Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro‐organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function . Trait‐based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and ‐omics‐based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun^Fun). Fun^Fun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait‐based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.     

Fungal evolution: major ecological adaptations and evolutionary transitions

Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative‐genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome‐enabled inferences to envision plausible narratives and scenarios for important transitions.     

Revisiting the Holy Grail: using plant functional traits to understand ecological processes

One of ecology's grand challenges is developing general rules to explain and predict highly complex systems. Understanding and predicting ecological processes from species' traits has been considered a ‘Holy Grail’ in ecology. Plant functional traits are increasingly being used to develop mechanistic models that can predict how ecological communities will respond to abiotic and biotic perturbations and how species will affect ecosystem function and services in a rapidly changing world; however, significant challenges remain. In this review, we highlight recent work and outstanding questions in three areas: (i) selecting relevant traits; (ii) describing intraspecific trait variation and incorporating this variation into models; and (iii) scaling trait data to community‐ and ecosystem‐level processes. Over the past decade, there have been significant advances in the characterization of plant strategies based on traits and trait relationships, and the integration of traits into multivariate indices and models of community and ecosystem function. However, the utility of trait‐based approaches in ecology will benefit from efforts that demonstrate how these traits and indices influence organismal, community, and ecosystem processes across vegetation types, which may be achieved through meta‐analysis and enhancement of trait databases. Additionally, intraspecific trait variation and species interactions need to be incorporated into predictive models using tools such as Bayesian hierarchical modelling. Finally, existing models linking traits to community and ecosystem processes need to be empirically tested for their applicability to be realized.     

High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples

The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.     

The assembly of tropical tree communities – the advances and shortcomings of phylogenetic and functional trait analyses

Tropical tree communities present one of the most challenging systems for studying the processes underlying community assembly. Most community assembly hypotheses consider the relative importance of the ecological similarity of co‐occurring species. Quantifying this similarity is a daunting and potentially impossible task in species‐rich assemblages. During the past decade tropical tree ecologists have increasingly utilized phylogenetic trees and functional traits to estimate the ecological similarity of species in order to test mechanistic community assembly hypotheses. A large amount of work has resulted with many important advances having been made along the way. That said, there are still many outstanding challenges facing those utilizing phylogenetic and functional trait approaches to study community assembly. Here I review the conceptual background, major advances and major remaining challenges in phylogenetic‐ and trait‐based approaches to community ecology with a specific focus on tropical trees. I argue that both approaches tremendously improve our understanding of tropical tree community ecology, but neither approach has fully reached its potential thus far.     

Strong coupling of plant and fungal community structure across western Amazonian rainforests

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant–fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.     

Neighboring trees regulate the root‐associated pathogenic fungi on the host plant in a subtropical forest

Root‐associated fungi and host‐specific pathogens are major determinants of species coexistence in forests. Phylogenetically related neighboring trees can strongly affect the fungal community structure of the host plant, which, in turn, will affect the ecological processes. Unfortunately, our understanding of the factors influencing fungal community composition in forests is still limited. In particular, investigation of the relationship between the phytopathogenic fungal community and neighboring trees is incomplete. In the current study, we tested the host specificity of members of the root‐associated fungal community collected from seven tree species and determined the influence of neighboring trees and habitat variation on the composition of the phytopathogenic fungal community of the focal plant in a subtropical evergreen forest. Using high‐throughput sequencing data with respect to the internal transcribed spacer (ITS) region, we characterized the community composition of the root‐associated fungi and found significant differences with respect to fungal groups among the seven tree species. The density of conspecific neighboring trees had a significantly positive influence on the relative abundance of phytopathogens, especially host‐specific pathogens, while the heterospecific neighbor density had a significant negative impact on the species richness of host‐specific pathogens, as well as phytopathogens. Our work provides evidence that the root‐associated phytopathogenic fungi of a host plant depend greatly on the tree neighbors of the host plant.     

动物个性研究进展

"个性"是指不同时空条件下动物种群个体间行为的稳定差异。大量的理论和实验性研究表明,个性差异在动物界普遍存在,其是种群多度和分布、物种共存及群落构建的重要驱动因子。介绍了动物个性的概念、分类及衡量指标,将前人测量个性类型的方法加以总结;随后介绍了动物个性的生态学意义,尤其是个性对动物生活史策略、种群分布与多度、群落结构和动态、生态系统功能和过程以及疾病与信息传播等的影响。在此基础上,进一步分析了在人类活动增加等全球变化背景下,动物个性如何调控动物个体行为、种群和群落动态对这些环境变化的响应。阐述了动物个性的形成与维持机制,并对未来的研究方向进行了展望。     

Endophytic fungi from Peruvian highland and lowland habitats form distinctive and host plant-specific assemblages

Biodiversity and biogeography of leaf-inhabiting endophytic fungi have not been resolved yet. This is because host specificity, life cycles and species concepts, in this heterogeneous ecological guild of plant-associated microfungi, are far from being understood. Even though it is known that culture-based collection techniques are often biased, this has been the method of choice for studying fungal endophytes. Isolation of fungal endophytes only through culture-based methods could potentially mask slow growing species as well as species with low prevalence, preventing the capture of the communities’ real diversity and composition. This bias can be partially resolved by the use of cultivation-independent approaches such as direct sequencing of plant tissue by next generation techniques. Irrespective of the chosen sampling method, an efficient analysis of community ecology is urgently needed in order to evaluate the driving forces acting on fungal endophytic communities. In the present study, endophytic ascomyceteous fungi from three different plant genera (Vasconcellea microcarpa, Tillandsia spp., and Hevea brasiliensis) distributed in Peru, were isolated through culture-based sampling techniques and sequenced for their ITS rDNA region. These data sets were used to assess host preferences and biogeographic patterns of endophytic assemblages. This study showed that the effect of the host’s genetic background (identity) has a significant effect on the composition of the fungal endophytic community. In other words, the composition of the fungal endophytic community was significantly related to their host’s taxonomic identity. However, this was not true for all endophytic groups, since we found some endophytic groups (e.g. Xylariales and Pleosporales) occurring in more than one host genus. Findings from this study promote the formulation of hypotheses related to the effect of altitudinal changes on the endophytic communities along the Eastern Andean slopes. These hypotheses and perspectives for fungal biodiversity research and conservation in Peru are addressed and discussed.     

Plant identity strongly structures the root-associated fungal community in a diverse subtropical forest

Revealing the relationship between plants and root-associated fungi is very important in understanding diversity maintenance and community assembly in ecosystems. However, the community assembly of root-associated fungi of focal plant species along a subtropical plant species diversity gradient is less documented. Here, we examined root-associated fungal communities associated with five ectomycorrhizal (EM) plant species (Betula luminifera, Castanea henryi, Castanopsis fargesii, C. sclerophylla, and Quercus serrate) in a Chinese subtropical woody plant species diversity (1, 2, 4, 8, 16 and 24 species) experiment, using paired-end Illumina MiSeq sequencing of the ITS2 region. In total, we detected 1933 root-associated fungal operational taxonomic units (OTUs) at a 97% sequence similarity level. Plant identity had a significant effect on total and saprotrophic fungal OTU richness, but plant species diversity level had a significant effect on saprotrophic and pathogenic fungal OTU richness. The community composition of total, saprotrophic and EM fungi was structured by plant identity and plant species diversity level. However, the community composition of pathogenic fungi was only shaped by plant identity. This study highlights that plant identity has a stronger effect on the root-associated fungal community than plant species diversity level in a diverse subtropical forest ecosystem.     

Foraging speed and precision of arbuscular mycorrhizal fungi under field conditions: An experimental approach

To better understand the ecology of arbuscular mycorrhizal (AM) symbiosis, we need to measure functional traits of individual fungal virtual taxa under field conditions. The efficiency of AM fungi in locating nutrient‐rich patches in soil space is one of their central traits in this symbiotic relationship. We used plots of a long‐term field experiment in grassland with manipulated functional group composition of host plant community to establish ingrowth patches with substrate free of roots and fungi and with varying nutrient availability. Comparison of the original AM fungal community before patch creation with that present 9 weeks after patch establishment enabled us to estimate relative hyphal foraging speed for 41 fungal taxa, and a comparison of the fungal community in neighbouring patches differing in nutrient availability provided estimates of hyphal foraging precision for 22 taxa. Members of two dominant fungal families, Glomeraceae and Claroideoglomeraceae, differed in their foraging speed and precision. Glomeraceae taxa responded more slowly, but with a higher focus on enriched patches. We further demonstrated the usefulness of the obtained fungal functional traits by testing the differences between grass and dicotyledonous plant hosts using a data set obtained in another experiment at the same plots. Grass species hosted AM fungal communities with higher foraging speed, but lower foraging precision than the dicotyledonous species. Our study results support the use of field experiments for measuring comparative characteristics of AM fungi, which are highly elusive (or misrepresented) under controlled conditions.     

MycoRed: Betalain pigments enable in vivo real-time visualisation of arbuscular mycorrhizal colonisation

Arbuscular mycorrhiza (AM) are mutualistic interactions formed between soil fungi and plant roots. AM symbiosis is a fundamental and widespread trait in plants with the potential to sustainably enhance future crop yields. However, improving AM fungal association in crop species requires a fundamental understanding of host colonisation dynamics across varying agronomic and ecological contexts. To this end, we demonstrate the use of betalain pigments as in vivo visual markers for the occurrence and distribution of AM fungal colonisation by Rhizophagus irregularis in Medicago truncatula and Nicotiana benthamiana roots. Using established and novel AM-responsive promoters, we assembled multigene reporter constructs that enable the AM-controlled expression of the core betalain synthesis genes. We show that betalain colouration is specifically induced in root tissues and cells where fungal colonisation has occurred. In a rhizotron setup, we also demonstrate that betalain staining allows for the noninvasive tracing of fungal colonisation along the root system over time. We present MycoRed, a useful innovative method that will expand and complement currently used fungal visualisation techniques to advance knowledge in the field of AM symbiosis.

Arbuscular mycorrhiza are mutualistic interactions formed between soil fungi and plant roots. This study presents the MycoRed system, which uses red plant pigments derived from beetroot to reveal how fungi establish symbiosis with living legume and wild tobacco roots.     

Trait‐based partner selection drives mycorrhizal network assembly

Plants and their microbial symbionts are often found to interact non‐randomly in nature, but we have yet to understand the mechanisms responsible for such preferential species associations. Theory predicts that host plants should select symbiotic partners bearing traits complementary to their own, as this should favor cooperation and evolutionary stability of mutualisms. Here, we present the first field‐based empirical test for this hypothesis using arbuscular mycorrhizas (AM), the oldest and most widespread plant symbiosis. Preferential associations occurring within a local plant–AM fungal community could not be predicted by the spatial distributions of interacting partners, nor by gradients in soil properties. Rather, plants with similar traits preferentially hosted similar AM fungi and, likewise, phylogenetically related AM fungi (assumed to have similar functional traits) interacted with similar plants. Our results suggest that trait‐based partner selection may have been a strong force in maintaining plant–AM fungal symbioses since the evolution of land plants.     

Leaf traits and performance vary with plant age and water availability in Artemisia californica

Background and AimsLeaf functional traits are strongly tied to growth strategies and ecological processes across species, but few efforts have linked intraspecific trait variation to performance across ontogenetic and environmental gradients. Plants are believed to shift towards more resource-conservative traits in stressful environments and as they age. However, uncertainty as to how intraspecific trait variation aligns with plant age and performance in the context of environmental variation may limit our ability to use traits to infer ecological processes at larger scales.MethodsWe measured leaf physiological and morphological traits, canopy volume and flowering effort for Artemisia californica (California sagebrush), a dominant shrub species in the coastal sage scrub community, under conditions of 50, 100 and 150 % ambient precipitation for 3 years.Key ResultsPlant age was a stronger driver of variation in traits and performance than water availability. Older plants demonstrated trait values consistent with a more conservative resource-use strategy, and trait values were less sensitive to drought. Several trait correlations were consistent across years and treatments; for example, plants with high photosynthetic rates tended to have high stomatal conductance, leaf nitrogen concentration and light-use efficiency. However, the trade-off between leaf construction and leaf nitrogen evident in older plants was absent for first-year plants. While few traits correlated with plant growth and flowering effort, we observed a positive correlation between leaf mass per area and performance in some groups of older plants.ConclusionsOverall, our results suggest that trait sensitivity to the environment is most visible during earlier stages of development, after which intraspecific trait variation and relationships may stabilize. While plant age plays a major role in intraspecific trait variation and sensitivity (and thus trait-based inferences), the direct influence of environment on growth and fecundity is just as critical to predicting plant performance in a changing environment.     

Both traits and phylogenetic history influence community structure in snakes over steep environmental gradients

Assemblages of closely related organisms are generated on axes of deep time diversification, biogeographic processes related to dispersal and habitat filtering, and competition. Using models that account for phylogeny, ecology, and traits, we examine how the interaction among biogeography, habitat filtering, and trait convergence influences community assemblage in Nearctic snakes. With 122 community surveys, environmental niche, trait data including size, diet, parity and habitat preference, and a nearly complete phylogeny of snakes from the United States, we ask 1) do phylogenetic species variability (PSV) and traits change in predictable and correlated ways given ecology and geographic distance, 2) are the measured traits variable within and across communities and how is this related to PSV at local scales, and 3) is there evidence of habitat filtering or trait divergence? Following a general trend of western to eastern North American origin and dispersal of major groups, we similarly show a significant decrease in PSV in this direction but unexpectedly with stable trait variance, showing that traits and phylogenetic variability are disconnected at the community level. We also demonstrate that trait variability and not PSV dominates local communities. Finally, regardless of phylogeny, we show that certain traits, such as reproductive mode (parity) frequency, change within communities in response to steep ecological gradients.     

The interactions between plant life form and fungal traits of arbuscular mycorrhizal fungi determine the symbiotic community

Arbuscular mycorrhizal (AM) fungi have traditionally been considered generalist symbionts. However, an increasing number of studies are pointing out the selectivity potential of plant hosts. Plant life form, determined by plant life history traits, seems to drive the AM fungal community composition. The AM fungi also exhibit a wide diversity of functional traits known to be responsible for their distribution in natural ecosystems. However, little is known about the role of plant and fungal traits driving the resultant symbiotic assemblages. With the aim of testing the feedback relationship between plant and fungal traits on the resulting AM fungal community, we inoculated three different plant life forms, i.e. annual herbs, perennial herbs and perennial semi-woody plants, with AM fungal communities sampled in different seasons. We hypothesized that the annual climate variation will induce changes in the mean traits of the AM fungal communities present in the soil throughout the year. Furthermore, the association of plants with different life forms with AM fungi with contrasting life history traits will show certain preferences according to reciprocal traits of the plants and fungi. We found changes in the AM fungal community throughout the year, which were differentially disrupted by disturbance and altered by plant growth form and plant biomass. Both plant and fungal traits clearly contributed to the resultant AM fungal communities. The revealed process can have implications for the functioning of ecosystems since changes in dominant plant life forms or climatic variables could influence the traits of AM fungal communities in soil and hence ecosystem processes.     

The role of in vitro cultivation on symbiotic trait and function variation in a single species of arbuscular mycorrhizal fungus

In vitro propagation of AM fungi using transformed root cultures (TRC) is commonly used to obtain pure AM fungal propagules for use in research and industry. Early observations indicate that such an artificial environment can alter traits and function of AM fungi over time. We hypothesized that increased in vitro cultivation may promote ruderal strategies in fungi by enhancing propagule production and reducing mutualistic quality. To examine the effect of in vitro cultivation on the trait and function of AM fungi, we inoculated plants with 11 Rhizoglomus irregulare isolates which fell along a cultivation gradient spanning 80 generations. We harvested plants at 10, 20 and 30 d post inoculation to observe differences in fungal and plant traits post infection. In vitro cultivation led to increased spore production but reduced plant shoot phosphorus. Our results indicate that in vitro propagation may indirectly select for traits that affect symbiotic quality.     

Sharing of Diverse Mycorrhizal and Root-Endophytic Fungi among Plant Species in an Oak-Dominated Cool–Temperate Forest

Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through belowground plant–fungal interactions, dominant plants can benefit by interacting with host-specific mutualistic fungi and proliferate in a community based on positive plant–mutualistic fungal feedback. On the other hand, subordinate plant species may persist in the community by sharing other sets (functional groups) of fungal symbionts with each other. Therefore, revealing how diverse clades of root-associated fungi are differentially hosted by dominant and subordinate plant species is essential for understanding plant community structure and dynamics. Based on 454-pyrosequencing, we determined the community composition of root-associated fungi on 36 co-occurring plant species in an oak-dominated forest in northern Japan and statistically evaluated the host preference phenotypes of diverse mycorrhizal and root-endophytic fungi. An analysis of 278 fungal taxa indicated that an ectomycorrhizal basidiomycete fungus in the genus Lactarius and a possibly endophytic ascomycete fungus in the order Helotiales significantly favored the dominant oak (Quercus) species. In contrast, arbuscular mycorrhizal fungi were generally shared among subordinate plant species. Although fungi with host preferences contributed to the compartmentalization of belowground plant–fungal associations, diverse clades of ectomycorrhizal fungi and possible root endophytes were associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant-ectomycorrhizal and subordinate plant species can host different subsets of root-associated fungi, and diverse clades of generalist fungi can counterbalance the compartmentalization of plant–fungal associations. Such insights into the overall structure of belowground plant–fungal associations will help us understand the mechanisms that facilitate the coexistence of plant species in natural communities.