Sophie van Rijssel

It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.

Aims Saprophytic fungi are important agents of soil mineralization and carbon cycling. Their community structure is known to be affected by soil conditions such as organic matter and pH. However, the effect of plant species, whose roots provide the litter input into the soil, on the saprophytic fungal community is largely unknown. Methods We examined the saprophytic fungi in a grassland biodiversity experiment with eight plant species belonging to two functional groups (grasses and forbs), combining DNA extraction from plant roots, next-generation sequencing and literature research. Results We found that saprophyte richness increased with plant species richness, but plant functional group richness was the best predictor. Plant functional group was also the main factor driving fungal saprophytic community structure. This effect was correlated with differences in root lignin content and C:N ratio between grasses and forbs. In monocultures, root traits and plant functional group type explained 16% of the variation in community structure. The saprophyte taxa detected in mixed plant communities were to a large extent subsets of those found in monocultures. Conclusions Our work shows that the richness and community structure of the root-associated saprophytic fungi can largely be predicted by plant functional groups and their associated root traits. This means that the effects of plant diversity on ecosystem functions such as litter decomposition may also be predictable using information on plant functional groups in grasslands.

There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships.

Questions The rapid climate warming in tundra ecosystems can increase nutrient availability in the soil, which may initiate shifts in vegetation composition. The direction in which the vegetation shifts will co-determine whether Arctic warming is mitigated or accelerated, making the understanding of successional trajectories urgent. One of the key factors influencing the competitive relationships between plant species is their access to nutrients, depending on the depth where they take up most nutrients. However, nutrient uptake at different soil depths by tundra plant species that differ in rooting depth is unclear. Location Kytalyk Nature Reserve, northeast Siberia, Russia. Methods We injected 15N to 5 cm, 15 cm and the thaw front of the soil in a moist tussock tundra. The absorption of 15N by grasses, sedges, deciduous shrubs and evergreen shrubs from the three depths was compared. Results The results clearly show a vertical differentiation of N uptake by these plant functional types, corresponding to their rooting strategy. Shallow-rooting dwarf shrubs were more capable of absorbing nutrients from the upper soil than from deeper soil. Deep-rooting grasses and sedges were more capable of absorbing nutrients from deeper soil than the dwarf shrubs. The natural 15N abundances in control plants also indicate that graminoids can absorb more nutrients from the deeper soil than dwarf shrubs. Conclusions Our results show that graminoids and shrubs in the Arctic differ in their N uptake strategies, with graminoids profiting from nutrients released at the thaw front, while shrubs mainly forage in upper soil layers. Our results suggest that tundra vegetation will become graminoid-dominated as permafrost thaw progresses and nutrient availability increases in the deep soil.