Jenni Nordén

Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi.

Before the recent revolution in molecular biology, field studies on fungal communities were mostly confined to fruit bodies, whereas mycelial interactions were studied in the laboratory. Here we combine high-throughput sequencing with a fruit body inventory to study simultaneously mycelial and fruit body occurrences in a community of fungi inhabiting dead wood of Norway spruce. We studied mycelial occurrence by extracting DNA from wood samples followed by 454-sequencing of the ITS1 and ITS2 regions and an automated procedure for species identification. In total, we detected 198 species as mycelia and 137 species as fruit bodies. The correlation between mycelial and fruit body occurrences was high for the majority of the species, suggesting that high-throughput sequencing can successfully characterize the dominating fungal communities, despite possible biases related to sampling, PCR, sequencing and molecular identification. We used the fruit body and molecular data to test hypothesized links between life history and population dynamic parameters. We show that the species that have on average a high mycelial abundance also have a high fruiting rate and produce large fruit bodies, leading to a positive feedback loop in their population dynamics. Earlier studies have shown that species with specialized resource requirements are rarely seen fruiting, for which reason they are often classified as red-listed. We show with the help of high-throughput sequencing that some of these species are more abundant as mycelium in wood than what could be expected from their occurrence as fruit bodies.

Warming-induced shift in European mushroom fruiting phenology

In terrestrial ecosystems, fungi are the major agents of decomposition processes and nutrient cycling and of plant nutrient uptake. Hence, they have a vital impact on ecosystem processes and the terrestrial carbon cycle. Changes in productivity and phenology of fungal fruit bodies can give clues to changes in fungal activity, but understanding these changes in relation to a changing climate is a pending challenge among ecologists. Here we report on phenological changes in fungal fruiting in Europe over the past four decades. Analyses of 746,297 dated and geo-referenced mushroom records of 486 autumnal fruiting species from Austria, Norway, Switzerland, and the United Kingdom revealed a widening of the annual fruiting season in all countries during the period 1970–2007. The mean annual day of fruiting has become later in all countries. However, the interspecific variation in phenological responses was high. Most species moved toward a later ending of their annual fruiting period, a trend that was particularly strong in the United Kingdom, which may reflect regional variation in climate change and its effects. Fruiting of both saprotrophic and mycorrhizal fungi now continues later in the year, but mycorrhizal fungi generally have a more compressed season than saprotrophs. This difference is probably due to the fruiting of mycorrhizal fungi partly depending on cues from the host plant. Extension of the European fungal fruiting season parallels an extended vegetation season in Europe. Changes in fruiting phenology imply changes in mycelia activity, with implications for ecosystem function.

High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples.

In this methodological study, we compare 454 sequencing and a conventional cloning and Sanger sequencing approach in their ability to characterize fungal communities PCR amplified from four root systems of the ectomycorrhizal plant Bistorta vivipara. To examine variation introduced by stochastic processes during the laboratory work, we replicated all analyses using two independently obtained DNA extractions from the same root systems. The ITS1 region was used as DNA barcode and the sequences were clustered into OTUs as proxies for species using single linkage clustering (BLASTClust) and 97% sequence similarity cut-off. A relatively low overlap in fungal OTUs was observed between the 454 and the clone library datasets — even among the most abundant OTUs. In a non-metric multidimensional scaling analysis, the samples grouped more according to methodology compared to plant. Some OTUs frequently detected by 454, most notably those OTUs with taxonomic affinity to Glomales, were not detected in the Sanger dataset. Likewise, a few OTUs, including Cenococcum sp., only appeared in the clone libraries. Surprisingly, we observed a significant relationship between GC/AT content of the OTUs and their proportional abundances in the 454 versus the clone library datasets. Reassuringly, a very good consistency in OTU recovery was observed between replicate runs of both sequencing methods. This indicates that stochastic processes had little impact when applying the same sequencing technique on replicate samples.

A fungal perspective on conservation biology

Hitherto fungi have rarely been considered in conservation biology, but this is changing as the field moves from addressing single species issues to an integrative ecosystem-based approach. The current emphasis on biodiversity as a provider of ecosystem services throws the spotlight on the vast diversity of fungi, their crucial roles in terrestrial ecosystems, and the benefits of considering fungi in concert with animals and plants. We reviewed the role of fungi in ecosystems and composed an overview of the current state of conservation of fungi. There are 5 areas in which fungi can be readily integrated into conservation: as providers of habitats and processes important for other organisms; as indicators of desired or undesired trends in ecosystem functioning; as indicators of habitats of conservation value; as providers of powerful links between human societies and the natural world because of their value as food, medicine, and biotechnological tools; and as sources of novel tools and approaches for conservation of megadiverse organism groups. We hope conservation professionals will value the potential of fungi, engage mycologists in their work, and appreciate the crucial role of fungi in nature.

Evaluating citizen science data for forecasting species responses to national forest management

Abstract The extensive spatial and temporal coverage of many citizen science datasets (CSD) makes them appealing for use in species distribution modeling and forecasting. However, a frequent limitation is the inability to validate results. Here, we aim to assess the reliability of CSD for forecasting species occurrence in response to national forest management projections (representing 160,366 km2) by comparison against forecasts from a model based on systematically collected colonization–extinction data. We fitted species distribution models using citizen science observations of an old‐forest indicator fungus Phellinus ferrugineofuscus. We applied five modeling approaches (generalized linear model, Poisson process model, Bayesian occupancy model, and two MaxEnt models). Models were used to forecast changes in occurrence in response to national forest management for 2020‐2110. Forecasts of species occurrence from models based on CSD were congruent with forecasts made using the colonization–extinction model based on systematically collected data, although different modeling methods indicated different levels of change. All models projected increased occurrence in set‐aside forest from 2020 to 2110: the projected increase varied between 125% and 195% among models based on CSD, in comparison with an increase of 129% according to the colonization–extinction model. All but one model based on CSD projected a decline in production forest, which varied between 11% and 49%, compared to a decline of 41% using the colonization–extinction model. All models thus highlighted the importance of protected old forest for P. ferrugineofuscus persistence. We conclude that models based on CSD can reproduce forecasts from models based on systematically collected colonization–extinction data and so lead to the same forest management conclusions. Our results show that the use of a suite of models allows CSD to be reliably applied to land management and conservation decision making, demonstrating that widely available CSD can be a valuable forecasting resource.

Reply to Gange et al.: Climate-driven changes in the fungal fruiting season in the United Kingdom.

The first comprehensive study of phenological changes in wild fungi (1) revealed a significantly earlier start and later end of the fungal fruiting season than nowadays, based on a dataset collected in a small area (30-mile radius) in southern England during 1950–2005. To determine whether these interesting results were reflected on a larger scale, we analyzed nationwide datasets from Austria, Norway, Switzerland, and the United Kingdom (2). Our analyses confirmed that, for the United Kingdom, the fruiting season has widened over the last half century. Like Gange et al. (1), we hypothesized that these changes are mainly driven by climatic variation. We are, therefore, surprised …