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Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity., (© 2019 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

Aridity, which is increasing worldwide because of climate change, affects the structure and functioning of dryland ecosystems. Whether aridification leads to gradual (versus abrupt) and systemic (versus specific) ecosystem changes is largely unknown. We investigated how 20 structural and functional ecosystem attributes respond to aridity in global drylands. Aridification led to systemic and abrupt changes in multiple ecosystem attributes. These changes occurred sequentially in three phases characterized by abrupt decays in plant productivity, soil fertility, and plant cover and richness at aridity values of 0.54, 0.7, and 0.8, respectively. More than 20% of the terrestrial surface will cross one or several of these thresholds by 2100, which calls for immediate actions to minimize the negative impacts of aridification on essential ecosystem services for the more than 2 billion people living in drylands., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Employing mycorrhiza-defective mutants and their progenitors does not require inoculation or elimination of the resident microbial community in the experimental study of mycorrhizal soil ecology. We aimed to examine the suitability of mycorrhiza-defective rice (non-mycorrhizal, Oryza sativa L., cv. Nipponbare) and its progenitor (mycorrhizal) to evaluate nitrogen (N) loss control from paddy fields via arbuscular mycorrhizal (AM) fungi. We grew the two rice lines in soils with the full community of AM fungi and investigated root AM colonization. In the absence of AM fungi, we estimated rice N content, soil N concentration and microbial community on the basis of phospholipid fatty acids; we also quantified N loss via NH 3 volatilization, N 2 O emission, runoff and leaching. In the presence of AM fungi, we did not find any evidence of AM colonization for non-mycorrhizal rice while mycorrhizal rice was colonized and percentage of root colonization was 17-24%. In the absence of AM fungi, the two rice lines had similar N content, soil N concentration and microbial community. Importantly, there was no significant difference in N loss via all the four pathways between mycorrhizal and non-mycorrhizal systems. This mycorrhizal/non-mycorrhizal rice pair is suitable for further research on the role of AM fungi in the control of soil N loss in paddy fields., (Copyright © 2020 Zhang, You, Guo, Yun, Xia and Rillig.)

Denitrification is an ecosystem process linked to ongoing climate change, because it releases nitrous oxide (N2O) into the atmosphere. To date, the literature covers mostly how aboveground (i.e. plant community structure) and belowground (i.e. plant-associated soil microbes) biota separately influence denitrification in isolation of each other. We here present a mesocosm experiment where we combine a manipulation of belowground biota (i.e. addition of Rhizophagus irregularis propagules to the indigenous mycorrhizal community) with a realized gradient in plant diversity. We used a seed mix containing plant species representative of mesophytic European grasslands and by stochastic differences in species establishment across the sixteen replicates per treatment level a spontaneously established gradient in plant diversity. We address mycorrhizal-induced and plant-diversity mediated changes on denitrification potential parameters and how these differ from the existing literature that studies them independently of each other. We show that unlike denitrification potential, N2O potential emissions do not change with mycorrhiza and depend instead on realized plant diversity. By linking mycorrhizal ecology to an N-cycling process, we present a comprehensive assessment of terrestrial denitrification dynamics when diverse plants co-occur., (© FEMS 2019.)

Soil structure, the complex arrangement of soil into aggregates and pore spaces, is a key feature of soils and soil biota. Among them, filamentous saprobic fungi have well-documented effects on soil aggregation. However, it is unclear what properties, or traits, determine the overall positive effect of fungi on soil aggregation. To achieve progress, it would be helpful to systematically investigate a broad suite of fungal species for their trait expression and the relation of these traits to soil aggregation. Here, we apply a trait-based approach to a set of 15 traits measured under standardized conditions on 31 fungal strains including Ascomycota, Basidiomycota, and Mucoromycota, all isolated from the same soil. We find large differences among these fungi in their ability to aggregate soil, including neutral to positive effects, and we document large differences in trait expression among strains. We identify biomass density, i.e., the density with which a mycelium grows (positive effects), leucine aminopeptidase activity (negative effects) and phylogeny as important factors explaining differences in soil aggregate formation (SAF) among fungal strains; importantly, growth rate was not among the important traits. Our results point to a typical suite of traits characterizing fungi that are good soil aggregators, and our findings illustrate the power of employing a trait-based approach to unravel biological mechanisms underpinning soil aggregation. Such an approach could now be extended also to other soil biota groups. In an applied context of restoration and agriculture, such trait information can inform management, for example to prioritize practices that favor the expression of more desirable fungal traits., (Copyright © 2020 Lehmann, Zheng, Ryo, Soutschek, Roy, Rongstock, Maaß and Rillig.)

Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses., (© 2019 The Authors Research Synthesis Methods Published by John Wiley & Sons Ltd.)

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., (© 2019 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Movement ecology aims to provide common terminology and an integrative framework of movement research across all groups of organisms. Yet such work has focused on unitary organisms so far, and thus the important group of filamentous fungi has not been considered in this context. With the exception of spore dispersal, movement in filamentous fungi has not been integrated into the movement ecology field. At the same time, the field of fungal ecology has been advancing research on topics like informed growth , mycelial translocations , or fungal highways using its own terminology and frameworks, overlooking the theoretical developments within movement ecology. We provide a conceptual and terminological framework for interdisciplinary collaboration between these two disciplines, and show how both can benefit from closer links: We show how placing the knowledge from fungal biology and ecology into the framework of movement ecology can inspire both theoretical and empirical developments, eventually leading towards a better understanding of fungal ecology and community assembly. Conversely, by a greater focus on movement specificities of filamentous fungi, movement ecology stands to benefit from the challenge to evolve its concepts and terminology towards even greater universality. We show how our concept can be applied for other modular organisms (such as clonal plants and slime molds), and how this can lead towards comparative studies with the relationship between organismal movement and ecosystems in the focus., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s). 2019.)

Soils underpin terrestrial ecosystem functions, but they face numerous anthropogenic pressures. Despite their crucial ecological role, we know little about how soils react to more than two environmental factors at a time. Here, we show experimentally that increasing the number of simultaneous global change factors (up to 10) caused increasing directional changes in soil properties, soil processes, and microbial communities, though there was greater uncertainty in predicting the magnitude of change. Our study provides a blueprint for addressing multifactor change with an efficient, broadly applicable experimental design for studying the impacts of global environmental change., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Biochar is being discussed as a soil amendment to improve soil fertility and mitigate climate change. While biochar interactions with soil microbial biota have been frequently studied, interactions with soil mesofauna are understudied. We here present an experiment in which we tested if the collembolan Folsomia candida I) can transport biochar particles, II) if yes, how far the particles are distributed within 10 days, and III) if it shows a preference among biochars made from different feedstocks, i.e. pine wood, pine bark and spelt husks. In general, biochar particles based on pine bark and pine wood were consistently distributed significantly more than those made of spelt husks, but all types were transported more than 4cm within 10 days. Additionally, we provide evidence that biochar particles can become readily attached to the cuticle of collembolans and hence be transported, potentially even over large distances. Our study shows that the soil mesofauna can indeed act as a vector for the transport of biochar particles and show clear preferences depending on the respective feedstock, which would need to be studied in more detail in the future., Competing Interests: The authors have declared that no competing interests exist.

Global change has complex eco-evolutionary consequences for organisms and ecosystems, but related concepts (e.g., novel ecosystems) do not cover their full range. Here we propose an umbrella concept of "ecological novelty" comprising (1) a site-specific and (2) an organism-centered, eco-evolutionary perspective. Under this umbrella, complementary options for studying and communicating effects of global change on organisms, ecosystems, and landscapes can be included in a toolbox. This allows researchers to address ecological novelty from different perspectives, e.g., by defining it based on (a) categorical or continuous measures, (b) reference conditions related to sites or organisms, and (c) types of human activities. We suggest striving for a descriptive, non-normative usage of the term "ecological novelty" in science. Normative evaluations and decisions about conservation policies or management are important, but require additional societal processes and engagement with multiple stakeholders., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)

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., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The fungal mycelium represents the essence of the fungal lifestyle, and understanding how a mycelium is constructed is of fundamental importance in fungal biology and ecology. Previous studies have examined initial developmental patterns or focused on a few strains, often mutants of model species, and frequently grown under non-harmonized growth conditions; these factors currently collectively hamper systematic insights into rules of mycelium architecture. To address this, we here use a broader suite of fungi (31 species including members of the Ascomycota, Basidiomycota and Mucoromycota), all isolated from the same soil, and tested for ten architectural traits under standardized laboratory conditions. We find great variability in traits among the saprobic fungal species, and detect several clear tradeoffs in mycelial architecture, for example between internodal length and hyphal diameter. Within the constraints so identified, we document otherwise great versatility in mycelium architecture in this set of fungi, and there was no evidence of trait 'syndromes' as might be expected. Our results point to an important dimension of fungal properties with likely consequences for coexistence within local communities, as well as for functional complementarity (e.g. decomposition, soil aggregation).

The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment., (© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust.)

Microplastic pollution and increasing temperature have potential to influence soil quality; yet little is known about their effects on soil aggregation, a key determinant of soil quality. Given the importance of fungi for soil aggregation, we investigated the impacts of increasing temperature and microplastic fibers on aggregation by carrying out a soil incubation experiment in which we inoculated soil individually with 5 specific strains of soil saprobic fungi. Our treatments were temperature (ambient temperature of 25°C or temperature increased by 3°C, abruptly versus gradually) and microplastic fibers (control and 0.4% w/w). We evaluated the percentage of water stable aggregates (WSA) and hydrolysis of fluorescein diacetate (FDA) as an indicator of fungal biomass. Microplastic fiber addition was the main factor influencing the WSA, decreasing the percentage of WSA except in soil incubated with strain RLCS 01, and mitigated the effects of temperature or even caused more pronounced decrease in WSA under increasing temperature. We also observed clear differences between temperature change patterns. Our study shows that the interactive effects of warming and microplastic fibers are important to consider when evaluating effects of global change on soil aggregation and potentially other soil processes.

All ecological disciplines consider temporal dynamics, although relevant concepts have been developed almost independently. We here introduce basic principles of temporal dynamics in ecology. We figured out essential features that describe temporal dynamics by finding similarities among about 60 ecological concepts and theories. We found that considering the hierarchically nested structure of complexity in temporal patterns (i.e. hierarchical complexity) can well describe the fundamental nature of temporal dynamics by expressing which patterns are observed at each scale. Across all ecological levels, driver-response relationships can be temporally variant and dependent on both short- and long-term past conditions. The framework can help with designing experiments, improving predictive power of statistics, and enhancing communications among ecological disciplines., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Microplastic effects in terrestrial ecosystems have recently moved into focus, after about a decade of research being limited to aquatic systems. While effects on soil physical properties and soil biota are starting to become apparent, there is not much information on the consequences for plant performance. We here propose and discuss mechanistic pathways through which microplastics could impact plant growth, either positively or negatively. These effects will vary as a function of plant species, and plastic type, and thus are likely to translate to changes in plant community composition and perhaps primary production. Our mechanistic framework serves to guide ongoing and future research on this important topic., (© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust.)

Stable soils provide valuable ecosystem services and mechanical soil stability is enhanced by the presence of arbuscular mycorrhizal fungi (AMF). Soil aggregation, which is the major driver of mechanical soil stability, is often treated as a static phenomenon, even though aggregate turnover is continually ongoing. In fact, some breakdown of macroaggregates is necessary to allow new aggregate formation and inclusion of new organic matter into microaggregates. We determined how aggregate turnover times were affected by AMF by tracking movement of rare earth elements (REE), applied as their immobile oxides, between aggregate size classes, and using X-ray fluorescence microscopy to spatially localize REEs in a sample of aggregates. Here we show that AMF increased large macroaggregate formation and slowed down disintegration of large and small macroaggregates. Microaggregate turnover was increased in the presence of AMF. Internal aggregate organization suggested that although formation of microaggregates by accretion of soil to particulate organic matter is common, it is not the only mechanism in operation.

Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.

Microplastic pollution is increasingly considered to be a factor of global change: in addition to aquatic ecosystems, this persistent contaminant is also found in terrestrial systems and soils. Microplastics have been chiefly examined in soils in terms of the presence and potential effects on soil biota. Given the persistence and widespread distribution of microplastics, it is also important to consider potential evolutionary implications of the presence of microplastics in soil; we offer such a perspective for soil microbiota. We discuss the range of selection pressures likely to act upon soil microbes, highlight approaches for the study of evolutionary responses to microplastics, and present the obstacles to be overcome. Pondering the evolutionary consequences of microplastics in soils can yield new insights into the effects of this group of pollutants, including establishing 'true' baselines in soil ecology, and understanding future responses of soil microbial populations and communities., Competing Interests: Conflicts of interest The authors declare no conflicts of interest.

Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensive survey of a 10 m 2 grassland plot in Germany, focusing on a major group of protists, the Cercozoa. From 177 soil samples, collected from April to November, we obtained 694 Operational Taxonomy Units representing >6 million Illumina reads. All major cercozoan taxonomic and functional groups were present, dominated by the small flagellates of the Glissomonadida. We found evidence of environmental selection structuring the cercozoan communities both spatially and seasonally. Spatial analyses indicated that communities were correlated within a range of 3.5 m. Seasonal variations in the abundance of bacterivores and bacteria, followed by that of omnivores suggested a dynamic prey-predator succession. The most influential edaphic properties were moisture and clay content, which differentially affected each functional group. Our study is based on an intense sampling of protists at a small scale, thus providing a detailed description of the biodiversity of different taxa/functional groups and the ecological processes involved in shaping their distribution.

Awareness that our planet is a self-supporting biosphere with sunlight as its major source of energy for life has resulted in a long-term historical fascination with the workings of self-supporting ecological systems. However, the studies of such systems have never entered the canon of ecological or evolutionary tools and instead, have led a fringe existence connected to life support system engineering and space travel. We here introduce a framework for a renaissance in biospherics based on the study of matter-closed, energy-open ecosystems at a microbial level (microbial biospherics). Recent progress in genomics, robotics, and sensor technology makes the study of closed systems now much more tractable than in the past, and we argue that the time has come to emancipate the study of closed systems from this fringe context and bring them into a mainstream approach for studying ecosystem processes. By permitting highly replicated long-term studies, especially on predetermined and simplified systems, microbial biospheres offer the opportunity to test and develop strong hypotheses about ecosystem function and the ecological and evolutionary determinants of long-term system failure or persistence. Unlike many sciences, ecosystem ecology has never fully embraced a reductionist approach and has remained focused on the natural world in all its complexity. We argue that a reductionist approach to ecosystem ecology, using microbial biospheres, based on a combination of theory and the replicated study of much simpler self-enclosed microsystems could pay huge dividends., Competing Interests: The authors declare no conflict of interest.

Microplastics can affect biophysical properties of the soil. However, little is known about the cascade of events in fundamental levels of terrestrial ecosystems, i.e., starting with the changes in soil abiotic properties and propagating across the various components of soil-plant interactions, including soil microbial communities and plant traits. We investigated here the effects of six different microplastics (polyester fibers, polyamide beads, and four fragment types: polyethylene, polyester terephthalate, polypropylene, and polystyrene) on a broad suite of proxies for soil health and performance of spring onion ( Allium fistulosum). Significant changes were observed in plant biomass, tissue elemental composition, root traits, and soil microbial activities. These plant and soil responses to microplastic exposure were used to propose a causal model for the mechanism of the effects. Impacts were dependent on particle type, i.e., microplastics with a shape similar to other natural soil particles elicited smaller differences from control. Changes in soil structure and water dynamics may explain the observed results in which polyester fibers and polyamide beads triggered the most pronounced impacts on plant traits and function. The findings reported here imply that the pervasive microplastic contamination in soil may have consequences for plant performance and thus for agroecosystems and terrestrial biodiversity.

With growing populations and climate change, assuring food and nutrition security is an increasingly challenging task. Climate-smart and sustainable agriculture, that is, conceiving agriculture to be resistant and resilient to a changing climate while keeping it viable in the long term, is probably the best solution. The role of soil biota and particularly arbuscular mycorrhizal (AM) fungi in this new agriculture is believed to be of paramount importance. However, the large nutrient pools and the microbiota of subsoils are rarely considered in the equation. Here we explore the potential contributions of subsoil AM fungi to a reduced and more efficient fertilization, carbon sequestration, and reduction of greenhouse gas emissions in agriculture. We discuss the use of crop rotations and cover cropping with deep rooting mycorrhizal plants, and low-disturbance management, as means of fostering subsoil AM communities. Finally, we suggest future research goals that would allow us to maximize these benefits.

Increasing grain yields of food cereal crops is a major goal in future sustainable agriculture. We quantitatively analyzed the potential role of arbuscular mycorrhizal (AM) fungi in enhancing grain yields of seven cereal crops with exceptional importance for human nutrition across the globe: corn, wheat, rice, barley, sorghum, millet and oat. We conducted a meta-analysis for three datasets including both English and Chinese language publications: the 'whole' dataset including both laboratory and field studies (168 articles); the 'field' dataset comprising only field studies (97 studies); and the 'field-inoculation' dataset including only AM fungal inoculation studies conducted in field conditions (70 articles). We found that the AM fungal effect on grain yield was less pronounced in field and noninoculation studies. AM fungal inoculation in field led to a 16% increase (overall effect) based on the 'field-inoculation' dataset; this effect was variable (77% trials had positive values), crop-specific, lower for new cultivars released after 1950 and further modulated by soil pH. Although there are neutral and negative effects of AM fungi on grain yields, we emphasize the importance of integrating AM fungi in sustainable agriculture to increase grain yields of cereal crops., (© 2018 Nanjing Tech University New Phytologist © 2018 New Phytologist Trust.)

Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major group of protists, at two depths; 10-30 cm (topsoil) and 60-75 cm (subsoil) in an agricultural field in Germany. At the two depths, we also distinguished among three soil compartments: rhizosphere, drilosphere (earthworm burrows) and bulk soil. With increasing depth, we found an overall decline in richness, but we were able to detect subsoil specific phylotypes and contrasting relative abundance patterns between topsoil and subsoil for different clades. We also found that the compartment effect disappeared in the subsoil when compared to the topsoil. More studies are now needed to describe and isolate these possibly subsoil specific phylotypes and better understand their ecology and function., (© FEMS 2019.)

Offspring size is a key trait for understanding the reproductive ecology of species, yet studies addressing the ecological meaning of offspring size have so far been limited to macro-organisms. We consider this a missed opportunity in microbial ecology and provide what we believe is the first formal study of offspring-size variation in microbes using reproductive models developed for macro-organisms. We mapped the entire distribution of fungal spore size in the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina) and tested allometric expectations of this trait to offspring (spore) output and body size. Our results reveal a potential paradox in the reproductive ecology of AM fungi: while large spore-size variation is maintained through evolutionary time (independent of body size), increases in spore size trade off with spore output. That is, parental mycelia of large-spored species produce fewer spores and thus may have a fitness disadvantage compared to small-spored species. The persistence of the large-spore strategy, despite this apparent fitness disadvantage, suggests the existence of advantages to large-spored species that could manifest later in fungal life history. Thus, we consider that solving this paradox opens the door to fruitful future research establishing the relationship between offspring size and other AM life history traits.

Many experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal.

High biodiversity aboveground tends to increase the stability of ecosystem functioning when faced with a changing environment. However, whether and how soil biota affect ecosystem stability is less clear. Here, we introduce a framework for understanding the effects of soil biota on variation in ecosystem functioning under environmental changes. We conclude that soil biota may be a neglected factor determining ecosystem stability through their direct and indirect effects on plant diversity, the net productivity of an ecosystem, and compensatory dynamics among plant species, and via altering ecosystem resistance and resilience. Furthermore, future research needs to consider that effects of soil biota on ecosystem stability will vary depending on extrinsic factors, and for a given perturbation and ecosystem function., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Contents Summary 1059 I. Introduction: pathways of influence and pervasiveness of effects 1060 II. AM fungal richness effects on ecosystem functions 1062 III. Other dimensions of biodiversity 1062 IV. Back to basics - primary axes of niche differentiation by AM fungi 1066 V. Functional diversity of AM fungi - a role for biological stoichiometry? 1067 VI. Past, novel and future ecosystems 1068 VII. Opportunities and the way forward 1071 Acknowledgements 1072 References 1072 SUMMARY: Arbuscular mycorrhizal (AM) fungi play important functional roles in ecosystems, including the uptake and transfer of nutrients, modification of the physical soil environment and alteration of plant interactions with other biota. Several studies have demonstrated the potential for variation in AM fungal diversity to also affect ecosystem functioning, mainly via effects on primary productivity. Diversity in these studies is usually characterized in terms of the number of species, unique evolutionary lineages or complementary mycorrhizal traits, as well as the ability of plants to discriminate among AM fungi in space and time. However, the emergent outcomes of these relationships are usually indirect, and thus context dependent, and difficult to predict with certainty. Here, we advocate a fungal-centric view of AM fungal biodiversity-ecosystem function relationships that focuses on the direct and specific links between AM fungal fitness and consequences for their roles in ecosystems, especially highlighting functional diversity in hyphal resource economics. We conclude by arguing that an understanding of AM fungal functional diversity is fundamental to determine whether AM fungi have a role in the exploitation of marginal/novel environments (whether past, present or future) and highlight avenues for future research., (© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.)

Biodiversity increases ecosystem functions underpinning a suite of services valued by society, including services provided by soils. To test whether, and how, future environments alter the relationship between biodiversity and multiple ecosystem functions, we measured grassland plant diversity effects on single soil functions and ecosystem multifunctionality, and compared relationships in four environments: ambient conditions, elevated atmospheric CO 2 , enriched N supply, and elevated CO 2 and N in combination. Our results showed that plant diversity increased three out of four soil functions and, consequently, ecosystem multifunctionality. Remarkably, biodiversity-ecosystem function relationships were similarly significant under current and future environmental conditions, yet weaker with enriched N supply. Structural equation models revealed that plant diversity enhanced ecosystem multifunctionality by increasing plant community functional diversity, and the even provision of multiple functions. Conserving local plant diversity is therefore a robust strategy to maintain multiple valuable ecosystem services in both present and future environmental conditions., Competing Interests: NE, JH, FI, Fv, SH, CK, AL, ML, AL, MR, AV, KW, PR No competing interests declared, (© 2018, Eisenhauer et al.)

Research on mycorrhizal interactions has traditionally developed into separate disciplines addressing different organizational levels. This separation has led to an incomplete understanding of mycorrhizal functioning. Integration of mycorrhiza research at different scales is needed to understand the mechanisms underlying the context dependency of mycorrhizal associations, and to use mycorrhizae for solving environmental issues. Here, we provide a road map for the integration of mycorrhiza research into a unique framework that spans genes to ecosystems. Using two key topics, we identify parallels in mycorrhiza research at different organizational levels. Based on two current projects, we show how scientific integration creates synergies, and discuss future directions. Only by overcoming disciplinary boundaries, we will achieve a more comprehensive understanding of the functioning of mycorrhizal associations., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Flows of water, soil, litter, and anthropogenic materials in and around rivers lead to the mixing of their resident microbial communities and subsequently to a resultant community distinct from its precursors. Consideration of these events through a new conceptual lens, namely, community coalescence, could provide a means of integrating physical, environmental, and ecological mechanisms to predict microbial community assembly patterns better in these habitats. Here, we review field studies of microbial communities in riverine habitats where environmental mixing regularly occurs, interpret some of these studies within the community coalescence framework and posit novel hypotheses and insights that may be gained in riverine microbial ecology through the application of this concept. Particularly in the face of a changing climate and rivers under increasing anthropogenic pressures, knowledge about the factors governing microbial community assembly is essential to forecast and/or respond to changes in ecosystem function. Additionally, there is the potential for microbial ecology studies in rivers to become a driver of theory development: riverine systems are ideal for coalescence studies because regular and predictable environmental mixing occurs. Data appropriate for testing community coalescence theory could be collected with minimal alteration to existing study designs., (© 2018 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

Microplastic is an emerging contaminant of concern in soils globally, probably gradually increasing in soil due to slow degradation. Few studies on microplastic effects on soil biota are available, and no study in a microplastic contamination context has specifically addressed soil protists. Soil protists, a phylogenetically and functionally diverse group of eukaryotic, unicellular soil organisms, are major consumers of bacteria in soils and are potentially important vehicles for the delivery of microplastics into the soil food chain. Here we build a case for focusing research on soil protists by drawing on data from previous, older studies of phagocytosis in protist taxa, which have long made use of polystyrene latex beads (microspheres). Various soil-borne taxa, including ciliates, flagellates and amoebae take up microplastic beads in the size range of a few micrometers. This included filter feeders as well as amoebae which engulf their prey. Discrimination in microplastic particle uptake depended on species, physiological state as well as particle size. Based on the results of the studies we review here, there is now a need to study microplastic effects in a pollution ecology context: this means considering a broad range of particle types under realistic conditions in the soil, and exploring longer-term effects on soil protist communities and functions., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Soils are essential components of terrestrial ecosystems that experience strong pollution pressure. Microplastic contamination of soils is being increasingly documented, with potential consequences for soil biodiversity and function. Notwithstanding, data on effects of such contaminants on fundamental properties potentially impacting soil biota are lacking. The present study explores the potential of microplastics to disturb vital relationships between soil and water, as well as its consequences for soil structure and microbial function. During a 5-weeks garden experiment we exposed a loamy sand soil to environmentally relevant nominal concentrations (up to 2%) of four common microplastic types (polyacrylic fibers, polyamide beads, polyester fibers, and polyethylene fragments). Then, we measured bulk density, water holding capacity, hydraulic conductivity, soil aggregation, and microbial activity. Microplastics affected the bulk density, water holding capacity, and the functional relationship between the microbial activity and water stable aggregates. The effects are underestimated if idiosyncrasies of particle type and concentrations are neglected, suggesting that purely qualitative environmental microplastic data might be of limited value for the assessment of effects in soil. If extended to other soils and plastic types, the processes unravelled here suggest that microplastics are relevant long-term anthropogenic stressors and drivers of global change in terrestrial ecosystems.

The arbuscular mycorrhizal (AM) symbiosis is key to plant nutrition, and hence is potentially key in sustainable agriculture. Fertilization and other agricultural practices reduce soil AM fungi and root colonization. Such conditions might promote the evolution of low mycorrhizal responsive crops. Therefore, we ask if and how evolution under domestication has altered AM symbioses of crops. We measured the effect of domestication on mycorrhizal responsiveness across 27 crop species and their wild progenitors. Additionally, in a subset of 14 crops, we tested if domestication effects differed under contrasting phosphorus (P) availabilities. The response of AM symbiosis to domestication varied with P availability. On average, wild progenitors benefited from the AM symbiosis irrespective of P availability, while domesticated crops only profited under P-limited conditions. Magnitudes and directions of response were diverse among the 27 crops, and were unrelated to phylogenetic affinities or to the coordinated evolution with fine root traits. Our results indicate disruptions in the efficiency of the AM symbiosis linked to domestication. Under high fertilization, domestication could have altered the regulation of resource trafficking between AM fungi and associated plant hosts. Provided that crops are commonly raised under high fertilization, this result has important implications for sustainable agriculture., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

Microplastics (plastics <5 mm, including nanoplastics which are <0.1 μm) originate from the fragmentation of large plastic litter or from direct environmental emission. Their potential impacts in terrestrial ecosystems remain largely unexplored despite numerous reported effects on marine organisms. Most plastics arriving in the oceans were produced, used, and often disposed on land. Hence, it is within terrestrial systems that microplastics might first interact with biota eliciting ecologically relevant impacts. This article introduces the pervasive microplastic contamination as a potential agent of global change in terrestrial systems, highlights the physical and chemical nature of the respective observed effects, and discusses the broad toxicity of nanoplastics derived from plastic breakdown. Making relevant links to the fate of microplastics in aquatic continental systems, we here present new insights into the mechanisms of impacts on terrestrial geochemistry, the biophysical environment, and ecotoxicology. Broad changes in continental environments are possible even in particle-rich habitats such as soils. Furthermore, there is a growing body of evidence indicating that microplastics interact with terrestrial organisms that mediate essential ecosystem services and functions, such as soil dwelling invertebrates, terrestrial fungi, and plant-pollinators. Therefore, research is needed to clarify the terrestrial fate and effects of microplastics. We suggest that due to the widespread presence, environmental persistence, and various interactions with continental biota, microplastic pollution might represent an emerging global change threat to terrestrial ecosystems., (© 2017 John Wiley & Sons Ltd.)

The socio-economic values of fertile and carbon-rich Dark Earth soils are well described from the Amazon region. Very recently, Dark Earth soils were also identified in tropical West Africa, with comparable beneficial soil properties and plant growth-promoting effects. The impact of this management technique on soil microbial communities, however, is less well understood, especially with respect to the ecologically relevant group of arbuscular mycorrhizal (AM) fungi. Thus, we tested the hypotheses that (1) improved soil quality in African Dark Earth (AfDE) will increase soil microbial biomass and shift community composition and (2) concurrently increased nutrient availability will negatively affect AM fungal communities. Microbial communities were distinct in AfDE in comparison to adjacent sites, with an increased fungal:bacterial ratio of 71%, a pattern mainly related to shifts in pH. AM fungal abundance and diversity, however, did not differ despite clearly increased soil fertility in AfDE, with 3.7 and 1.7 times greater extractable P and total N content, respectively. The absence of detrimental effects on AM fungi, often seen following applications of inorganic fertilizers, and the enhanced role of saprobic fungi relevant for mineralization and C sequestration support previous assertions of this management type as a sustainable alternative agricultural practice.

Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi with a broad distribution, and many taxa have physiological and ecological adaptations to specific environments, including semiarid ecosystems. Our aim was to address regional distribution patterns of AMF communities in such semiarid environments based on spore morphological techniques. We assessed AMF spores at the bottom and top of inselbergs distributed throughout the tropical dry forest in the Northeast region of Brazil. Across 10 replicate inselbergs and the surrounding area, spanning a range of altitude between 140 and 2000 m, we scored the AMF soil diversity and properties in 52 plots. We fitted parsimonious ordination analyses and variance partitioning models to determine the environmental factors which explained the variation in AMF community, based on morphological spore analysis. The diversity of AMF was similar at the bottom and top of inselbergs; however, we detected high variation in abundance and richness across sites. We formulated a parsimonious richness model that used physical soil factors as predictors. The AMF community structure could be best explained through the variables coarse and total sand, iron, organic matter, potassium, silt, and sodium which together accounted for 17.8% of total variance. Several AMF species were indicators of either deficiency or high values of specific soil properties. We demonstrated that habitat isolation of the inselbergs compared with surrounding areas did not trigger differences in AMF communities in semiarid regions of Brazil. At the regional scale, soil predictors across sites drove the distribution of symbiotic mycorrhizal fungi.

Our knowledge of soil biodiversity in agriculture in general is currently increasing rapidly. However, almost all studies have stopped with the quantification of soil biodiversity effects on crops at harvest time, ignoring subsequent processes along the agrifood chain until food arrives on our plates. Here we develop a conceptual framework for the study of such postharvest effects. We present the main mechanisms (direct and indirect) via which soil biodiversity can influence crop quality aspects and give examples of how effects at harvest time may become attenuated through postharvest operations and how biodiversity may also affect some of these operations (i.e., storage) themselves. Future research with a broader focus has the potential to unveil how soil biodiversity may benefit from what ends up on our forks., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

When methane-producing microbial communities are mixed experimentally, the resulting community is dominated by the community with the greatest resource-use efficiency. These results suggest a degree of community cohesion, or the maintenance of that initial community in the mix., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Root traits are often thought to be analogues of leaf traits along the plant economics spectrum. But evolutionary pressures have most likely shaped above- and belowground patterns differentially. Here, we aimed to identify the most important aboveground traits for explaining root traits without an a priori focus on known concepts. We measured morphological root traits in a glasshouse experiment on 141 common Central European grassland species. Using random forest algorithms, we built predictive models of six root traits from 97 aboveground morphological, ecological and life history traits. Root tissue density was best predicted by leaf dry matter content, whereas traits related to root fineness were best predicted by diaspore mass: the heavier the diaspore, the coarser the root system. Specific leaf area (SLA) was not an important predictor for any of the root traits. This study confirms the hypothesis that root traits are more than analogues of leaf traits within a plant economics spectrum. The results reveal a novel ecological pattern and highlight the power of root data to close important knowledge gaps in trait-based ecology., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)