Defoliation effects on the community structure of arbuscular mycorrhizal fungi based on 18S rDNA sequences

Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands

Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.

Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments

Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.

Precipitation shapes communities of arbuscular mycorrhizal fungi in Tibetan alpine steppe

Tibetan Plateau is one of the largest and most unique habitats for organisms including arbuscular mycorrhizal fungi (AMF). However, it remains unclear how AMF communities respond to key environmental changes in this harsh environment. To test if precipitation could be a driving force in shaping AMF community structures at regional scale, we examined AMF communities associated with dominant plant species along a precipitation gradient in Tibetan alpine steppe. Rhizosphere soils were collected from five sites with annual precipitation decreasing from 400 to 50 mm. A total of 31 AMF operational taxonomic units (OTUs) were identified. AMF community composition varied significantly among sites, whereas AMF community composition did not vary among plant species. Path analysis revealed that precipitation directly affected AMF hyphal length density, and indirectly influenced AMF species richness likely through the mediation of plant coverage. Our results suggested that water availability could drive the changes of AMF communities at regional scale. Given the important roles AMF could play in the dynamics of plant communities, exploring the changes of AMF communities along key environmental gradients would help us better predict the ecosystem level responses of the Tibetan vegetation to future climate change.

Impacts of drought stress on soluble carbohydrates and respiratory enzymes in fruit body of Auricularia auricula

In order to study the survival mechanisms to drought stress for fruit body of Auricularia auricula, soluble carbohydrates and respiratory enzymes were investigated. Fruit bodies were exposed to sunlight and were naturally dehydrated. Samples were taken at different levels of water loss (0%, 10%, 30%, 50% and 70%) to measure the content of soluble sugars and polysaccharides. The activities of phosphoglucose isomerase (PGI), combined glucose-6-phosphate dehydrogenase (G-6-PDH) and 6-phosphogluconate dehydrogenase (6-PGDH), and malate dehydrogenase (MDH), were also determined. The results showed that with the increase in water loss, soluble sugars and MDH activity declined, whereas the activities of G-6-PDH and 6-PGDH increased. Soluble polysaccharides content and PGI activity decreased with water loss up to 30% and increased afterwards. These results suggested that the pentose phosphate pathway (PPP), as demonstrated by activities of G-6-PDH and 6-PGDH, could be one of the mechanisms for survival during drought stress in the fruit body of A. auricula. Moreover, soluble polysaccharides may play a part in protecting the fruit body in further drought stress.

Significant difference in mycorrhizal specificity between an autotrophic and its sister mycoheterotrophic plant species of Petrosaviaceae

Petrosaviaceae is a monocotyledonous plant family that comprises two genera: the autotrophic Japonolirion and the mycoheterotrophic Petrosavia. Accordingly, this plant family provides an excellent system to examine specificity differences in mycobionts between autotrophic and closely related mycoheterotrophic plant species. We investigated mycobionts of Japonolirion osense, the sole species of the monotypic genus, from all known habitats of this species by molecular identification and detected 22 arbuscular mycorrhizal (AM) fungal phylotypes in Archaesporales, Diversisporales, and Glomerales. In contrast, only one AM fungal phylotype in Glomerales was predominantly detected from the mycoheterotrophic Petrosavia sakuraii in a previous study. The high mycobiont diversity in J. osense and in an outgroup plant, Miscanthus sinensis (Poaceae), indicates that fungal specificity increased during the evolution of mycohetrotrophy in Petrosaviaceae. Furthermore, some AM fungal sequences of J. osense showed >99% sequence similarity to the dominant fungal phylotype of P. sakuraii, and one of them was nested within a clade of P. sakuraii mycobionts. These results indicate that fungal partners are not necessarily shifted, but rather selected for in the course of the evolution of mycoheterotrophy. We also confirmed the Paris-type mycorrhiza in J. osense.

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities

Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status.

Community analysis of arbuscular mycorrhizal fungi in roots of Poncirus trifoliata and Citrus reticulata based on SSU rDNA

Morphological observation of arbuscular mycorrhizal fungi (AMF) species in rhizospheric soil could not accurately reflect the actual AMF colonizing status in roots, while molecular identification of indigenous AMF colonizing citrus rootstocks at present was rare in China. In our study, community of AMF colonizing trifoliate orange (Poncirus trifoliata L. Raf.) and red tangerine (Citrus reticulata Blanco) were analyzed based on small subunit of ribosomal DNA genes. Morphological observation showed that arbuscular mycorrhizal (AM) colonization, spore density, and hyphal length did not differ significantly between two rootstocks. Phylogenetic analysis showed that 173 screened AMF sequences clustered in at least 10 discrete groups (GLO1~GLO10), all belonging to the genus of Glomus Sensu Lato. Among them, GLO1 clade (clustering with uncultured Glomus) accounting for 54.43% clones was the most common in trifoliate orange roots, while GLO6 clade (clustering with Glomus intraradices) accounting for 35.00% clones was the most common in red tangerine roots. Although, Shannon-Wiener indices exhibited no notable differences between both rootstocks, relative proportions of observed clades analysis revealed that composition of AMF communities colonizing two rootstocks varied severely. The results indicated that native AMF species in citrus rhizosphere had diverse colonization potential between two different rootstocks in the present orchards.

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

• Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.

Mycorrhizal fungal-plant-insect interactions: the importance of a community approach

Mycorrhizal fungi and insects are important components of most ecosystems that are likely to interact with one another indirectly through a common host plant. In this paper, we review the literature examining the effects of insects on mycorrhizal fungi and the effects of mycorrhizal fungi on insects and show that both groups of organisms can indirectly and, occasionally directly, influence each other. We explore the mechanisms for these interactions and test a recently proposed model predicting mycorrhizal fungal community responses to herbivory. We emphasize the results of several recent studies that showed that experiments conducted in isolation are unlikely to predict the outcome of interactions between insects, plants, and mycorrhizal fungi, and we highlight the need for a community approach to the study of mycorrhizal fungal-plant-insect interactions.

Impacts of plant symbiotic fungi on insect herbivores: mutualism in a multitrophic context

We consider how fungi that form symbiotic associations with plants interact with insect herbivores attacking the same plants. Both endophytes and mycorrhizae have significant impacts on herbivores with which they are in relatively intimate contact, but weaker effects on those from which they are spatially separated. Generalist insects are usually adversely affected by the presence of endophytes and mycorrhizae, whereas specialist insects may often benefit. Effects on feeding guilds vary according to type of fungi; for example, aphids are often negatively affected by endophytes but respond positively to mycorrhizae, and leaf-chewers are usually negatively affected by both types of fungi. There is a strong taxonomic bias in the literature and many interactions remain little studied; laboratory studies predominate over field studies. Although some patterns emerge, there is a large amount of specificity and context dependency in the outcome of interactions, reflecting the influence of fungal and host genotype, fungal, host, and insect species, and environmental factors. Whereas some of the mechanisms underpinning these interactions are relatively well characterized, others remain unclear and await elucidation by molecular and metabolomic techniques.

Seasonal dynamics of arbuscular mycorrhizal fungal communities in roots in a seminatural grassland

Symbiotic arbuscular mycorrhizal fungi (AMF) have been shown to influence both the diversity and productivity of grassland plant communities. These effects have been postulated to depend on the differential effects of individual mycorrhizal taxa on different plant species; however, so far there are few detailed studies of the dynamics of AMF colonization of different plant species. In this study, we characterized the communities of AMF colonizing the roots of two plant species, Prunella vulgaris and Antennaria dioica, in a Swedish seminatural grassland at different times of the year. The AMF small subunit rRNA genes were subjected to PCR, cloning, sequencing, and phylogenetic analysis. Nineteen discrete sequence types belonging to Glomus groups A and B and to the genus Acaulospora were distinguished. No significant seasonal changes in the species compositions of the AMF communities as a whole were observed. However, the two plant species hosted significantly different AMF communities. P. vulgaris hosted a rich AMF community throughout the entire growing season. The presence of AMF in A. dioica decreased dramatically in autumn, while an increased presence of Ascomycetes species was detected.

Above-ground herbivory causes rapid and sustained changes in mycorrhizal colonization of grasses

Arbuscular mycorrhizal fungi (AMF) play a vital role in ecosystem functioning. In most grasslands, herbivory by both vertebrate and invertebrate herbivores is common and thus in order to assess herbivore effects on multitrophic-level interactions both should be considered. This study investigated the effects of grazing by rabbit and insect herbivores on root-colonization of grasses by AMF in two lowland grasslands in southern England, UK. A long-term exclosure site was used to provide a temporal assessment in order to elucidate whether any short-term responses to herbivore removal were sustained. Root samples from three grass species at each site were analysed in terms of total mycorrhizal colonization and proportional colonization by individual mycorrhizal structures. Colonization levels were up to 1.6 times greater under moderate levels of rabbit grazing (with summer maxima of 25% and winter minima of 11%) than in intensely grazed swards or fenced plots at both sites. The change was fast (within 8 weeks), consistent throughout the sampled field plots, and temporally sustainable over a 19-year period. There was no significant effect of insect herbivory on total colonization but proportional colonization by different AM structures was affected on some sample dates where vertebrate herbivores had been removed, indicating a slight effect on fungal structure allocation. The results suggest that the type of herbivore and perhaps more importantly the intensity of grazing are key determinants of below-ground effects upon mycorrhizal-host plant symbiosis. The data suggest that the extent of mycorrhizal colonization within grass host plants is strongly influenced by C assimilation and allocation.

Two threatened coexisting indigenous conifer species in the dry Afromontane forests of Ethiopia are associated with distinct arbuscular mycorrhizal fungal communities

The molecular diversity of arbuscular mycorrhizal (AM) fungi colonizing roots of Podocarpus falcatus (Thunb.) R.Br. (Podocarpaceae) in the dry Afromontane forests of Ethiopia was investigated. The nuclear gene coding for small subunit ribosomal RNA (nucSSU rDNA) was amplified from colonized roots of P. falcatus, cloned, and sequenced using AM fungal specific primers. Phylogenetic analyses revealed that the glomeromycetous sequences from mycorrhizae of P. falcatus belong to the Glomeraceae, Diversisporaceae, and Archaeosporaceae. Overall, 16 Glomus , three Diversispora , and one Archaeospora sequence types were identified. These sequence types were distinct and only distantly related to sequences from the available defined species. The composition of the AM fungal communities differed significantly between the two study sites. Comparison of the AM fungal community composition of P. falcatus with that of previously investigated Juniperus procera Hochst. ex Endl. (Cupressaceae), the only coexisting indigenous conifer tree species in the dry Afromontane forest ecosystem, yields that the two tree species are colonized by distinct AM fungal communities. This suggests that fungal communities are host plant specific in the natural stand conditions. Therefore, in the conservation of these endangered species and restoration of the degraded ecosystem, the use of appropriate mycorrhizal fungi should be taken into account in future projects.

Phylogenetic analysis of nuclear small subunit rDNA sequences suggests that the endangered African Pencil Cedar, Juniperus procera, is associated with distinct members of Glomeraceae

The endangered indigenous tree species Juniperus procera, commonly known as African Pencil Cedar, is an important component of the dry Afromontane vegetation of Ethiopia and was shown to be AM in earlier studies. Here we describe the composition of AM fungi in colonized roots of J. procera from two dry Afromontane forests of Ethiopia. The nuSSU rDNA gene was amplified from colonized roots, cloned and sequenced using AM fungal specific primers that were partly developed for this study. Molecular phylogenetic analysis revealed that all the glomeralean sequences obtained belonged exclusively to the genus Glomus (Glomeraceae). Seven distinct Glomus sequence types were identified that all are new to science. The composition of the AM fungal communities between the sampled trees, and between the two study sites in general, differed significantly. Isolation and utilization of the indigenous AM fungal taxa from the respective sites might be required for successful enrichment plantation of this threatened Juniperus species.

The effects of agricultural practices on arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants, including many important agricultural crops. These fungi facilitate plant nutrient uptake, promote soil aggregation and use a significant portion of reduced carbon from the plants. AMF functional traits differ considerably among and within species, meaning that functional properties of a mycorrhizal community depend on its composition. Here we review studies exploring the effects of agricultural practices such as tillage, crop rotation, fertilization, pesticide application, irrigation and grazing on AMF communities. Although it is difficult to generalize the results of studies performed under different soil and climatic conditions, some universal patterns emerge. For example, soil tillage reduces the abundance of Scutellospora spp.; phosphorus fertilization lowers the extent of AMF root colonization; and diversification of crops results in more diverse AMF communities. We now need to design simple and reliable field tests for quantifying the effects of AMF communities on crop growth, yields and sustainability of the agro-ecosystems.