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Fluorescent nanoparticles (FNPs) have been widely used in chemistry and medicine for decades, but their employment in biology is relatively recent. Past reviews on FNPs have focused on chemical, physical or medical uses, making the extrapolation to biological applications difficult. In biology, FNPs have largely been used for biosensing and molecular tracking. However, concerns over toxicity in early types of FNPs, such as cadmium-containing quantum dots (QDs), may have prevented wide adoption. Recent developments, especially in non-Cd-containing FNPs, have alleviated toxicity problems, facilitating the use of FNPs for addressing ecological, physiological and molecule-level processes in biological research. Standardised protocols from synthesis to application and interdisciplinary approaches are critical for establishing FNPs in the biologists’ tool kit. Here, we present an introduction to FNPs, summarise their use in biological applications, and discuss technical issues such as data reliability and biocompatibility. We assess whether biological research can benefit from FNPs and suggest ways in which FNPs can be applied to answer questions in biology. We conclude that FNPs have a great potential for studying various biological processes, especially tracking, sensing and imaging in physiology and ecology.

Microbiota of crop ancestors may offer a way to enhance sustainable food production

Arbuscular mycorrhizal fungi function as conduits for underground nutrient transport. While the fungal partner is dependent on the plant host for its carbon (C) needs, the amount of nutrients that the fungus allocates to hosts can vary with context. Because fungal allocation patterns to hosts can change over time, they have historically been difficult to quantify accurately. We developed a technique to tag rock phosphorus (P) apatite with fluorescent quantum-dot (QD) nanoparticles of three different colors, allowing us to study nutrient transfer in an in vitro fungal network formed between two host roots of different ages and different P demands over a 3-week period. Using confocal microscopy and raster image correlation spectroscopy, we could distinguish between P transfer from the hyphae to the roots and P retention in the hyphae. By tracking QD-apatite from its point of origin, we found that the P demands of the younger root influenced both: (1) how the fungus distributed nutrients among different root hosts and (2) the storage patterns in the fungus itself. Our work highlights that fungal trade strategies are highly dynamic over time to local conditions, and stresses the need for precise measurements of symbiotic nutrient transfer across both space and time.

High-throughput sequencing (e.g., amplicon and shotgun) has provided new insight into the diversity and distribution of fungi around the globe, but developing a framework to understand this diversity has proved challenging. Here we review key ecological strategy theories developed for macro-organisms and discuss ways that they can be applied to fungi. We suggest that while certain elements may be applied, an easy translation does not exist. Particular aspects of fungal ecology, such as body size and growth architecture, which are critical to many existing strategy schemes, as well as guild shifting, need special consideration in fungi. Moreover, data on shifts in traits across environments, important to the development of strategy schemes for macro-organisms, also does not yet exist for fungi. We end by suggesting a way forward to add data. Additional data can open the door to the development of fungi-specific strategy schemes and an associated understanding of the trait and ecological strategy dimensions employed by the world's fungi.

Diverse forms of cultivation have evolved across the tree of life. Efficient farming requires that the farmer deciphers and actively promotes conditions that increase crop yield. For plant cultivation, this can include evaluating tradeoffs among light, nutrients, and protection against herbivores. It is not understood if, or how, nonhuman farmers evaluate local conditions to increase payoffs. Here, we address this question using an obligate farming mutualism between the ant Philidris nagasau and epiphytic plants in the genus Squamellaria that are cultivated for their nesting sites and floral rewards. We focused on the ants' active fertilization of their crops and their protection against herbivory. We found that ants benefited from cultivating plants in full sun, receiving 7.5-fold more floral food rewards compared to shade-cultivated plants. The higher reward levels correlated with higher levels of crop protection provided by the ants. However, while high-light planting yielded the greatest immediate food rewards, sun-grown crops contained less nitrogen compared to shade-grown crops. This was due to lower nitrogen input from ants feeding on floral rewards instead of insect protein gained from predation. Despite this tradeoff, farming ants optimize crop yield by selectively planting their crops in full sun. Ancestral state reconstructions across this ant-plant clade show that a full-sun farming strategy has existed for millions of years, suggesting that nonhuman farmers have evolved the means to evaluate and balance conflicting crop needs to their own benefit.

The nutrient exchange mutualism between arbuscular mycorrhizal fungi (AMFs) and their host plants qualifies as a biological market, but several complications have hindered its appropriate use. First, fungal ‘trading agents’ are hard to identify because AMFs are potentially heterokaryotic, that is, they may contain large numbers of polymorphic nuclei. This means it is difficult to define and study a fungal ‘individual’ acting as an independent agent with a specific trading strategy. Second, because nutrient exchanges occur via communal structures (arbuscules), this temporarily reduces outbidding competition and transaction costs and hence resembles exchanges among divisions of firms, rather than traditional trade on markets. We discuss how fungal nuclei may coordinate their trading strategies, but nevertheless retain some independence, similar to human co-operatives (co-ops).

In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.

The functional relationship between arbuscular mycorrhizal fungi (AMF) and their hosts is variable on small spatial scales. Here, we hypothesized that herbivore exclusion changes the AMF community and alters the ability of AMF to enhance plant tolerance to grazing. We grew the perennial bunchgrass, Themeda triandra Forssk in inoculum from soils collected in the Kenya Long-term Exclosure Experiment where treatments representing different levels of herbivory have been in place since 1995. We assessed AMF diversity in the field, using terminal restriction fragment length polymorphism and compared fungal diversity among treatments. We conducted clipping experiments in the greenhouse and field and assessed regrowth. Plants inoculated with AMF from areas accessed by wild herbivores and cattle had greater biomass than non-inoculated controls, while plants inoculated with AMF from where large herbivores were excluded did not benefit from AMF in terms of biomass production. However, only the inoculation with AMF from areas with wild herbivores and no cattle had a positive effect on regrowth, relative to clipped plants grown without AMF. Similarly, in the field, regrowth of plants after clipping in areas with only native herbivores was higher than other treatments. Functional differences in AMF were evident despite little difference in AMF species richness or community composition. Our findings suggest that differences in large herbivore communities over nearly two decades has resulted in localized, functional changes in AMF communities. Our results add to the accumulating evidence that mycorrhizae are locally adapted and that functional differences can evolve within small geographical areas.

Liming and fertilization of grasslands have been used for centuries to sustain hay production. Besides improving hay yields, these practices induce compositional shifts in plant and soil microbial communities, including symbiotic arbuscular mycorrhizal (AM) fungi. However, in spite of increasing interest in soil carbon (C) sequestration to offset anthropogenic CO2 emissions, little is known about the long-term effects of these agronomic interventions on soil C stocks. We examined how plants, AM fungi, and soil C respond to more than seven decades of annual applications of lime, mineral nitrogen (N), and mineral phosphorus (P) to test the hypotheses that (1) management practices increasing aboveground plant production decrease C allocation to roots, AM fungi and the soil; and (2) the relative availability of N and P predicts belowground C allocation in a consistent manner. Our study was conducted at the Rengen Grassland Experiment, established in 1941. Lime combined with N increased hay yields and promoted development of AM fungal hyphae in soil, while reducing relative C allocation to roots. Simultaneous enrichment of soil with lime, N, and P further boosted hay production, promoted grasses and suppressed other plant functional groups. This treatment also decreased soil organic C and strongly suppressed AM fungi in the soil, although the response to P varied among different AM fungal taxa. Our results indicate that agricultural management practices aimed at maximization of hay production may, in the long run, significantly (−20%) reduce belowground C storage. This is a great concern with respect to the intended use of grasslands as anthropogenic CO2 sinks because the fertilization-induced decrease in soil C stocks can partly or fully negate the C sequestration potential of the grassland ecosystems as a whole.

International audience; Plants are exemplified by high plasticity in resource allocation strategies which allows them to maximize their fitness under changing resource conditions. In many plant species, obtaining resources involves mutualistic interactions with arbuscular mycorrhizal fungi (AMF), where plants provide the AMF with sugars in exchange for soil nutrients like phosphorus (P). These nutrient exchange rates have high context dependency, influenced by both the cooperative level of the AMF species involved (a qualitative trait) and the ambient nutrient concentrations in the soil (a quantitative value). Because this context dependency arises from a mix of both quantitative and qualitative factors, standard ordinary differential equation (ODE) modeling methods often complicate the representation of resource allocation strategies. Here, we explore the utility of a hybrid automata modeling framework that can intuitively combine the qualitative AMF traits and quantitative nutrient concentrations. This allows for a better analysis and understanding of phenotypic plasticity in resource allocation in the plant–AMF, and other nutrient exchange mutualisms. We consider a focal strategy in which nutrients are allocated to growth at times of nutrient limitations, and to storage otherwise and ask how this changes plant allocation to growth vs. storage. We first model this system dynamically to show how the plant responds to different environmental conditions and interacts with AMF and show that our hybrid automata model can replicate experimental data from the plant–AMF system. From our work, novel perceptions into the well-studied plant–AMF symbiosis and testable hypotheses can be underlined: (1) leaf biomass does not increase proportionally with the level of AMF cooperation; (2) in the context of multiple AMF simultaneously colonizing a host–plant, a narrow variance of response is observed and explained by an auction-like mechanism of the AMF to acquire C from the plant.

Priority effects - the impact of a species' arrival on subsequent community development - have been shown to influence species composition in many organisms. Whether priority effects among arbuscular mycorrhizal fungi (AMF) structure fungal root communities is not well understood. Here, we investigated whether priority effects influence the success of two closely related AMF species (Rhizophagus irregularis and Glomus aggregatum), hypothesizing that a resident AMF suppresses invader success, this effect is time-dependent and a resident will experience reduced growth when invaded. We performed two glasshouse experiments using modified pots, which permitted direct inoculation of resident and invading AMF on the roots. We quantified intraradical AMF abundances using quantitative PCR and visual colonization percentages. We found that both fungi suppressed the invading species and that this effect was strongly dependent on the time lag between inoculations. In contrast to our expectations, neither resident AMF was negatively affected by invasion. We show that order of arrival can influence the abundance of AMF species colonizing a host. These priority effects can have important implications for AMF ecology and the use of fungal inocula in sustainable agriculture.

There is a widespread recognition that above- and below-ground organisms are linked through their interactions with host plants that span terrestrial subsystems. In addition to direct effects on plants, soil organisms such as root herbivores can indirectly alter interactions between plants and other community members, with potentially important effects on plant growth and fitness. We manipulated root herbivory by Acalymma vittatum in Cucumis sativus to determine indirect effects on arbuscular mycorrhizal fungi, leaf herbivory, the leaf pathogen downy mildew and pollinators. We also manipulated pollen receipt by plants to determine whether root herbivory reduced plant reproduction through changes in pollinator visitation. Overall, root herbivory had strong net negative effects on plant growth and fitness, with 34% reductions in both leaf and fruit production by high root damage levels relative to control, despite reduced infection by downy mildew. High root herbivory also reduced floral visitation by 39%, apparently due to lower flower production, as flower size and scent were unaffected. Above-ground herbivory was not affected by root herbivores. Although root herbivory reduced pollinator visits, pollen receipt manipulations had no effect on fruit set, indicating that reduced pollinator service did not affect plant reproduction. Synthesis. Root herbivory had indirect effects on a range of community members, including mutualists and antagonists both above- and below-ground. Although reduced pathogen infection associated with root herbivory would be expected to benefit plants, root herbivory had an overall strong negative effect on plant growth and reproduction, indicating that direct negative effects over-rode any potential indirect benefits. Soil organisms such as root herbivores can indirectly alter interactions between plants and other community members. Here, root damage had indirect effects on a range of community members, including mutualists and antagonists both above- and below-ground. However, direct negative effects of root herbivory were more important for reducing plant growth and fitness.

It has been argued that cooperative behavior in the plant-mycorrhizal mutualism resembles trade in a market economy and can be understood using economic tools. Here, we assess the validity of this "biological market" analogy by investigating whether a market mechanism--that is, competition between partners over the price at which they provide goods--could be the outcome of natural selection. Then, we consider the conditions under which this market mechanism is sufficient to maintain mutualistic trade. We find that: (i) as in a market, individuals are favored to divide resources among trading partners in direct relation to the relative amount of resources received, termed linear proportional discrimination; (ii) mutualistic trade is more likely to be favored when individuals are able to interact with more partners of both species, and when there is a greater relative difference between the species in their ability to directly acquire different resources; (iii) if trade is favored, then either one or both species is favored to give up acquiring one resource directly, and vice versa. We then formulate testable predictions as to how environmental changes and coevolved responses of plants and mycorrhizal fungi will influence plant fitness (crop yields) in agricultural ecosystems.

Symbiotic partnerships are a major source of evolutionary innovation. They have driven rapid diversification of organisms, allowed hosts to harness new forms of energy, and radically modified Earth's nutrient cycles. The application of next-generation sequencing and advanced microscopic techniques has revealed not only the ubiquity of symbiotic partnerships, but the extent to which partnerships can become physically, genomically, and metabolically integrated ( 1 ). When and why does this integration of once free-living organisms happen?

International audience; Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.

Statistical models of ecosystem functioning based on species traits are valuable tools for predicting how nutrient cycling will respond to global change. However, species such as arbuscular mycorrhizal fungi (AMF) have evolved high intraspecific trait variation, making trait characterization and inclusion in functional trait models difficult. We present a five-part framework based on experimental designs from the phenotypic plasticity literature to quantify AMF intraspecific trait variation in a nutrient cycling context. Framework experiments involve exposing AMF replicates to different environmental conditions and recording trait values to quantify the (i) degree of variation, (ii) reversibility of traits, (iii) relationships among traits, (iv) adaptive nature of traits and (v) potential for trait variation to evolve. We include a phenotypic trajectory analysis of a simulated data set to illustrate relationships among traits. To focus future research, we provide a synthesis of AMF traits whose evolution is particularly relevant to nutrient cycling and environmental factors that induce variation in those traits. Synthesis. Characterizing the depth and range of arbuscular mycorrhizal fungal trait variation is essential for predicting responses to natural and anthropogenic environmental changes, as well as understanding past and future fungal trait evolutionary trajectories in the Tree of Life. Characterizing the depth and range of arbuscular mycorrhizal fungal trait variation is essential for predicting responses to natural and anthropogenic environmental changes, as well as understanding past and future fungal trait evolutionary trajectories in the Tree of Life. Here, we present an experimental framework for characterizing arbuscular mycorrhizal fungal trait variation. © 2014 British Ecological Society.

Agricultural management has profound effects on soil communities. Activities such as fertilizer inputs can modify the composition of arbuscular mycorrhizal fungi (AMF) communities, which form important symbioses with the roots of most crop plants. Intensive conventional agricultural management may select for less mutualistic AMF with reduced benefits to host plants compared to organic management, but these differences are poorly understood. AMF are generally evaluated based on their direct growth effects on plants. However, mycorrhizal colonization also may alter plant traits such as tissue nutrients, defensive chemistry, or floral traits, which mediate important plant-insect interactions like herbivory and pollination. To determine the effect of AMF from different farming practices on plant performance and traits that putatively mediate species interactions, we performed a greenhouse study by inoculating Cucumis sativus (cucumber, Cucurbitaceae) with AMF from conventional farms, organic farms, and a commercial AMF inoculum. We measured growth and a suite of plant traits hypothesized to be important predictors of herbivore resistance and pollinator attraction. Several leaf and root traits and flower production were significantly affected by AMF inoculum. Both conventional and organic AMF reduced leaf P content but increased Na content compared to control and commercial AMF. Leaf defenses were unaffected by AMF treatments, but conventional AMF increased root cucurbitacin C, the primary defensive chemical of C. sativus, compared to organic AMF. These effects may have important consequences for herbivore preference and population dynamics. AMF from both organic and conventional farms decreased flower production relative to commercial and control treatments, which may reduce pollinator attraction and plant reproduction. AMF from both farm types also reduced seed germination, but effects on plant growth were limited. Our results suggest that studies only considering AMF effects on growth may overlook changes in plant traits that have the potential to influence interactions, and hence yield, on farms. Given the effects of AMF on plant traits documented here, and the great importance of both herbivores and pollinators to wild and cultivated plants, we advocate for comprehensive assessments of mycorrhizal effects in complex community contexts, with the aim of incorporating multispecies interactions both above and below the soil surface. © 2013 by the Ecological Society of America.

Herbivores affect plants through direct effects, such as tissue damage, and through indirect effects that alter species interactions. Interactions may be positive or negative, so indirect effects have the potential to enhance or lessen the net impacts of herbivores. Despite the ubiquity of these interactions, the indirect pathways are considerably less understood than the direct effects of herbivores, and multiple indirect pathways are rarely studied simultaneously. We placed herbivore effects in a comprehensive community context by studying how herbivory influences plant interactions with antagonists and mutualists both aboveground and belowground. We manipulated early-season aboveground herbivore damage to Cucumis sativus (cucumber, Cucurbitaceae) and measured interactions with subsequent aboveground herbivores, root-feeding herbivores, pollinators, and arbuscular mycorrhizal fungi (AMF). We quantified plant growth and reproduction and used an enhanced pollination treatment to determine if plants were pollen limited. Increased herbivory reduced interactions with both antagonists and mutualists. Plants with high levels of early herbivory were significantly less likely to suffer leaf damage later in the summer and tended to be less attacked by root herbivores. Herbivory also reduced pollinator visitation, likely due to fewer and smaller flowers, and reduced AMF colonization. The net effect of herbivory on plant growth and reproduction was strongly negative, but lower fruit and seed production were not due to reduced pollinator visits, because reproduction was not pollen limited. Although herbivores influenced interactions between plants and other organisms, these effects appear to be weaker than the direct negative effects of early-season tissue loss. © 2012 by the Ecological Society of America.

The cultivation of genetically modified (GM) crops has increased significantly over the last decades. However, concerns have been raised that some GM traits may negatively affect beneficial soil biota, such as arbuscular mycorrhizal fungi (AMF), potentially leading to alterations in soil functioning. Here, we test two maize varieties expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) for their effects on soil AM fungal communities. We target both fungal DNA and RNA, which is new for AM fungi, and we use two strategies as an inclusive and robust way of detecting community differences: (i) 454 pyrosequencing using general fungal rRNA gene-directed primers and (ii) terminal restriction fragment length polymorphism (T-RFLP) profiling using AM fungus-specific markers. Potential GM-induced effects were compared to the normal natural variation of AM fungal communities across 15 different agricultural fields. AM fungi were found to be abundant in the experiment, accounting for 8% and 21% of total recovered DNA- and RNA-derived fungal sequences, respectively, after 104 days of plant growth. RNA- and DNA-based sequence analyses yielded most of the same AM fungal lineages. Our research yielded three major conclusions. First, no consistent differences were detected between AM fungal communities associated with GM plants and non-GM plants. Second, temporal variation in AMF community composition (between two measured time points) was bigger than GM trait-induced variation. Third, natural variation of AMF communities across 15 agricultural fields in The Netherlands, as well as within-field temporal variation, was much higher than GM-induced variation. In conclusion, we found no indication that Bt maize cultivation poses a risk for AMF.

The root systems of most agronomic crops are colonized by diverse assemblages of arbuscular mycorrhizal fungi (AMF), varying in the functional benefits (e.g. nutrient transfer, pathogen protection, water uptake) provided to hosts. Little is known about the evolutionary processes that shape the composition of these fungal assemblages, nor is it known whether more diverse assemblages are beneficial to crop productivity. In this review we aim to identify the evolutionary selection pressures that shape AMF diversity in agricultural systems and explore whether promotion of AMF diversity can convincingly be linked to increases in agricultural productivity and/or sustainability. We then ask whether farmers can (and should) actively modify evolutionary selection pressures to increase AMF functioning. We focus on three agriculturally imposed selection regimes: tillage, fertilization, and continuous monoculture. We find that the uniform nature of these practices strongly selects for dominance of few AMF species. These species exhibit predictable, generally non-beneficial traits, namely heavy investment in reproduction at the expense of nutrient scavenging and transfer processes that are beneficial for hosts. A number of focus-points are given based on empirical and theoretical evidence that could be utilized to slow down negative selection pressures on AMF functioning, therein increasing crop benefit.

Summary 1. Plants use a range of sophisticated strategies to protect themselves against herbivores and pathogens, such as the production of jasmonates, a group of plant hormones that prime the plant’s defense system upon attack. However, defense-related mechanisms, such as the jasmonate response, play a more diverse role than previously appreciated. Jasmonates also regulate key mutualist relationships, leading to a suit of potential conflicting selection pressures as a single response is employed to mediate multiple species interactions. 2. Here, we experimentally manipulate the host’s jasmonate response and document the impact on two key plant mutualisms: (i) changes to arbuscular mycorrhizal symbionts belowground (ii) modifications to floral traits affecting pollinator mutualists aboveground. By exogenously applying a range of methyl jasmonate solutions to cucumber plant roots grown with and without mycorrhizal fungi, we are able to examine the potential costs of the jasmonate response to both above and belowground mutualists. 3. We demonstrate that the negative effect of jasmonates on floral traits depends on whether the plant is mycorrhizal or nonmycorrhizal. Mycorrhization had a positive effect on floral traits, but benefits were lost with jasmonate application. While low levels of jasmonate decreased floral traits, these same jasmonate levels increased colonization by the mycorrhizal symbiont threefold, but only under high phosphorus conditions. 4. Our results highlight potential conflicts for the host in the regulation of their mutualists under different conditions and suggest that the overall impact of the jasmonate response depends on the plant mycorrhizal status and its nutrient context. 5. These findings suggest that increasing the jasmonate response may lead to differential costs and benefits for plants and their mutualists, and highlight potential conflict in planta ,w ith mycorrhizal symbionts benefiting from intermediate levels of jasmonates while certain floral traits can be depressed at this same level.

There are both costs and benefits for host plants that associate with microbes in the rhizosphere. Typically, an individual plant associates with multiple microbial genotypes varying in mutualistic benefit. This creates a potential tragedy of the commons where less-mutualistic strains potentially share in the collective benefits, while paying less of the costs. Therefore, maintaining cooperation over the course of evolution requires specific mechanisms that reduce the fitness benefits from “cheating.” Sanctions that discriminate among partners based on actual symbiotic performance are a key mechanism in rhizobia and may exist in many rhizosphere mutualisms, including rhizobia, mycorrhizal fungi, root endophytes, and perhaps free-living rhizosphere microbes. Where they exist, sanctions may take different forms depending on the system. Despite sanctions, less-effective symbionts still persist. We suggest this is because of mixed infection at spatial scales that limit the effects of sanctions, variation among plants in the strength of sanctions, and conflicting selection regimes.

The 450-million-year-old symbiosis between the majority of land plants and arbuscular mycorrhizal fungi (AMF) is one of the most ancient, abundant, and ecologically important mutualisms on Earth. Yet, the evolutionary stability of mycorrhizal associations is still poorly understood, as it follows none of the constraints thought to stabilize cooperation in other well-known mutualisms. The capacity of both host and symbiont to simultaneously interact with several partners introduces a unique dilemma; detecting and punishing those exploiting the mutualism becomes increasingly difficult if these individuals can continue to access resources from alternative sources. Here, we explore four hypotheses to explain evolutionary cooperation in the arbuscular mycorrhizal symbiosis: (1) pseudo-vertical transmission and spatial structuring of plant and fungal populations leading to local adaptation of partners; (2) luxury resource exchange in which plants trade surplus carbon for excess fungal nutrients; (3) partner choice allowing partners to associate with better cooperators; and (4) host and symbiont sanctions which actively reward good partners and punish less cooperative ones. We propose that mycorrhizal cooperation is promoted by an exchange of surplus resources between partners and enforced through sanctions by one or both partners. These mechanisms may allow plant and fungal genotypes to discriminate against individuals employing exploitative strategies, promoting patterns of partner choice. Together these selection pressures provide a framework for understanding the stabilization of mycorrhizal cooperation over evolutionary time.

Explaining mutualistic cooperation between species remains one of the greatest problems for evolutionary biology. Why do symbionts provide costly services to a host, indirectly benefiting competitors sharing the same individual host? Host monitoring of symbiont performance and the imposition of sanctions on 'cheats' could stabilize mutualism. Here we show that soybeans penalize rhizobia that fail to fix N(2) inside their root nodules. We prevented a normally mutualistic rhizobium strain from cooperating (fixing N(2)) by replacing air with an N(2)-free atmosphere (Ar:O(2)). A series of experiments at three spatial scales (whole plants, half root systems and individual nodules) demonstrated that forcing non-cooperation (analogous to cheating) decreased the reproductive success of rhizobia by about 50%. Non-invasive monitoring implicated decreased O(2) supply as a possible mechanism for sanctions against cheating rhizobia. More generally, such sanctions by one or both partners may be important in stabilizing a wide range of mutualistic symbioses.

Progress in genetic improvement of crop yield potential has slowed since 1985. Simultaneously, more sustainable management of agricultural ecosystems is needed. A better understanding of natural selection can help solve both problems. We illustrate this point with two specific examples. First, the genetic legacy of crop plants has been refined by millions of years of natural selection, often driven by competition among plants. We therefore suggest that most simple, tradeoff-free options to increase competitiveness (e.g., increased gene expression, or minor modifications of existing plant genes) have already been tested by natural selection. Further genetic improvement of crop yield potential over the next decade will mainly involve tradeoffs, either between fitness in past versus present environments, or between individual competitiveness and the collective performance of plant communities. Eventually, we may develop the ability to predict the consequences of genetic alterations so radical that they have not yet been tested by natural selection. Second, natural selection acts mainly at the level of genes, individuals, and family groups, rather than ecosystems as a whole. Consequently, there is no reason to expect the structure of natural ecosystems (diversity, spatial, or temporal patterns) to be a reliable blueprint for agricultural ecosystems. Natural ecosystems are nonetheless an important source of information that could be used to improve agriculture.

Summary 1. Root symbionts (rhizobia and arbuscular mycorrhizae) are often assumed to increase agricultural productivity consistently. However, rhizobial and mycorrhizal strains vary in effectiveness, resulting in symbiotic associations that range from parasitic to mutualistic. 2. The extent to which different farming practices mediate evolutionary changes along this continuum of symbiont effectiveness is rarely discussed. However, evolutionary theory suggests that (i) fertilizer use will favour parasitism unless host-plants impose sanctions against less-effective mutualists; (ii) tillage will have contrasting effects because it decreases within-plant symbiont relatedness but also decreases the risk that mutualism will benefit future competitors; (iii) crop rotation can act as a selective agent against dominating symbiont genotypes; and (iv) rhizobial inoculation adds beneficial strains to the soil but may increase the frequency of mixed nodules that allow parasitic strains to escape host sanctions. 3. However, the existing empirical data are inadequate to test our predictions thoroughly. Changes in species composition have been documented as a result of management practices, but evolutionary changes in symbiont effectiveness are difficult to detect. Therefore, a major aim of this study was to stimulate research that will assesses directly changes in symbiotic effectiveness as a function of management practices.

Why do mutualists perform costly behaviours that benefit individuals of a different species? One of the factors that may stabilize mutualistic interactions is when individuals preferentially reward more mutualistic (beneficial) behaviour and/or punish less mutualistic (more parasitic) behaviour. We develop a model that shows how such sanctions provide a fitness benefit to the individuals that carry them out. Although this approach could be applied to a number of symbioses, we focus on how it could be applied to the legume-rhizobia interaction. Specifically, we demonstrate how plants can be selected to supply preferentially more resources to (or be less likely to senesce) nodules that are fixing more N-2 (termed plant sanctions). We have previously argued that appreciable levels of N-2 fixation by rhizobia are only likely to be selected for in response to plant sanctions. Therefore, by showing that plant sanctions can also be favoured by natural selection, we are able to provide an explanation for the stability of the plant-legume mutualism, Why do mutualists perform costly behaviours that benefit individuals of a different species? One of the factors that may stabilize mutualistic interactions is when individuals preferentially reward more mutualistic (beneficial) behaviour and/or punish less mutualistic (more parasitic) behaviour. We develop a model that shows how such sanctions provide a fitness benefit to the individuals that carry them out. Although this approach could be applied to a number of symbioses, we focus on how it could be applied to the legume-rhizobia interaction. Specifically, we demonstrate how plants can be selected to supply preferentially more resources to (or be less likely to senesce) nodules that are fixing more N2 (termed plant sanctions). We have previously argued that appreciable levels of N2 fixation by rhizobia are only likely to be selected for in response to plant sanctions. Therefore, by showing that plant sanctions can also be favoured by natural selection, we are able to provide an explanation for the stability of the plant-legume mutualism.

Ecology Letters (2010) 13: 1459-1474 ABSTRACT: There is growing concern that rapid environmental degradation threatens mutualistic interactions. Because mutualisms can bind species to a common fate, mutualism breakdown has the potential to expand and accelerate effects of global change on biodiversity loss and ecosystem disruption. The current focus on the ecological dynamics of mutualism under global change has skirted fundamental evolutionary issues. Here, we develop an evolutionary perspective on mutualism breakdown to complement the ecological perspective, by focusing on three processes: (1) shifts from mutualism to antagonism, (2) switches to novel partners and (3) mutualism abandonment. We then identify the evolutionary factors that may make particular classes of mutualisms especially susceptible or resistant to breakdown and discuss how communities harbouring mutualisms may be affected by these evolutionary responses. We propose a template for evolutionary research on mutualism resilience and identify conservation approaches that may help conserve targeted mutualisms in the face of environmental change.

The root systems of most agronomic crops are colonized by diverse assemblages of arbuscular mycorrhizal fungi (AMF), varying in the functional benefits (e.g. nutrient transfer, pathogen protection, water uptake) provided to hosts. Little is known about the evolutionary processes that shape the composition of these fungal assemblages, nor is it known whether more diverse assemblages are beneficial to crop productivity. In this review we aim to identify the evolutionary selection pressures that shape AMF diversity in agricultural systems and explore whether promotion of AMF diversity can convincingly be linked to increases in agricultural productivity and/or sustainability. We then ask whether farmers can (and should) actively modify evolutionary selection pressures to increase AMF functioning. We focus on three agriculturally imposed selection regimes: tillage, fertilization, and continuous monoculture. We find that the uniform nature of these practices strongly selects for dominance of few AMF species. These species exhibit predictable, generally non-beneficial traits, namely heavy investment in reproduction at the expense of nutrient scavenging and transfer processes that are beneficial for hosts. A number of focus-points are given based on empirical and theoretical evidence that could be utilized to slow down negative selection pressures on AMF functioning, therein increasing crop benefit.

Enforcement mechanisms are thought to be important in maintaining mutualistic cooperation between species. A clear example of an enforcement mechanism is how legumes impose sanctions on rhizobial symbionts that fail to provide sufficient fixed N 2 . However, with domestication and breeding in high-soil-N environments, humans may have altered these natural legume defences and reduced the agricultural benefits of the symbiosis. Using six genotypes of soya beans, representing 60 years of breeding, we show that, as a group, older cultivars were better able to maintain fitness than newer cultivars (seed production) when infected with a mixture of effective and ineffective rhizobial strains. Additionally, we found small differences among cultivars in the ratio of effective : ineffective rhizobia released from their nodules, an indicator of future rhizobial strain fitness. When infected by symbionts varying in quality, legume defences against poor-quality partners have apparently worsened under decades of artificial selection.

Several studies have shown that soil biotic communities from organically managed fields are more diverse and exhibit higher activity levels compared to conventionally managed fields. The impact of these different soil communities on plant productivity and the provision of soil ecosystem services are, however, still unclear. Here, we test the effects of soil inoculation from each of three organic and three conventional maize fields on maize productivity and nutrient loss during leaching events induced by simulated rain. In particular, we examine whether differences in productivity and nutrient loss are related to the abundance and species composition of arbuscular mycorrhizal (AM) fungi. We hypothesized that soil biota from organically managed fields would improve maize growth and reduce nutrient leaching significantly more than those from conventionally managed fields. In contrast to our hypothesis, we found that plant productivity was negatively affected by soil inoculation, and this effect was stronger with inoculum from organic fields. Plant productivity was inversely correlated with AMF abundance, suggesting that enhanced carbon allocation to AMF is at least in part responsible for plant growth reduction under our experimental conditions. However, soil inoculation did alter the ecological functioning of the system by reducing phosphorus leaching losses after simulated rain. Moreover, these leaching losses were lower with increased hyphal density and were related with abundance of particular AMF types, suggesting that abundance of AMF and their community composition may be useful indicators of phosphorus leaching losses. The results demonstrate that soil communities from different agricultural fields vary in their impact on plant productivity and nutrient leaching losses. The results further indicate that there is a potential tradeoff between positive effects of soil communities on sustainability and negative effects on crop productivity. © 2011 The Author(s).