John Davison’s research while affiliated with University of Tartu and other places

Mycorrhizal symbiosis, specifically arbuscular mycorrhiza, is one of Earth's oldest and most widespread symbiosis. Existing evidence suggests that plant species differ in their associations with mycorrhizal partners, with different species reported to be always (obligately mycorrhizal, OM), sometimes (facultatively mycorrhizal, FM) or never (non‐mycorrhizal, NM) associating with arbuscular mycorrhizal (AM) fungi and this plant reliance on AM fungi is called plant mycorrhizal status. However, very little is known about how host plant mycorrhizal status shapes the network topology of interacting AM fungi. Here, we use a standardized sampling scheme to test whether plant species with different mycorrhizal statuses differ in mean AM fungal hyphal colonization and various indices of the AM fungal networks such as nestedness rank and resource range. We collected the roots and rhizosphere soil of 19 plant species representing five families. Each plant species was sampled from three distinct habitats. We determined AM fungal colonization in the roots and AM fungal community composition in roots and rhizosphere soil using molecular methods. We found that previously reported NM plant species had lower mean AM fungal colonization than FM plant species, but no differences were found between FM and OM plant species. Network analyses indicated that AM fungal communities in the roots of FM plant species had higher nestedness rank and resource range than networks associated with OM plant species, suggesting that OM plant species are more generalist regarding partner selection and interact with a wider range of fungal partners. Our results suggest that plant mycorrhizal status conveys useful information about the characteristics of AM fungal interaction networks, revealing that plant species consistently associated with AM fungi are less selective towards their fungal partners. Read the free Plain Language Summary for this article on the Journal blog.

Increasing extreme climatic events threaten the functioning of terrestrial ecosystems1,2. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning3,4. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils. Soil microbiomes exhibited a small, but highly consistent and phylogenetically conserved, response under the imposed extreme events. Heat treatment most strongly impacted soil microbiomes, enhancing dormancy and sporulation genes and decreasing metabolic versatility. Microbiome response to heat in particular could be predicted by local climatic conditions and soil properties, with soils that do not normally experience the extreme conditions being imposed being most vulnerable. Our results suggest that soil microbiomes from different climates share unified responses to extreme climatic events, but that predicting the extent of community change may require knowledge of the local microbiome. These findings advance our understanding of soil microbial responses to extreme events, and provide a first step for making general predictions about the impact of extreme climatic events on soil functioning.

We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant‐associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.

European dry thin-soil calcareous grasslands (alvars) are species-rich semi-natural habitats. Cessation of traditional management, such as mowing and grazing, leads to shrub and tree encroachment and the local extinction of characteristic alvar species. While soil microbes are known to play a critical role in driving vegetation and ecosystem dynamics, more information is needed about their composition and function in grasslands of different dynamic stages. Here we assess the composition of soil fungal, prokaryotic, and plant communities using soil environmental DNA from restored alvar grasslands in Estonia. The study areas included grasslands that had experienced different degrees of woody encroachment prior to restoration (woody plant removal and grazing), as well as unmanaged open grasslands. We found that, in general, different taxonomic groups exhibited correlated patterns of between-community variation. Previous forest sites, which had prior to restoration experienced a high degree of woody encroachment by ectomycorrhizal Scots pine, were compositionally most distinct from managed open grasslands, which had little woody vegetation even prior to restoration. The functional structure of plant and fungal communities varied in ways that were consistent with the representation of mycorrhizal types in the ecosystems prior to restoration. Compositional differences between managed and unmanaged open grasslands reflecting the implementation of grazing without further management interventions were clearer among fungal, and to an extent prokaryotic, communities than among plant communities. While previous studies have shown that during woody encroachment of alvar grassland, plant communities change first and fungal communities follow, our DNA-based results suggest that microbial communities reacted faster than plant communities during the restoration of grazing management in alvar grassland. We conclude that while the plant community responds faster to cessation of management, the fungal community responds faster to restoration of management. This may indicate hysteresis, where the eventual pathway back to the original state (grazed ecosystem) differs from the pathway taken towards the alternative state (abandoned semi-natural grassland ecosystem).

Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche‐based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche.

Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.

Mycorrhizal symbioses are known to strongly influence plant performance, structure plant communities and shape ecosystem dynamics. Plant mycorrhizal traits, such as those characterising mycorrhizal type (arbuscular (AM), ecto‐, ericoid or orchid mycorrhiza) and status (obligately (OM), facultatively (FM) or non‐mycorrhizal) offer valuable insight into plant belowground functionality. Here, we compile available plant mycorrhizal trait information and global occurrence data (∼$\sim$100 million records) for 11,770 vascular plant species. Using a plant phylogenetic mega‐tree and high‐resolution climatic and edaphic data layers, we assess phylogenetic and environmental correlates of plant mycorrhizal traits. We find that plant mycorrhizal type is more phylogenetically conserved than plant mycorrhizal status, while environmental variables (both climatic and edaphic; notably soil texture) explain more variation in mycorrhizal status, especially FM. The previously underestimated role of environmental conditions has far‐reaching implications for our understanding of ecosystem functioning under changing climatic and soil conditions.

Arbuscular mycorrhizal (AM) fungi can benefit plants under environmental stress, and influence plant adaptation to warmer climates. However, very little is known about the ecology of these fungi in alpine environments. We sampled plant roots along a large fraction (1941–6150 m asl) of the longest terrestrial elevational gradient on Earth and used DNA metabarcoding to identify AM fungi. We hypothesized that AM fungal alpha and beta diversity decreases with increasing elevation, and that different vegetation types comprise dissimilar communities, with cultured (putatively ruderal) taxa increasingly represented at high elevations. We found that alpha diversity of AM fungal communities declined linearly with elevation, whereas within-site taxon turnover (beta diversity) was unimodally related to elevation. Composition of AM fungal communities differed between vegetation types and was influenced by elevation, mean annual temperature and precipitation. In general, Glomeraceae taxa dominated at all elevations and vegetation types, however, higher elevations were associated with increased presence of Acaulosporaceae, Ambisporaceae and Claroideoglomeraceae. Contrary to our expectation, the proportion of cultured AM fungal taxa in communities decreased with elevation. These results suggest that, in this system, climate-induced shifts in habitat conditions may facilitate more diverse AM fungal communities at higher elevations but could also favour ruderal taxa.

Introduction Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.