Using niche breadth theory to explain generalization in mutualisms

Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis

The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.

Complex parental effects impact variation in larval thermal tolerance in a vertically transmitting coral

Coral populations must be able to adapt to changing environmental conditions for coral reefs to persist under climate change. The adaptive potential of these organisms is difficult to forecast due to complex interactions between the host animal, dinoflagellate symbionts and the environment. Here we created 26 larval families from six Montipora capitata colonies from a single reef, showing significant, heritable variation in thermal tolerance. Our results indicate that 9.1% of larvae are expected to exhibit four times the thermal tolerance of the general population. Differences in larval thermotolerance were driven mainly by maternal contributions, but we found no evidence that these effects were driven by symbiont identity despite vertical transmission from the dam. We also document no evidence of reproductive incompatibility attributable to symbiont identity. These data demonstrate significant genetic variation within this population which provides the raw material upon which natural selection can act.

Symbiont plasticity as a driver of plant success

We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant-associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.

Mutualisms drive plant trait evolution beyond interaction-related traits

Mutualisms have driven the evolution of extraordinary structures and behavioural traits, but their impact on traits beyond those directly involved in the interaction remains unclear. We addressed this gap using a highly evolutionarily replicated system - epiphytes in the Rubiaceae forming symbioses with ants. We employed models that allow us to test the influence of discrete mutualistic traits on continuous non-mutualistic traits. Our findings are consistent with mutualism shaping the pace of morphological evolution, strength of selection and long-term mean of non-mutualistic traits in function of mutualistic dependency. While specialised and obligate mutualisms are associated with slower trait change, less intimate, facultative and generalist mutualistic interactions - which are the most common - have a greater impact on non-mutualistic trait evolution. These results challenge the prevailing notion that mutualisms solely affect the evolution of interaction-related traits via stabilizing selection and instead demonstrate a broader role for mutualisms in shaping trait evolution.

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.

Generalized mutualisms promote range expansion in both plant and ant partners

Mutualism improves organismal fitness, but strong dependence on another species can also limit a species' ability to thrive in a new range if its partner is absent. We assembled a large, global dataset on mutualistic traits and species ranges to investigate how multiple plant-animal and plant-microbe mutualisms affect the spread of legumes and ants to novel ranges. We found that generalized mutualisms increase the likelihood that a species establishes and thrives beyond its native range, whereas specialized mutualisms either do not affect or reduce non-native spread. This pattern held in both legumes and ants, indicating that specificity between mutualistic partners is a key determinant of ecological success in a new habitat. Our global analysis shows that mutualism plays an important, if often overlooked, role in plant and insect invasions.

Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes

AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.

Paraburkholderia symbionts isolated from Dictyostelium discoideum induce bacterial carriage in other Dictyostelium species

The social amoeba Dictyostelium discoideum engages in a complex relationship with bacterial endosymbionts in the genus Paraburkholderia, which can benefit their host by imbuing it with the ability to carry prey bacteria throughout its life cycle. The relationship between D. discoideum and Paraburkholderia has been shown to take place across many strains and a large geographical area, but little is known about Paraburkholderia's potential interaction with other dictyostelid species. We explore the ability of three Paraburkholderia species to stably infect and induce bacterial carriage in other dictyostelid hosts. We found that all three Paraburkholderia species successfully infected and induced carriage in seven species of Dictyostelium hosts. While the overall behaviour was qualitatively similar to that previously observed in infections of D. discoideum, differences in the outcomes of different host/symbiont combinations suggest a degree of specialization between partners. Paraburkholderia was unable to maintain a stable association with the more distantly related host Polysphondylium violaceum. Our results suggest that the mechanisms and evolutionary history of Paraburkholderia's symbiotic relationships may be general within Dictyostelium hosts, but not so general that it can associate with hosts of other genera. Our work further develops an emerging model system for the study of symbiosis in microbes.

Specialization patterns in symbiotic associations: A community perspective over spatial scales

Specialization, contextualized in a resource axis of an organism niche, is a core concept in ecology. In biotic interactions, specialization can be determined by the range of interacting partners. Evolutionary and ecological factors, in combination with the surveyed scale (spatial, temporal, biological, and/or taxonomic), influence the conception of specialization. This study aimed to assess the specialization patterns and drivers in the lichen symbiosis, considering the interaction between the principal fungus (mycobiont) and the associated Nostoc (cyanobiont), from a community perspective considering different spatial scales. Thus, we determined Nostoc phylogroup richness and composition of lichen communities in 11 Nothofagus pumilio forests across a wide latitudinal gradient in Chile. To measure specialization, cyanobiont richness, Simpson's and d' indices were estimated for 37 mycobiont species in these communities. Potential drivers that might shape Nostoc composition and specialization measures along the environmental gradient were analysed. Limitations in lichen distributional ranges due to the availability of their cyanobionts were studied. Turnover patterns of cyanobionts were identified at multiple spatial scales. The results showed that environmental factors shaped the Nostoc composition of these communities, thus limiting cyanobiont availability to establish the symbiotic association. Besides, specialization changed with the spatial scale and with the metric considered. Cyanolichens were more specialized than cephalolichens when considering partner richness and Simpson's index, whereas the d' index was mostly explained by mycobiont identity. Little evidence of lichen distributional ranges due to the distribution of their cyanobionts was found. Thus, lichens with broad distributional ranges either associated with several cyanobionts or with widely distributed cyanobionts. Comparisons between local and regional scales showed a decreasing degree of specialization at larger scales due to an increase in cyanobiont richness. The results support the context dependency of specialization and how its consideration changes with the metric and the spatial scale considered. Subsequently, we suggest considering the entire community and widening the spatial scale studied as it is crucial to understand factors determining specialization.

Transmission of beneficial yeasts accompanies offspring production in Drosophila-An initial evolutionary stage of insect maternal care through manipulation of microbial load?

Parent-to-offspring transmission of beneficial microorganisms is intimately interwoven with the evolution of social behaviors. Ancestral stages of complex sociality-microbe vectoring interrelationships may be characterized by high costs of intensive parental care and hence only a weak link between the transmission of microbial symbionts and offspring production. We investigate the relationship between yeast symbiont transmission and egg-laying, as well as some general factors thought to drive the "farming" of microscopic fungi by the fruit fly Drosophila melanogaster, an insect with no obvious parental care but which is highly dependent on dietary microbes during offspring development. The process of transmitting microbes involves flies ingesting microbes from their previous environment, storing and vectoring them, and finally depositing them to a new environment. This study revealed that fecal materials of adult flies play a significant role in this process, as they contain viable yeast cells that support larval development. During single patch visits, egg-laying female flies transmitted more yeast cells than non-egg-laying females, suggesting that dietary symbiont transmission is not random, but linked to offspring production. The crop, an extension of the foregut, was identified as an organ capable of storing viable yeast cells during travel between egg-laying sites. However, the amount of yeast in the crop reduced rapidly during periods of starvation. Although females starved for 24 h deposited a smaller amount of yeast than those starved for 6 h, the yeast inoculum produced still promoted the development of larval offspring. The results of these experiments suggest that female Drosophila fruit flies have the ability to store and regulate the transfer of microorganisms beneficial to their offspring via the shedding of fecal material. We argue that our observation may represent an initial evolutionary stage of maternal care through the manipulation of microbial load, from which more specialized feedbacks of sociality and microbe management may evolve.

Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels

Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.

Bee breweries: The unusually fermentative, lactobacilli-dominated brood cell microbiomes of cellophane bees

Pathogens and parasites of solitary bees have been studied for decades, but the microbiome as a whole is poorly understood for most taxa. Comparative analyses of microbiome features such as composition, abundance, and specificity, can shed light on bee ecology and the evolution of host–microbe interactions. Here we study microbiomes of ground-nesting cellophane bees (Colletidae: Diphaglossinae). From a microbial point of view, the diphaglossine genus Ptiloglossa is particularly remarkable: their larval provisions are liquid and smell consistently of fermentation. We sampled larval provisions and various life stages from wild nests of Ptiloglossa arizonensis and two species of closely related genera: Caupolicana yarrowi and Crawfordapis luctuosa. We also sampled nectar collected by P. arizonensis. Using 16S rRNA gene sequencing, we find that larval provisions of all three bee species are near-monocultures of lactobacilli. Nectar communities are more diverse, suggesting ecological filtering. Shotgun metagenomic and phylogenetic data indicate that Ptiloglossa culture multiple species and strains of Apilactobacillus, which circulate among bees and flowers. Larval lactobacilli disappear before pupation, and hence are likely not vertically transmitted, but rather reacquired from flowers as adults. Thus, brood cell microbiomes are qualitatively similar between diphaglossine bees and other solitary bees: lactobacilli-dominated, environmentally acquired, and non-species-specific. However, shotgun metagenomes provide evidence of a shift in bacterial abundance. As compared with several other bee species, Ptiloglossa have much higher ratios of bacterial to plant biomass in larval provisions, matching the unusually fermentative smell of their brood cells. Overall, Ptiloglossa illustrate a path by which hosts can evolve quantitatively novel symbioses: not by acquiring or domesticating novel symbionts, but by altering the microenvironment to favor growth of already widespread and generalist microbes.

Toxicity sharing model of earthworm intestinal microbiome reveals shared functional genes are more powerful than species in resisting pesticide stress

Earthworm intestinal bacteria and indigenous soil bacteria work closely during various biochemical processes and play a crucial role in maintaining the internal stability of the soil environment. However, the response mechanism of these bacterial communities to external pesticide disturbance is unknown. In this study, soil and earthworm gut contents were metagenomically sequenced after exposure to various concentrations of nitrochlorobenzene (0-1026.7 mg kg^-1). A high degree of similarity was found between the microbial community composition and abundance in the worm gut and soil, both of which decreased significantly (P < 0.05) under elevated pesticide stress. The toxicity sharing model (TSM) showed that the toxicity sharing capacity was 97.4-125.7 % and 100.4-130.2 % for E_genes (genes in the worm gut) and E_met(degradation genes in the worm gut) in the earthworm intestinal microbiome, respectively. This indicated that the earthworm intestinal microbiome assisted in relieving the pesticide toxicity of the indigenous soil microbiome. This study showed that the TSM could quantitatively describe the toxic effect of pesticides on the earthworm intestinal microbiome. It provides a new analytical model for investigating the ecological alliance between earthworm intestinal microbiome and indigenous soil microbiome under pesticide stress while contributing a more profound understanding of the potential to use earthworms to mitigate pesticide pollution in soils and develop earthworm-based soil remediation techniques.

Co-occurring epiphytic orchids have specialized mycorrhizal fungal niches that are also linked to ontogeny

Mycorrhizal symbiosis has been related to the coexistence and community assembly of coexisting orchids in few studies despite their obligate dependence on mycorrhizal partners to establish and survive. In hyper-diverse environments like tropical rain forests, coexistence of epiphytic orchids may be facilitated through mycorrhizal fungal specialization (i.e., sets of unique and dominant mycorrhizal fungi associated with a particular host species). However, information on the role of orchid mycorrhizal fungi (OMF) in niche differentiation and coexistence of epiphytic orchids is still scarce. In this study, we sought to identify the variation in fungal preferences of four co-occurring epiphytic orchids in a tropical rainforest in Costa Rica by addressing the identity and composition of their endophytic fungal and OMF communities across species and life stages. We show that the endophytic fungal communities are formed mainly of previously recognized OMF taxa, and that the four coexisting orchid species have both a set of shared mycorrhizal fungi and a group of fungi unique to an orchid species. We also found that adult plants keep the OMF of the juvenile stage while adding new mycobionts over time. This study provides evidence for the utilization of specific OMF that may be involved in niche segregation, and for an aggregation mechanism where adult orchids keep initial fungal mycobionts of the juvenile stage while adding others.

Low Specificity but Dissimilar Mycorrhizal Communities Associating with Roots May Contribute to the Spatial Pattern of Four Co-Occurring Habenaria (Orchidaceae) Species

Fungi with orchid roots have been increasingly proven to play important roles in orchid growth, spatial distribution, and coexistence of natural communities. Here, we used 454 amplicon pyrosequencing with two different primer combinations to investigate the spatial variations in the community of OMF and endophytic fungi associates within the roots of four co-occurring Habenaria species. The results showed that all investigated Habenaria species were generalists and the different fungi communities may contribute to the spatial separation of the four Habenaria species. Firstly, the fungal OTUs identified in the roots of the four species overlapped but their presence differed amongst species and numerous distinct OMF families were unique to each species. Second, NMDS clustering showed samples clustered together based on associated species and PERMANOVA analyses indicated that fungi communities in the roots differed significantly between the Habenaria species, both for all endophytic fungi communities and for OMF communities. Third, the network structure of epiphytic fungi was highly specialized and modular but demonstrated lowly connected and anti-nested properties. However, it calls for more soil nutrition and soil fungal communities' studies to elucidate the contribution of habitat-specific adaptations in general and mycorrhizal divergence.

The patterns of co-occurrence variation are explained by the low dependence of bark beetles (Coleoptera: Scolytinae and Platypodinae) on hosts along altitude gradients

Background

Separation of biotic and abiotic impacts on species diversity distribution patterns across a significant climatic gradient is a challenge in the study of diversity maintenance mechanisms. The basic task is to reconcile scale-dependent effects of abiotic and biotic processes on species distribution models. Here, we used a hierarchical modeling method to detect the host specificities of bark beetles (Scolytinae and Platypodinae) with their dependent tree communities across a steep climatic gradient, which was embedded within a relatively homogenous spatial niche.

Results

Species turnover of both trees and bark beetles have an opposite pattern along the climatic proxy (represented by the elevation gradients) at the regional scale, but not at local spatial scales. This pattern confirmed the hypothesis wherein emphasis was on influences of macro-climate on local biotic interactions between trees and hosted bark beetle communities, whereas local biotic relations, represented by host specificity dependence, were regionally conserved.

Conclusions

At a confined spatial scale, cross-taxa comparisons of β-diversity highlighted the importance of simultaneous impacts from both extrinsic factors related to geography and environment, and intrinsic factors related to organism characteristics. The effects of tree abundance and phylogeny diversity on bark beetle diversity were, to a large extent, indirect, operating via changes in bark beetle abundance through spatial and temporal dynamics of resources distribution. Tree host dependence, which was considered and represented by host specificities, plays a minor role on the hosted beetle community in this concealed wood decomposing interacting system.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12983-022-00455-y.

Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks

Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss.

Symbiotic germination and development of fully mycoheterotrophic plants convergently targeting similar Glomeraceae taxa

Plants producing dust seeds often meet their carbon demands by exploiting fungi at the seedling stage. This germination strategy (i.e. mycoheterotrophic germination) has been investigated among orchidaceous and ericaceous plants exploiting Ascomycota or Basidiomycota. Although several other angiosperm lineages have evolved fully mycoheterotrophic relationships with Glomeromycota, the fungal identities involved in mycoheterotrophic germination remain largely unknown. Here, we conducted in situ seed baiting and high-throughput DNA barcoding to identify mycobionts associated with seedlings of Burmannia championii (Burmanniaceae: Dioscoreales) and Sciaphila megastyla (Triuridaceae: Pandanales), which have independently evolved full mycoheterotrophy. Subsequently, we revealed that both seedlings and adults in B. championii and S. megastyla predominantly associate with Glomeraceae. However, mycorrhizal communities are somewhat distinct between seedling and adult stages, particularly in S. megastyla. Notably, the dissimilarity of mycorrhizal communities between S. megastyla adult samples and S. megastyla seedling samples is significantly higher than that between B. championi adult samples and S. megastyla adult samples, based on some indices. This pattern is possibly due to both mycorrhizal shifts during ontogenetic development and convergent recruitment of cheating-susceptible fungi. The extensive fungal overlap in two unrelated mycoheterotrophic plants indicates that both species convergently exploit specific AM fungal phylotypes.

Temporal turnover in mycorrhizal interactions: a proof of concept with orchids

Temporal turnover events in biotic interactions involving plants are rarely assessed, although such changes might afford a considerable acclimation potential to the plant. This could enable fairly rapid responses to short-term fluctuations in growth conditions as well as lasting responses to long-term climatic trends. Here, we present a classification of temporal turnover encompassing 11 possible scenarios. Using orchid mycorrhiza as a study model, we show that temporal changes are common, and discuss under which conditions temporal turnover of fungal symbiont is expected. We provide six research questions and identify technical challenges that we deem most important for future studies. Finally, we discuss how the same framework can be applied to other types of biotic interactions.

Context Dependency in Bark Beetle-Fungus Mutualisms Revisited: Assessing Potential Shifts in Interaction Outcomes Against Varied Genetic, Ecological, and Evolutionary Backgrounds

Context dependency occurs when biological interactions shift in sign or magnitude depending upon genetic, abiotic, and biotic context. Most models of mutualism address systems where interaction outcomes slide along a mutualism-antagonism continuum as environmental conditions vary altering cost-benefit relationships. However, these models do not apply to the many mutualisms that involve by-product benefits and others that do not have antagonistic alternate states. The ubiquity of such mutualisms indicates a need for different approaches and models to understand how environmental variability influences their strength, stability, and ecological roles. In this paper, we apply the concept of context dependency to mutualisms among bark beetles and fungi that span a variety of life strategies and exposures to environmental variability. Bark beetles and their mutualist fungi co-construct a niche based on by-product benefits that allows them to exist in a resource that is otherwise intractable or inaccessible. For the closest of these partnerships, this has resulted in some of the most influential agents of forest mortality in conifer forests worldwide. Understanding these symbioses is key to understanding their influence on forest structure and dynamics and responses to change. We found no evidence that bark beetle mutualisms change in sign as conditions vary, only in magnitude, and that the "closest" (and most environmentally influential) of these partnerships have evolved behaviors and mechanisms to reduce context-dependency and stabilize benefit delivery. The bark beetle-fungus symbioses most likely to slide along a mutualism-antagonism continuum are those involving loosely associated facultative symbionts that may provide benefits under some circumstances and that are horizontally transmitted by the beetle host. Additionally, some symbiotic fungi are never mutualists - these "third party" fungi are exploiters and may shift from commensalism to antagonism depending on environmental context. Our assessment indicates that a careful differentiation between bark beetle-fungus partnerships is crucial to understanding how they influence forests and respond to environmental variability.

Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

For successful colonization of host roots, ectomycorrhizal (EM) fungi must overcome host defense systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defense systems, but it is not yet understood whether variation in these constitutive defenses can result in variation in the colonization of hosts by specific fungal species.We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After 3 months, we characterized the mycorrhizal fungal community of each seedling using a combination of morphological categorization and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling's mycorrhizal community.While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotype or a seedling's terpene chemodiversity affected associations with EM fungi. Instead, we found that the location of seedlings, both within and among sites, was the only determinant of the diversity and makeup of EM communities.These results show that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealizable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings.

Polyploidy: an evolutionary and ecological force in stressful times

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.

From Binary Model Systems to the Human Microbiome: Factors That Drive Strain Specificity in Host-Symbiont Associations

Microbial symbionts are ubiquitous and can have significant impact on hosts. These impacts can vary in the sign (positive or negative) and degree depending on the identity of the interacting partners. Studies on host-symbiont associations indicate that subspecies (strain) genetic variation can influence interaction outcomes, making it necessary to go beyond species-level distinction to understand host-symbiont dynamics. In this review, we discuss examples of strain specificity found in host-symbiont associations, from binary model systems to the human microbiome. Although host and bacterial factors identified as mediators for specificity could be distinct at the molecular level, they generally fall into two broad functional categories: (1) those that contribute a required activity in support of the association and (2) those involved in antagonistic interactions with organisms outside of the association. We argue here based on current literature that factors from these two categories can work in concert to drive strain specificity and that this strain specificity must be considered to fully understand the molecular and ecological dynamics of host-symbiont associations, including the human microbiome.

Consistency in mutualism relies on local, rather than wider community biodiversity

Mutualistic interactions play a major role in shaping the Earth’s biodiversity, yet the consistent drivers governing these beneficial interactions are unknown. Using a long-term (8 year, including > 256 h behavioural observations) dataset of the interaction patterns of a service-resource mutualism (the cleaner-client interaction), we identified consistent and dynamic predictors of mutualistic outcomes. We showed that cleaning was consistently more frequent when the presence of third-party species and client partner abundance locally increased (creating choice options), whilst partner identity regulated client behaviours. Eight of our 12 predictors of cleaner and client behaviour played a dynamic role in predicting both the quality (duration) and quantity (frequency) of interactions, and we suggest that the environmental context acting on these predictors at a specific time point will indirectly regulate their role in cleaner-client interaction patterns: context-dependency can hence regulate mutualisms both directly and indirectly. Together our study highlights that consistency in cleaner-client mutualisms relies strongly on the local, rather than wider community—with biodiversity loss threatening all environments this presents a worrying future for the pervasiveness of mutualisms.

The Potential for Genotype-by-Environment Interactions to Maintain Genetic Variation in a Model Legume-Rhizobia Mutualism

The maintenance of genetic variation in mutualism-related traits is key for understanding mutualism evolution, yet the mechanisms maintaining variation remain unclear. We asked whether genotype-by-environment (G×E) interaction is a potential mechanism maintaining variation in the model legume-rhizobia system, Medicago truncatula-Ensifer meliloti. We planted 50 legume genotypes in a greenhouse under ambient light and shade to reflect reduced carbon availability for plants. We found an expected reduction under shaded conditions for plant performance traits, such as leaf number, aboveground and belowground biomass, and a mutualism-related trait, nodule number. We also found G×E for nodule number, with ∼83% of this interaction due to shifts in genotype fitness rank order across light environments, coupled with strong positive directional selection on nodule number regardless of light environment. Our results suggest that G×E can maintain genetic variation in a mutualism-related trait that is under consistent positive directional selection across light environments.

The Evolution of Mutualistic Dependence

While the importance of mutualisms across the tree of life is recognized, it is not understood why some organisms evolve high levels of dependence on mutualistic partnerships, while other species remain autonomous or retain or regain minimal dependence on partners. We identify four main pathways leading to the evolution of mutualistic dependence. Then, we evaluate current evidence for three predictions: ( a) Mutualisms with different levels of dependence have distinct stabilizing mechanisms against exploitation and cheating, ( b) less dependent mutualists will return to autonomy more often than those that are highly dependent, and ( c) obligate mutualisms should be less context dependent than facultative ones. Although we find evidence supporting all three predictions, we stress that mutualistic partners follow diverse paths toward—and away from—dependence. We also highlight the need to better examine asymmetry in partner dependence. Recognizing how variation in dependence influences the stability, breakdown, and context dependence of mutualisms generates new hypotheses regarding how and why the benefits of mutualistic partnerships differ over time and space.

Co-Cultures of Mycorrhizal Fungi Do Not Increase Germination and Seedling Development in the Epiphytic Orchid Dendrobium nobile

Orchids are highly dependent on mycorrhizal fungi for seed germination and subsequent growth to a seedling as they provide essential carbon, water, and mineral nutrients to developing seeds. Although there is mounting evidence that orchid seeds are often colonized by multiple fungi simultaneously, most in vitro germination experiments focus on mycorrhizal monocultures and little is known about how mycorrhizal assemblages affect seed germination and growth of seedlings. In this study, we compared the effects of mycorrhizal monocultures and co-cultures on seed germination and seedling growth of the epiphytic orchid Dendrobium nobile. In situ baiting was used to isolate mycorrhizal fungi from protocorms for germination experiments. Germination experiments were conducted under two light regimes for 90 days. In total, five fungal strains were isolated from protocorms of D. nobile, indicating that the species was not highly specific to its fungal partners. Four strains (JC-01, JC-02, JC-04, and JC-05) belonged to the Serendipitaceae and one (JC-03) to the Tulasnellaceae. In vitro germination experiments showed that germination percentages were higher under light-dark conditions than under complete dark conditions, supporting previous findings that light facilitates germination in epiphytic orchids. While all strains were able to induce protocorm formation and growth into the seedling stage, large differences between fungal strains were observed. Co-cultures did not result in significantly higher seed germination percentages and seedling development than monocultures. Taken together, these results demonstrate that effects of fungal assemblages are not predictable from those of component species, and that more work is needed to better understand the role of fungal assemblages determining seed germination and subsequent growth under natural conditions.

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

BACKGROUND

Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities.

RESULTS

Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere.

CONCLUSIONS

Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes. Video Abstract.

Interactions among interactions: The dynamical consequences of antagonism between mutualists

Species often interact with multiple mutualistic partners that provide functionally different benefits and/or that interact with different life-history stages. These functionally different partners, however, may also interact directly with one another in other ways, indirectly altering net outcomes and persistence of the mutualistic system as a whole. We present a population dynamical model of a three-species system involving antagonism between species sharing a mutualist partner species with two explicit life stages. We find that, regardless of whether the antagonism is predatory or non-consumptive, persistence of the shared mutualist is possible only under a restrictive set of conditions. As the rate of antagonism between the species sharing the mutualist increases, indirect rather than direct interactions increasingly determine species' densities and sometimes result in complex, oscillatory dynamics for all species. Surprisingly, persistence of the mutualistic system is particularly dependent upon the degree to which each of the two mutualistic interactions is specialized. Our work investigates a novel mechanism by which changing ecological conditions can lead to extinction of mutualist partners and provides testable predictions regarding the interactive roles of mutualism and antagonism in net outcomes for species' densities.

Compartmentalization drives the evolution of symbiotic cooperation

Across the tree of life, hosts have evolved mechanisms to control and mediate interactions with symbiotic partners. We suggest that the evolution of physical structures that allow hosts to spatially separate symbionts, termed compartmentalization, is a common mechanism used by hosts. Such compartmentalization allows hosts to: (i) isolate symbionts and control their reproduction; (ii) reward cooperative symbionts and punish or stop interactions with non-cooperative symbionts; and (iii) reduce direct conflict among different symbionts strains in a single host. Compartmentalization has allowed hosts to increase the benefits that they obtain from symbiotic partners across a diversity of interactions, including legumes and rhizobia, plants and fungi, squid and Vibrio, insects and nutrient provisioning bacteria, plants and insects, and the human microbiome. In cases where compartmentalization has not evolved, we ask why not. We argue that when partners interact in a competitive hierarchy, or when hosts engage in partnerships which are less costly, compartmentalization is less likely to evolve. We conclude that compartmentalization is key to understanding the evolution of symbiotic cooperation. This article is part of the theme issue 'The role of the microbiome in host evolution'.

Polyploid plants obtain greater fitness benefits from a nutrient acquisition mutualism

Polyploidy is a key driver of ecological and evolutionary processes in plants, yet little is known about its effects on biotic interactions. This gap in knowledge is especially profound for nutrient acquisition mutualisms, despite the fact that they regulate global nutrient cycles and structure ecosystems. Generalism in mutualistic interactions depends on the range of potential partners (niche breadth), the benefits obtained and ability to maintain benefits across a variety of partners (fitness plasticity). Here, we determine how each of these is influenced by polyploidy in the legume-rhizobium mutualism. We inoculated a broad geographic sample of natural diploid and autotetraploid alfalfa (Medicago sativa) lineages with a diverse panel of Sinorhizobium bacterial symbionts. To analyze the extent and mechanism of generalism, we measured host growth benefits and functional traits. Autotetraploid plants obtained greater fitness enhancement from mutualistic interactions and were better able to maintain this across diverse rhizobial partners (i.e. low plasticity in fitness) relative to diploids. These benefits were not attributed to increases in niche breadth, but instead reflect increased rewards from investment in the mutualism. Polyploid plants displayed greater generalization in bacterial mutualisms relative to diploids, illustrating another axis of advantage for polyploids over diploids.

Connecting signals and benefits through partner choice in plant-microbe interactions

Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.

Heritable genetic variation but no local adaptation in a pine-ectomycorrhizal interaction

Local adaptation of plants to mycorrhizal fungi helps determine the outcome of mycorrhizal interactions. However, there is comparatively little work exploring the potential for evolution in interactions with ectomycorrhizal fungi, and fewer studies have explored the heritability of mycorrhizal responsiveness, which is required for local adaptation to occur. We set up a reciprocal inoculation experiment using seedlings and soil from four populations of Scots pine (Pinus sylvestris) from Scotland, measuring seedling response to mycorrhizal inoculation after 4 months. We estimated heritability for the response traits and tested for genotype × environment interactions. While we found that ectomycorrhizal responsiveness was highly heritable, we found no evidence that pine populations were locally adapted to fungal communities. Instead, we found a complex suite of interactions between pine population and soil inoculum. Our results suggest that, while Scots pine has the potential to evolve in response to mycorrhizal fungi, evolution in Scotland has not resulted in local adaptation. Long generation times and potential for rapid shifts in fungal communities in response to environmental change may preclude the opportunity for such adaptation in this species, and selection for other factors such as resistance to fungal pathogens may explain the pattern of interactions found.

Expanding the mutualistic niche: parallel symbiont turnover along climatic gradients

Keystone mutualisms, such as corals, lichens or mycorrhizae, sustain fundamental ecosystem functions. Range dynamics of these symbioses are, however, inherently difficult to predict because host species may switch between different symbiont partners in different environments, thereby altering the range of the mutualism as a functional unit. Biogeographic models of mutualisms thus have to consider both the ecological amplitudes of various symbiont partners and the abiotic conditions that trigger symbiont replacement. To address this challenge, we here investigate 'symbiont turnover zones'--defined as demarcated regions where symbiont replacement is most likely to occur, as indicated by overlapping abundances of symbiont ecotypes. Mapping the distribution of algal symbionts from two species of lichen-forming fungi along four independent altitudinal gradients, we detected an abrupt and consistent β-diversity turnover suggesting parallel niche partitioning. Modelling contrasting environmental response functions obtained from latitudinal distributions of algal ecotypes consistently predicted a confined altitudinal turnover zone. In all gradients this symbiont turnover zone is characterized by approximately 12°C average annual temperature and approximately 5°C mean temperature of the coldest quarter, marking the transition from Mediterranean to cool temperate bioregions. Integrating the conditions of symbiont turnover into biogeographic models of mutualisms is an important step towards a comprehensive understanding of biodiversity dynamics under ongoing environmental change.

Environmental variation impacts trait expression and selection in the legume-rhizobium symbiosis

PREMISE

The ecological outcomes of mutualism are well known to shift across abiotic or biotic environments, but few studies have addressed how different environments impact evolutionary responses, including the intensity of selection on and the expression of genetic variance in key mutualism-related traits.

METHODS

We planted 30 maternal lines of the legume Medicago lupulina in four field common gardens and compared our measures of selection on and genetic variance in nodulation, a key trait reflecting legume investment in the symbiosis, with those from a previous greenhouse experiment using the same 30 M. lupulina lines.

RESULTS

We found that both the mean and genetic variance for nodulation were much greater in the greenhouse than in the field and that the form of selection on nodulation significantly differed across environments. We also found significant genotype-by-environment (G × E) effects for fitness-related traits that were generated by differences in the rank order of plant lines among environments.

CONCLUSIONS

Overall, our results suggest that the expression of genotypic variation and selection on nodulation differ across environments. In the field, significant rank-order changes for plant fitness potentially help maintain genetic variation in natural populations, even in the face of directional or stabilizing selection.

Using text-mined trait data to test for cooperate-and-radiate co-evolution between ants and plants

Mutualisms may be “key innovations” that spur lineage diversification by augmenting niche breadth, geographic range, or population size, thereby increasing speciation rates or decreasing extinction rates. Whether mutualism accelerates diversification in both interacting lineages is an open question. Research suggests that plants that attract ant mutualists have higher diversification rates than non-ant associated lineages. We ask whether the reciprocal is true: does the interaction between ants and plants also accelerate diversification in ants, i.e. do ants and plants cooperate-and-radiate? We used a novel text-mining approach to determine which ant species associate with plants in defensive or seed dispersal mutualisms. We investigated patterns of lineage diversification across a recent ant phylogeny using BiSSE, BAMM, and HiSSE models. Ants that associate mutualistically with plants had elevated diversification rates compared to non-mutualistic ants in the BiSSE model, with a similar trend in BAMM, suggesting ants and plants cooperate-and-radiate. However, the best-fitting model was a HiSSE model with a hidden state, meaning that diversification models that do not account for unmeasured traits are inappropriate to assess the relationship between mutualism and ant diversification. Against a backdrop of diversification rate heterogeneity, the best-fitting HiSSE model found that mutualism actually decreases diversification: mutualism evolved much more frequently in rapidly diversifying ant lineages, but then subsequently slowed diversification. Thus, it appears that ant lineages first radiated, then cooperated with plants.

Many plants and animals depend on other species for nutrition, protection, or dispersal, a type of ecological interaction known as mutualism. Mutualisms often help organisms thrive in new or harsh environments, thereby increasing their ecological success. We studied whether mutualism also increases evolutionary success by affecting lineage diversification, or the net result of the formation and loss of species over evolutionary time (i.e., speciation minus extinction). We focused on the widespread mutualism between ants and plants, in which ants act as protective ‘bodyguards’ or seed dispersers for plants and gain food or shelter in return. Previous research has found that the evolution of ant-plant mutualisms increased plant diversification. Here, we asked whether the same is true for ant diversification. We used a novel, automated approach to gather trait data from the abstracts of over 89,000 scientific articles about ants, and identified 432 mutualistic ant species and 2,909 non-mutualistic ant species. We then used this trait information to model how mutualism has evolved and influenced diversification across a recent ant phylogeny. Our analysis suggests that instead of causally enhancing diversification, mutualism evolves more often in lineages that are already diversifying quickly and then slows ant diversification.

On the Consequences of the Interdependence of Stabilizing and Equalizing Mechanisms

We present an overlooked but important property of modern coexistence theory (MCT), along with two key new results and their consequences. The overlooked property is that stabilizing mechanisms (increasing species' niche differences) and equalizing mechanisms (reducing species' fitness differences) have two distinct sets of meanings within MCT: one in a two-species context and another in a general multispecies context. We demonstrate that the two-species framework is not a special case of the multispecies one, and therefore these two parallel frameworks must be studied independently. Our first result is that, using the two-species framework and mechanistic consumer-resource models, stabilizing and equalizing mechanisms exhibit complex interdependence, such that changing one will simultaneously change the other. Furthermore, the nature and direction of this simultaneous change sensitively depend on model parameters. The second result states that while MCT is often seen as bridging niche and neutral modes of coexistence by building a niche-neutrality continuum, the interdependence between stabilizing and equalizing mechanisms acts to break this continuum under almost any biologically relevant circumstance. We conclude that the complex entanglement of stabilizing and equalizing terms makes their impact on coexistence difficult to understand, but by seeing them as aggregated effects (rather than underlying causes) of coexistence, we may increase our understanding of ecological dynamics.

A selective fungal transport organ (mycangium) maintains coarse phylogenetic congruence between fungus-farming ambrosia beetles and their symbionts

Thousands of species of ambrosia beetles excavate tunnels in wood to farm fungi. They maintain associations with particular lineages of fungi, but the phylogenetic extent and mechanisms of fidelity are unknown. We test the hypothesis that selectivity of their mycangium enforces fidelity at coarse phylogenetic scales, while permitting promiscuity among closely related fungal mutualists. We confirm a single evolutionary origin of the Xylosandrus complex-a group of several xyleborine genera that farm fungi in the genus Ambrosiella. Multi-level co-phylogenetic analysis revealed frequent symbiont switching within major Ambrosiella clades, but not between clades. The loss of the mycangium in Diuncus, a genus of evolutionary cheaters, was commensurate with the loss of fidelity to fungal clades, supporting the hypothesis that the mycangium reinforces fidelity. Finally, in vivo experiments tracked symbiotic compatibility throughout the symbiotic life cycle of Xylosandrus compactus and demonstrated that closely related Ambrosiella symbionts are interchangeable, but the probability of fungal uptake in the mycangium was significantly lower in more phylogenetically distant species of symbionts. Symbiont loads in experimental subjects were similar to wild-caught beetles. We conclude that partner choice in ambrosia beetles is achieved in the mycangium, and co-phylogenetic inferences can be used to predict the likelihood of specific symbiont switches.

More partners, more ranges: generalist legumes spread more easily around the globe

How does mutualism affect range expansion? On the one hand, mutualists might thrive in new habitats thanks to the resources, stress tolerance or defence provided by their partners. On the other, specialized mutualists might fail to find compatible partners beyond their range margins, limiting further spread. A recent global analysis of legume ranges found that non-symbiotic legumes have been successfully introduced to more ranges than legumes that form symbioses with rhizobia, but there is still abundant unexplained variation in introduction success within symbiotic legumes. We test the hypothesis that generalist legumes have spread to more ranges than specialist legumes. We used published data and rhizobial 16S rRNA sequences from GenBank to quantify the number of rhizobia partners that associate with 159 legume species, spanning the legume phylogeny and the globe. We found that generalist legumes occur in more introduced ranges than specialist legumes, suggesting that among mutualists, specialization hinders range expansions.