Spatial characterization of arbuscular mycorrhizal fungal molecular diversity at the submetre scale in a temperate grassland

Impact of agricultural systems on arbuscular mycorrhizal fungi community composition in robusta coffee roots in the Democratic Republic of congo

Robusta coffee, grown by 25 million farmers across more than 50 countries, plays an important role in smallholder farmers' livelihoods and the economies of many low-income countries. Coffee establishes a mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF); however, the impact of agricultural practices and soil characteristics on AMF diversity and community composition is not well understood. To address this, we characterised the AMF community composition of robusta coffee in part of its region of origin, the Democratic Republic of Congo. AMF diversity and community composition were compared between coffee monoculture, agroforestry systems and wild robusta in its native rainforest habitat. Using Illumina sequencing on 304 root samples, we identified 307 AMF operational taxonomic units (OTUs), dominated by the genera Glomus and Acaulospora. OTU richness did not vary across the three studied systems, yet large differences in community composition were found. Many unique OTUs were only observed in the coffee in the rainforest. In general, lower available soil phosphorus (P) and lower soil bulk density increased AMF diversity, yet higher available soil P and pH increased AMF diversity in the wild forest coffee. Shifts in AMF community composition across coffee systems were driven by canopy closure, soil pH, available soil P and soil bulk density. Our study is the first to characterise mycorrhizal communities in wild robusta coffee in its region of origin and shows that even low-input agricultural practices result in major AMF community shifts as compared to a natural baseline.

Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition

Ectomycorrhizal and saprotrophic fungi respond differently to changing edaphic conditions caused by atmospheric deposition. Within each guild, responses can vary significantly, reflecting the diversity of species and their specific adaptations to environmental changes. Metal contaminants are often deposited onto earth's surface through atmospheric deposition, yet few studies have assessed the relationship between soil metal contamination and fungal communities. The goal of this study was to understand how soil metal contamination and other edaphic factors vary across the spruce-fir ecosystem in the Southern Appalachians and influence fungal diversity and function. Here, we characterize soil fungal communities using high-throughput sequencing of the ITS2 gene region and found that higher soil lead (Pb) concentrations were associated with lower fungal diversity. Ectomycorrhizal fungi were less diverse (specifically hydrophilic ectomycorrhizal functional types) at plots with elevated soil Pb concentrations, while saprotrophic fungi were less diverse at plots with elevated soil carbon:nitrogen ratios. Fungal community composition was significantly influenced by pH, Pb, and spatial factors. This study identifies important relationships between fungal diversity and soil Pb concentrations and indicates variable responses of genera within well-defined ecological guilds. Our work highlights the need to characterize poorly understood taxonomic groups of fungi and their function prior to further environmental degradation.

Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach

Backgorund

The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.

Methods

In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.

Results

Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.

Discussion

This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.

Response of Sagebrush Steppe Grass Species to AMF Inoculum Sources and Biochar

The sagebrush steppe has presented increasing levels of degradation. The addition of arbuscular mycorrhizal fungi (AMF) and biochar have been suggested to restore ecosystems. However, little is known about their effects on sagebrush steppe plants. We tested three sources of AMF inoculum: soil from a disturbed site (Inoculum A), soil from an undisturbed site (Inoculum B), and commercial inoculum (Inoculum C), all with and without biochar, to test if they could mediate growth of Pseudoroegneria spicata (native perennial), Taeniatherum caput-medusae (early seral; exotic annual) and Ventenata dubia (early seral; exotic annual) under greenhouse conditions. We measured AMF colonization and biomass. We hypothesized that the plant species would be differently affected by the inoculum types. The colonization of T. caput-medusae and V. dubia was greatest when inoculated with Inoculum A (38.8% and 19.6%). In contrast, the colonization of P. spicata was greatest with Inoculum B and Inoculum C (32.1% and 32.2). Biochar decreased biomass production but increased colonization with Inoculum A for P. spicata and V. dubia and with Inoculum C for T. caput-medusae. This study reveals the response of early and late seral sagebrush steppe grass species to contrasting sources of AMF and suggests that late seral plant species respond better to late seral inocula.

The temporal and spatial dimensions of plant-soil feedbacks

Feedbacks between plants and soil microbes form a keystone to terrestrial community and ecosystem dynamics. Recent advances in dissecting the spatial and temporal dynamics of plant-soil feedbacks (PSFs) have challenged longstanding assumptions of spatially well-mixed microbial communities and exceedingly fast microbial assembly dynamics relative to plant lifespans. Instead, PSFs emerge from interactions that are inherently mismatched in spatial and temporal scales, and explicitly considering these spatial and temporal dynamics is crucial to understanding the contribution of PSFs to foundational ecological patterns. I propose a synthetic spatiotemporal framework for future research that pairs experimental and modeling approaches grounded in mechanism to improve predictability and generalizability of PSFs.

Farm-scale differentiation of active microbial colonizers

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.

Epiphytic fungal communities vary by substrate type and at sub-meter spatial scales

Fungal species have numerous important environmental functions. Where these functions occur will depend on how fungi are spatially distributed, but spatial structures of fungal communities are largely unknown, especially in understudied hyperdiverse tropical tree canopy systems. We explore fungal communities in a Costa Rican tropical rainforest canopy, with a focus on local-scale spatial structure and substrate specificity of fungi. Samples of ~1 cm³ were collected from 135 points along 5 adjacent tree branches, with inter-sample distances from 1 to 800 cm, and dissected into four substrates: outer host tree bark, inner bark, dead bryophytes, and living bryophytes. We sequenced the ITS2 region to characterize total fungal communities. Fungal community composition and diversity varied among substrate types, even when multiple substrates were in direct contact. Fungi were most diverse in living bryophytes, with 39% of all OTUs found exclusively in this substrate, and the least diverse in inner bark. Fungal communities had significant positive spatial autocorrelation and distance decay of similarity only at distances less than one meter. Similarity among samples declines by half in less than ten cm, and even at these short distances, similarities are low with few OTUs shared among samples. These results indicate that community turnover is high and occurs at very small spatial scales, with any two locations sharing very few fungi in common. High heterogeneity of fungal communities in space and among substrates may have implications for the distributions, population dynamics, and diversity of other tree canopy organisms, including epiphytic plants.

Temporal turnover of the soil microbiome composition is guild-specific

Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.

Three decades post-reforestation has not led to the reassembly of arbuscular mycorrhizal fungal communities associated with remnant primary forests

The negative effects of deforestation can potentially be ameliorated through ecological restoration. However, reforestation alone may not reassemble the same ecological communities or functions as primary forests. In part, this failure may be owed to forest ecosystems inherently involving complex interactions among guilds of organisms. Plants, which structure forest food webs, rely on intimate associations with symbiotic microbes such as root-inhabiting mycorrhizal fungi. Here, we leverage a large-scale reforestation project on Hawai'i Island underway for over three decades to assess whether arbuscular mycorrhizal (AM) fungal communities have concurrently been restored. The reference ecosystem for this restoration project is a remnant montane native Hawaiian forest that provides critical habitat for endangered birds. We sampled soils from 12 plots within remnant and restored forest patches and characterized AM fungal communities using high-throughput amplicon sequencing. While some AM fungal community metrics were comparable between remnant and restored forest (e.g. species richness), other key characteristics were not. Specifically, community membership and the identity of AM fungal keystone species differed between the two habitat types, as well as the primary environmental factors influencing community composition. Remnant forest AM fungal communities were strongly associated with soil chemical properties, especially pH, while restored forest communities were influenced by the spatial proximity to remnant forests. We posit that combined, these differences in soil AM fungal communities could be negatively affecting the recruitment of native plant hosts and that future restoration efforts should consider plant-microbe interactions as an important facet of forest health.

Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean

Background

Understanding the role of communities of arbuscular mycorrhizal fungi (AMF) in agricultural systems is imperative for enhancing crop production. The key variables influencing change in AMF communities are the type of cover crop species or the type of subsequent host crop species. However, how maize and soybean performance is related to the diversity of AMF communities in cover cropping systems remains unclear. We therefore investigated which cover cropping or host identity is the most important factor in shaping AMF community structure in subsequent crop roots using an Illumina Miseq platform amplicon sequencing.

Methods

In this study, we established three cover crop systems (Italian ryegrass, hairy vetch, and brown mustard) or bare fallow prior to planting maize and soybean as cash crops. After cover cropping, we divided the cover crop experimental plots into two subsequent crop plots (maize and soybean) to understand which cover cropping or host crop identity is an important factor for determining the AMF communities and diversity both in maize and soybeans.

Results

We found that most of the operational taxonomic units (OTUs) in root samples were common in both maize and soybean, and the proportion of common generalists in this experiment for maize and soybean roots was 79.5% according to the multinomial species classification method (CLAM test). The proportion of OTUs specifically detected in only maize and soybean was 9.6% and 10.8%, respectively. Additionally, the cover cropping noticeably altered the AMF community structure in the maize and soybean roots. However, the differentiation of AMF communities between maize and soybean was not significantly different.

Discussion

Our results suggest cover cropping prior to planting maize and soybean may be a strong factor for shaping AMF community structure in subsequent maize and soybean roots rather than two host crop identities. Additionally, we could not determine the suitable rotational combination for cover crops and subsequent maize and soybean crops to improve the diversity of the AMF communities in their roots. However, our findings may have implications for understanding suitable rotational combinations between cover crops and subsequent cash crops and further research should investigate in-depth the benefit of AMF on cash crop performances in cover crop rotational systems.

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb

Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.

Sympatric diploid and tetraploid cytotypes of Centaurea stoebe s.l. do not differ in arbuscular mycorrhizal communities and mycorrhizal growth response

PREMISE OF THE STUDY

Genome duplication is associated with multiple changes at different levels, including interactions with pollinators and herbivores. Yet little is known whether polyploidy may also shape belowground interactions.

METHODS

To elucidate potential ploidy-specific interactions with arbuscular mycorrhizal fungi (AMF), we compared mycorrhizal colonization and assembly of AMF communities in roots of diploid and tetraploid Centaurea stoebe s.l. (Asteraceae) co-occurring in a Central European population. In a follow-up greenhouse experiment, we tested inter-cytotype differences in mycorrhizal growth response by combining ploidy, substrate, and inoculation with native AMF in a full-factorial design.

KEY RESULTS

All sampled plants were highly colonized by AMF, with the Glomeraceae predominating. AMF-community composition revealed by 454-pyrosequencing reflected the spatial distribution of the hosts, but not their ploidy level or soil characteristics. In the greenhouse experiment, the tetraploids produced more shoot biomass than the diploids did when grown in a more fertile substrate, while no inter-cytotype differences were found in a less fertile substrate. AMF inoculation significantly reduced plant growth and improved P uptake, but its effects did not differ between the cytotypes.

CONCLUSIONS

The results do not support our hypotheses that the cytotype structure in a mixed-ploidy population of C. stoebe is mirrored in AMF-community composition and that ploidy-specific fungal communities contribute to cytotype co-existence. Causes and implications of the observed negative growth response to AMF are discussed.

Symbiosis Specificity of the Preceding Host Plant Can Dominate but Not Obliterate the Association Between Wheat and Its Arbuscular Mycorrhizal Fungal Partners

The symbiosis established between arbuscular mycorrhizal fungi (AMF) and roots of most land plants plays a key role in plant nutrient acquisition and alleviation of environmental stresses. Despite the ubiquity of the symbiosis, AMF and host species display significant specificity in their interactions. To clarify preferential associations between wheat (Triticum aestivum) and AMF, we characterized root AMF communities in the transition from two first host species, ryegrass (Lolium rigidum) and yellow-serradella (Ornithopus compressus), grown separately or together, to a second host (wheat), by sequencing the large subunit ribosomal DNA (LSU rDNA) gene. The response of AMF communities in wheat to prior soil disturbance – and consequently of the mycelial network [intact extraradical mycelium (ERM) vs. disrupted mycelium] established with either of the first hosts – was also investigated. Since the outcome of a specific host–symbiont interaction depends on the molecular responses of the host plant upon microbial colonization, we studied the expression of six key symbiosis-related genes in wheat roots. AMF communities on L. rigidum and O. compressus roots were clearly distinct. Within an undisturbed ERM, wheat AMF communities were similar to that of previous host, and O. compressus-wheat-AMF interactions supported a greater growth of wheat than L. rigidum-wheat-AMF interactions. This effect declined when ERM was disrupted, but generated a greater activation of symbiotic genes in wheat, indicating that plant symbiotic program depends on some extent on the colonizing symbiont propagule type. When a mixture of L. rigidum and O. compressus was planted, the wheat colonization pattern resembled that of O. compressus, although this was not reflected in a greater growth. These results show a lasting effect of previous hosts in shaping wheat AMF communities through an efficient use of the established ERM, although not completely obliterating host–symbiont specificity.

Linking the community structure of arbuscular mycorrhizal fungi and plants: a story of interdependence?

Arbuscular mycorrhizal fungi (AMF) are crucial to plants and vice versa, but little is known about the factors linking the community structure of the two groups. We investigated the association between AMF and the plant community structure in the nearest neighborhood of Festuca brevipila in a semiarid grassland with steep environmental gradients, using high-throughput sequencing of the Glomeromycotina (former Glomeromycota). We focused on the Passenger, Driver and Habitat hypotheses: (i) plant communities drive AMF (passenger); (ii) AMF communities drive the plants (driver); (iii) the environment shapes both communities causing covariation. The null hypothesis is that the two assemblages are independent and this study offers a spatially explicit novel test of it in the field at multiple, small scales. The AMF community consisted of 71 operational taxonomic units, the plant community of 47 species. Spatial distance and spatial variation in the environment were the main determinants of the AMF community. The structure of the plant community around the focal plant was a poor predictor of AMF communities, also in terms of phylogenetic community structure. Some evidence supports the passenger hypothesis, but the relative roles of the factors structuring the two groups clearly differed, leading to an apparent decoupling of the two assemblages at the relatively small scale of this study. Community phylogenetic structure in AMF suggests an important role of within-assemblage interactions.

Community assembly and coexistence in communities of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi are asexual, obligately symbiotic fungi with unique morphology and genomic structure, which occupy a dual niche, that is, the soil and the host root. Consequently, the direct adoption of models for community assembly developed for other organism groups is not evident. In this paper we adapted modern coexistence and assembly theory to arbuscular mycorrhizal fungi. We review research on the elements of community assembly and coexistence of arbuscular mycorrhizal fungi, highlighting recent studies using molecular methods. By addressing several points from the individual to the community level where the application of modern community ecology terms runs into problems when arbuscular mycorrhizal fungi are concerned, we aim to account for these special circumstances from a mycocentric point of view. We suggest that hierarchical spatial structure of arbuscular mycorrhizal fungal communities should be explicitly taken into account in future studies. The conceptual framework we develop here for arbuscular mycorrhizal fungi is also adaptable for other host-associated microbial communities.

Impact of an invasive nitrogen-fixing tree on arbuscular mycorrhizal fungi and the development of native species

Arbuscular mycorrhizal fungi (AMF) are obligate soil biotrophs that establish intimate relationships with 80 % of terrestrial plant families. Arbuscular mycorrhizal fungi obtain carbon from host plants and contribute to the acquisition of mineral nutrients, mainly phosphorus. The presence of invasive plants has been identified as a soil disturbance factor, often conditioning the structure and function of soil microorganisms. Despite the investigation of many aspects related to the invasion ofAcacia dealbata, the effect produced on the structure of AMF communities has never been assessed. We hypothesize thatA. dealbatamodifies the structure of AMF community, influencing the establishment and growth of plants that are dependent on these mutualisms. To validate our hypothesis, we carried out denaturing gradient gel electrophoresis (DGGE) analysis and also grew plants ofPlantago lanceolatain pots using roots of native shrublands or fromA. dealbata, as inoculum of AMF. Cluster analyses from DGGE indicated an alteration in the structure of AMF communities in invaded soils. After 15 weeks, we found that plants grown in pots containing native roots presented higher stem and root growth and also produced higher biomass in comparison with plants grown withA. dealbatainoculum. Furthermore, plants that presented the highest biomass and growth exhibited the maximum mycorrhizal colonization and phosphorus content. Moreover, fluorescence measurements indicated that plants grown withA. dealbatainoculum even presented higher photosynthetic damage. Our results indicate that the presence of the invaderA. dealbatamodify the composition of the arbuscular fungal community, conditioning the establishment of native plants.

Molecular diversity and distribution of indigenous arbuscular mycorrhizal communities colonizing roots of two different winter cover crops in response to their root proliferation

A clear understanding of how crop root proliferation affects the distribution of the spore abundance of arbuscular mycorrhizal fungi (AMF) and the composition of AMF communities in agricultural fields is imperative to identify the potential roles of AMF in winter cover crop rotational systems. Toward this goal, we conducted a field trial using wheat (Triticum aestivum L.) or red clover (Trifolium pratense L.) grown during the winter season. We conducted a molecular analysis to compare the diversity and distribution of AMF communities in roots and spore abundance in soil cropped with wheat and red clover. The AMF spore abundance, AMF root colonization, and abundance of root length were investigated at three different distances from winter crops (0 cm, 7.5 cm, and 15 cm), and differences in these variables were found between the two crops. The distribution of specific AMF communities and variables responded to the two winter cover crops. The majority of Glomerales phylotypes were common to the roots of both winter cover crops, but Gigaspora phylotypes in Gigasporales were found only in red clover roots. These results also demonstrated that the diversity of the AMF colonizing the roots did not significantly change with the three distances from the crop within each rotation but was strongly influenced by the host crop identity. The distribution of specific AMF phylotypes responded to the presence of wheat and red clover roots, indicating that the host crop identity was much more important than the proliferation of crop roots in determining the diversity of the AMF communities.

Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.

Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes

Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant roots. Plants were harvested 60 days after sowing, and data were collected on plant growth and per cent AMF colonization of roots. AMF community composition in roots was assessed using 454 pyrosequencing of the 28S rRNA genes, and spatial variation in mycorrhizal communities within replicated experimental field plots was examined. Growth responses, per cent AMF colonization of roots and AMF community diversity in roots did not differ between Bt and non-Bt maize, but root and shoot biomass and per cent colonization by arbuscules varied by maize cultivar. Plot identity had the most significant effect on plant growth, AMF colonization and AMF community composition in roots, indicating spatial heterogeneity in the field. Mycorrhizal fungal communities in maize roots were autocorrelated within approximately 1 m, but at greater distances, AMF community composition of roots differed between plants. Our findings indicate that spatial variation and heterogeneity in the field has a greater effect on the structure of AMF communities than host plant cultivar or modification by Bt toxin genes.

The composition of arbuscular mycorrhizal fungal communities differs among the roots, spores and extraradical mycelia associated with five Mediterranean plant species

Arbuscular mycorrhizal fungi (AMF) are essential constituents of most terrestrial ecosystems. AMF species differ in terms of propagation strategies and the major propagules they form. This study compared the AMF community composition of different propagule fractions - colonized roots, spores and extraradical mycelium (ERM) - associated with five Mediterranean plant species in Sierra de Baza Natural Park (Granada, Spain). AMF were identified using 454 pyrosequencing of the SSU rRNA gene. A total of 96 AMF phylogroups [virtual taxa (VT)] were detected in the study site, including 31 novel VT. After per-sample sequencing depth standardization, 71 VT were recorded from plant roots, and 47 from each of the spore and ERM fractions. AMF communities differed significantly among the propagule fractions, and the root-colonizing fraction differed among host plant species. Indicator VT were detected for the root (13 Glomus VT), spore (Paraglomus VT281, VT336, Pacispora VT284) and ERM (Diversispora VT62) fractions. This study provides detailed evidence from a natural system that AMF taxa are differentially allocated among soil mycelium, soil spores and colonized root propagules. This has important implications for interpreting AMF diversity surveys and designing applications of AMF in vegetation restoration.

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi

Knowledge of spatiotemporal patterns in species distribution is fundamental to understanding the ecological and evolutionary processes shaping communities. The emergence of DNA-based tools has expanded the geographic and taxonomic scope of studies examining spatial and temporal distribution of mycorrhizal fungi. However, the nature of spatiotemporal patterns documented and subsequent interpretation of ecological processes can vary significantly from study to study. In order to look for general patterns we synthesize the available data across different sampling scales and mycorrhizal types. The results of this analysis shed light on the relative importance of space, time and vertical soil structure on community variability across different mycorrhizal types. Although we found no significant trend in spatiotemporal variation amongmycorrhizal types, the vertical community variation was distinctly greater than the spatial and temporal variability in mycorrhizal fungal communities. Both spatial and temporal variability of communities was greater in topsoil compared with lower horizons, suggesting that greater environmental heterogeneity drives community variation on a fine scale. This further emphasizes the importance of both niche differentiation and environmental filtering in maintaining diverse fungal communities.

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

The common occurrence of mutualistic interactions between plants and root symbionts is problematic. As the delivery of benefit to hosts involves costs to symbionts, symbionts that provide reduced benefit to their host are expected to increase in frequency. Plants have been shown to allocate preferentially to the most efficient symbiont and this preferential allocation may stabilize the mutualism. I construct a general model of the interactive feedbacks of host preferential allocation and the dynamics of root symbiont populations to evaluate the stability of nutritional mutualisms. Preferential allocation can promote the evolution of mutualism even when the cost to the symbiont is very large. Moreover, the physiological plasticity of preferential allocation likely leads to coexistence of beneficial and nonbeneficial symbionts. For arbuscular mycorrhizal fungi, which facilitate plant uptake of phosphorus (P), the model predicts greater P transfer from these fungi per unit carbon invested with decreasing concentrations of soil P and with increasing concentrations of atmospheric CO2 , patterns that have been observed in laboratory and field studies. This framework connects physiological plasticity in plant allocation to population processes that determine mutualism stability and, as such, represents a significant step in understanding the stability and environmental patterns in mutualism.

Spatial structuring of arbuscular mycorrhizal communities in benchmark and modified temperate eucalypt woodlands

Arbuscular mycorrhizal fungi (AMF) are crucial to the functioning of the plant-soil system, but little is known about the spatial structuring of AMF communities across landscapes modified by agriculture. AMF community composition was characterized across four sites in the highly cleared south-western Australian wheatbelt that were originally dominated by forb-rich eucalypt woodlands. Environmentally induced spatial structuring in AMF composition was examined at four scales: the regional scale associated with location, the site scale associated with past management (benchmark woodlands with no agricultural management history, livestock grazing, recent revegetation), the patch scale associated with trees and canopy gaps, and the fine scale associated with the herbaceous plant species beneath which soils were sourced. Field-collected soils were cultured in trap pots; then, AMF composition was determined by identifying spores and through ITS1 sequencing. Structuring was strongest at site scales, where composition was strongly related to prior management and associated changes in soil phosphorus. The two fields were dominated by the genera Funneliformis and Paraglomus, with little convergence back to woodland composition after revegetation. The two benchmark woodlands were characterized by Ambispora gerdemannii and taxa from Gigasporaceae. Their AMF communities were strongly structured at patch scales associated with trees and gaps, in turn most strongly related to soil N. By contrast, there were few patterns at fine scales related to different herbaceous plant species, or at regional scales associated with the 175 km distance between benchmark woodlands. Important areas for future investigation are to identify the circumstances in which recolonization by woodland AMF may be limited by fungal propagule availability, reduced plant diversity and/or altered chemistry in agricultural soils.

Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales

Next-generation sequencing technologies with markers covering the full Glomeromycota phylum were used to uncover phylogenetic community structure of arbuscular mycorrhizal fungi (AMF) associated with Festuca brevipila. The study system was a semi-arid grassland with high plant diversity and a steep environmental gradient in pH, C, N, P and soil water content. The AMF community in roots and rhizosphere soil were analyzed separately and consisted of 74 distinct operational taxonomic units (OTUs) in total. Community-level variance partitioning showed that the role of environmental factors in determining AM species composition was marginal when controlling for spatial autocorrelation at multiple scales. Instead, phylogenetic distance and spatial distance were major correlates of AMF communities: OTUs that were more closely related (and which therefore may have similar traits) were more likely to co-occur. This pattern was insensitive to phylogenetic sampling breadth. Given the minor effects of the environment, we propose that at small scales closely related AMF positively associate through biotic factors such as plant-AMF filtering and interactions within the soil biota.

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.

Contrasting the community structure of arbuscular mycorrhizal fungi from hydrocarbon-contaminated and uncontaminated soils following willow (Salix spp. L.) planting

Phytoremediation is a potentially inexpensive alternative to chemical treatment of hydrocarbon-contaminated soils, but its success depends heavily on identifying factors that govern the success of root-associated microorganisms involved in hydrocarbon degradation and plant growth stimulation. Arbuscular mycorrhizal fungi (AMF) form symbioses with many terrestrial plants, and are known to stimulate plant growth, although both species identity and the environment influence this relationship. Although AMF are suspected to play a role in plant adaptation to hydrocarbon contamination, their distribution in hydrocarbon-contaminated soils is not well known. In this study, we examined how AMF communities were structured within the rhizosphere of 11 introduced willow cultivars as well as unplanted controls across uncontaminated and hydrocarbon-contaminated soils at the site of a former petrochemical plant. We obtained 69 282 AMF-specific 18S rDNA sequences using 454-pyrosequencing, representing 27 OTUs. Contaminant concentration was the major influence on AMF community structure, with different AMF families dominating at each contaminant level. The most abundant operational taxonomic unit in each sample represented a large proportion of the total community, and this proportion was positively associated with increasing contamination, and seemingly, by planting as well. The most contaminated soils were dominated by three phylotypes closely related to Rhizophagus irregularis, while these OTUs represented only a small proportion of sequences in uncontaminated and moderately contaminated soils. These results suggest that in situ inoculation of AMF strains could be an important component of phytoremediation treatments, but that strains should be selected from the narrow group that is both adapted to contaminant toxicity and able to compete with indigenous AMF species.

Soil nutrient content influences the abundance of soil microbes but not plant biomass at the small-scale

Small-scale heterogeneity of abiotic and biotic factors is expected to play a crucial role in species coexistence. It is known that plants are able to concentrate their root biomass into areas with high nutrient content and also acquire nutrients via symbiotic microorganisms such as arbuscular mycorrhizal (AM) fungi. At the same time, little is known about the small-scale distribution of soil nutrients, microbes and plant biomass occurring in the same area. We examined small-scale temporal and spatial variation as well as covariation of soil nutrients, microbial biomass (using soil fatty acid biomarker content) and above- and belowground biomass of herbaceous plants in a natural herb-rich boreonemoral spruce forest. The abundance of AM fungi and bacteria decreased during the plant growing season while soil nutrient content rather increased. The abundance of all microbes studied also varied in space and was affected by soil nutrient content. In particular, the abundance of AM fungi was negatively related to soil phosphorus and positively influenced by soil nitrogen content. Neither shoot nor root biomass of herbaceous plants showed any significant relationship with variation in soil nutrient content or the abundance of soil microbes. Our study suggests that plants can compensate for low soil phosphorus concentration via interactions with soil microbes, most probably due to a more efficient symbiosis with AM fungi. This compensation results in relatively constant plant biomass despite variation in soil phosphorous content and in the abundance of AM fungi. Hence, it is crucial to consider both soil nutrient content and the abundance of soil microbes when exploring the mechanisms driving vegetation patterns.

Contrasting arbuscular mycorrhizal communities colonizing different host plants show a similar response to a soil phosphorus concentration gradient

High soil phosphorus (P) concentration is frequently shown to reduce root colonization by arbuscular mycorrhizal (AM) fungi, but the influence of P on the diversity of colonizing AM fungi is uncertain. We used terminal restriction fragment length polymorphism (T-RFLP) of 18S rDNA and cloning to assess diversity of AM fungi colonizing maize (Zea mays), soybean (Glycene max) and field violet (Viola arvensis) at three time points in one season along a P gradient of 10-280 mg l(-1) in the field. Percentage AM colonization changed between sampling time points but was not reduced by high soil P except in maize. There was no significant difference in AM diversity between sampling time points. Diversity was reduced at concentrations of P > 25 mg l(-1), particularly in maize and soybean. Both cloning and T-RFLP indicated differences between AM communities in the different host species. Host species was more important than soil P in determining the AM community, except at the highest P concentration. Our results show that the impact of soil P on the diversity of AM fungi colonizing plants was broadly similar, despite the fact that different plants contained different communities. However, subtle differences in the response of the AM community in each host were evident.

Positive diversity-invasibility relationship in species-rich semi-natural grassland at the neighbourhood scale

BACKGROUND AND AIMS

Attempts to answer the old question of whether high diversity causes high invasion resistance have resulted in an invasion paradox: while large-scale studies often find a positive relationship between diversity and invasibility, small-scale experimental studies often find a negative relationship. Many of the small-scale studies are conducted in artificial communities of even-aged plants. Species in natural communities, however, do not represent one simultaneous cohort and occur at various levels of spatial aggregation at different scales. This study used natural patterns of diversity to assess the relationship between diversity and invasibility within a uniformly managed, semi-natural community.

METHODS

In species-rich grassland, one seed of each of ten species was added to each of 50 contiguous 16 cm(2) quadrats within seven plots (8 × 100 cm). The emergence of these species was recorded in seven control plots, and establishment success was measured in relation to the species diversity of the resident vegetation at two spatial scales, quadrat (64 cm(2)) within plots (800 cm(2)) and between plots within the site (approx. 400 m(2)) over 46 months.

KEY RESULTS

Invader success was positively related to resident species diversity and richness over a range of 28-37 species per plot. This relationship emerged 7 months after seed addition and remained over time despite continuous mortality of invaders.

CONCLUSIONS

Biotic resistance to plant invasion may play only a sub-ordinate role in species-rich, semi-natural grassland. As possible alternative explanations for the positive diversity-invasibility relationship are not clear, it is recommended that future studies elaborate fine-scale environmental heterogeneity in resource supplies or potential resource flows from resident species to seedlings by means of soil biological networks established by arbuscular mycorrhizal fungi.

Communities of arbuscular mycorrhizal fungi detected in forest soil are spatially heterogeneous but do not vary throughout the growing season

Despite the important ecosystem role played by arbuscular mycorrhizal fungi (AMF), little is known about spatial and temporal variation in soil AMF communities. We used pyrosequencing to characterise AMF communities in soil samples (n = 44) from a natural forest ecosystem. Fungal taxa were identified by BLAST matching of reads against the MaarjAM database of AMF SSU rRNA gene diversity. Sub-sampling within our dataset and experimental shortening of a set of long reads indicated that our approaches to taxonomic identification and diversity analysis were robust to variations in pyrosequencing read length and numbers of reads per sample. Different forest plots (each 10×10 m and separated from one another by 30 m) contained significantly different soil AMF communities, and the pairwise similarity of communities decreased with distance up to 50 m. However, there were no significant changes in community composition between different time points in the growing season (May-September). Spatial structure in soil AMF communities may be related to the heterogeneous vegetation of the natural forest study system, while the temporal stability of communities suggests that AMF in soil represent a fairly constant local species pool from which mycorrhizae form and disband during the season.

Phylogenetic and trait-based assembly of arbuscular mycorrhizal fungal communities

Both competition and environmental filtering are expected to influence the community structure of microbes, but there are few tests of the relative importance of these processes because trait data on these organisms is often difficult to obtain. Using phylogenetic and functional trait information, we tested whether arbuscular mycorrhizal (AM) fungal community composition in an old field was influenced by competitive exclusion and/or environmental filtering. Communities at the site were dominated by species from the most speciose family of AM fungi, the Glomeraceae, though species from two other lineages, the Acaulosporaceae and Gigasporaceae were also found. Despite the dominance of species from a single family, AM fungal species most frequently co-existed when they were distantly related and when they differed in the ability to colonize root space on host plants. The ability of AM fungal species to colonize soil did not influence co-existence. These results suggest that competition between closely related and functionally similar species for space on plant roots influences community assembly. Nevertheless, in a substantial minority of cases communities were phylogenetically clustered, indicating that closely related species could also co-occur, as would be expected if i) the environment restricted community membership to single functional type or ii) competition among functionally similar species was weak. Our results therefore also suggest that competition for niche space between closely related fungi is not the sole influence of mycorrhizal community structure in field situations, but may be of greater relative importance than other ecological mechanisms.

The network structure of plant-arbuscular mycorrhizal fungi

Ecological network theory predicts that in mutualistic systems specialists tend to interact with a subset of species with which generalists interact (i.e. nestedness). Approaching plant-arbuscular mycorrhizal fungi (AMF) association using network analyses will allow the generality of this pattern to be expanded to the ubiquitous plant-AMF mutualism. Based on certain plant-AMF specificity recently suggested, networks are expected to be nested as a result of their mutualistic nature, and modular, with certain species interacting more tightly than others. Network analyses were used to test for nestedness and modularity and to compare the different contribution of plant and AMF to the overall nestedness. Plant-AMF networks share general network properties with other mutualisms. Plant species with few AMFs in their roots tend to associate with those AMFs recorded in most plant species. AMFs present in a few plant species occur in plant species sheltering most AMF (i.e. nestedness). This plant-AMF network presents weakly interlinked subsets of species, strongly connected internally (i.e. modularity). Both plants and AMF show a nested structure, although AMFs have lower nestedness than plants. The plant-AMF interaction pattern is interpreted in the context of how plant-AMF associations can be underlying mechanisms shaping plant community assemblages.

Spatial structure and interspecific cooperation: theory and an empirical test using the mycorrhizal mutualism

Explaining mutualistic cooperation between species remains a major challenge for evolutionary biology. Why cooperate if defection potentially reaps greater benefits? It is commonly assumed that spatial structure (limited dispersal) aligns the interests of mutualistic partners. But does spatial structure consistently promote cooperation? Here, we formally model the role of spatial structure in maintaining mutualism. We show theoretically that spatial structure can actually disfavor cooperation by limiting the suite of potential partners. The effect of spatial structuring depends on the scale (fine or coarse level) at which hosts reward their partners. We then test our predictions by using molecular methods to track the abundance of competing, closely related, cooperative, and less cooperative arbuscular mycorrhizal (AM) fungal symbionts on host roots over multiple generations. We find that when spatial structure is reduced by mixing soil, the relative success of the more cooperative AM fungal species increases. This challenges previous suggestions that high spatial structuring is critical for stabilizing cooperation in the mycorrhizal mutualism. More generally, our results show, both theoretically and empirically, that contrary to expectations, spatial structuring can select against cooperation.

Niche differentiation of two sympatric species of Microdochium colonizing the roots of common reed

BACKGROUND

Fungal endophyte communities are often comprised of many species colonizing the same host. However, little is known about the causes of this diversity. On the one hand, the apparent coexistence of closely related species may be explained by the traditional niche differentiation hypothesis, which suggests that abiotic and/or biotic factors mediate partitioning. For endophytes, such factors are difficult to identify, and are therefore in most cases unknown. On the other hand, there is the neutral hypothesis, which suggests that stochastic factors may explain high species diversity. There is a need to investigate to what extent each of these hypotheses may apply to endophytes.

RESULTS

The niche partitioning of two closely related fungal endophytes, Microdochium bolleyi and M. phragmitis, colonizing Phragmites australis, was investigated. The occurrences of each species were assessed using specific nested-PCR assays for 251 field samples of common reed from Lake Constance, Germany. These analyses revealed niche preferences for both fungi. From three niche factors assessed, i.e. host habitat, host organ and season, host habitat significantly differentiated the two species. M. bolleyi preferred dry habitats, whereas M. phragmitis prevailed in flooded habitats. In contrast, both species exhibited a significant preference for the same host organ, i.e. roots. Likewise the third factor, season, did not significantly distinguish the two species. Differences in carbon utilization and growth temperature could not conclusively explain the niches. The inclusion of three unrelated species of Ascomycota, which also colonize P. australis at the same locations, indicated spatio-temporal niche partitioning between all fungi. None of the species exhibited the same preferences for all three factors, i.e. host habitat, host organ, and time of the season.

CONCLUSIONS

The fungal species colonizing common reed investigated in this study seem to exploit niche differences leading to a separation in space and time, which may allow for their coexistence on the same host. A purely neutral model is unlikely to explain the coexistence of closely related endophytes on common reed.

Determining a minimum detection threshold in terminal restriction fragment length polymorphism analysis

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common technique used to characterize soil microbial diversity. The fidelity of this technique in accurately reporting diversity has not been thoroughly evaluated. Here we determine if rare fungal species can be reliably detected by T-RFLP analysis. Spores from three arbuscular mycorrhizal fungal species were each mixed at a range of concentrations (1%, 10%, 50%, and 100%) with Glomus irregulare to establish a minimum detection threshold. T-RFLP analysis was capable of detecting diagnostic peaks of rare taxa at concentrations as low as 1%. The relative proportion of the target taxa in the sample and DNA concentration influenced peak detection reliability. However, low concentrations produced small, inconsistent electropherogram peaks contributing to difficulty in differentiating true peaks from signal noise. The results of this experiment suggest T-RFLP is a reproducible and high fidelity procedure, which requires careful data interpretation in order to accurately characterize sample diversity.

Analysis of ribosomal RNA indicates seasonal fungal community dynamics in Andropogon gerardii roots

Use of the reverse-transcribed small subunit of the ribosomal RNA (rRNA) was tested for exploring seasonal dynamics of fungal communities associated with the roots of the dominant tallgrass prairie grass, Andropogon gerardii. Ribosomal RNA was extracted, reverse-transcribed, and PCR-amplified in four sampling events in May, July, September, and November. Analyses of cloned PCR amplicons indicated that the A. gerardii rhizospheres host phylogenetically diverse fungal communities and that these communities are seasonally dynamic. Operational taxonomic units with Basic Local Alignment Search Tool affinities within the order Helotiales were dominant in the rhizosphere in May. These putative saprobes were largely replaced by arbuscular mycorrhizal fungi with likely affinities within Glomerales suggesting that the fungal communities are not only compositionally but also functionally dynamic. These data suggest replacement of functional guilds comprised of saprobic fungi by mutualistic fungi in the course of a growing season.

Differentiating between effects of invasion and diversity: impacts of aboveground plant communities on belowground fungal communities

Exotic plant species can affect soil microbial communities with the potential for community and ecosystem feedbacks. Yet, separating the effects of exotics from confounded changes in plant community diversity still remains a challenge. We focused on how plant diversity and native or exotic life history affected root fungi because of their significant roles in community and ecosystem processes. Specifically, we examined how fungi colonizing plant roots were affected by plant richness (one, two or four species) replicated across a range of plant community mixtures (natives, exotics, native-exotic mixtures). Fungal biomass inside roots was affected independently by plant richness and mixture, while root fungal community composition was affected only by plant richness. Extraradical networks also increased in size with plant richness. By contrast, plant biomass was a function of plant mixture, with natives consistently smaller than exotics and native-exotic mixtures intermediate. Plant invasions may have an impact on the belowground community primarily through their effects on diversity, at least in the short-term. Disentangling the effects of diversity and invasion on belowground microbial communities can help us to understand both the controllers of belowground resilience and mechanisms of successful colonization and spread of exotic plants.

Intraspecific variation in allelochemistry determines an invasive species' impact on soil microbial communities

Invasive species can benefit from altered species interactions in their new range, and by interfering with species interactions among native competitors. Since exotic invasions are generally studied at the species level, relatively little is known about intraspecific variation in the traits that determine an invader's effect on native species. Alliaria petiolata is a widespread and aggressive invader of forest understories that succeeds in part by interfering with mutualistic interactions between native plants and soil fungi. Here, I show that the impact of A. petiolata on soil microbial communities varied among individuals due to variation in their allelochemical concentrations. The differential impacts translated into varied effects on native tree growth, partly because A. petiolata's allelochemicals preferentially affected the most mutualistic fungal taxa. These results highlight the importance of considering the spatial and temporal variation in an invasive species' impacts for understanding and managing the invasion process.