Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts

Community composition of phytopathogenic fungi significantly influences ectomycorrhizal fungal communities during subtropical forest succession

Ectomycorrhizal fungi (EMF) can form symbiotic relationships with plants, aiding in plant growth by providing access to nutrients and defense against phytopathogenic fungi. In this context, factors such as plant assemblages and soil properties can impact the interaction between EMF and phytopathogenic fungi in forest soil. However, there is little understanding of how these fungal interactions evolve as forests move through succession stages. In this study, we used high-throughput sequencing to investigate fungal communities in young, intermediate, and old subtropical forests. At the genus level, EMF communities were dominated by Sebacina, Russula, and Lactarius, while Mycena was the most abundant genus in pathogenic fungal communities. The relative abundances of EMF and phytopathogenic fungi in different stages showed no significant difference with the regulation of different factors. We discovered that interactions between phytopathogenic fungi and EMF maintained a dynamic balance under the influence of the differences in soil quality attributed to each forest successional stage. The community composition of phytopathogenic fungi is one of the strong drivers in shaping EMF communities over successions. In addition, the EMF diversity was significantly related to plant diversity, and these relationships varied among successional stages. Despite the regulation of various factors, the positive relationship between the diversity of phytopathogenic fungi and EMF remained unchanged. However, there is no significant difference in the ratio of the abundance of EMF and phytopathogenic fungi over the course of successions. These results will advance our understanding of the biodiversity-ecosystem functioning during forest succession. KEY POINTS: •Community composition of both EMF and phytopathogenic fungi changed significantly over forest succession. •Phytopathogenic fungi is a key driver in shaping EMF community. •The effect of plant Shannon's diversity on EMF communities changed during the forest aging process.

Arbuscular mycorrhizal fungal spore communities and co-occurrence networks demonstrate host-specific variation throughout the growing season

Microbial community assembly involves a series of ecological filtering mechanisms that determine the composition of microbial communities. While the importance of both broad and local level factors on microbial communities has been reasonably well studied, this work often is limited to single observations and neglects to consider how communities change over time (i.e., seasonal variation). Because seasonal variation is an important determinant of community assembly and determines the relative importance of community assembly filters, this represents a key knowledge gap. Due to their close associations with seasonal variation in plant growth and fitness, arbuscular mycorrhizal (AM) fungi are useful groups for assessing the importance of seasonal dynamics in microbial community assembly. We tested how seasonal variation (spring vs. summer), plant life history stage (vegetative vs. flowering), and host plant species (Baptisia bracteata var. leucophaea & Andropogon gerardii) influenced AM fungal spore community assembly. AM fungal spore community temporal dynamics were closely linked to plant host species and life history stage. While AM fungal spore communities demonstrated strong turnover between the spring (e.g., higher sporulation) and late summer (e.g., higher diversity), the strength and direction of these changes was modified by host plant species. Here we demonstrate the importance of considering temporal variation in microbial community assembly, and also show how plant-microbe interactions can modify seasonal trends in microbial community dynamics.

The complex circuitry of interactions determining coexistence among plants and mycorrhizal fungi

We present a mechanistic model of coexistence among a mycorrhizal fungus and one or two plant species that compete for a single nutrient. Plant-fungal coexistence is more likely if the fungus is better at extracting the environmental nutrient than the plant and the fungus acquires carbon from the plant above a minimum rate. When they coexist, their interaction can shift from mutualistic to parasitic at high nutrient availability. The fungus is a second nutrient source for plants and can promote the coexistence of two plant competitors if one is better at environmental nutrient extraction and the other is better at acquiring the nutrient from the fungus. Because it extracts carbon from both plants, the fungus also serves as a conduit of apparent competition between the plants. Consequently, the plant with the lower environmental nutrient extraction rate can drive the plant with the higher environmental nutrient extraction rate extinct at high carbon supply rates. This model illustrates mechanisms to explain several observed patterns, including shifts in plant-mycorrhizal growth responses and coexistence along nutrient gradients, equivocal results among experiments testing the effect of mycorrhizal fungi on plant diversity, and differences in plant diversity among ecosystems dominated by different mycorrhizal groups.

Mutualism at the leading edge: insights into the eco-evolutionary dynamics of host-symbiont communities during range expansion

The evolution of mutualism between host and symbiont communities plays an essential role in maintaining ecosystem function and should therefore have a profound effect on their range expansion dynamics. In particular, the presence of mutualistic symbionts at the leading edge of a host-symbiont community should enhance its propagation in space. We develop a theoretical framework that captures the eco-evolutionary dynamics of host-symbiont communities, to investigate how the evolution of resource exchange may shape community structure during range expansion. We consider a community with symbionts that are mutualistic or parasitic to various degrees, where parasitic symbionts receive the same amount of resource from the host as mutualistic symbionts, but at a lower cost. The selective advantage of parasitic symbionts over mutualistic ones is increased with resource availability (i.e. with host density), promoting mutualism at the range edges, where host density is low, and parasitism at the population core, where host density is higher. This spatial selection also influences the speed of spread. We find that the host growth rate (which depends on the average benefit provided by the symbionts) is maximal at the range edges, where symbionts are more mutualistic, and that host-symbiont communities with high symbiont density at their core (e.g. resulting from more mutualistic hosts) spread faster into new territories. These results indicate that the expansion of host-symbiont communities is pulled by the hosts but pushed by the symbionts, in a unique push-pull dynamic where both the host and symbionts are active and tightly-linked players.

Plant choice between arbuscular mycorrhizal fungal species results in increased plant P acquisition

Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that provide phosphorus (P) to plants in exchange for photosynthetically fixed carbon (C). Previous research has shown that plants-given a choice among AMF species-may preferentially allocate C to AMF species that provide more P. However, these investigations rested on a limited set of plant and AMF species, and it therefore remains unclear how general this phenomenon is. Here, we combined 4 plant and 6 AMF species in 24 distinct plant-AMF species compositions in split-root microcosms, manipulating the species identity of AMF in either side of the root system. Using 14C and 32P/33P radioisotope tracers, we tracked the transfer of C and P between plants and AMF, respectively. We found that when plants had a choice of AMF species, AMF species which transferred more P acquired more C. Evidence for preferential C allocation to more beneficial AMF species within individual plant roots was equivocal. However, AMF species which transferred more P to plants did so at lower C-to-P ratios, highlighting the importance both of absolute and relative costs of P acquisition from AMF. When plants had a choice of AMF species, their shoots contained a larger total amount of P at higher concentrations. Our results thus highlight the benefits of plant C choice among AMF for plant P acquisition.

Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities

Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional structure. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e. plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly through increasing the maximum plant height, rather than altering soil properties. Our results highlight the importance of plant height in driving AMF community dynamics under N enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic N deposition.

Impact of intercropping grass on the soil rhizosphere microbial community and soil ecosystem function in a walnut orchard

The intercropping of grass in orchards has beneficial effects on soil properties and soil microbial communities and is an important soil management measure for improving orchard productivity and land-use efficiency. However, few studies have explored the effects of grass intercropping on rhizosphere microorganisms in walnut orchards. In this study, we explored the microbial communities of clear tillage (CT), walnut/ryegrass (Lolium perenne L.) (Lp), and walnut/hairy vetch (Vicia villosa Roth.) (Vv) intercropping system using MiSeq sequencing and metagenomic sequencing. The results revealed that the composition and structure of the soil bacterial community changed significantly with walnut/Vv intercropping compared to CT and walnut/Lp intercropping. Moreover, the walnut/hairy vetch intercropping system had the most complex connections between bacterial taxa. In addition, we found that the soil microorganisms of walnut/Vv intercropping had a higher potential for nitrogen cycling and carbohydrate metabolism, which may be related to the functions of Burkholderia, Rhodopseudomonas, Pseudomonas, Agrobacterium, Paraburkholderia, and Flavobacterium. Overall, this study provided a theoretical basis for understanding the microbial communities associated with grass intercropping in walnut orchards, providing better guidance for the management of walnut orchards.

Competitive interactions in two different plant species: Do grassland mycorrhizal communities and nitrogen addition play the same game?

In the Tibetan Plateau grassland ecosystems, nitrogen (N) availability is rising dramatically; however, the influence of higher N on the arbuscular mycorrhizal fungi (AMF) might impact on plant competitive interactions. Therefore, understanding the part played by AMF in the competition between Vicia faba and Brassica napus and its dependence on the N-addition status is necessary. To address this, a glasshouse experiment was conducted to examine whether the grassland AMF community's inocula (AMF and NAMF) and N-addition levels (N-0 and N-15) alter plant competition between V. faba and B. napus. Two harvests took day 45 (1^st harvest) and day 90 (2^nd harvest), respectively. The findings showed that compared to B. napus, AMF inoculation significantly improved the competitive potential of the V. faba. In the occurrence of AMF, V. faba was the strongest competitor being facilitated by B. napus in both harvests. While under N-15, AMF significantly enhanced tissue N:P ratio in B. napus mixed-culture at 1^st harvest, the opposite trend was observed in 2^nd harvest. The mycorrhizal growth dependency slightly negatively affected mixed-culture compared to monoculture under both N-addition treatments. The aggressivity index of AMF plants was higher than NAMF plants with both N-addition and harvests. Our observation highlights that mycorrhizal associations might facilitate host plant species in mixed-culture with non-host plant species. Additionally, interacting with N-addition, AMF could impact the competitive ability of the host plant not only directly but also indirectly, thereby changing the growth and nutrient uptake of competing plant species.

Interactive responses of root and shoot of camphor tree (Cinnamomum camphora L.) to asymmetric disturbance treatments

Plant root and shoot growth are closely interrelated, though the connotation of root-shoot balance should not be limited to their connectivity in biomass and physiological indicators. Their directional distribution of mass in architecture and the resulting root-shoot interactions are the keys to understanding the dynamic balance of the below- and above-ground organs related to tree anchorage. This study focuses on the 4-year-old camphor tree (Cinnamomum camphora L.) as a system to observe the biomass distribution in response to the asymmetric disturbance treatments of biased root (BRT), inclined trunk (ITT), and half-crown (HCT) in a controlled cultivation experiment using the minirhizotron technique. We found an inverse relationship of biomass distribution of crowns to roots in BRT and opposite asymmetries of roots with crowns in response to the ITT and HCT treatments. We also observed higher net photosynthesis rate (P_n ), water use efficiency, and chlorophyll content in the leaves on the side opposite the lean in ITT, and higher P_n , transpiration rate, and chlorophyll content on the root-bias side in BRT, which is consistent with the nutrient allocation strategies of allocating nutrients across plant organs in an optimal way to obtain 'functional equilibrium' and adapt to the stressed environment. Furthermore, the asymmetrical growth transformation of first-level branch length from the root-bias side to the opposite side in BRT, and a similar transformation of root length from the crown-bias side to the opposite side in HCT, imbues further theoretical support of the nutrient allocation strategy and the biomechanical stability principle, respectively. In summary, this study is the first to identify opposite interaction between below- and above-ground biomass distributions of the camphor tree. The findings enrich the connotation of root-shoot interactions and help to realize root design for the silviculture management of urban forests.

Evolution of manipulative microbial behaviors in the rhizosphere

The rhizosphere has been called "one of the most complex ecosystems on earth" because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed a plant-centric perspective when trying to harness the potential of microbiome-derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, a microbe-centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context-dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production.

Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype

The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and evolution of rhizobia and their symbiotic interactions with hosts. We examined how host genotype, nitrogen addition, rhizobial density, and community complexity affected selection on 68 rhizobial strains in the Sinorhizobium meliloti-Medicago truncatula mutualism. As expected, host genotype had a substantial effect on the size, number, and strain composition of root nodules (the symbiotic organ). The understudied environmental variable of rhizobial density had a stronger effect on nodule strain frequency than the addition of low nitrogen levels. Higher inoculum density resulted in a nodule community that was less diverse and more beneficial but only in the context of the more selective host genotype. Higher density resulted in more diverse and less beneficial nodule communities with the less selective host. Density effects on strain composition deserve additional scrutiny as they can create feedback between ecological and evolutionary processes. Finally, we found that relative strain rankings were stable across increasing community complexity (2, 3, 8, or 68 strains). This unexpected result suggests that higher-order interactions between strains are rare in the context of nodule formation and development. Our work highlights the importance of examining mechanisms of density-dependent strain fitness and developing theoretical predictions that incorporate density dependence. Furthermore, our results have translational relevance for overcoming establishment barriers in bioinoculants and motivating breeding programs that maintain beneficial plant-microbe interactions across diverse agroecological contexts. IMPORTANCE Legume crops establish beneficial associations with rhizobial bacteria that perform biological nitrogen fixation, providing nitrogen to plants without the economic and greenhouse gas emission costs of chemical nitrogen inputs. Here, we examine the influence of three environmental factors that vary in agricultural fields on strain relative fitness in nodules. In addition to manipulating nitrogen, we also use two biotic variables that have rarely been examined: the rhizobial community's density and complexity. Taken together, our results suggest that (i) breeding legume varieties that select beneficial strains despite environmental variation is possible, (ii) changes in rhizobial population densities that occur routinely in agricultural fields could drive evolutionary changes in rhizobial populations, and (iii) the lack of higher-order interactions between strains will allow the high-throughput assessments of rhizobia winners and losers during plant interactions.

Changes to bacterial communities and soil metabolites in an apple orchard as a legacy effect of different intercropping plants and soil management practices

Intercropping is an important soil management practice for increasing orchard productivity and land-use efficiency because it has beneficial effects on soil microbial communities and soil properties. However, there is relatively little information available regarding the effects of different crops/grasses on soil microbial communities and soil metabolic products in apple orchards in arid and semi-arid regions. In this study, we showed the microbial communities of apple, intercropping plants, and sandy waste soil, using the third-generation PacBio SMRT long-read sequencing technology. Our results also revealed that the microbial communities and soil metabolic properties differed significantly between apple and the sandy waste soil and the intercropping plants. Intercropping could significantly enrich diverse microbial species, microbial nitrogen, and microbial carbon of soil. Moreover, intercropping with licorice showed better effects in recruiting beneficial microbes, compared to grass and pepper, significantly enriching species belonging to some well-known taxa with beneficial effects, including Bacillus, Ensifer, Paenibacillus, Rhizobium, and Sphingomonas. Thus, intercropping with licorice may improve apple tree growth and disease resistance. Furthermore, Bradyrhizobium and Rubrobacter were included among the keystone taxa of apple, whereas Bacillus, Chitinophaga, Stenotrophobacter, Rubrobacter, and Luteimonas were the keystone taxa of the intercropping plants. The results of our study suggest that intercropping with licorice is a viable option for increasing apple orchard productivity.

Plant Interaction Patterns Shape the Soil Microbial Community and Nutrient Cycling in Different Intercropping Scenarios of Aromatic Plant Species

Intercropping systems improve the soil nutrient cycle through microbial community activity and then land productivity. However, their interactions mechanism underlying that the mixed aromatic plant species intercropping regulate the soil microbiome and nutrient cycling on the perennial woody orchard is still uncovered. We designed treatments with 0, 1, and 3 aromatic plant species intercropped in two scenarios of clean tillage (T model, T1, T2, and T4) and natural grass (G model, G1, G2, and G4) in apple orchards, and investigated intercrops effects at the branch growing stage (BGS) and fruit development stage (FDS), respectively. Compared with T model, G model in FDS increased alpha diversity of bacterial community and Shannon index fungal community, the relative abundance of dominant taxa, such as Acidobacteria and Actinobacteria, and also the numbers of up and down-regulated OTUs, the most of indices of co-occurrence network in both bacterial and fungal community, and then improved invertase activity and available nitrogen content. Relative to G1, G2 and G4 reduced diversity bacterial community in FDS, the relative abundance of dominant taxa, the most of indices of co-occurrence network, and then improved soil invertase activity and total phosphorus content in soil. Moreover, Shannon index of fungal community, the altered number of OTUs and the most indices of co-occurrence network were higher in G4 than those in G2 in FDS. These changes above in FDS were more markedly than those in BGS, suggesting that chemical diversity of litter from mixed species of aromatic plants in natural grass scenario led to diversity, complexity, and stability of soil microbial community and then nutrient cycling. It provided a novel highlight and method to modulate biocenosis and then improve the soil nutrient cycling.

Specific Plant Mycorrhizal Responses Are Linked to Mycorrhizal Fungal Species Interactions

Effects of arbuscular mycorrhizal fungi (AMF) on plants span the continuum from mutualism to parasitism due to the plant-AMF specificity, which obscures the utilization of AMF in the restoration of degraded lands. Caragana korshinskii, Hedysarum laeve, Caragana microphylla, and Poa annua are the most frequently used plants for revegetation in Kubuqi Desert, China, and the influence of AMF on their re-establishment remains to be explored further. Herein, using a greenhouse experiment, we tested the plant-AMF feedbacks between the four plant species and their conspecific or heterospecific AMF, retrieved from their rhizosphere in the Kubuqi Desert. AMF showed beneficial effects on plant growth for all these plant-AMF pairs. Generally, AMF increased the biomass of C. korshinskii, H. laeve, C. microphylla, and P. annua by 97.6, 50.6, 46.5, and 381.1%, respectively, relative to control. In addition, the AMF-plant specificity was detected. P. annua grew best, but C. microphylla grew worst with conspecific AMF communities. AMF community from P. annua showed the largest beneficial effect on all the plants (with biomass increased by 63.9-734.4%), while the AMF community from C. microphylla showed the least beneficial effect on all the plants (with biomass increased by 9.9-59.1%), except for P. annua (a 292.4% increase in biomass). The magnitude of AMF effects on plant growth was negatively correlated with the complexity of the corresponding AMF co-occurrence networks. Overall, this study suggests that AMF effects on plant growth vary due to plant-AMF specificity. We also observed the broad-spectrum benefits of the native AMF from P. annua, which indicates its potential utilization in the restoration of the desert vegetation.

Microbial mediators of plant community response to long-term N and P fertilization: Evidence of a role of plant responsiveness to mycorrhizal fungi

Climate changes and anthropogenic nutrient enrichment widely threaten plant diversity and ecosystem functions. Understanding the mechanisms governing plant species turnover across nutrient gradients is crucial to developing successful management and restoration strategies. We tested whether and how soil microbes, particularly arbuscular mycorrhizal fungi (AMF), could mediate plant community response to a 15 years long-term N (0, 4, 8, and 16 g N m^-2  year^-1 ) and P (0 and 8 g N m^-2  year^-1 ) enrichment in a grassland system. We found N and P enrichment resulted in plant community diversity decrease and composition change, in which perennial C₄  graminoids were dramatically reduced while annuals and perennial forbs increased. Metabarcoding analysis of soil fungal community showed that N and P changed fungal diversity and composition, of which only a cluster of AMF identified by the co-occurrence networks analysis was highly sensitive to P treatments and was negatively correlated with shifts in percentage cover of perennial C₄  graminoids. Moreover, by estimating the mycorrhizal responsiveness (MR) of 41 plant species in the field experiment from 264 independent tests, we found that the community weighted mean MR of the plant community was substantially reduced with nutrient enrichment and was positively correlated with C₄  graminoids percentage cover. Both analyses of covariance and structural equation modeling indicated that the shift in MR rather than AMF composition change was the primary predictor of the decline in perennial C₄  graminoids, suggesting that the energy cost invested by C₄ plants on those sensitive AMF might drive the inferior competitive abilities compared with other groups. Our results suggest that shifts in the competitive ability of mycorrhizal responsive plants can drive plant community change to anthropogenic eutrophication, suggesting a functional benefit of mycorrhizal mutualism in ecological restoration following climatic or anthropogenic degradation of soil communities.

Host age and surrounding vegetation affect the community and colonization rates of arbuscular mycorrhizal fungi in a temperate grassland

Arbuscular mycorrhizal fungi (AMF) are important symbionts for the majority of terrestrial vascular plants, yet the drivers of the compositional variation in AMF communities need to be better understood. What effects does the ontogenetic stage of host plants have and do these effects differ between plant functional groups? Are the AMF communities modified by the properties of surrounding vegetation, such as the proportion of different functional groups or nonmycorrhizal plants ? We addressed these questions in a temperate grassland and studied AMF communities using next-generation sequencing and light microscopy, evaluating their composition, taxonomic, phylogenetic and functional diversity, functional traits and root colonization levels. We found important differences between AMF communities and their diversity between seedlings and adults which are larger than the differences among host species or between functional groups. The proportion of nonmycorrhizal plants in the surrounding affected AMF community composition and increased its richness. Our results highlight the need for further investigating the existence of a common mycelial networks. The decision to use seedlings for experimental work can affect the results more than the chosen host species.

Optimal Allocation Ratios: A Square Root Relationship between the Ratios of Symbiotic Costs and Benefits

AbstractAll organisms struggle to make sense of environmental stimuli in order to maximize their fitness. For animals, the responses of single cells and superorganisms to stimuli are generally proportional to stimulus ratios, a phenomenon described by Weber's law. However, Weber's law has not yet been used to predict how plants respond to stimuli generated from their symbiotic partners. Here we develop a model for quantitatively predicting the ratios of carbon (C) allocation to symbionts that provide nutrients to their plant host. Consistent with Weber's law, our model demonstrates that the optimal ratio of resources allocated to a less beneficial relative to a more beneficial symbiont scale to the ratio of the growth benefits of the two strains. As C allocation to symbionts increases, the ratio of C allocation to two strains approaches the square root of the ratio of symbiotic growth benefits (e.g., a worse symbiont providing one-fourth the benefits gets 1/4=1/2 the C of a better symbiont). We document a compelling correspondence between our square root model prediction and a meta-analysis of experimental literature on C allocation. This type of preferential allocation can promote coexistence between more beneficial and less beneficial symbionts, offering a potential mechanism behind the high diversity of microbial symbionts observed in nature.

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.

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.

Compatible Mycorrhizal Types Contribute to a Better Design for Mixed Eucalyptus Plantations

Mixed-species forest plantation is a sound option to facilitate ecological restoration, plant diversity and ecosystem functions. Compatible species combinations are conducive to reconstruct plant communities that can persist at a low cost without further management and even develop into natural forest communities. However, our understanding of how the compatibility of mycorrhizal types mediates species coexistence is still limited, especially in a novel agroforestry system. Here, we assessed the effects of mycorrhizal association type on the survival and growth of native woody species in mixed-species Eucalyptus plantations. To uncover how mycorrhizal type regulates plant-soil feedbacks, we first conducted a pot experiments by treating distinct mycorrhizal plants with soil microbes from their own or other mycorrhizal types. We then compared the growth response of arbuscular mycorrhizal plants and ectomycorrhizal plants to different soil microbial compositions associated with Eucalyptus plants. We found that the type of mycorrhizal association had a significant impact on the survival and growth of native tree species in the Eucalyptus plantations. The strength and direction of the plant-soil feedbacks of focal tree species depended on mycorrhizal type. Non-mycorrhizal plants had consistent negative feedbacks with the highest survival in the Eucalyptus plantations, whereas nitrogen-fixing plants had consistent positive feedbacks and the lowest survival. Arbuscular mycorrhizal and ectomycorrhizal plants performed varied feedback responses to soil microbes from distinct mycorrhizal plant species. Non-mycorrhizal plants grew better with Eucalyptus soil microbes while nitrogen-fixing plants grew worse with their own conspecific soil microbes. Different soil microbial compositions of Eucalyptus consistently increased the aboveground growth of arbuscular mycorrhizal plants, but the non-mycorrhizal microbial composition of the Eucalyptus soil resulted in greater belowground growth of ectomycorrhizal plants. Overall, Eucalyptus plants induced an unfavorable soil community, impeding coexistence with other mycorrhizal plants. Our study provides consistent observational and experimental evidence that mycorrhizal-mediated plant-microbial feedback on species coexistence among woody species. These findings are with important implications to optimize the species combinations for better design of mixed forest plantations.

Decreased coevolutionary potential and increased symbiont fecundity during the biological invasion of a legume-rhizobium mutualism

Although most invasive species engage in mutualism, we know little about how mutualism evolves as partners colonize novel environments. Selection on cooperation and standing genetic variation for mutualism traits may differ between a mutualism's invaded and native ranges, which could alter cooperation and coevolutionary dynamics. To test for such differences, we compare mutualism traits between invaded- and native-range host-symbiont genotype combinations of the weedy legume, Medicago polymorpha, and its nitrogen-fixing rhizobium symbiont, Ensifer medicae, which have coinvaded North America. We find that mutualism benefits for plants are indistinguishable between invaded- and native-range symbioses. However, rhizobia gain greater fitness from invaded-range mutualisms than from native-range mutualisms, and this enhancement of symbiont fecundity could increase the mutualism's spread by increasing symbiont availability during plant colonization. Furthermore, mutualism traits in invaded-range symbioses show lower genetic variance and a simpler partitioning of genetic variance between host and symbiont sources, compared to native-range symbioses. This suggests that biological invasion has reduced mutualists' potential to respond to coevolutionary selection. Additionally, rhizobia bearing a locus (hrrP) that can enhance symbiotic fitness have more exploitative phenotypes in invaded-range than in native-range symbioses. These findings highlight the impacts of biological invasion on the evolution of mutualistic interactions.

Light availability and light demand of plants shape the arbuscular mycorrhizal fungal communities in their roots

Plants involved in the arbuscular mycorrhizal (AM) symbiosis trade photosynthetically derived carbon for fungal-provided soil nutrients. However, little is known about how plant light demand and ambient light conditions influence root-associating AM fungal communities. We conducted a manipulative field experiment to test whether plants' shade-tolerance influences their root AM fungal communities in open and shaded grassland sites. We found similar light-dependent shifts in AM fungal community structure for experimental bait plant roots and the surrounding soil. Yet, deviation from the surrounding soil towards lower AM fungal beta-diversity in the roots of shade-intolerant plants in shade suggested preferential carbon allocation to specific AM fungi in conditions where plant-assimilated carbon available to fungi was limited. We conclude that favourable environmental conditions widen the plant biotic niche, as demonstrated here with optimal light availability reducing plants' selectivity for specific AM fungi, and promote compatibility with a larger number of AM fungal taxa.

Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop

Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.

Connections and Feedback: Aquatic, Plant, and Soil Microbiomes in Heterogeneous and Changing Environments

Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model

Empirical studies show that plant-soil feedbacks (PSF) can generate negative density dependent (NDD) recruitment capable of maintaining plant community diversity at landscape scales. However, the observation that common plants often exhibit relatively weaker NDD than rare plants at local scales is difficult to reconcile with the maintenance of overall plant diversity. We develop a spatially explicit simulation model that tracks the community dynamics of microbial mutualists, pathogens, and their plant hosts. We find that net PSF effects vary as a function of both host abundance and key microbial traits (e.g., host affinity) in ways that are compatible with both common plants exhibiting relatively weaker local NDD, while promoting overall species diversity. The model generates a series of testable predictions linking key microbial traits and the relative abundance of host species, to the strength and scale of PSF and overall plant community diversity.

How mycorrhizal associations drive plant population and community biology

Mycorrhizal fungi provide plants with a range of benefits, including mineral nutrients and protection from stress and pathogens. Here we synthesize current information about how the presence and type of mycorrhizal association affect plant communities. We argue that mycorrhizal fungi regulate seedling establishment and species coexistence through stabilizing and equalizing mechanisms such as soil nutrient partitioning, feedback to soil antagonists, differential mycorrhizal benefits, and nutrient trade. Mycorrhizal fungi have strong effects on plant population and community biology, with mycorrhizal type-specific effects on seed dispersal, seedling establishment, and soil niche differentiation, as well as interspecific and intraspecific competition and hence plant diversity.

Carbon for nutrient exchange between arbuscular mycorrhizal fungi and wheat varies according to cultivar and changes in atmospheric carbon dioxide concentration

Arbuscular mycorrhizal fungi (AMF) form symbioses with most crops, potentially improving their nutrient assimilation and growth. The effects of cultivar and atmospheric CO2 concentration ([CO2 ]) on wheat-AMF carbon-for-nutrient exchange remain critical knowledge gaps in the exploitation of AMF for future sustainable agricultural practices within the context of global climate change. We used stable and radioisotope tracers (15 N, 33 P, 14 C) to quantify AMF-mediated nutrient uptake and fungal acquisition of plant carbon in three wheat (Triticum aestivum L.) cultivars. We grew plants under current ambient (440 ppm) and projected future atmospheric CO2 concentrations (800 ppm). We found significant 15 N transfer from fungus to plant in all cultivars, and cultivar-specific differences in total N content. There was a trend for reduced N uptake under elevated atmospheric [CO2 ]. Similarly, 33 P uptake via AMF was affected by cultivar and atmospheric [CO2 ]. Total P uptake varied significantly among wheat cultivars and was greater at the future than current atmospheric [CO2 ]. We found limited evidence of cultivar or atmospheric [CO2 ] effects on plant-fixed carbon transfer to the mycorrhizal fungi. Our results suggest that AMF will continue to provide a route for nutrient uptake by wheat in the future, despite predicted rises in atmospheric [CO2 ]. Consideration should therefore be paid to cultivar-specific AMF receptivity and function in the development of climate smart germplasm for the future.

Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis

PREMISE

Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen. Because partner quality in mutualisms is genotype-dependent, within-species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here we ask whether partner quality variation in rhizobia mediates the response of host plants to changing light availability, and conversely, whether light alters the expression of partner quality variation.

METHODS

We inoculated clover hosts with 11 strains of Rhizobium leguminosarum that differed in partner quality, grew plants under either ambient or low light conditions in the greenhouse, and measured plant growth, nodule traits, and foliar nutrient composition.

RESULTS

Light availability and rhizobium inoculum interactively determined plant growth, and variation in rhizobium partner quality was more apparent in ambient light.

CONCLUSIONS

Our results suggest that variation in the costs and benefits of rhizobium symbionts mediate host responses to light availability and that rhizobium strain variation might more important in higher-light environments. Our work adds to a growing appreciation for the role of microbial intraspecific and interspecific diversity in mediating extended phenotypes in their hosts and suggests an important role for light availability in the ecology and evolution of legume-rhizobium symbiosis.

Testing for loss of Epichloë and non-epichloid symbionts under altered rainfall regimes

PREMISE

Microbial symbionts can buffer plant hosts from environmental change. Therefore, understanding how global change factors alter the associations between hosts and their microbial symbionts may improve predictions of future changes in host population dynamics and microbial diversity. Here, we investigated how one global change factor, precipitation, affected the maintenance or loss of symbiotic fungal endophytes in a C₃ grass host. Specifically, we examined the distinct responses of Epichloë (vertically transmitted and systemic) and non-epichloid endophytes (typically horizontally transmitted and localized) by considering (1) how precipitation altered associations with Epichloë and non-epichloid endophytic taxa across host ontogeny, and (2) interactive effects of water availability and Epichloë on early seedling life history stages.

METHODS

We manipulated the presence of Epichloë amarillans in American beachgrass (Ammophila breviligulata) in a multiyear field experiment that imposed three precipitation regimes (ambient or ±30% rainfall). In laboratory assays, we investigated the interactive effects of water availability and Epichloë on seed viability and germination.

RESULTS

Reduced precipitation decreased the incidence of Epichloë in leaves in the final sampling period, but had no effect on associations with non-epichloid taxa. Epichloë reduced the incidence of non-epichloid endophytes, including systemic p-endophytes, in seeds. Laboratory assays suggested that association with Epichloë is likely maintained, in part, due to increased seed viability and germination regardless of water availability.

CONCLUSIONS

Our study empirically demonstrates several pathways for plant symbionts to be lost or maintained across host ontogeny and suggests that reductions in precipitation can drive the loss of a plant's microbial symbionts.

Foliar endophytic fungi alter patterns of nitrogen uptake and distribution in Theobroma cacao

Colonization by foliar endophytic fungi can affect the expression of host plant defenses and other ecologically important traits. However, whether endophyte colonization affects the uptake or redistribution of resources within and among host plant tissues remains unstudied. We inoculated leaves of Theobroma cacao with four common colonizers that range in their effect from protective to pathogenic (Colletotrichum tropicale, Pestalotiopsis sp., Colletotrichum theobromicola, or Phytophthora palmivora). We pulsed the soil with nitrogen-15 (¹⁵ N) and then traced ¹⁵ N uptake and its subsequent distribution to whole plants and individual leaves. At a whole-plant level, C. tropicale-inoculated plants showed significantly greater ¹⁵ N uptake than endophyte-free plants did in the same pot. Among leaves within plants, younger leaves were particularly enriched in ¹⁵ N, but endophyte inoculation at the individual leaf level did not alter ¹⁵ N distribution within plants. However, leaves co-inoculated with pathogenic Phytophthora and protective C. tropicale experienced significantly elevated ¹⁵ N content as pathogen damage increased, compared with leaves inoculated only with the pathogen. Further, endophyte-pathogen co-infection also increased total plant biomass. Our results indicate that colonization by foliar endophytes significantly affects N uptake and distribution among and within host plants in ways that appear to be context dependent on other microbiome components.

Host investment into symbiosis varies among genotypes of the legume Acmispon strigosus, but host sanctions are uniform

Efficient host control predicts the extirpation of ineffective symbionts, but they are nonetheless widespread in nature. We tested three hypotheses for the maintenance of symbiotic variation in rhizobia that associate with a native legume: partner mismatch between host and symbiont, such that symbiont effectiveness varies with host genotype; resource satiation, whereby extrinsic sources of nutrients relax host control; and variation in host control among host genotypes. We inoculated Acmispon strigosus from six populations with three Bradyrhizobium strains that vary in symbiotic effectiveness on sympatric hosts. We measured proxies of host and symbiont fitness in single- and co-inoculations under fertilization treatments of zero added nitrogen (N) and near-growth-saturating N. We examined two components of host control: 'host investment' into nodule size during single- and co-inoculations, and 'host sanctions' against less effective strains during co-inoculations. The Bradyrhizobium strains displayed conserved growth effects on hosts, and host control did not decline under experimental fertilization. Host sanctions were robust in all hosts, but host lines from different populations varied significantly in measures of host investment in both single- and co-inoculation experiments. Variation in host investment could promote variation in symbiotic effectiveness and prevent the extinction of ineffective Bradyrhizobium from natural populations.

Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks

Plants may actively cultivate microorganisms in their roots and rhizosphere that enhance their nutrition. To develop cropping strategies that substitute mineral fertilizers for beneficial root symbioses, we must first understand how microbial communities associated with plant roots differ among plant taxa and how they respond to fertilization. Arbuscular mycorrhizal (AM) fungi and rhizobacteria are of particular interest because they enhance nutrient availability to plants and perform a suite of nutrient cycling functions. The purpose of this experiment is to examine the root and soil microbiome in a long-term switchgrass (Panicum virgatum) biofuel feedstock experiment and determine how AM fungi and rhizobacteria respond to plant diversity and soil fertility. We hypothesize that intra- and interspecific plant diversity, nitrogen fertilization (+N), and their interaction will influence the biomass and community composition of AM fungi and rhizobacteria. We further hypothesize that +N will reduce the abundance of nitrogenase-encoding nifH genes on the rhizoplane. Roots and soils were sampled from three switchgrass cultivars (Cave-in-Rock, Kanlow, Southlow) grown in monoculture, intraspecific mixture, and interspecific planting mixtures with either Andropogon gerardii or diverse native tallgrass prairie species. Molecular sequencing was performed on root and soil samples, fatty acid extractions were assessed to determine microbial biomass, and quantitative polymerase chain reaction (qPCR) was performed on nifH genes from the rhizoplane. Sequence data determined core AM fungal and bacterial microbiomes and indicator taxa for plant diversity and +N treatments. We found that plant diversity and +N influenced AM fungal biomass and community structure. Across all plant diversity treatments, +N reduced the biomass of AM fungi and nifH gene abundance by more than 40%. The AM fungal genus Scutellospora was an indicator for +N, with relative abundance significantly greater under +N and in monoculture treatments. Community composition of rhizobacteria was influenced by plant diversity but not by +N. Verrucomicrobia and Proteobacteria were the dominant bacterial phyla in both roots and soils. Our findings provide evidence that soil fertility and plant diversity structure the root and soil microbiome. Optimization of soil communities for switchgrass production must take into account differences among cultivars and their unique responses to shifts in soil fertility.

Plant-mycorrhizal interactions mediate plant community coexistence by altering resource demand

As the diversity of plants increases in an ecosystem, so does resource competition for soil nutrients, a process that mycorrhizal fungi can mediate. The influence of mycorrhizal fungi on plant biodiversity likely depends on the strength of the symbiosis between the plant and fungi, the differential plant growth responses to mycorrhizal inoculation, and the transfer rate of nutrients from the fungus to plant. However, our current understanding of how nutrient-plant-mycorrhizal interactions influence plant coexistence is conceptual and thus lacks a unified quantitative framework. To quantify the conditions of plant coexistence mediated by mycorrhizal fungi, we developed a mechanistic resource competition model that explicitly included plant-mycorrhizal symbioses. We found that plant-mycorrhizal interactions shape plant coexistence patterns by creating a tradeoff in resource competition. Especially, a tradeoff in resource competition was caused by differential payback in the carbon resources that plants invested in the fungal symbiosis and/or by the stoichiometric constraints on plants that required additional, less-beneficial, resources to sustain growth. Our results suggested that resource availability and the variation in plant-mycorrhizal interactions act in concert to drive plant coexistence patterns. Applying our framework, future empirical studies should investigate plant-mycorrhizal interactions under multiple levels of resource availability.

Responses of arbuscular mycorrhizal fungi to long-term inorganic and organic nutrient addition in a lowland tropical forest

Improved understanding of the nutritional ecology of arbuscular mycorrhizal (AM) fungi is important in understanding how tropical forests maintain high productivity on low-fertility soils. Relatively little is known about how AM fungi will respond to changes in nutrient inputs in tropical forests, which hampers our ability to assess how forest productivity will be influenced by anthropogenic change. Here we assessed the influence of long-term inorganic and organic nutrient additions and nutrient depletion on AM fungi, using two adjacent experiments in a lowland tropical forest in Panama. We characterised AM fungal communities in soil and roots using 454-pyrosequencing, and quantified AM fungal abundance using microscopy and a lipid biomarker. Phosphorus and nitrogen addition reduced the abundance of AM fungi to a similar extent, but affected community composition in different ways. Nutrient depletion (removal of leaf litter) had a pronounced effect on AM fungal community composition, affecting nearly as many OTUs as phosphorus addition. The addition of nutrients in organic form (leaf litter) had little effect on any AM fungal parameter. Soil AM fungal communities responded more strongly to changes in nutrient availability than communities in roots. This suggests that the 'dual niches' of AM fungi in soil versus roots are structured to different degrees by abiotic environmental filters, and biotic filters imposed by the plant host. Our findings indicate that AM fungal communities are fine-tuned to nutrient regimes, and support future studies aiming to link AM fungal community dynamics with ecosystem function.

Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium

Research on mutualism seeks to explain how cooperation can be maintained when uncooperative mutants co-occur with cooperative kin. Gains and losses of the gene modules required for cooperation punctuate symbiont phylogenies and drive lifestyle transitions between cooperative symbionts and uncooperative free-living lineages over evolutionary time. Yet whether uncooperative symbionts commonly evolve from within cooperative symbiont populations or from within distantly related lineages with antagonistic or free-living lifestyles (i.e., third-party mutualism exploiters or parasites), remains controversial. We use genomic data to show that genotypes that differ in the presence or absence of large islands of symbiosis genes are common within a single wild recombining population of Mesorhizobium symbionts isolated from host tissues and are an important source of standing heritable variation in cooperation in this population. In a focal population of Mesorhizobium, uncooperative variants that lack a symbiosis island segregate at 16% frequency in nodules, and genome size and symbiosis gene number are positively correlated with cooperation. This finding contrasts with the genomic architecture of variation in cooperation in other symbiont populations isolated from host tissues in which the islands of genes underlying cooperation are ubiquitous and variation in cooperation is primarily driven by allelic substitution and individual gene gain and loss events. Our study demonstrates that uncooperative mutants within mutualist populations can comprise a significant component of genetic variation in nature, providing biological rationale for models and experiments that seek to explain the maintenance of mutualism in the face of non-cooperators.