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

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

Effect of plant communities on bacterial and fungal communities in a Central European grassland

BACKGROUND

Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains poorly understood. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in a wooded meadow of Čertoryje (White Carpathians, Czech Republic), a European hotspot of plant species diversity.

RESULTS

High plant diversity was associated with treeless grassland areas with high primary productivity and high contents of soil nitrogen and organic carbon. In contrast, low plant diversity occurred in grasslands near solitary trees and forest edges. Fungal communities differed between low-diversity and high-diversity grasslands more strongly than bacterial communities, while the difference in arbuscular mycorrhizal fungi (AMF) depended on their location in soil versus plant roots. Compared to grasslands with low plant diversity, high-diversity plant communities had a higher diversity of fungi including soil AMF, a different fungal and soil AMF community composition and higher bacterial and soil AMF biomass. Root AMF composition differed only slightly between grasslands with low and high plant diversity. Trees dominated the belowground plant community in low-diversity grasslands, which influenced microbial diversity and composition.

CONCLUSIONS

The determinants of microbiome abundance and composition in grasslands are complex. Soil chemistry mainly influenced bacterial communities, while plant community type mainly affected fungal (including AMF) communities. Further studies on the functional roles of microbial communities are needed to understand plant-soil-microbe interactions and their involvement in grassland ecosystem services.

"Ectomycorrhizal exploration type" could be a functional trait explaining the spatial distribution of tree symbiotic fungi as a function of forest humus forms

In European forests, most tree species form symbioses with ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi. The EM fungi are classified into different morphological types based on the development and structure of their extraradical mycelium. These structures could be root extensions that help trees to acquire nutrients. However, the relationship between these morphological traits and functions involved in soil nutrient foraging is still under debate.We described the composition of mycorrhizal fungal communities under 23 tree species in a wide range of climates and humus forms in Europe and investigated the exploratory types of EM fungi. We assessed the response of this tree extended phenotype to humus forms, as an indicator of the functioning and quality of forest soils. We found a significant relationship between the relative proportion of the two broad categories of EM exploration types (short- or long-distance) and the humus form, showing a greater proportion of long-distance types in the least dynamic soils. As past land-use and host tree species are significant factors structuring fungal communities, we showed this relationship was modulated by host trait (gymnosperms versus angiosperms), soil depth and past land use (farmland or forest).We propose that this potential functional trait of EM fungi be used in future studies to improve predictive models of forest soil functioning and tree adaptation to environmental nutrient conditions.

Co-occurring tree species drive arbuscular mycorrhizal fungi diversity in tropical forest

It is still uncertain whether environment or host plant species is more important in determining AMF diversity; although, plant roots are usually associated with abundant AMF species in different environments. This study explored the effect of plant species and environmental factors on AMF diversity based on three co-occurring tree species (Glochidion coccineum, Schefflera octophylla, and Schima superba) on six elevations of Mt. Jianfengling. A total of 185 OTUs (operational taxonomic units) of AMF were found in the three co-occurring dominant tree species. Of which 109 unique OTUs were identified in the three co-occurring plant species, which accounted for the total number of 58.92%. Forty-five OTUs were shared by the three co-occurring tree species, accounting for a total number of 24.32%. The plant species of Schefflera octophylla was identified as having the highest AMF diversity with the largest number of OTUs of 143. The fungi in the genus of Glomus were the dominant AMF species in the three co-occurring tree species. AMF communities and diversity are quite different, either within different plant species at the same elevation or within the same plant species at different elevations. However, the altitude had no significant effect on the ACE index. Therefore, the results suggest that plant species have a more important effect on AMF diversity and community composition.

Soil mycobiomes in native European aspen forests and hybrid aspen plantations have a similar fungal richness but different compositions, mainly driven by edaphic and floristic factors

Background

The cultivation of short-rotation tree species on non-forest land is increasing due to the growing demand for woody biomass for the future bioeconomy and to mitigate climate change impacts. However, forest plantations are often seen as a trade-off between climate benefits and low biodiversity. The diversity and composition of soil fungal biota in plantations of hybrid aspen, one of the most planted tree species for short-rotation forestry in Northern Europe, are poorly studied.

Methods

The goal of this study was to obtain baseline knowledge about the soil fungal biota and the edaphic, floristic and management factors that drive fungal richness and communities in 18-year-old hybrid aspen plantations on former agricultural soils and compare the fungal biota with those of European aspen stands on native forest land in a 130-year chronosequence. Sites were categorized as hybrid aspen (17-18-year-old plantations) and native aspen stands of three age classes (8-29, 30-55, and 65-131-year-old stands). High-throughput sequencing was applied to soil samples to investigate fungal diversity and assemblages.

Results

Native aspen forests showed a higher ectomycorrhizal (EcM) fungal OTU richness than plantations, regardless of forest age. Short-distance type EcM genera dominated in both plantations and forests. The richness of saprotrophic fungi was similar between native forest and plantation sites and was highest in the middle-aged class (30-55-year-old stands) in the native aspen stands. The fungal communities of native forests and plantations were significantly different. Community composition varied more, and the natural forest sites were more diverse than the relatively homogeneous plantations. Soil pH was the best explanatory variable to describe soil fungal communities in hybrid aspen stands. Soil fungal community composition did not show any clear patterns between the age classes of native aspen stands.

Conclusion

We conclude that edaphic factors are more important in describing fungal communities in both native aspen forest sites and hybrid aspen plantation sites than forest thinning, age, or former land use for plantations. Although first-generation hybrid aspen plantations and native forests are similar in overall fungal diversity, their taxonomic and functional composition is strikingly different. Therefore, hybrid aspen plantations can be used to reduce felling pressure on native forests; however, our knowledge is still insufficient to conclude that plantations could replace native aspen forests from the soil biodiversity perspective.

Characterization of the arbuscular mycorrhizal fungal community associated with rosewood in threatened Miombo forests

Understanding the dynamics of arbuscular mycorrhizal fungi (AMF) in response to land use change is important for the restoration of degraded forests. Here, we investigated the AMF community composition in the roots of Pterocarpus tinctorius sampled from agricultural and forest fallow soils rich in aluminum and iron. By sequencing the large subunit region of the rRNA gene, we identified a total of 30 operational taxonomic units (OTUs) in 33 root samples. These OTUs belonged to the genera Rhizophagus, Dominikia, Glomus, Sclerocystis, and Scutellospora. The majority of these OTUs did not closely match any known AMF species. We found that AMF species richness was significantly influenced by soil properties and overall tree density. Acidic soils with high levels of aluminum and iron had a low mean AMF species richness of 3.2. Indicator species analyses revealed several AMF OTUs associated with base saturation (4 OTUs), high aluminum (3 OTUs), and iron (2 OTUs). OTUs positively correlated with acidity (1 OTU), iron, and available phosphorus (2 OTUs) were assigned to the genus Rhizophagus, suggesting their tolerance to aluminum and iron. The results highlight the potential of leguminous trees in tropical dry forests as a reservoir of unknown AMF species. The baseline data obtained in this study opens new avenues for future studies, including the use of indigenous AMF-based biofertilizers to implement ecological revegetation strategies and improve land use.

Disturbance induces similar shifts in arbuscular mycorrhizal fungal communities from grassland and arable field soils

Anthropogenic disturbances play an increasingly important role in structuring the diversity and functioning of soil organisms such as arbuscular mycorrhizal (AM) fungi. Frequently, multiple land-use practices, which may represent disturbances for AM fungal communities, operate simultaneously in different habitats. It is not known, however, how previous land-use history and specific habitat type influence AM fungal community response to disturbances. We applied mechanical (cutting to stimulate tillage) and chemical (herbicide addition) disturbances to AM fungal communities from meadow and arable field soils. Our results indicated that AM fungal communities from meadows, which previously had experienced mowing, were more species rich than communities from fields that had experienced intensive land-use practices. There were no significant differences, however, in the responses to disturbance of the AM fungal communities from field and meadow soils. We expected mechanical disturbance to promote taxa from the family Glomeraceae which are expected to exhibit a ruderal life-history strategy; instead, the abundance of this family increased in response to chemical disturbance. Simultaneous application of mechanical disturbance and herbicide decreased only the abundance of Diversisporaceae. No AM fungal families increased in abundance when both mechanical and chemical disturbances were applied simultaneously, but all disturbances increased the abundance of culturable AM fungi. Our study demonstrates that although chemical and mechanical forms of disturbance favor different AM fungal families, existing information about family-level characteristics may not adequately characterize the life history strategies of AM fungus species.

Hedgerows increase the diversity and modify the composition of arbuscular mycorrhizal fungi in Mediterranean agricultural landscapes

Sustainable agriculture is essential to address global challenges such as climate change and biodiversity loss. Hedgerows enhance aboveground biodiversity and provide ecosystem services, but little is known about their impact on soil biota. Arbuscular mycorrhizal (AM) fungi are one of the key components of belowground biodiversity. We compared the diversity and composition of AM fungal communities at four farmland sites located in Central Spain, where 132 soil samples in total were collected to assess soil physical and chemical properties and the AM fungal communities. We compared the richness (number of AM fungal taxa), taxonomic, functional, and phylogenetic diversity, and structure of the AM fungal communities across three farmland habitat types, namely hedgerows, woody crops (olive groves and vineyard), and herbaceous crops (barley, sunflower, and wheat). Our results showed positive effects of hedgerows on most diversity metrics. Almost 60% of the AM fungal taxa were shared among the three farmland habitat types. Hedgerows increased AM fungal taxonomic richness (31%) and alpha diversity (25%), and especially so compared to herbaceous crops (45% and 28%, respectively). Hedgerows harbored elevated proportions of AM fungi with non-ruderal life-history strategies. AM fungal communities were more similar between hedgerows and woody crops than between hedgerows and adjacent herbaceous crops, possibly because of differences in tillage and fertilization. Unexpectedly, hedgerows reduced phylogenetic diversity, which might be related to more selective associations of AM fungi with woody plants than with herbaceous crops. Overall, the results suggest that planting hedgerows contributes to maintain belowground diversity. Thus, European farmers should plant more hedgerows to attain the goals of the EU Biodiversity Strategy for 2030.

Soil microbial communities shift along an urban gradient in Berlin, Germany

The microbial communities inhabiting urban soils determine the functioning of these soils, in regards to their ability to cycle nutrients and support plant communities. In an increasingly urbanized world these properties are of the utmost importance, and the microbial communities responsible are worthy of exploration. We used 53 grassland sites spread across Berlin to describe and explain the impacts of urbanity and other environmental parameters upon the diversity and community composition of four microbial groups. These groups were (i) the Fungi, with a separate dataset for (ii) the Glomeromycota, (iii) the Bacteria, and (iv) the protist phylum Cercozoa. We found that urbanity had distinct impacts on fungal richness, which tended to increase. Geographic distance between sites and soil chemistry, in addition to urbanity, drove microbial community composition, with site connectivity being important for Glomeromycotan communities, potentially due to plant host communities. Our findings suggest that many microbial species are well adapted to urban soils, as supported by an increase in diversity being a far more common result of urbanity than the reverse. However, we also found distinctly separate distributions of operational taxonomic unit (OTU)s from the same species, shedding doubt of the reliability of indicator species, and the use of taxonomy to draw conclusion on functionality. Our observational study employed an extensive set of sites across an urbanity gradient, in the region of the German capital, to produce a rich microbial dataset; as such it can serve as a blueprint for other such investigations.

Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant-Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient

The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.

Climate warming promotes deterministic assembly of arbuscular mycorrhizal fungal communities

Arbuscular mycorrhizal fungi (AMF) significantly contribute to plant resource acquisition and play important roles in mediating plant interactions and soil carbon (C) dynamics. However, it remains unclear how AMF communities respond to climate change. We assessed impacts of warming and precipitation alterations (30% increase or decrease) on soil AMF communities, and examined major ecological processes shaping the AMF community assemblage in a Tibetan alpine meadow. Our results showed that warming significantly increased root biomass, and available nitrogen (N) and phosphorus (P) in soil. While precipitation alterations increased AMF abundances, they did not significantly affect the composition or diversity of AMF communities. In contrast, warming altered the composition of AMF communities and reduced their Shannon-Wiener index and Pielou's evenness. In particular, warming shifted the AMF community composition in favor of Diversisporaceae over Glomeraceae, likely through its impact on soil N and P availability. In addition, AMF communities were phylogenetically random in the unwarmed control but clustered in warming plots, implying more deterministic community assembly under climate warming. Warming enhancement of root growth, N and P availability likely reduced plant C-allocation to AMF, imposing stronger environmental filtering on AMF communities. We further proposed a conceptual framework that integrates biological and geochemical processes into a mechanistic understanding of warming and precipitation changes' effects on AMF. Taken together, these results suggest that soil AMF communities may be more sensitive to warming than expected, highlighting the need to monitor their community structure and associated functional consequences on plant communities and soil C dynamics under the future warmer climate.

Agricultural land-use favours Mucoromycotinian, but not Glomeromycotinian, arbuscular mycorrhizal fungi across ten biomes

Globally, agricultural land-use negatively affects soil biota that contribute to ecosystem functions such as nutrient cycling, yet arbuscular mycorrhizal fungi (AMF) are promoted as essential components of agroecosystems. Arbuscular mycorrhizal fungi include Glomeromycotinian AMF (G-AMF) and the arbuscule-producing fine root endophytes, recently re-classified into the Endogonales order within Mucoromycotina. The correct classification of Mucoromycotinian AMF (M-AMF) and the availability of new molecular tools can guide research to better the understanding of their diversity and ecology. To investigate the impact on G-AMF and M-AMF of agricultural land-use at a continental scale, we sampled DNA from paired farm and native sites across 10 Australian biomes. Glomeromycotinian AMF were present in both native and farm sites in all biomes. Putative M-AMF were favoured by farm sites, rare or absent in native sites, and almost entirely absent in tropical biomes. Temperature, rainfall, and soil pH were strong drivers of richness and community composition of both groups, and plant richness was an important mediator. Both fungal groups occupy different, but overlapping, ecological niches, with M-AMF thriving in temperate agricultural landscapes. Our findings invite exploration of the origin and spread of M-AMF and continued efforts to resolve the phylogeny of this newly reclassified group of AMF.

Arbuscular mycorrhizal fungi promote small-scale vegetation recovery in the forest understorey

Root-associating arbuscular mycorrhizal (AM) fungi foster vegetation recovery in degraded habitats. AM fungi increase nutrient availability for host plants; therefore, their importance is expected to be higher when nutrient availability is low. However, little is known about how small-scale variation in nutrient availability influences plant and AM fungal communities in a stable ecosystem. We conducted a 2-year field study in the understorey of a boreonemoral forest where we examined plant and AM fungal communities at microsites (15 cm diameter) with intact vegetation cover and at disturbed microsites where vegetation was cleared away and soil was sterilized to remove soil biota. We manipulated soil nutrient content (increased with fertilizer, unchanged, or decreased with sucrose addition) and fungal activity (natural or suppressed by fungicide addition) at these microsites. After two vegetation seasons, manipulations with nutrient content resulted in significant, although moderate, differences in the content of soil nutrients (e.g. in soil phosphorus). Suppression of fungal activity resulted in lower richness, abundance and phylogenetic diversity of AM fungal community, independently of microsite type and soil fertility level. Plant species richness and diversity decreased when fungal activity was suppressed at disturbed but not in intact microsites. The correlation between plant and AM fungal communities was not influenced by microsite type or soil fertility. We conclude that small-scale variation in soil fertility and habitat integrity does not influence the interactions between plants and AM fungi. The richness, but not composition, of AM fungal communities recovered fast after small-scale disturbance and supported the recovery of species-rich vegetation.

Hierarchical spatial sampling reveals factors influencing arbuscular mycorrhizal fungus diversity in Côte d'Ivoire cocoa plantations

While many molecular studies have documented arbuscular mycorrhizal fungi (AMF) communities in temperate ecosystems, very few studies exist in which molecular techniques have been used to study tropical AMF communities. Understanding the composition of AMF communities in tropical areas gains special relevance as crop productivity in typically low fertility tropical soils can be improved with the use of AMF. We used a hierarchical sampling approach in which we sampled soil from cocoa (Theobroma cacao L.) plantations nested in localities, and in which localities were nested within each of three regions of Côte d'Ivoire. This sampling strategy, combined with 18S rRNA gene sequencing and a dedicated de novo OTU-picking model, allowed us to study AMF community composition and how it is influenced at different geographical scales and across environmental gradients. Several factors, including pH, influenced overall AMF alpha diversity and differential abundance of specific taxa and families of the Glomeromycotina. Assemblages and diversity metrics at the local scale did not reliably predict those at regional scales. The amount of variation explained by soil, climate, and geography variables left a large proportion of the variance to be explained by other processes, likely happening at smaller scales than the ones considered in this study. Gaining a better understanding of processes involved in shaping tropical AMF community composition and AMF establishment are much needed and could allow for the development of sustainable, productive tropical agroecosystems.

Organic agricultural practice enhances arbuscular mycorrhizal symbiosis in correspondence to soil warming and altered precipitation patterns

Climate and agricultural practice interact to influence both crop production and soil microbes in agroecosystems. Here, we carried out a unique experiment in Central Germany to simultaneously investigate the effects of climates (ambient climate vs. future climate expected in 50-70 years), agricultural practices (conventional vs. organic farming), and their interaction on arbuscular mycorrhizal fungi (AMF) inside wheat (Triticum aestivum L.) roots. AMF communities were characterized using Illumina sequencing of 18S rRNA gene amplicons. We showed that climatic conditions and agricultural practices significantly altered total AMF community composition. Conventional farming significantly affected the AMF community and caused a decline in AMF richness. Factors shaping AMF community composition and richness at family level differed greatly among Glomeraceae, Gigasporaceae and Diversisporaceae. An interactive impact of climate and agricultural practices was detected in the community composition of Diversisporaceae. Organic farming mitigated the negative effect of future climate and promoted total AMF and Gigasporaceae richness. AMF richness was significantly linked with nutrient content of wheat grains under both agricultural practices.

Molecular Diversity and Distribution of Arbuscular Mycorrhizal Fungi at Different Elevations in Mt. Taibai of Qinling Mountain

Arbuscular mycorrhizal fungi (AMFs) play a vital role in ecosystems, especially in ecosystem variability, diversity, and function. Understanding the AMF diversity, distribution, and their driver at different altitudinal gradients is a benefit for understanding the ecological function of AMF in mountain ecosystems. In this study, we explored the AMF molecular diversity and their distribution from 660 to 3,500 m a.s.l. in Mount Taibai of Qinling Mountains based on high-throughput sequencing technology. A total of 702 operational taxonomic units (OTUs) in 103 species of AMF are isolated from soil samples, which belong to 18 identified and 1 unidentified genus in 10 families. The fungi in the genus of Glomus is the most dominant, with the occurrence frequency of 100% and the relative abundance of 42.268% and 33.048% on the species and OTU level, respectively. The AMF colonization in root could be simulated by a cubic function with the change of altitudes with the peak and trough at a.s.l. 1,170 and 2,850 m, respectively. Further, AMF diversity indices including Sob, Shannon diversity, and Pielou evenness also showed the same cubic function change trends with increasing altitude at OTU and species levels. However, the average values of diversity indices at OTU level are always higher than these at the species level. Based on the OTU level, the highest and lowest values of Shannon and Pielou indices are observed at the altitudes of 1,400 and 2,800 m, respectively. The pattern of AMF community distribution in Mt. Taibai is driven by altitude with the characteristics of more abundance in the medium- to low-altitude than high-altitude areas. In general, abundant AMF molecular diversity and species exit in different elevations of Mt. Taibai, which indicate gradient changes with elevations.

Understanding Multilevel Selection May Facilitate Management of Arbuscular Mycorrhizae in Sustainable Agroecosystems

Studies in natural ecosystems show that adaptation of arbuscular mycorrhizal (AM) fungi and other microbial plant symbionts to local environmental conditions can help ameliorate stress and optimize plant fitness. This local adaptation arises from the process of multilevel selection, which is the simultaneous selection of a hierarchy of groups. Studies of multilevel selection in natural ecosystems may inform the creation of sustainable agroecosystems through developing strategies to effectively manage crop microbiomes including AM symbioses. Field experiments show that the species composition of AM fungal communities varies across environmental gradients, and that the biomass of AM fungi and their benefits for plants generally diminish when fertilization and irrigation eliminate nutrient and water limitations. Furthermore, pathogen protection by mycorrhizas is only important in environments prone to plant damage due to pathogens. Consequently, certain agricultural practices may inadvertently select for less beneficial root symbioses because the conventional agricultural practices of fertilization, irrigation, and use of pesticides can make these symbioses superfluous for optimizing crop performance. The purpose of this paper is to examine how multilevel selection influences the flow of matter, energy, and genetic information through mycorrhizal microbiomes in natural and agricultural ecosystems, and propose testable hypotheses about how mycorrhizae may be actively managed to increase agricultural sustainability.

Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert Habitats

Deserts cover a significant proportion of the Earth’s surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages.

Different wheat cultivars exhibit variable responses to inoculation with arbuscular mycorrhizal fungi from organic and conventional farms

The present study aimed to investigate the effects of arbuscular mycorrhizal (AM) fungal communities originating from organic and conventional agriculture on wheat growth and yield. Six different spring wheat cultivars released in different years in north and central European countries were considered. We hypothesised that AM fungal inoculum collected from organic agricultural fields would elicit a greater positive growth response than inoculum collected from conventional agricultural fields; and that older cultivars, which were developed under conditions of low fertilizer input, would exhibit overall greater growth responses to the presence of AM fungi, compared with more recent cultivars, and that AM fungal inoculum from conventional fields might have the most beneficial effect on the growth and yield of recent cultivars. The results showed that the overall effects on the growth and yield of spring wheat grown with organic and conventional AM fungal inocula did not differ greatly. However, the inoculation growth response, showing the difference of the effects of organic and conventional inocula, varied between particular wheat cultivars. Inoculation growth response of the cultivar Pikker (released in 1959) was the most positive, while that of the cultivar Arabella (released in 2012) was the most negative. The use of AM fungal inoculum from organic fields resulted in slightly taller plant individuals. Pikker showed relatively higher yield and stronger growth when the organic AM fungal inoculum was used. Arabella exhibited relatively lower yield and weaker growth when the organic inoculum was used. Whether the positive response of Pikker to Estonian organic inoculation reflects adaptation to the locally occurring AM fungal community needs to be established by further studies of the communities of AM fungi colonizing wheat roots.

Trait-based aerial dispersal of arbuscular mycorrhizal fungi

Dispersal is a key process driving local-scale community assembly and global-scale biogeography of plant symbiotic arbuscular mycorrhizal (AM) fungal communities. A trait-based approach could improve predictions regarding how AM fungal aerial dispersal varies by species. We conducted month-long collections of aerial AM fungi for 12 consecutive months in an urban mesic environment at heights of 20 m. We measured morphological functional traits of collected spores and assessed aerial AM fungal community structure both morphologically and with high-throughput sequencing. Large numbers of AM fungal spores were present in the air over the course of one year and these spores exhibited traits that facilitate aerial dispersal. Measured aerial spores were smaller than average for Glomeromycotinan fungi. Trait-based predictions indicate that nearly 1/3 of described species from diverse genera demonstrate the potential for aerial dispersal. Diversity of aerial AM fungi was relatively high (20 spore species and 17 virtual taxa) and both spore abundance and community structure shifted temporally. The prevalence of aerial dispersal in AM fungi is perhaps greater than previously indicated and a hypothesized model of AM fungal aerial dispersal mechanisms is presented. Anthropogenic soil impacts may liberate AM fungal propagules initiating the dispersal of ruderal species.

Environmental factors driving arbuscular mycorrhizal fungal communities associated with endemic woody plant Picconiaazorica on native forest of Azores

Abstract

Purpose

Arbuscular mycorrhizal fungi (AMF) play important key roles in the soil ecosystems as they link plants to the root-inaccessible part of soil. The aims of this study were to investigate which environmental factors influence the spatial and temporal structuring of AMF communities associated to Picconia azorica in two Azorean islands (Terceira and São Miguel islands), and investigate the seasonal variation in AMF communities between the two islands.

Methods

Communities of AMF associated with P. azorica in native forest of two Azorean islands (Terceira and São Miguel) were characterised by spore morphology or molecular analysis.

Results

Forty-five AMF spore morphotypes were detected from the four fragments of P. azorica forest representing nine families of AMF. Acaulosporaceae (14) and Glomeraceae (9) were the most abundant families. AMF density and root colonisation varied significantly between islands and sampling sites. Root colonisation and spore density exhibited temporal patterns, which peaked in spring and were higher in Terceira than in São Miguel. The relative contribution of environmental factors showed that factors such as elevation, relative air humidity, soil pH, and soil available P, K, and Mg influenced AMF spore production and root colonisation.

Conclusion

Different sporulation patterns exhibited by the members of the commonest families suggested different life strategies. Adaptation to a particular climatic and soil condition and host phenology may explain seasonal differences in sporulation patterns. Cohorts of AMF associated to P. azorica are shaped by regional processes including environmental filters such as soil properties and natural disturbance.

Rehabilitation time has greater influences on soil mechanical composition and erodibility than does rehabilitation land type in the hilly-gully region of the Loess Plateau, China

Background

The major landscape in the hilly-gully region of the Loess Plateau is greatly affected by vegetation rehabilitation on abandoned cropland. Although many studies have shown that the rehabilitation have greatly improved soil conditions and protected them from erosion, these effectiveness were not always in consensus possibly due to the land type of vegetation or to the rehabilitation time. To close this gap, we conducted a long term experiment as follows.

Methods

In this study, we analysed four land types of vegetation rehabilitation (shrub land, woodland, naturally revegetated grassland, and orchard land) with different rehabilitation times and investigated the mechanical composition and erodibility of the soil. Areas of slope croplandand natural forest were selected as controls.

Results

The results showed that soil depth, rehabilitation time and rehabilitation land type had strong impacts on soil mechanical composition, micro-aggregation and erodibility. Following rehabilitation, naturally revegetated grassland and shrub land had lower fractal dimensions of particle size distribution (fractal dimensions of PSD), fractal dimensions of micro-aggregation, and erodibility (K factor) than did cropland. Compared to the positive effects of rehabilitation mainly happened in the topsoil layer at other rehabilitation land type, that of woodland happened in the deeper soil layer. Besides, the indispensable rehabilitation time for the significant improvement of soil condition was shorter at naturally revegetated grassland than that at shrub land and woodland.

Discussion

Although rehabilitation time was more influential than was rehabilitation land type or soil depth, the differences among the rehabilitation land types showed that naturally revegetated grassland with native plants is the most time-saving rehabilitation vegetation for the Loess Plateau in the conversion from slope cropland. The success of rehabilitation in this forestry practice was mainly contributed by the suited species of rehabilitation land type to the local climate and soil. Based on the differences of rehabilitation effectiveness resulting from land type, we should be cautious to choose land types for the rehabilitation of soil conditions in the Loess Plateau.

Impact of biochar application dose on soil microbial communities associated with rubber trees in North East Thailand

Biochar is a potential tool to mitigate climate change by enhancing C sequestration in soils, but its use as a soil amendment to improve soil fertility and crop yields is still a contentious subject. In North East (NE) Thailand, biochar has been promoted to restore soil fertility in rubber tree plantations. Despite this, there is scarce information on the impact of biochar application on the soil biota, particularly on microbial communities associated with rubber trees. The effects of increasing doses of biochar on microbial communities were investigated in a rubber tree plantation in NE Thailand, 28 months after application. Biochar application resulted in increases of soil pH and nutrient contents and also had an impact on both bacterial and fungal communities. Changes in microbial composition and structure were observed although fungal communities were more markedly affected than bacterial communities. The nature and magnitude of the observed changes were strongly related to soil properties (pH, soil moisture and P content), while biochar dose (5, 10 or 20 tons/ha) effect was not significant. Our results highlight the need for additional research for a better understanding of the impact of biochar application on soil microbial communities and further cascading effects on ecosystem functions.

Soil Organic Carbon Shapes AMF Communities in Soils and Roots of Cynodon dactylon under Anti-Seasonal Drying-Wetting Cycles

Anti-seasonal drying-wetting cycles since 2010 have substantially altered its soil and vegetation status in the drawdown zone of China’s Three Gorges Reservoir (TGR). Such alternations may thus affect the composition and functioning of soil microbial communities, including the beneficial arbuscular mycorrhizal fungi (AMF), which enhance plant performance. Moreover, limited information is available if AMF communities are different in soils and roots, particularly under contrasting land-use changes. By combining the Illumina Miseq sequencing with bioinformatics analyses, AMF communities in both rhizosphere soils and roots of a stoloniferous and rhizomatous C4 perennial of Cynodon dactylon were characterized under three land-use types: (1) crop cultivated, (2) non-cultivated non-disturbed, and (3) disturbed non-cultivated land. A total of 35 and 26 AMF taxa were respectively detected from C. dactylon rhizosphere soils and roots from these three land-use types, which had endured four anti-seasonal drying/summer-wetting/winter cycles. Contrasting differentiations in the AMF community composition and structure were displayed in the C. dactylon rhizosphere soils and roots, and between land-use types. Nonmetric multidimensional scaling analyses revealed that AMF communities significantly correlated to soil organic carbon in the rhizosphere soils and roots of C. dactylon, to land-use types only in rhizosphere soils, whereas to soil moisture only in roots. Our results highlight the effects of soil nutrients and land-use changes on AMF community composition and diversity under the canopy of C. dactylon in TGR. The identified dominant AMF taxa can be employed to vegetation restoration in such degraded habitats globally.

Impacts of long-term elevated atmospheric CO2 concentrations on communities of arbuscular mycorrhizal fungi

The ecological impacts of long-term elevated atmospheric CO2 (eCO2 ) levels on soil microbiota remain largely unknown. This is particularly true for the arbuscular mycorrhizal (AM) fungi, which form mutualistic associations with over two-thirds of terrestrial plant species and are entirely dependent on their plant hosts for carbon. Here, we use high-resolution amplicon sequencing (Illumina, HiSeq) to quantify the response of AM fungal communities to the longest running (>15 years) free-air carbon dioxide enrichment (FACE) experiment in the Northern Hemisphere (GiFACE); providing the first evaluation of these responses from old-growth (>100 years) semi-natural grasslands subjected to a 20% increase in atmospheric CO2 . eCO2 significantly increased AM fungal richness but had a less-pronounced impact on the composition of their communities. However, while broader changes in community composition were not observed, more subtle responses of specific AM fungal taxa were with populations both increasing and decreasing in abundance in response to eCO2 . Most population-level responses to eCO2 were not consistent through time, with a significant interaction between sampling time and eCO2 treatment being observed. This suggests that the temporal dynamics of AM fungal populations may be disturbed by anthropogenic stressors. As AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in population densities in response to eCO2 may significantly impact terrestrial plant communities and their productivity. Thus, predictions regarding future terrestrial ecosystems must consider changes both aboveground and belowground, but avoid relying on broad-scale community-level responses of soil microbes observed on single occasions.

Land Use Change and Water Quality Use for Irrigation Alters Drylands Soil Fungal Community in the Mezquital Valley, Mexico

Soil fungal communities provide important ecosystem services, however, some soil borne representatives damage agricultural productivity. Composition under land-use change scenarios, especially in drylands, is rarely studied. Here, the soil fungal community composition and diversity of natural shrubland was analyzed and compared with agricultural systems irrigated with different water quality, namely rain, fresh water, dam-stored, and untreated wastewater. Superficial soil samples were collected during the dry and rainy seasons. Amplicon-based sequencing of the ITS2 region was performed on total DNA extractions and used the amplicon sequence variants to predict specific fungal trophic modes with FUNGuild. Additionally, we screened for potential pathogens of crops and humans and assessed potential risks. Fungal diversity and richness were highest in shrubland and least in the wastewater-irrigated soil. Soil moisture together with soil pH and exchangeable sodium were the strongest drivers of the fungal community. The abundance of saprophytic fungi remained constant among the land use systems, while symbiotic and pathogenic fungi of plants and animals had the lowest abundance in soil irrigated with untreated wastewater. We found lineage-specific adaptations to each land use system: fungal families associated to shrubland, rainfed and part of the freshwater were adapted to drought, hence sensitive to exchangeable sodium content and most of them to N and P content. Taxa associated to freshwater, dam wastewater and untreated wastewater irrigated systems show the opposite trend. Additionally, we identified potentially harmful human pathogens that might be a health risk for the population.

Abiotic rather than biotic filtering shapes the arbuscular mycorrhizal fungal communities of European seminatural grasslands

Although it is well known that arbuscular mycorrhizal fungi (AMF) play a key role in the functioning of natural ecosystems, the underlying drivers determining the composition of AMF communities remain unclear. In this study, we established 138 sampling plots at 46 grassland sites, consisting of 26 acidic grasslands and 20 calcareous grasslands spread across eight European countries, to assess the relative importance of abiotic and biotic filtering in driving AMF community composition and structure in both the grassland soils and in the roots of 13 grassland plant species. Soil AMF communities differed significantly between acidic and calcareous grasslands. In root AMF communities, most variance was attributable to soil variables while very little variation was explained by host plant identity. Root AMF communities in host plant species occurring in only one grassland type closely resembled the soil AMF communities of that grassland type and the root AMF communities of other host plant species occurring in the same grassland type. The observed AMF-host plants networks were not modular but nested. Our results indicate that abiotic conditions, rather than biotic filtering through host plant specificity, are the most important drivers in shaping AMF communities in European seminatural grasslands.

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities

Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored taxa, indicating that dispersal may be human-mediated or require tolerance of significant environmental stress, such as exposure to sunlight or high salinity. The processes driving large-scale patterns of microbial diversity are a key consideration for attempts to conserve and restore functioning ecosystems in this era of rapid global change.

Arbuscular mycorrhizal fungal communities in tropical rain forest are resilient to slash-and-burn agriculture

Certain forestry and agricultural practices are known to affect arbuscular mycorrhizal (AM) fungal communities, but the effects of deforestation – including slash-and-burn management and other more severe disturbances – in tropical rain forests are poorly understood. We addressed the effects of anthropogenic disturbance on rain-forest AM fungal communities in French Guiana, by comparing mature tropical rain forest, slash-and-burn (5 y old) and clearcut areas (8 y old). A total of 36 soil samples were collected in six plots and sequenced using a high throughput 454-pyrosequencing platform. A total of 32649 sequences from 103 AM fungal virtual taxa (VT) were recorded. Whereas alpha diversity of AM fungi did not decrease due to land-use intensification, with average richness ranging from 17 to 21 taxa per plot, beta diversity (average distance to multivariate centroid) dropped by 28% from 0.46 in rain forest to 0.33 under clearcutting. AM fungal community composition was correlated with land use and soil chemical properties. Clearcut areas were characterized by the more frequent occurrence of specialist AM fungi, compared with mature forest or slash-and-burn areas. Specifically, clearcuts contained the highest proportions of VT that were geographic (21%), habitat (31%), abundance (97%) or host (97%) specialists based on VT metadata contained in the MaarjAM database. This suggests that certain AM fungi with narrow ecological niches have traits that allow them to exploit conditions of severe disturbance. In conclusion, slash-and-burn management appears to allow diverse AM fungal communities to persist, and may favour regeneration of tropical rain forest after abandonment. More severe disturbance in the form of clearcutting resulted in marked changes in AM fungal communities.

Anthropogenic disturbance equalizes diversity levels in arbuscular mycorrhizal fungal communities

The arbuscular mycorrhizal (AM) symbiosis is a key plant-microbe interaction in sustainable functioning ecosystems. Increasing anthropogenic disturbance poses a threat to AM fungal communities worldwide, but there is little empirical evidence about its potential negative consequences. In this global study, we sequenced AM fungal DNA in soil samples collected from pairs of natural (undisturbed) and anthropogenic (disturbed) plots in two ecosystem types (10 naturally wooded and six naturally unwooded ecosystems). We found that ecosystem type had stronger directional effects than anthropogenic disturbance on AM fungal alpha and beta diversity. However, disturbance increased alpha and beta diversity at sites where natural diversity was low and decreased diversity at sites where natural diversity was high. Cultured AM fungal taxa were more prevalent in anthropogenic than natural plots, probably due to their efficient colonization strategies and ability to recover from disturbance. We conclude that anthropogenic disturbance does not have a consistent directional effect on AM fungal diversity; rather, disturbance equalizes levels of diversity at large scales and causes changes in community functional structure.

Effects of land use on arbuscular mycorrhizal fungal communities in Estonia

Arbuscular mycorrhizal (AM) fungal communities vary across habitat types, as well as across different land use types. Most relevant research, however, has focused on agricultural or other severely human-impacted ecosystems. Here, we compared AM fungal communities across six habitat types: calcareous grassland, overgrown ungrazed calcareous grassland, wooded meadow, farmyard lawn, boreonemoral forest, and boreonemoral forest clear-cut, exhibiting contrasting modes of land use. AM fungi in the roots of a single host plant species, Prunella vulgaris, and in its rhizosphere soil were identified using 454-sequencing from a total of 103 samples from 12 sites in Estonia. Mean AM fungal taxon richness per sample did not differ among habitats. AM fungal community composition, however, was significantly different among habitat types. Both abandonment and land use intensification (clearcutting; trampling combined with frequent mowing) changed AM fungal community composition. The AM fungal communities in different habitat types were most similar in the roots of the single host plant species and most distinct in soil samples, suggesting a non-random pattern in host-fungal taxon interactions. The results show that AM fungal taxon composition is driven by habitat type and land use intensity, while the plant host may act as an additional filter between the available and realized AM fungal species pool.

Disturbance reduces the differentiation of mycorrhizal fungal communities in grasslands along a precipitation gradient

Given that mycorrhizal fungi play key roles in shaping plant communities, greater attention should be focused on factors that determine the composition of mycorrhizal fungal communities and their sensitivity to anthropogenic disturbance. We investigate changes in arbuscular mycorrhizal (AM) fungal community composition across a precipitation gradient in North American grasslands as well as changes occurring with varying degrees of site disturbance that have resulted in invasive plant establishment. We find strong differentiation of AM fungal communities in undisturbed remnant grasslands across the precipitation gradient, whereas communities in disturbed grasslands were more homogeneous. These changes in community differentiation with disturbance are consistent with more stringent environmental filtering of AM fungal communities in undisturbed sites that may also be promoted by more rigid functional constraints imposed on AM fungi by the native plant communities in these areas. The AM fungal communities in eastern grasslands were particularly sensitive to anthropogenic disturbance, with disturbed sites having low numbers of AM fungal operational taxonomic units (OTUs) commonly found in undisturbed sites, and also the proliferation of AM fungal OTUs in disturbed sites. This proliferation of AM fungi in eastern disturbed sites coincided with increased soil phosphorus availability and is consistent with evidence suggesting the fungi represented by these OTUs would provide reduced benefits to native plants. The differentiation of AM fungal communities along the precipitation gradient in undisturbed grasslands but not in disturbed sites is consistent with AM fungi aiding plant adaptation to climate, and suggests they may be especially important targets for conservation and restoration in order to help maintain or re-establish diverse grassland plant communities.

Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi

The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes. We then calculated community completeness, an index showing the fraction of the species pool present, which is expected to reflect local processes. We found significant spatial variation, globally in species pool size, as well as in local and dark diversity (absent members of the species pool). Species pool size was larger close to areas containing tropical grasslands during the last glacial maximum, which are possible centres of diversification. Community completeness was greater in regions of high wilderness (remoteness from human disturbance). Local diversity was correlated with wilderness and current connectivity to mountain grasslands. Applying the species pool concept to symbiotic fungi facilitated a better understanding of how biodiversity can be jointly shaped by large-scale historical processes and recent human disturbance.