Mycorrhizal Community Structure Research Articles

Impact of hurricane disturbance on mycorrhizal co-occurrence networks: Resilience and community dynamics in the Neotropics

Extreme climatic events and related disturbances such as hurricanes are increasingly altering forest ecosystems. How these events impact forest fungal communities is poorly characterized. We examined the effect of a hurricane on mycorrhizal community structure and potential interspecific fungal interactions, inferred from OTU co-occurrences. We characterized the root fungal communities of dual-mycorrhizal plants from nine plots during two consecutive years after a category four hurricane impacted the coastal Mexican Pacific tropical forest in Jalisco. Presence-abundance matrices were used to calculate properties of mycorrhizal networks including nestedness and modularity, and to infer patterns of co-occurrence. One year after the hurricane there was a loss of links between plants and fungi. Increased network modularity and connectivity were observed after two years. We also found that disturbance changed arbuscular mycorrhizal fungal network structure more strongly than ectomycorrhizal fungal networks. Fungal guilds changed their putative interspecific interactions, from mutual exclusion in the first year to a significant increase in co-occurrence of plant pathogens, saprotrophs, and endophytes in the second year. Our results suggest that in the short term, rhizospheric interactions can be resilient to hurricanes, but fungal guilds may have divergent responses.

Contrasting structure of root mycorrhizal communities of black spruce and trembling aspen in different layers of the soil profile in the boreal mixedwoods of eastern Canada

Contrasting structure of root mycorrhizal communities of black spruce and trembling aspen in different layers of the soil profile in the boreal mixedwoods of eastern Canada

Elevation, space and host plant species structure Ericaceae root-associated fungal communities in Papua New Guinea

Abstract Our study aimed to identify significant predictors (spatial distance, elevation, host plant taxonomy) which shape the structure of endophytic fungal (ENDF) and putative ericoid mycorrhizal (ErMF) communities associated with roots of Ericaceae in Papua New Guinea. Roots of five Ericaceae together with one non-Ericaceae species were sampled at an experimental site and one common Ericaceae species was chosen for sampling along an elevation gradient. ENDF and putative ErMF communities were determined using the 454-sequencing approach. ENDF as well as putative ErMF communities were affected by interacting host plant. While the putative ErMF community was structured by host plants at the genus level, the ENDF community was affected by host plant subfamily level. Composition of ENDF as well as putative ErMF communities were affected by elevation. Non-Ericaceae plant species (Hypericum sp.) harbored similar communities of ENDF as well as putative ErMF as Ericaceae plants. Our study provides a first insight into ErMF and ENDF community ecology of Ericaceae in Papua New Guinea.

Are there keystone mycorrhizal fungi associated to tropical epiphytic orchids?

In epiphytic orchids, distinctive groups of fungi are involved in the symbiotic association. However, little is known about the factors that determine the mycorrhizal community structure. Here, we analyzed the orchid mycorrhizal fungi communities associated with three sympatric Cymbidieae epiphytic tropical orchids (Cyrtochilum flexuosum, Cyrtochilum myanthum, and Maxillaria calantha) at two sites located within the mountain rainforest of southern Ecuador. To characterize these communities at each orchid population, the ITS2 region was analyzed by Illumina MiSeq technology. Fifty-five mycorrhizal fungi operational taxonomic units (OTUs) putatively attributed to members of Serendipitaceae, Ceratobasidiaceae and Tulasnellaceae were identified. Significant differences in mycorrhizal communities were detected between the three sympatric orchid species as well as among sites/populations. Interestingly, some mycorrhizal OTUs overlapped among orchid populations. Our results suggested that populations of studied epiphytic orchids have site-adjusted mycorrhizal communities structured around keystone fungal species. Interaction with multiple mycorrhizal fungi could favor orchid site occurrence and co-existence among several orchid species.

Bradyrhizobium inoculation alters indigenous AMF community assemblages and interacts positively with AMF inoculum to improve cowpea performance

Legumes are a major component in sustainable agricultural systems since they can fix atmospheric nitrogen and form effective associations with both nitrogen fixing bacteria (NFB) and arbuscular mycorrhizal fungi (AMF). However, the impact of NFB inoculation on the indigenous AMF community structure in legumes has been overlooked. In the current study, we investigated the influence of a Bradhyrhizobium isolate together with a commercial mycorrhizal inoculum on the performance of cowpea, along with its endophytic mycorrhizal community structure. A three-way factorial randomized design was established in sterilized and non-sterilized soils, including control plants (without inoculation), inoculated plants with a Bradyrhizobium (NFB) strain, a commercial mycorrhizal inoculum (AMF) and their combination (AMF+/NFB+). All inoculation treatments under sterile and non-sterile soil conditions resulted in a significant increase in the shoot biomass, which was positively correlated with AMF colonization, and the number of nodules found in cowpea roots. Mycorrhizal colonization and nodule formation in control plants grown in non-sterilized soils, suggested an active and functional local mycorrhizal and rhizobial community in the soil, which was further supported by the molecular fingerprints. Growth of control plants in sterile soil resulted in lower shoot biomass that was in line with the absence of the respective microbial assemblages. Interestingly, the local AMF community pattern of cowpea roots was drastically altered after the NFB application. Molecular fingerprinting, through cloning of PCR amplified sequences of 18sRNA revealed that cowpea plants were colonized by Rhizophagus, Funneliformis, Claroideoglomus and Paraglomus related species. The results support the notion that the introduced Bradyrhizobium strain interacted drastically with the indigenous AMF community, leading to a more diverse colonization pattern of cowpea roots. These findings enhance our understanding of how these microorganisms interact to affect plant performance and increase agricultural sustainability.

Hierarchical neighbor effects on mycorrhizal community structure and function.

Theory predicts that neighboring communities can shape one another's composition and function, for example, through the exchange of member species. However, empirical tests of the directionality and strength of these effects are rare. We determined the effects of neighboring communities on one another through experimental manipulation of a plant‐fungal model system. We first established distinct ectomycorrhizal fungal communities on Douglas‐fir seedlings that were initially grown in three soil environments. We then transplanted seedlings and mycorrhizal communities in a fully factorial experiment designed to quantify the direction and strength of neighbor effects by focusing on changes in fungal community species composition and implications for seedling growth (a proxy for community function). We found that neighbor effects on the composition and function of adjacent communities follow a dominance hierarchy. Specifically, mycorrhizal communities established from soils collected in Douglas‐fir plantations were both the least sensitive to neighbor effects, and exerted the strongest influence on their neighbors by driving convergence in neighbor community composition and increasing neighbor seedling vigor. These results demonstrate that asymmetric neighbor effects mediated by ecological history can determine both community composition and function.

Arbuscular mycorrhizal community structure on co-existing tropical legume trees in French Guiana

We aimed to characterise the arbuscular mycorrhizal fungal (AMF) community structure and potential edaphic determinants in the dominating, but poorly described, root-colonizing Paris-type AMF community on co-occurring Amazonian leguminous trees. Three highly productive leguminous trees (Dicorynia guianensis, Eperua falcata and Tachigali melinonii were targeted) in species-rich forests on contrasting soil types at the Nouragues Research Station in central French Guiana. Abundant AMF SSU rRNA amplicons (NS31-AM1 & AML1-AML2 primers) from roots identified via trnL profiling were subjected to denaturing gradient gel electrophoresis (DGGE), clone library sequencing and phylogenetic analysis. Classical approaches targeting abundant SSU amplicons highlighted a diverse root-colonizing symbiotic AMF community dominated by members of the Glomeraceae. DGGE profiling indicated that, of the edaphic factors investigated, soil nitrogen was most important in influencing the AMF community and this was more important than any host tree species effect. Dominating Paris-type mycorrhizal leguminous trees in Amazonian soils host diverse and novel taxa within the Glomeraceae that appear under edaphic selection in the investigated tropical forests. Linking symbiotic diversity of identified AMF taxa to ecological processes is the next challenge ahead.

Colonization of new land by arbuscular mycorrhizal fungi

The study describes the primary assembly of arbuscular mycorrhizal communities on a newly constructed island Peberholm between Denmark and Sweden. The AM fungal community on Peberholm was compared with the neighboring natural island Saltholm. The structure of arbuscular mycorrhizal communities was assessed through 454 pyrosequencing. Internal community structure was investigated through fitting the rank-abundance of Operational Taxonomic Units to different models. Heterogeneity of communities within islands was assessed by analysis of group dispersion. The mean OTU richness per sample was significantly lower on the artificial island than on the neighboring natural island, indicating that richness of the colonizing AM fungal community is restricted by limited dispersal. The AM fungal communities colonizing the new island appeared to be a non-random subset of communities on the natural and much older neighboring island, which points to high colonization potential of certain – probably early successional – mycorrhizal fungi, likely assisted by migratory birds.

Is root DNA a reliable proxy to assess arbuscular mycorrhizal community structure?

Arbuscular mycorrhizal (AM) fungi are widespread plant symbionts that extensively colonize both soil and roots. Given their influence on ecosystem processes, such as plant growth, soil carbon storage, and nutrient cycling, there is great interest in understanding the drivers of their community structure. AM fungal communities are increasingly characterized by selectively amplifying their DNA from plant roots, thus assuming that AM fungal community structure within roots provides a reliable portrait of the total (i.e., soil + roots) community. Through numerical simulations, we test this assumption using published data. We show that community structure and diversity is well preserved when analyzing only a subset of the community biomass (i.e., roots or soil), provided that the community shows a typical skewed abundance distribution, with few very dominant species and a high prevalence of rare species. Given that this community structure has been shown to be common in natural AM fungal communities, the present work would suggest that characterizing AM fungal communities using only roots or soil can provide a reliable portrait of the overall community. However, we show through additional analyses that the proportion of sample biomass used for molecular methods must be over a minimal threshold to properly characterize the community. Using published molecular data sets, we validate those results, which suggest that typical molecular protocols using low amounts of biomass may strongly influence AM fungal community characterization. Finally, we also discuss other assumptions implied by the molecular analysis of AM fungal communities, and point out urgent knowledge gaps.

Impact of 12-year field treatments with organic and inorganic fertilizers on crop productivity and mycorrhizal community structure

The effect of manure and mineral fertilization on the arbuscular mycorrhizal (AM) fungal community structure of sunflower (Helianthus annuus L.) plants was studied. Soils were collected from a field experiment treated for 12 years with equivalent nitrogen (N) doses of inorganic N, dairy manure slurry, or without N fertilization. Fresh roots of tall fescue (Festuca arundinacea Schreb.) grass collected from the field plots without N fertilization and unfumigated field soils were used as native microbial inoculum sources. Sunflower plants were sown in pots containing these soils, and three different means of manipulating the microbial community were set: unfumigated soil with fresh grass roots, fumigated soil with fresh grass roots, or fumigated soil with sterilized grass roots. Assessing the implications with respect to plant productivity and mycorrhizal community structure was investigated. Twelve AM fungal OTUs were identified from root or soil samples as different taxa of Acaulospora, Claroideoglomus, Funneliformis, Rhizophagus, and uncultured Glomus, using PCR-DGGE and sequencing of an 18S rRNA gene fragment. Sunflower plants grown in manure-fertilized soils had a distinct AMF community structure from plants either fertilized with mineral N or unfertilized, with an abundance of Rhizophagus intraradices-like (B2). The results also showed that AM inoculation increased P and N contents in inorganic N-fertilized or unfertilized plants, but not in manure-fertilized plants.

Response of soil microbial communities to contrasted histories of phosphorus fertilisation in pastures

Several microbial taxa that potentially affect soil phosphorus (P) biogeochemical cycling and plant nutrition have been identified, in particular some members of the Actinobacteria, Pseudomonas, and arbuscular mycorrhizal fungi (AMF) have been found to solubilise P and enhance P uptake. This study investigated the diversity of selected key taxa within a pastoral agricultural system, to address the hypothesis that if these taxa have an intrinsic association to soil P, long-term P-manipulation should present a selective pressure. We defined this selective pressure as a shift in community assemblage, based on either PCR-DGGE banding patterns or taxon-specific quantitative polymerase chain reaction (qPCR) (mycorrhizae). The work was conducted on a long-term fertiliser field trial site where soil P status had been altered for ∼40 years, with total P ranging from 464 to 1102mgkg−1 soil. The structure of both Actinobacteria and Pseudomonas communities was found to differ according to fertiliser treatment (P<0.05). However, only the Actinobacteria were associated with the underlying P fertility gradient (soil C:P ratio; ρ=0.481; P=0.019); no significant links between the Pseudomonas community and soil physicochemical properties were found. As the structure of the general bacterial or α-Proteobacterial communities did not vary between treatments (P>0.05), the hypothesis that Actinobacteria communities are intrinsically linked to soil P cycling is supported. Similarly, mycorrhizal community structure was strongly influenced by soil P status (P=0.002), with particularly strong differences between the control treatments (no P fertiliser) and fertilised plots, meaning the addition of fertiliser P to soil per se was more important than quantity. P-fertilizer application increased the diversity of AMF. The AMF community of the control plot was dominated by Glomus intraradices and Glomus claroideum; these taxa may have had the highest fitness under the low P conditions. The total fungal community structure, assessed by denaturing gradient gel electrophoresis (DGGE), also varied over the fertiliser trial (P=0.001), however the variation was not correlated with soil P status (biota and/or environment matching; BIO-ENV test). Our results expand our knowledge on the microbiology supporting soil P cycling in pasture soils. Furthermore, we demonstrate that communities of Actinobacteria and AMF, proposed to be involved in supplying P to pasture plants, are linked to the underlying soil P status.

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.

Using ecological network theory to evaluate the causes and consequences of arbuscular mycorrhizal community structure

See also the Commentary by Öpik and Moora

Influence of trees on the spatial structure of arbuscular mycorrhizal communities in a temperate tree-based intercropping system

Tree-based intercropping (TBI) is an ecologically sustainable agricultural practice that may promote a more diverse arbuscular mycorrhizal (AM) fungal community compared to conventional systems, but the influence of the dynamics of these systems on AM fungi has not been established. Soil and root samples were collected in the intercropping alleys along transects perpendicular to tree rows occupied by white ash ( Fraxinus americana), poplar ( Populus deltoids × nigra), Norway spruce ( Picea abies), and rows without trees (control). Molecular analysis of the AM fungal community at the TBI site revealed 17 phylotypes belonging to the Glomeraceae. Overall, the AM fungal community in the TBI site was comparable to other conventional agricultural systems; with the majority of phylotypes belonging to Glomus group A. AM fungal phylotype richness and community composition significantly differed among the treatments in the TBI site. AM fungal communities were more diverse in cropping alleys adjacent to trees that associate with AM fungi than trees that do not associate with AM fungi. Norway spruce had a negative influence on the AM fungal community as tree rows and bordering intercropping alleys had a significantly lower phylotype richness and different community composition. These results suggest that to maintain a diverse AM fungal community throughout TBI systems, it may be best to incorporate tree species that associate with AM fungi.

Arbuscular Mycorrhizas: Drivers or Passengers of Alien Plant Invasion

Observational and manipulative studies have revealed that alien plant invasions are an outcome of interplay between a myriad of biotic and abiotic factors operating at various spatio-temporal stages and scales. Despite the salient role of ubiquitous arbuscular mycorrhizal (AM) fungi in plant interactions, studies exploring the role of such symbionts in invasiveness of alien species and invasibility of communities are limited, in part because of difficult-culturablilty of AM fungi on artificial media and apparent complexities in manipulations of AM-plant interactions in field and laboratory experiments. Moreover, analysis of the AM-plant invasion studies conducted so far have yielded contradictory results with some indicating facilitation of invasion by AM fungi and others its inhibition. Other studies have indicated that arbuscular mycorrhizal symbiosis has no effect on invasiveness of alien plants. While arbuscular mycorrhizas may facilitate invasiveness of some alien plants, such plants may also potentially impact mycorrhizal community structure and functions in the invaded habitats in different ways. The present review addresses these paradoxically conflicting observations in the context of mutualism-commensalism-parasitism gradient that characterizes the relationship between AM fungi and their alien vs. native hosts and also discusses the influence of alien invasive plants on mycorrhizal community structure of invaded ecosystems. Through critical analysis of costs and benefits for invasive plants that associate with AM fungi in their introduced range, invasion-induced shifts in AM mutualism are evaluated in the context of their impact on native biodiversity. Underlining limitations of methodologies and experimental designs usually employed to understand AM-mediated plant invasiveness, we proposes herein some alternative frameworks and experimental approaches to overcome these limitations.

Interactions among Prescribed Fire, Soil Attributes, and Mycorrhizal Community Structure at Crater Lake National Park, Oregon, USA

We identified relationships between prescribed burn treatments and selected soil and fuel attributes on mycorrhizal fungus fruiting patterns in an old-growth ponderosa pine (Pinus ponderosa) and white fir (Abies concolor) stand in Crater Lake National Park, Oregon, USA. Three prescribed burn treatments (early spring, late spring, and fall burns) plus non-burned controls were applied to 24 ∼3 ha units in 2002. We sampled mycorrhizal fungus sporocarp production in the spring and fall in the ensuing three years, and collected data on surface fuels, soil C and N concentrations, δ13C and δ15N signatures, pH, and mineral soil bulk density. A gradient of C:N ratios and other soil attributes across the study area facilitated separation of the effect of fire from the effects of soil attributes on fungal fruiting patterns. Distinct guilds of fungal indicator species were identified, correlating more closely with soil C:N ratios than prescribed burn treatments. Although other habitat attributes (such as fuel levels) were correlated with C:N ratios, the C:N ratios were the most consistent predictor of fungal fruiting patterns. The fall burn treatment did reduce soil C:N ratios, and most of the fall burned units produced the fungal indicator species associated with lower C:N ratios, but the same fungal indicator species also fruited in the non-burned control units with lower C:N ratios. The spring burn treatments did not differ significantly from non-burned controls in fungal fruiting patterns or C:N ratios. Fall burn treatment units produced significantly fewer fungal species and collections than spring burn units, but did not differ significantly in fungal diversity and abundance from non-burned controls.

Structure and activities of ectomycorrhizal and microbial communities in the rhizosphere of Fagus sylvatica under ozone and pathogen stress in a lysimeter study

The aim was to study the influence of abiotic (elevated ozone) or biotic stress (Phytophthora citricola) or their combination on soil biological components and processes in the rhizosphere of young beech trees. Ectomycorrhizal and overall microbial community composition was studied at two soil depths in a lysimeter experiment with 7 year old trees of Fagus sylvatica. As a functional parameter, potential enzyme activities were measured in mycorrhizosphere soil and on excised mycorrhizal tips. The degree of mycorrhization, structure and potential enzymatic activities of mycorrhizal communities were only slightly influenced by treatments. Soil enzyme activities were depressed under elevated ozone and stimulated by P. citricola under ambient but not under elevated ozone. Overall microbial community composition (PLFA) and ectomycorrhizal diversity changed with depth. PLFA analyses not only suggested a reaction of the microbial community to elevated ozone but also indicated an increase in plant stress related components. No influence of the biotic stress on ectomycorrhizal or overall microbial community structure was detected. Changes in the mycorrhizosphere community structure and function due to ozone may be explained by the quality of plant derived carbon.

Diversity and seasonal variations of mycorrhiza and rhizosphere bacteria in three common plant species at the Slovenian Ljubljana Marsh

Interactions between plants and microorganisms can significantly affect plant health and productivity as well as ecosystem functioning. Detailed knowledge of the tripartite relationships between plants, fungi, and bacteria, and their environment is still limited. In the present study, the soils adjacent to three plant species (Cruciata laevipes, Mentha piperita, Equisetum arvense) in the Ljubljana Marsh and the bulk, plant-free soil were analyzed for their bacterial community structure in June and October 2006. The terminal restriction fragment length polymorphism analysis indicated a different bacterial community structure in the rhizosphere and in bulk soil, however, with almost no seasonal changes between late spring and autumn samples and no apparent impact of the three plant species. In addition, root colonization of the three plant species by arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) was microscopically assessed monthly from May until October 2006. A presumably accidental correlation between monthly precipitation and the degree of arbuscule formation, with the latter lagging 1 month, was noted for M. piperita, the most heavily colonized of the three plant species. With all three plants, the phosphorus content in roots correlated positively with most AMF structures. Microsclerotia of DSE were mainly abundant in autumn samples. Fungal diversity in roots was estimated using temporal temperature gradient gel electrophoresis separation of the fungal polymerase chain reaction products obtained for both 18S-rDNA and the 5.8S-ITS2-28S rDNA segments. No specific effects of either plant species or seasonal changes on mycorrhizal community structure were discernible.

Molecular analysis of arbuscular mycorrhizal community structure and spores distribution in tree-based intercropping and forest systems

Due to their potential to enhance soil biodiversity and fertility, tree-based intercropping (TBI) systems are recognized as promising agrotechnologies. However, few studies have examined the effects of TBI on the diversity of arbuscular mycorrhizal (AM) fungi. To investigate this aspect, and to compare TBI with a more typical forest plantation (FO) system, a field experiment using soybean ( Glycine max (L.) Merr. cv. SO3-W4) and poplar ( Populus nigra L. × P. maximowiczii cv. A. Henry ‘Max 5’) was conducted on an arable field site in southwestern Québec. The species of AM fungi colonizing the roots were assessed by PCR-RFLP and DNA sequence analyses of SSU rRNA genes. A total of 13 different phylotypes were identified. Phylogenetic analyses demonstrated that these belonged to the genera Glomus (11), Acaulospora (1) and Scutellospora (1). The AM fungal diversity, as expressed by the Shannon–Wiener indices, were 0.82 ± 0.08 for the soybean and 0.70 ± 0.11 for poplar under the TBI system, and 0.53 ± 0.08 for poplar under the FO system. The study also investigated the distribution of AM fungal spores in the soil, and this differed in the two systems. Under the TBI system, spore abundance increased with increasing distance from the poplar trunk, while it remained relatively constant under the FO system. Our results also show that neighbouring trees and soybean plants hosted different AM fungal communities, suggesting that TBI systems may enhance AM fungal richness compared to monocultures.

Mycorrhizal community structure, microbial biomass P and phosphatase activities under Salix polaris as influenced by nutrient availability

Low supply of the nutrients nitrogen (N) and phosphorus (P) limit plant growth and spreading, and increase the plant-microbial nutrient competition in subarctic and arctic regions. We investigated the mycorrhizal community structure of a polar shrub willow ( Salix polaris) and the microbial turnover in its rhizosphere to explore the adaptation of a mycorrhizal plant in the subarctic tundra. The ectomycorrhizal colonisation ranged from 35 to 64% of the fine root tips and decreased with an increasing soil C/N ratio. In total, 16 ectomycorrhizal morphotypes were found under S. polaris (eight to 13 morphotypes per site, five morphotypes at all four sites). Cenococcum sp. was the most common EM fungus (32% of the ectomycorrhizal fine roots). The abundance of Cenococcum sp. increased with an increasing organic matter content and N/P ratio in the soil. Arbuscular mycorrhizal colonisation of S. polaris was absent or less than 1% of the fine root length. Microbial biomass P accounted for 21–75% of the organic soil P and 6–49% of the total soil P. Microbial biomass P, alkaline and acid phosphatase activities in the rhizosphere increased with increasing soil N concentration. We conclude that a higher N supply decreases the diversity in the mycorrhizal community on polar willows and increases the role of P turnover from the soil microbial biomass for the nutrient supply.