webs by historical land management may alter the response of ecosystem processes to climate extremes, but empirical support for this is limited and the mechanisms involved remain unclear. Here, we quantified how historical grassland management modifies transfers of recent photosynthate and soil nitrogen through plants and...

Early terrestrial plants colonizing land likely relied on arbuscular mycorrhizal (AM) associations to meet their nutrient needs (Smith and Read 2008 but see Bidartondo et al. 2011). Despite occasional diversifications towards other mycorrhizal association strategies (Hoeksema 2010; Feijen et al. 2018), the AM symbiosis shows a remarkable persistenc...

The effects of plants on the biosphere, atmosphere, and geosphere are key determinants of terrestrial ecosystem functioning. However, despite substantial progress made regarding plant belowground components, we are still only beginning to explore the complex relationships between root traits and functions. Drawing on literature in plant physiology,...

Grasslands are under severe threat from ongoing degradation, undermining their capacity to support biodiversity, ecosystem services and human well-being. Yet, grasslands are largely ignored in sustainable development agendas. In this Perspective, we examine the current state of global grasslands and explore the extent and dominant drivers of their...

This special issue, brought together during a time of unprecedented global change, represents a unique collection of papers that shed light on the current and future significance of mycorrhiza‐forming fungi in the human world. Across this selection of papers, we explore the significance and potential of mycorrhizal fungi to contribute towards our a...

While the effect of drought on plant communities and their associated ecosystem functions is well studied, little research has considered how responses are modified by soil depth and depth heterogeneity. We conducted a mesocosm study comprising shallow and deep soils, and variable and uniform soil depths, and two levels of plant community compositi...

It is widely accepted that the measurement of organic and inorganic forms of carbon (C) and nitrogen (N) in soils should be performed on fresh extracts taken from fresh soil samples. However, this is often not possible, and it is common practice to store samples (soils and/or extracts), despite a lack of guidance on best practice. We utilised a cas...

Plant–soil feedbacks regulate plant productivity and diversity, but potential mechanisms underpinning such feedbacks, such as the allocation of recent plant assimilate, remain largely untested especially for plants forming tripartite symbioses. We tested how soils from under alder Alnus glutinosa and beneath other species of the same and different...

Food systems are significant sources of global greenhouse gas emissions (GHGE). Since emission intensity varies greatly between different foods, changing food choices towards those with lower GHGE could make an important contribution to mitigating climate change. Public engagement events offer an opportunity to communicate these multifaceted issues...

Societal Impact Statement Mycorrhizal fungi are key components of soil biodiversity that offer potential to provide sustainable solutions for land management, notably in agriculture and forestry. Several studies conducted in controlled environments show that key functional attributes of common mycorrhizal networks (CMNs), which inter‐link different...

Pathogenic and mutualistic fungi have contrasting effects on seedling establishment, but it remains unclear whether density‐dependent survival and growth are regulated by access to different types of mycorrhizal fungal networks supported by neighbouring adult trees. Here, we conducted an extensive field survey to test how mycorrhizal and pathogenic...

It is widely accepted that the measurement of organic and inorganic forms of carbon (C) and nitrogen (N) in soils should be performed on fresh extracts taken from fresh soil samples. However, this is often not possible, and it is common practice to store samples (soils and/or extracts), despite a lack of guidance on best practice. Here, we demonstr...

The rainforests of Southeast Asia are a global biodiversity hotspot under increasing pressure from human activity. Selective logging and forest conversion to oil palm plantation has major implications for biogeochemical cycling and carbon storage that are underpinned by plant-soil interactions. Soil fungi are key regulators of carbon and mineral nu...

The mechanisms regulating community composition and local dominance of trees in species-rich forests are poorly resolved, but the importance of interactions with soil microbes is increasingly acknowledged. Here, we show that tree seedlings that interact via root-associated fungal hyphae with soils beneath neighbouring adult trees grow faster and ha...

Root systems show a tremendous diversity both between and within species, suggesting a large variability in plant functioning and effects on ecosystem properties and processes. In recent decades, developments in many areas of root research have brought considerable advances in our understanding of root traits and their contribution to plant and eco...

Soil carbon (C) pools and plant community composition are regulated by nitrogen (N) and phosphorus (P) availability. Atmospheric N deposition impacts ecosystem C storage, but the direction of response varies between systems. Phosphorus limitation may constrain C storage response to N, hence P application to increase plant productivity and thus C se...

In arctic ecosystems, climate change has increased plant productivity. As arctic carbon (C) stocks predominantly are located belowground, the effects of greater plant productivity on soil C storage will significantly determine the net sink/source potential of these ecosystems, but vegetation controls on soil CO 2 efflux remain poorly resolved. In o...

Societal Impact Statement Mycorrhizal fungi are of huge significance for plants, people, and the planet. In addition to the fruiting bodies of many mycorrhizal fungi having great culinary, medical, and sometimes religious significance, by forming partnerships with the vast majority of land plants, mycorrhizal fungi are essential in the formation an...

Logging, pervasive across the lowland tropics, affects millions of hectares of forest, yet its influence on nutrient cycling remains poorly understood. One hypothesis is that logging influences phosphorus (P) cycling, because this scarce nutrient is removed in extracted timber and eroded soil, leading to shifts in ecosystem functioning and communit...

Despite great advances, experiments concerning the response of ecosystems to climate change still face considerable challenges, including the high complexity of climate change in terms of environmental variables, constraints in the number and amplitude of climate treatment levels, and the limited scope of responses and interactions covered. Drawing...

The relationship between plant diversity and productivity and the mechanisms underpinning that relationship remain poorly resolved in species-rich forests. We combined extensive field observations and experimental manipulations in a subtropical forest to test how species richness (SR) and phylogenetic diversity (PD) interact with putative root-asso...

Invasive plants depositing recalcitrant, polyphenol-rich leaf litter may alter decomposition dynamics, leading to an accumulation of soil organic matter. Removing invasives is critical in restoring native habitats, but our understanding of its impacts upon soil processes remains limited. Here, we test the hypothesis that clearing of Rhododendron po...

Theory suggests that more complex food webs promote stability and can buffer the effects of perturbations, such as drought, on soil organisms and ecosystem functions. Here, we tested experimentally how soil food web trophic complexity modulates the response to drought of soil functions related to carbon cycling and the capture and transfer below‐gr...

If water saving methods of rice management are to be adopted, the interaction between rice plants and arbuscular mycorrhizal (AM) fungi will grow in agronomic significance. As yet there are very few studies on the interaction between rice and AM fungi and none on host genetics. A subset 334 cultivars from the Rice Diversity Panel 1 were grown in 25...

Most terrestrial plants depend strongly on associations with arbuscular mycorrhizal (AM) fungi (Subphylum: Glomeromycotina) to establish and survive (Bever, 2002; van der Heijden et al., 1998; Klironomos et al., 2011; Veresoglou et al., 2017), and have evolved a nutritional mutualism. In this mutualism, the plant provides carbon to the fungus, usua...

Maternal effects (i.e. trans‐generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects of these factors on plant growth dynamics remain poorly understood. We used soil and seeds from a...

The use of plant traits to predict ecosystem functions has been gaining growing attention. Above‐ground plant traits, such as leaf nitrogen (N) content and specific leaf area (SLA), have been shown to strongly relate to ecosystem productivity, respiration and nutrient cycling. Furthermore, increasing plant functional trait diversity has been sugges...

The maternal rearing environment can affect offspring fitness or phenotype indirectly via ‘maternal effects’ and can also influence a mother’s behaviour and fecundity directly. However, it remains uncertain how the effects of the maternal rearing environment cascade through multiple trophic levels, such as in plant-insect herbivore-natural enemy in...

Details on plants used in G0 pea aphid choice tests. Weight (g) and leaf nitrogen concentration (% dry mass) of 3-week old bean. Values are means (± SEM) of n = 12 plants. Significant differences are highlighted in bold. (DOCX)

Statistical summaries of two-way ANOVAs for pea aphid performance. G1 intrinsic rate of population increase (Rm), G2 nymph dry weight and G1 survival for pea aphids used in performance assays (Fig 4). Significant differences are highlighted in bold. (DOCX)

Statistical summaries of the pea aphid and wasp choice tests shown in Fig 3. Negative estimates and z values indicate preference for the ‘alternative’ compared to the ‘same’ host environment (Fig 1) presented in the choice tests. Significant preferences are highlighted in bold. (DOCX)

Quality of aphids used in G0 wasp choice tests. Aphid dry weight (mg) for (A) the Plant Comparison and (C) the Plant-Aphid Comparison. Aphid nitrogen concentration for (B) the Plant Comparison and (D) the Plant-Aphid Comparison. Values are means (± SEM) of n = 20 for pea aphids reared on bean plants and n = 19 pea aphids reared on pea plants in the...

Details on plants used in G1 pea aphid performance assays. Weight (g) and leaf nitrogen concentration (% dry mass) of six-week old bean and pea plants, after being infested with G1 pea aphids for three weeks. Significant differences are highlighted in bold. (DOCX)

Summary statistics of (general) linear mixed models ((G)LMMs) for wasp performance. GLMMS for G1 wasp survival and sex, and LMMs for G1 wasp weight were used to test for maternal effects for the Plant and Plant-Aphid Comparison (Fig 6). Statistical outputs are provided from the most simplified models (see text for details). Significant results are...

This article is a Commentary on Barnes et al., 220: 1171–1183.

Feedbacks between plants and soil microbial communities play an important role in vegetation dynamics, but the underlying mechanisms remain unresolved. Here, we show that the diversity of putative pathogenic, mycorrhizal, and saprotrophic fungi is a primary regulator of plant-soil feedbacks across a broad range of temperate grassland plant species....

Plant functional traits regulate ecosystem functions but little is known about how co‐occurring gradients of land use and edaphic conditions influence their expression. We test how gradients of logging disturbance and soil properties relate to community‐weighted mean traits in logged and old‐growth tropical forests in Borneo. We studied 32 physical...

Process‐based models describing biogeochemical cycling are crucial tools to understanding long‐term nutrient dynamics, especially in the context of perturbations, such as climate and land‐use change. Such models must effectively synthesize ecological processes and properties. For example, in terrestrial ecosystems, plants are the primary source of...

Association of plants with arbuscular mycorrhizal ( AM ) fungi may act as either an equalizing or a stabilizing mechanism of coexistence, but the effect of the symbiosis likely depends on the responsiveness to fungi of plant species within a community, rather than simply as a binary metric based on presence or absence of AM fungi. Here, we test the...

There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed tempe...

Partitioning of soil phosphorus (P) pools has been proposed as a key mechanism maintaining plant diversity, but experimental support is lacking. Here, we provided different chemical forms of P to 15 tree species with contrasting root symbiotic relationships to investigate plant P acquisition in both tropical and subtropical forests. Both ectomycorr...

Contents Summary I. Introduction II. Are there consistent patterns in diversity of mycorrhizal fungal genotypes and species across space? III. What is the variation in functional traits and genes of mycorrhizal fungi at different taxonomic scales? IV. How will environmental change impact the relationships between genotypic and species diversity of...

In hyperdiverse tropical forests, the key drivers of litter decomposition are poorly understood despite its crucial role in facilitating nutrient availability for plants and microbes. Selective logging is a pressing land use with potential for considerable impacts on plant–soil interactions, litter decomposition, and nutrient cycling. Here, in Born...

Effects of biodiversity on productivity are more likely to be expressed when there is greater potential for niche complementarity. In soil, chemically complex pools of nutrient resources should provide more opportunities for niche complementarity than chemically simple pools. Ectomycorrhizal (ECM) fungal genotypes can exhibit substantial variation...

An understanding of the environmental toxicology of ionizing radiation (IR) is needed because nuclear power production is expanding and there is increasing pressure to build nuclear waste repositories. The effects of IR in the environment have long been investigated but there have been fewer studies involving environmental microbiology than its imp...

Mycorrhizal fungi can interconnect individual plants to form common mycorrhizal networks (CMNs). Recent work has shown that these networks can transport signals produced by plants in response to herbivore and pathogen infestation to neighbouring plants before they are themselves attacked. The speed of transfer to uninfested plants is such that the...

A major gap in our understanding of biodiversity–ecosystem function relationships concerns the role of intra‐ and interspecific diversity of mycorrhizal fungi, which are critical for plant fitness, biogeochemical cycling and other processes. Here, we test the hypothesis that the identity and richness of ectomycorrhizal ( ECM ) fungi at the intra‐ a...

Understanding the climatic and biological factors that regulate soil carbon dioxide (CO2) efflux is crucial in peatlands because they contain a large proportion of terrestrial carbon (C). We predicted that rainfall reduction would increase soil CO2 efflux, and that cessation of below-ground allocation of recent plant assimilate would reduce soil CO...

Table S1. Surveyed long‐term upland exclosure details; location, age, size (m2) (calculated from http://digimap.edina.ac.uk/digimap/home), large herbivores excluded by fencing, mean annual rainfall, growing season length and growing season degree days (Met Office UKCP09 databases; http://www.metoffice.gov.uk/climatechange/science/monitoring/ukcp09/...

The mycelia of some symbiotic ectomycorrhizal fungi form extensive networks-the so called "wood-wide web"-that have key roles in biogeochemical cycling. By interacting with myriad soil organisms such as collembola, the fungi directly affect the functioning of above- and below-ground multitrophic interactions in ecosystems. Here we tested whether th...

Ecosystem carbon (C) accrual and storage can be enhanced by removing large herbivores as well as by the fertilizing effect of atmospheric nitrogen (N) deposition. These drivers are unlikely to operate independently, yet their combined effect on aboveground and belowground C storage remains largely unexplored. We sampled inside and outside 19 upland...

I. II. III. IV. V. VI. References SUMMARY: Mycorrhizal fungi can form common mycelial networks (CMNs) that interconnect plants. Here, we provide an insight into recent findings demonstrating that CMNs can be conduits for interplant signalling, influencing defence against insect herbivores and foliar necrotrophic fungi. A likely mechanism is direct...

Arbuscular mycorrhizal (AM) fungi, important plant mutualists, provide plants with nutrients such as phosphorus (P) in return for carbon. AM fungi also enhance the attractiveness of plants to aphids via effects on emissions of plant volatiles used in aphid host location. We tested whether increased P uptake by plants is the mechanism through which...

Root litter is the dominant soil carbon and nutrient input in many ecosystems, yet few studies have considered how root decomposition is regulated at the landscape scale and how this is mediated by land-use management practices. Large herbivores can potentially influence below-ground decomposition through changes in soil microclimate (temperature a...

Biplot of root decomposition measures mass and carbon loss CO2-C efflux; phenol peroxidase activity excluding loss of N from roots for 11 upland species and root decomposition measures excluding loss of N from roots and phenol peroxidase activity for 10 species without Ranunculus acris. Table S1 Spearman's rank correlation coefficients of paired ch...

Land management is a key control of terrestrial carbon (C) storage and can be used to mitigate rising CO 2 emissions. The UK uplands hold approximately one-third of national terrestrial C in their soils. The dominant land-use is extensive livestock grazing management. However, our understanding of the impact of grazing on upland C storage is limite...

Most plants interact with both arbuscular mycorrhizal ( AM ) fungi, which increase nutrient acquisition, and herbivores such as aphids, which drain nutrients from plants. Both AM fungi and aphids can affect plant metabolic pathways and may influence each other by altering the condition of the shared host plant. This study tests simultaneously the e...

The pressure of climate change is disproportionately high in mountainous regions, and small changes may push ecosystem processes beyond sensitivity thresholds, creating new dynamics of carbon and nutrient cycling. Given that the rate of organic matter decomposition is strongly dependent upon temperature and soil moisture, the sensitivity of soil re...