Estonian University of Life Sciences

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

Summary Here, we analysed a wide range of literature data on the leaf dry mass per unit area (LMA). In nature, LMA varies more than 100‐fold among species. Part of this variation ( c . 35%) can be ascribed to differences between functional groups, with evergreen species having the highest LMA, but most of the variation is within groups or biomes. When grown in the same controlled environment, leaf succulents and woody evergreen, perennial or slow‐growing species have inherently high LMA. Within most of the functional groups studied, high‐LMA species show higher leaf tissue densities. However, differences between evergreen and deciduous species result from larger volumes per area (thickness). Response curves constructed from experiments under controlled conditions showed that LMA varied strongly with light, temperature and submergence, moderately with CO 2 concentration and nutrient and water stress, and marginally under most other conditions. Functional groups differed in the plasticity of LMA to these gradients. The physiological regulation is still unclear, but the consequences of variation in LMA and the suite of traits interconnected with it are strong. This trait complex is an important factor determining the fitness of species in their environment and affects various ecosystem processes. Contents Summary 565 I. LMA in perspective 566 II. LMA in the field 567 III. Inherent differences 568 IV. Relation with anatomy and chemical composition 570 V. Environmental effects 572 VI. Differences in space and time 577 VII. Molecular regulation and physiology 579 VIII. Ecological consequences 580 IX. Conclusions and perspectives 582 Acknowledgements 582 References 582 Appendices 587

Abstract Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy‐in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log‐normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait‐based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Light gradients are ubiquitous in nature, so all plants are exposed to some degree of shade during their lifetime. The minimum light required for survival, shade tolerance, is a crucial life-history trait that plays a major role in plant community dynamics. There is consensus on the suites of traits that influence shade tolerance, but debate over the relative importance of traits maximizing photosynthetic carbon gain in low light versus those minimizing losses. Shade tolerance is influenced by plant ontogeny and by numerous biotic and abiotic factors. Although phenotypic plasticity tends to be low in shade-tolerant species (e.g., scant elongation in low light), plasticity for certain traits, particularly for morphological features optimizing light capture, can be high. Understanding differential competitive potentials among co-occurring species mediated by shade tolerance is critical to predict ecosystem responses to global change drivers such as elevated CO 2 , climate change and the spread of invasive species.

Summary 1. This synthesis examines 35 long‐term (5–35 years, mean: 16 years) lake re‐oligotrophication studies. It covers lakes ranging from shallow (mean depth <5 m and/or polymictic) to deep (mean depth up to 177 m), oligotrophic to hypertrophic (summer mean total phosphorus concentration from 7.5 to 3500 μ g L −1 before loading reduction), subtropical to temperate (latitude: 28–65°), and lowland to upland (altitude: 0–481 m). Shallow north‐temperate lakes were most abundant. 2. Reduction of external total phosphorus (TP) loading resulted in lower in‐lake TP concentration, lower chlorophyll a (chl a ) concentration and higher Secchi depth in most lakes. Internal loading delayed the recovery, but in most lakes a new equilibrium for TP was reached after 10–15 years, which was only marginally influenced by the hydraulic retention time of the lakes. With decreasing TP concentration, the concentration of soluble reactive phosphorus (SRP) also declined substantially. 3. Decreases (if any) in total nitrogen (TN) loading were lower than for TP in most lakes. As a result, the TN : TP ratio in lake water increased in 80% of the lakes. In lakes where the TN loading was reduced, the annual mean in‐lake TN concentration responded rapidly. Concentrations largely followed predictions derived from an empirical model developed earlier for Danish lakes, which includes external TN loading, hydraulic retention time and mean depth as explanatory variables. 4. Phytoplankton clearly responded to reduced nutrient loading, mainly reflecting declining TP concentrations. Declines in phytoplankton biomass were accompanied by shifts in community structure. In deep lakes, chrysophytes and dinophytes assumed greater importance at the expense of cyanobacteria. Diatoms, cryptophytes and chrysophytes became more dominant in shallow lakes, while no significant change was seen for cyanobacteria. 5. The observed declines in phytoplankton biomass and chl a may have been further augmented by enhanced zooplankton grazing, as indicated by increases in the zooplankton : phytoplankton biomass ratio and declines in the chl a : TP ratio at a summer mean TP concentration of <100–150 μ g L −1 . This effect was strongest in shallow lakes. This implies potentially higher rates of zooplankton grazing and may be ascribed to the observed large changes in fish community structure and biomass with decreasing TP contribution. In 82% of the lakes for which data on fish are available, fish biomass declined with TP. The percentage of piscivores increased in 80% of those lakes and often a shift occurred towards dominance by fish species characteristic of less eutrophic waters. 6. Data on macrophytes were available only for a small subsample of lakes. In several of those lakes, abundance, coverage, plant volume inhabited or depth distribution of submerged macrophytes increased during oligotrophication, but in others no changes were observed despite greater water clarity. 7. Recovery of lakes after nutrient loading reduction may be confounded by concomitant environmental changes such as global warming. However, effects of global change are likely to run counter to reductions in nutrient loading rather than reinforcing re‐oligotrophication.

In this paper, we reflect on the implications for science, policy and practice of the recently introduced concept of Nature-Based Solutions (NBS), with a focus on the European context. First, we analyse NBS in relation to similar concepts, and reflect on its relationship to sustainability as an overarching framework. From this, we derive a set of questions to be addressed and propose a general framework for how these might be addressed in NBS projects by funders, researchers, policy-makers and practitioners. We conclude that: NBS need to be developed and discussed in relation to existing concepts to clarify their added value; When considering and implementing NBS, the ‘relabelling’ of related concepts and the misuse of the concept have to be prevented in order to avoid misunderstanding, duplication and unintended consequences; NBS as currently framed by the European Commission provides an opportunity for: a) transdisciplinary research into the design and implementation of solutions based on nature; and b) overcoming a bias towards development alternatives with narrow perspectives that focus on short-term economic gains and effectiveness; The strength of the NBS concept is its integrative, systemic approach which prevents it from becoming just another “green communication tool” that provides justification for a classical model of natural resource exploitation and management measures. To realise their full potential, NBS must be developed by including the experience of all relevant stakeholders such that ‘solutions’ contribute to achieving all dimensions of sustainability. As NBS are developed, we must also moderate the expectations placed on them since the precedent provided by other initiatives whose aim was to manage nature sustainably demonstrates that we should not expect NBS to be cheap and easy, at least not in the short-term.

Abstract In this first worldwide synthesis of in situ and satellite‐derived lake data, we find that lake summer surface water temperatures rose rapidly (global mean = 0.34°C decade −1 ) between 1985 and 2009. Our analyses show that surface water warming rates are dependent on combinations of climate and local characteristics, rather than just lake location, leading to the counterintuitive result that regional consistency in lake warming is the exception, rather than the rule. The most rapidly warming lakes are widely geographically distributed, and their warming is associated with interactions among different climatic factors—from seasonally ice‐covered lakes in areas where temperature and solar radiation are increasing while cloud cover is diminishing (0.72°C decade −1 ) to ice‐free lakes experiencing increases in air temperature and solar radiation (0.53°C decade −1 ). The pervasive and rapid warming observed here signals the urgent need to incorporate climate impacts into vulnerability assessments and adaptation efforts for lakes.

• Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.

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Leaf size varies by over a 100,000-fold among species worldwide. Although 19th-century plant geographers noted that the wet tropics harbor plants with exceptionally large leaves, the latitudinal gradient of leaf size has not been well quantified nor the key climatic drivers convincingly identified. Here, we characterize worldwide patterns in leaf size. Large-leaved species predominate in wet, hot, sunny environments; small-leaved species typify hot, sunny environments only in arid conditions; small leaves are also found in high latitudes and elevations. By modeling the balance of leaf energy inputs and outputs, we show that daytime and nighttime leaf-to-air temperature differences are key to geographic gradients in leaf size. This knowledge can enrich "next-generation" vegetation models in which leaf temperature and water use during photosynthesis play key roles.

Abstract Dominance by cyanobacteria hampers human use of lakes and reservoirs worldwide. Previous studies indicate that excessive nutrient loading and warmer conditions promote dominance by cyanobacteria, but evidence from global scale field data has so far been scarce. Our analysis, based on a study of 143 lakes along a latitudinal transect ranging from subarctic Europe to southern South America, shows that although warmer climates do not result in higher overall phytoplankton biomass, the percentage of the total phytoplankton biovolume attributable to cyanobacteria increases steeply with temperature. Our results also reveal that the percent cyanobacteria is greater in lakes with high rates of light absorption. This points to a positive feedback because restriction of light availability is often a consequence of high phytoplankton biovolume, which in turn may be driven by nutrient loading. Our results indicate a synergistic effect of nutrients and climate. The implications are that in a future warmer climate, nutrient concentrations may have to be reduced substantially from present values in many lakes if cyanobacterial dominance is to be controlled.

Almost half of the total organic carbon (C) in terrestrial ecosystems is stored in forest soils. By altering rates of input or release of C from soils, forest management activities can influence soil C stocks in forests. In this review, we synthesize current evidence regarding the influences of 13 common forest management practices on forest soil C stocks. Afforestation of former croplands generally increases soil C stocks, whereas on former grasslands and peatlands, soil C stocks are unchanged or even reduced following afforestation. The conversion of primary forests to secondary forests generally reduces soil C stocks, particularly if the land is converted to an agricultural land-use prior to reforestation. Harvesting, particularly clear-cut harvesting, generally results in a reduction in soil C stocks, particularly in the forest floor and upper mineral soil. Removal of residues by harvesting whole-trees and stumps negatively affects soil C stocks. Soil disturbance from site preparation decreases soil C stocks, particularly in the organic top soil, however improved growth of tree seedlings may outweigh soil C losses over a rotation. Nitrogen (N) addition has an overall positive effect on soil C stocks across a wide range of forest ecosystems. Likewise, higher stocks and faster accumulation of soil C occur under tree species with N-fixing associates. Stocks and accumulation rates of soil C also differ under different tree species, with coniferous species accumulating more C in the forest floor and broadleaved species tending to store more C in the mineral soil. There is some evidence that increased tree species diversity could positively affect soil C stocks in temperate and subtropical forests, but tree species identity, particularly N-fixing species, seems to have a stronger impact on soil C stocks than tree species diversity. Management of stand density and thinning have small effects on forest soil C stocks. In forests with high populations of ungulate herbivores, reduction in herbivory levels can increase soil C stocks. Removal of plant biomass for fodder and fuel is related to a reduction in the soil C stocks. Fire management practices such as prescribed burning reduce soil C stocks, but less so than wildfires which are more intense. For each practice, we identify existing gaps in knowledge and suggest research to address the gaps.

Summary The leaf economics spectrum ( LES ) represents a suite of intercorrelated leaf traits concerning construction costs per unit leaf area, nutrient concentrations, and rates of carbon fixation and tissue turnover. Although broad trade‐offs among leaf structural and physiological traits have been demonstrated, we still do not have a comprehensive view of the fundamental constraints underlying the LES trade‐offs. Here, we investigated physiological and structural mechanisms underpinning the LES by analysing a novel data compilation incorporating rarely considered traits such as the dry mass fraction in cell walls, nitrogen allocation, mesophyll CO 2 diffusion and associated anatomical traits for hundreds of species covering major growth forms. The analysis demonstrates that cell wall constituents are major components of leaf dry mass (18–70%), especially in leaves with high leaf mass per unit area ( LMA ) and long lifespan. A greater fraction of leaf mass in cell walls is typically associated with a lower fraction of leaf nitrogen (N) invested in photosynthetic proteins; and lower within‐leaf CO 2 diffusion rates, as a result of thicker mesophyll cell walls. The costs associated with greater investments in cell walls underpin the LES : long leaf lifespans are achieved via higher LMA and in turn by higher cell wall mass fraction, but this inevitably reduces the efficiency of photosynthesis.

Water is the key resource limiting world agricultural production. Although an impressive number of research reports have been published on plant drought tolerance enhancement via genetic modifications during the last few years, progress has been slower than expected. We suggest a feasible alternative strategy by application of rhizospheric bacteria coevolved with plant roots in harsh environments over millions of years, and harboring adaptive traits improving plant fitness under biotic and abiotic stresses. We show the effect of bacterial priming on wheat drought stress tolerance enhancement, resulting in up to 78% greater plant biomass and five-fold higher survivorship under severe drought. We monitored emissions of seven stress-related volatiles from bacterially-primed drought-stressed wheat seedlings, and demonstrated that three of these volatiles are likely promising candidates for a rapid non-invasive technique to assess crop drought stress and its mitigation in early phases of stress development. We conclude that gauging stress by elicited volatiles provides an effectual platform for rapid screening of potent bacterial strains and that priming with isolates of rhizospheric bacteria from harsh environments is a promising, novel way to improve plant water use efficiency. These new advancements importantly contribute towards solving food security issues in changing climates.

The aim of this review is to present an overview of changes in the contemporary use of wild food plants in Europe, mainly using the examples of our home countries: Poland, Italy, Spain, Estonia and Sweden. We set the scene referring to the nutrition of 19th century peasants, involving many famine and emergency foods. Later we discuss such issues as children's wild snacks, the association between the decline of plant knowledge and the disappearance of plant use, the effects of over-exploitation, the decrease of the availability of plants due to ecosystem changes, land access rights for foragers and intoxication dangers. We also describe the 20th and 21st century vogues in wild plant use, particularly their shift into the domain of haute-cuisine.

Abstract Changes in the efficiency of light interception and in the costs for light harvesting along the light gradients from the top of the plant canopy to the bottom are the major means by which efficient light harvesting is achieved in ecosystems. In the current review analysis, leaf, shoot and canopy level determinants of plant light harvesting, the light‐driven plasticity in key traits altering light harvesting, and variations among different plant functional types and between species of different shade tolerance are analyzed. In addition, plant age‐ and size‐dependent alterations in light harvesting efficiency are also examined. At the leaf level, the variations in light harvesting are driven by alterations in leaf chlorophyll content modifies the fraction of incident light harvested by given leaf area, and in leaf dry mass per unit area ( M A ) that determines the amount of leaf area formed with certain fraction of plant biomass in the leaves. In needle‐leaved species with complex foliage cross‐section, the degree of foliage surface exposure also depends on the leaf total‐to‐projected surface area ratio. At the shoot scale, foliage inclination angle distribution and foliage spatial aggregation are the major determinants of light harvesting, while at the canopy scale, branching frequency, foliage distribution and biomass allocation to leaves ( F L ) modify light harvesting significantly. F L decreases with increasing plant size from herbs to shrubs to trees due to progressively larger support costs in plant functional types with greater stature. Among trees, F L and stand leaf area index scale positively with foliage longevity. Plant traits altering light harvesting have a large potential to adjust to light availability. Chlorophyll per mass increases, while M A , foliage inclination from the horizontal and degree of spatial aggregation decrease with decreasing light availability. In addition, branching frequency decreases and canopies become flatter in lower light. All these plastic modifications greatly enhance light harvesting in low light. Species with greater shade tolerance typically form a more extensive canopy by having lower M A in deciduous species and enhanced leaf longevity in evergreens. In addition, young plants of shade tolerators commonly have less strongly aggregated foliage and flatter canopies, while in adult plants partly exposed to high light, higher shade tolerance of foliage allows the shade tolerators to maintain more leaf layers, resulting in extended crowns. Within a given plant functional type, increases in plant age and size result in increases in M A , reductions in F L and increases in foliage aggregation, thereby reducing plant leaf area index and the efficiency of light harvesting. Such dynamic modifications in plant light harvesting play a key role in stand development and productivity. Overall, the current review analysis demonstrates that a suite of chemical and architectural traits at various scales and their plasticity drive plant light harvesting efficiency. Enhanced light harvesting can be achieved by various combinations of traits, and these suites of traits vary during plant ontogeny.

• Paleobotanists have long used models based on leaf size and shape to reconstruct paleoclimate. However, most models incorporate a single variable or use traits that are not physiologically or functionally linked to climate, limiting their predictive power. Further, they often underestimate paleotemperature relative to other proxies. • Here we quantify leaf-climate correlations from 92 globally distributed, climatically diverse sites, and explore potential confounding factors. Multiple linear regression models for mean annual temperature (MAT) and mean annual precipitation (MAP) are developed and applied to nine well-studied fossil floras. • We find that leaves in cold climates typically have larger, more numerous teeth, and are more highly dissected. Leaf habit (deciduous vs evergreen), local water availability, and phylogenetic history all affect these relationships. Leaves in wet climates are larger and have fewer, smaller teeth. Our multivariate MAT and MAP models offer moderate improvements in precision over univariate approaches (± 4.0 vs 4.8°C for MAT) and strong improvements in accuracy. For example, our provisional MAT estimates for most North American fossil floras are considerably warmer and in better agreement with independent paleoclimate evidence. • Our study demonstrates that the inclusion of additional leaf traits that are functionally linked to climate improves paleoclimate reconstructions. This work also illustrates the need for better understanding of the impact of phylogeny and leaf habit on leaf-climate relationships.

Floral plantings are promoted to foster ecological intensification of agriculture through provisioning of ecosystem services. However, a comprehensive assessment of the effectiveness of different floral plantings, their characteristics and consequences for crop yield is lacking. Here we quantified the impacts of flower strips and hedgerows on pest control (18 studies) and pollination services (17 studies) in adjacent crops in North America, Europe and New Zealand. Flower strips, but not hedgerows, enhanced pest control services in adjacent fields by 16% on average. However, effects on crop pollination and yield were more variable. Our synthesis identifies several important drivers of variability in effectiveness of plantings: pollination services declined exponentially with distance from plantings, and perennial and older flower strips with higher flowering plant diversity enhanced pollination more effectively. These findings provide promising pathways to optimise floral plantings to more effectively contribute to ecosystem service delivery and ecological intensification of agriculture in the future.