Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

Davison, John; Moora, Mari; Öpik, Maarja; Adholeya, Alok; Ainsaar, Leho; Bâ, Amadou; Sashidhar, Burla; Diédhiou, Abdoulaye; Hiiesalu, Inga; Jairus, Teele; Johnson, Nancy Collins; Kane, Aboubacry; Koorem, Kadri; Kochar, Mandira; Ndiaye, Cheikh; Pärtel, Meelis; Reier, Ülle; Saks, Ülle; Singh, Rajvikram; Vasar, Martti; Zobel, Martin

doi:10.1126/science.aab1161

Cited by 667 publications

(656 citation statements)

References 78 publications

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“…Arbuscular mycorrhizal (AM) fungi, contained within the subphylum Glomeromycotina, are obligate symbiotic partners of up to 82% of land plants (Davison et al, 2015). This symbiosis is crucial for the plant communities' health and the functioning of nutrient cycles at the ecosystem level (Castillo et al, 2006;Etcheverría et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Factors affecting arbuscular mycorrhizal fungi of Chilean temperate rainforests

Marín

Aguilera

Oehl

et al. 2017

J. Soil Sci. Plant Nutr.

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While arbuscular mycorrhizal (AM) fungi in Chile have been widely documented in agro-ecosystems, there is a knowledge gap regarding AM fungal diversity in Chilean temperate rainforests. AM fungal communities of these forests are affected by several factors: the mountain systems of Chile (Coastal Range or Andes Mountains), the mycorrhizal dominance of the forest (either ectomycorrhizal -EM-or AM), soil chemistry, and altitude. We tested the effects of mountain system, mycorrhizal dominance, soil chemistry, and altitude on AM fungal diversity. From 7,120 AM fungal spores recovered, we identified 14 species, that were found in 41 soil samples collected from 14 plots located in EM and AM forests of the Coastal Range and Andes Mountains of Southern Chile. Mountain system and mycorrhizal dominance affected AM fungal community composition, although neither fungal richness nor abundance were affected. Soil Olsen available P, Ca, Mg, and Na were the edaphic variables structuring AM fungal community composition. There was no relationship between altitude and AM fungal richness, however at high altitudes there was higher abundance. Finally, with this and other studies, a total of 59 AM fungal species, many of which were previously registered exclusively in agroecosystems, are registered on the Chilean AM fungal species list.

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Section: Introductionmentioning

confidence: 99%

Factors affecting arbuscular mycorrhizal fungi of Chilean temperate rainforests

Marín

Aguilera

Oehl

et al. 2017

J. Soil Sci. Plant Nutr.

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“…3). Caution should also be exercised when assigning taxonomic attributions to environmental sequences using phylogenetic differentiation, such as the generalized mixed Yule coalescent (GMYC) (33) and Poisson tree processes (PTP) (61) methods, or using entities like the virtual taxa that are represented by voucher sequences in the MaarjAM database on the basis of both phylogenetic monophyly and high sequence similarity (32,57,62). For example, these methods would consistently underrepresent the diversity in groups with a small amount of between-species sequence variation, like some species in the Gigasporaceae ( Fig.…”

Section: Fig 4 Mds Visualizations Of Otu Clusters For Isolates Of Spementioning

confidence: 99%

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

House

Ekanayake

Ruan

et al. 2016

Appl Environ Microbiol

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Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus-and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCEArbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over-or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account. Sequences of rRNA genes have revolutionized our understanding of microbial diversity (1, 2) and the factors structuring microbial communities (3). When used in combination with high-throughput sequencing, rRNA gene sequences have provided critical insights into the composition and dynami...

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“…There is clear evidence that AMF community composition and distribution at different sites or in different habitats are affected mainly by host plant species and environmental factors such as soil type (6,7,10,29,31,33,(39)(40)(41). If soil type determines the composition and species richness of AMF communities, what are the key soil parameters defining such communities?…”

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confidence: 99%

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils

Alguacil

Torres

Montesinos‐Navarro

et al. 2016

Appl Environ Microbiol

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We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. IMPORTANCECommunities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions.A rbuscular mycorrhizal fungi (AMF) represent an important soil microbial group that affects multiple ecosystem functions and processes, including nutrient cycling, plant productivity and competition, and plant diversity. As a consequence, the number of ecological studies concerning AMF has increased considerably in recent years (1-9). Those studies considered AMF communities associated with different host plants in many different ecosystems. However, studies comparing the occurrence of specific AMF species and communities in different soil types are scarce and have focused mainly on cultivated soils and different land uses (10-13). Differences in soil types have been reported to be key factors determining AMF community composition (10), and this is particularly relevant in stressed environments such as serpentine soi...

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Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

Cited by 667 publications

References 78 publications

Factors affecting arbuscular mycorrhizal fungi of Chilean temperate rainforests

Factors affecting arbuscular mycorrhizal fungi of Chilean temperate rainforests

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils

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