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• Andrew, Carrie (2025). Not always optimal: Fungal fruiting triggers indicate climate sensitivity in cooler regions. Fungal ecology. ISSN 1754-5048. 75. doi: 10.1016/j.funeco.2025.101416. Full text in Research Archive Show summary

  Many fungi have environmentally-based fruiting triggers, which requires their quantification within the context of climate change. Species' optima were modelled for 127 commonly recorded European taxa for climate and weather conditions that were associated with their fruiting occurrences. Trends were reported based on their land-use biome associations, and attributes of species’ nutritional modes and the substrates they fruit from. The optimal fruiting conditions for over one third of the species demonstrated likely sensitivity to climate warming, whose optima predominantly clustered in the boreal forest and tundra, i.e., in regions most in peril for further warming. Niche breadths were narrower for terrestrially fruiting species, which suggested that daily weather perturbations will cause greater knock-on effects to terrestrial than wood-inhabiting taxa. All species were sensitive to extremes in daily recorded temperatures. These results add to the mounting evidence that biodiversity in high-latitude regions is increasingly threatened from warming temperatures.

• Michaud, Talia J.; Pearse, Ian S.; Kauserud, Håvard; Andrew, Carrie & Kennedy, Peter G. (2024). Mast seeding in European beech (Fagus sylvatica L.) is associated with reduced fungal sporocarp production and community diversity. Ecology Letters. ISSN 1461-023X. 27(6). doi: 10.1111/ele.14460. Full text in Research Archive Show summary

  Mast seeding is a well-documented phenomenon across diverse forest ecosystems. While its effect on aboveground food webs has been thoroughly studied, how it impacts the soil fungi that drive soil carbon and nutrient cycling has not yet been explored. To evaluate the relationship between mast seeding and fungal resource availability, we paired a Swiss 29-year fungal sporocarp census with contemporaneous seed production for European beech (Fagus sylvatica L.). On average, mast seeding was associated with a 55% reduction in sporocarp production and a compositional community shift towards drought-tolerant taxa across both ectomycorrhizal and saprotrophic guilds. Among ectomycorrhizal fungi, traits associated with carbon cost did not explain species' sensitivity to seed production. Together, our results support a novel hypothesis that mast seeding limits annual resource availability and reproductive investment in soil fungi, creating an ecosystem ‘rhythm’ to forest processes that is synchronized above- and belowground.

• Chala, Desalegn; Kusch, Erik; Weiland, Claus; Andrew, Carrie; Grieb, Jonas & Rossi, Tuomas [Show all 8 contributors for this article] (2024). Prototype biodiversity digital twin: crop wild relatives genetic resources for food security. Research Ideas and Outcomes (RIO). 10. doi: 10.3897/rio.10.e125192. Full text in Research Archive Show summary

  Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal and insect pests, as well as various crop diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), wild plants in the same genus as the crop as well as wild populations belonging to the same species as the crop, offer novel genetic resources crucial for enhancing crop resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) to aid in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance resilience of various crops against diverse stress factors.

• Simpson, Hunter J.; Andrew, Carrie; Skrede, Inger; Kauserud, Håvard & Schilling, Jonathan S. (2024). Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates. New Phytologist. ISSN 0028-646X. 242(6). doi: 10.1111/nph.19723. Full text in Research Archive Show summary

  Unlike ‘white rot’ (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, ‘brown rot’ (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.

• Andrew, Carrie; Islam, Shariful; Weiland, Claus & Endresen, Dag (2024). Biodiversity data standards for the organization and dissemination of complex research projects and digital twins: a guide. arXiv.org. ISSN 2331-8422. doi: 10.48550/arXiv.2405.19857. Full text in Research Archive Show summary

  Biodiversity data are substantially increasing, spurred by technological advances and community (citizen) science initiatives. To integrate data is, likewise, becoming more commonplace. Open science promotes open sharing and data usage. Data standardization is an instrument for the organization and integration of biodiversity data, which is required for complex research projects and digital twins. However, just like with an actual instrument, there is a learning curve to understanding the data standards field. Here we provide a guide, for data providers and data users, on the logistics of compiling and utilizing biodiversity data. We emphasize data standards, because they are integral to data integration. Three primary avenues for compiling biodiversity data are compared, explaining the importance of research infrastructures for coordinated long-term data aggregation. We exemplify the Biodiversity Digital Twin (BioDT) as a case study. Four approaches to data standardization are presented in terms of the balance between practical constraints and the advancement of the data standards field. We aim for this paper to guide and raise awareness of the existing issues related to data standardization, and especially how data standards are key to data interoperability, i.e., machine accessibility. The future is promising for computational biodiversity advancements, such as with the BioDT project, but it rests upon the shoulders of machine actionability and readability, and that requires data standards for computational communication.

• Shumskaya, Maria; Filippova, Nina; Lorentzen, Laura; Blue, Shazneka; Andrew, Carrie Joy & Lorusso, Nicholas S. (2023). Citizen science helps in the study of fungal diversity in New Jersey. Scientific Data. 10. doi: 10.1038/s41597-022-01916-z. Full text in Research Archive
• Rustøen, Fredrik; Høiland, Klaus; Heegaard, Einar; Boddy, Lynne; Gange, Alan C. & Kauserud, Håvard [Show all 7 contributors for this article] (2023). Substrate affinities of wood decay fungi are foremost structured by wood properties not climate. Fungal ecology. ISSN 1754-5048. 63. doi: 10.1016/j.funeco.2023.101231. Full text in Research Archive Show summary

  Wood decomposing fungi differ in their substrate affinities, but to what extent factors like wood properties influence host specialization, compared to climate, is largely unknown. In this study, we analysed British field observations of 61 common wood decay species associated with 41 tree and shrub genera. While white rot fungi ranged from low-to high-substrate affinity, brown rot fungi were exclusively mid-to high-affinity. White rot fungi associated with dead fallen wood demonstrated the least substrate affinity. The composition of wood decomposer fungi was mostly structured by substrate properties, sorted between angiosperms and conifers. Any relationships with temporal and regional climate variability were of far less significance, but did predict community-based and substrate-usage host shifts, especially for fungi on fallen deadwood. Our results demonstrate that substrate shifts by wood-decay fungi will depend primarily upon their degree of affinity to, and the distribution of, related woody genera, followed less at regional levels by climate impacts.

• Diez, Jefferey M.; Kauserud, Håvard; Andrew, Carrie Joy; Heegaard, Einar; Krisai-Greilhüber, Irmgard & Senn-Irlet, Beatrice [Show all 9 contributors for this article] (2020). Altitudinal upwards shifts in fungal fruiting in the Alps. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. Full text in Research Archive
• Andrew, Carrie Joy; Büntgen, Ulf; Egli, Simon; Senn-Irlet, Beatrice; Grytnes, John-Arvid & Heilmann-Clausen, Jacob [Show all 15 contributors for this article] (2019). Open-source data reveal how collections-based fungal diversity is sensitive to global change. Applications in Plant Sciences. 7(3), p. 1–19. doi: 10.1002/aps3.1227. Full text in Research Archive Show summary

  Premise of the Study Fungal diversity (richness) trends at large scales are in urgent need of investigation, especially through novel situations that combine long‐term observational with environmental and remotely sensed open‐source data. Methods We modeled fungal richness, with collections‐based records of saprotrophic (decaying) and ectomycorrhizal (plant mutualistic) fungi, using an array of environmental variables across geographical gradients from northern to central Europe. Temporal differences in covariables granted insight into the impacts of the shorter‐ versus longer‐term environment on fungal richness. Results Fungal richness varied significantly across different land‐use types, with highest richness in forests and lowest in urban areas. Latitudinal trends supported a unimodal pattern in diversity across Europe. Temperature, both annual mean and range, was positively correlated with richness, indicating the importance of seasonality in increasing richness amounts. Precipitation seasonality notably affected saprotrophic fungal diversity (a unimodal relationship), as did daily precipitation of the collection day (negatively correlated). Ectomycorrhizal fungal richness differed from that of saprotrophs by being positively associated with tree species richness. Discussion Our results demonstrate that fungal richness is strongly correlated with land use and climate conditions, especially concerning seasonality, and that ongoing global change processes will affect fungal richness patterns at large scales.

• Gange, Alan C.; Allen, Lewis P; Nussbaumer, Aline; Gange, Edward G; Andrew, Carrie Joy & Egli, Simon [Show all 8 contributors for this article] (2019). Multiscale patterns of rarity in fungi, inferred from fruiting records. Global Ecology and Biogeography. ISSN 1466-822X. 28(8), p. 1106–1117. doi: 10.1111/geb.12918. Full text in Research Archive
• Aas, Anders Bjørnsgard; Andrew, Carrie Joy; Blaalid, Rakel; Vik, Unni; Kauserud, Håvard & Davey, Marie Louise (2019). Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms. FEMS Microbiology Ecology. ISSN 0168-6496. 95(6), p. 1–11. doi: 10.1093/femsec/fiz058. Full text in Research Archive Show summary

  The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.

• Leitão, Pedro J.; Andrew, Carrie Joy; Engelhardt, Eva Katharina; Graham, Catherine H.; Martinez-Almoyna, Camille & Mimet, Anne [Show all 11 contributors for this article] (2019). Macroecology as a hub between research disciplines: Opportunities, challenges and possible ways forward. Journal of Biogeography. ISSN 0305-0270. 47. doi: 10.1111/jbi.13751. Full text in Research Archive
• Andrew, Carrie Joy; Heegaard, Einar; Høiland, Klaus; Senn-Irlet, Beatrice; Kuyper, Thomas W. & Krisai-Greilhuber, Irmgard [Show all 14 contributors for this article] (2018). Explaining European fungal fruiting phenology with climate variability. Ecology. ISSN 0012-9658. 99(6), p. 1306–1315. doi: 10.1002/ecy.2237. Full text in Research Archive Show summary

  Here we assess the impact of geographically dependent (latitude, longitude, and altitude) changes in bioclimatic (temperature, precipitation, and primary productivity) variability on fungal fruiting phenology across Europe. Two main nutritional guilds of fungi, saprotrophic and ectomycorrhizal, were further separated into spring and autumn fruiters. We used a path analysis to investigate how biogeographic patterns in fungal fruiting phenology coincided with seasonal changes in climate and primary production. Across central to northern Europe, mean fruiting varied by approximately 25 d, primarily with latitude. Altitude affected fruiting by up to 30 d, with spring delays and autumnal accelerations. Fruiting was as much explained by the effects of bioclimatic variability as by their large‐scale spatial patterns. Temperature drove fruiting of autumnal ectomycorrhizal and saprotrophic groups as well as spring saprotrophic groups, while primary production and precipitation were major drivers for spring‐fruiting ectomycorrhizal fungi. Species‐specific phenology predictors were not stable, instead deviating from the overall mean. There is significant likelihood that further climatic change, especially in temperature, will impact fungal phenology patterns at large spatial scales. The ecological implications are diverse, potentially affecting food webs (asynchrony), nutrient cycling and the timing of nutrient availability in ecosystems.

• Andrew, Carrie Joy; Heegaard, Einar; Gange, Alan C.; Senn-Irlet, Beatrice; Egli, Simon & Kirk, Paul M. [Show all 9 contributors for this article] (2018). Congruency in fungal phenology patterns across dataset sources and scales. Fungal ecology. ISSN 1754-5048. 32, p. 9–17. doi: 10.1016/j.funeco.2017.11.009. Full text in Research Archive Show summary

  As citizen science and digitization projects bring greater and larger datasets to the scientific realm, wemust address the comparability of results across varying sources and spatial scales. Independentlyassembled fungal fruit body datasets from Switzerland and the UK were available at large, national-scales and more intensively surveyed, local-scales. Phenology responses of fungi between these data-sets at different scales (national, intermediate and local) resembled one another. Consistently with time,the fruiting season initiated earlier and extended later. Phenology better correlated across data sourcesand scales in the UK, which contain less landscape and environmental heterogeneity than Switzerland.Species-specific responses in seasonality varied more than overall responses, but generally fruiting startdates were later for most Swiss species compared with UK species, while end dates were later for both.The coherency of these results, across the data sources, supports the use of presence-only data obtainedby multiple recorders, and even across heterogeneous landscapes, for global change phenology research.

• Khomich, Maryia; Cox, Filipa; Andrew, Carrie Joy; Andersen, Tom; Kauserud, Håvard & Davey, Marie Louise (2018). Coming up short: Identifying substrate and geographic biases in fungal sequence databases. Fungal ecology. ISSN 1754-5048. 36, p. 75–80. doi: 10.1016/j.funeco.2018.08.002. Full text in Research Archive Show summary

  Insufficient reference database coverage is a widely recognized limitation of molecular ecology ap-proaches which are reliant on database matches for assignment of function or identity. Here, we use datafrom 65 amplicon high-throughput sequencing (HTS) datasets targeting the internal transcribed spacer(ITS) region of fungal rDNA to identify substrates and geographic areas whose underrepresentation in theavailable reference databases could have meaningful impact on our ability to draw ecological conclu-sions. A total of 14 different substrates were investigated. Database representation was particularly poorfor the fungal communities found in aquatic (freshwater and marine) and soil ecosystems. Aquaticecosystems are identified as priority targets for the recovery of novel fungal lineages. A subset of the datarepresenting soil samples with global distribution were used to identify geographic locations andterrestrial biomes with poor database representation. Database coverage was especially poor in tropical,subtropical, and Antarctic latitudes, and the Amazon, Southeast Asia, Australasia, and the Indian sub-continent are identified as priority areas for improving database coverage in fungi.

• Andrew, Carrie Joy; Halvorsen, Rune; Heegaard, Einar; Kuyper, Thomas W.; Heilmann-Clausen, Jacob & Krisai-Greilhuber, Irmgard [Show all 15 contributors for this article] (2018). Continental-scale macrofungal assemblage patterns correlate with climate, soil carbon and nitrogen deposition. Journal of Biogeography. ISSN 0305-0270. 45(8), p. 1942–1953. doi: 10.1111/jbi.13374. Full text in Research Archive Show summary

  Aim:Macroecological scales of species compositional trends are well documentedfor a variety of plant and animal groups, but remain sparse for fungi, despite theirecological importance in carbon and nutrient cycling. It is, thus, essential to under-stand the composition of fungal assemblages across broad geographical scales andthe underlying drivers. Our overall aim was to describe these patterns for fungiacross two nutritional modes (saprotrophic and ectomycorrhizal). Furthermore, weaimed to elucidate the temporal component of fruiting patterns and to relate theseto soil carbon and nitrogen deposition. Location:Central and Northern Europe.Methods:A total of 4.9 million fungal fruit body observations throughout Europe,collected between 1970 and 2010, were analysed to determine the two main envi-ronmental and geographical gradients structuring fungal assemblages for two mainnutritional modes, saprotrophic and ectomycorrhizal fungi. Results:Two main gradients explaining the geography of compositional patternswere identified, for each nutritional mode. Mean annual temperature (and relatedcollinear, seasonal measures) correlated most strongly with the first gradient forboth nutritional modes. Soil organic carbon was the highest correlate of the second compositional gradient for ectomycorrhizal fungi, suspected as an indicator of vege-tation- and pH-related covariates. In contrast, nitrogen deposition constituted asecond gradient for saprotrophic fungi, likely a proxy for anthropogenic pollution.Compositional gradients and environmental conditions correlated similarly whenthe data were divided into two time intervals of 1970–1990 and 1991–2010.Evidence of compositional temporal change was highest with increasing elevationand latitude. Main conclusions:Fungal assemblage patterns demonstrate clear biogeographicalpatterns that relate the nutritional modes to their main environmental correlates oftemperature, soil organic carbon and nitrogen deposition. With respect to globalchange impacts, the highest rates of compositional change by time suggest targetinghigher latitudes and elevations for a better understanding of fungal dynamics. We,finally, suggest further examination of the ranges and dispersal abilities of fungi tobetter assess responses to global change.

• Dawson, Samantha Katherine; Boddy, Lynne; Halbwachs, Hans; Bässler, Claus; Andrew, Carrie Joy & Crowther, Thomas Ward [Show all 10 contributors for this article] (2018). Handbook for the measurement of macrofungal functional traits: A start with basidiomycete wood fungi. Functional Ecology. ISSN 0269-8463. p. 372–387. doi: 10.1111/1365-2435.13239. Full text in Research Archive Show summary

  Chronic wasting disease (CWD) persists in cervid populations of North America and in 2016 was detected for the first time in Europe in a wild reindeer in Norway. We report the detection of CWD in 3 moose (Alces alces) in Norway, identified through a large scale surveillance program. The cases occurred in 13–14-year-old female moose, and we detected an abnormal form of prion protein (PrPSc) in the brain but not in lymphoid tissues. Immunohistochemistry revealed that the moose shared the same neuropathologic phenotype, characterized by mostly intraneuronal deposition of PrPSc. This pattern differed from that observed in reindeer and has not been previously reported in CWD-infected cervids. Moreover, Western blot revealed a PrPSc type distinguishable from previous CWD cases and from known ruminant prion diseases in Europe, with the possible exception of sheep CH1641. These findings suggest that these cases in moose represent a novel type of CWD.

• Gange, Alan C.; Heegaard, Einar; Boddy, Lynne; Andrew, Carrie Joy; Kirk, Paul M. & Halvorsen, Rune [Show all 13 contributors for this article] (2018). Trait-dependent distributional shifts in fruiting of common British fungi. Ecography. ISSN 0906-7590. 41(1), p. 51–61. doi: 10.1111/ecog.03233. Full text in Research Archive Show summary

  Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species‐specific fungal fruit body abundances have shifted across latitudes over time, using the UK national database of fruiting records. The data employed were recorded over 45 yr (1970–2014), and include 853 278 records of Agaricales, Boletales and Russulales, though we focus only on the most common species (with more than 3000 records each). The georeferenced observations were analysed by a Bayesian inference as a Gaussian additive model with a specification following a joint species distribution model. We used an offset, random contributions and fixed effects to isolate different potential biases from the trait‐specific interactions with latitude/climate and time. Our main aim was assessed by examination of the three‐way‐interaction of trait, predictor (latitude or climate) and time. The results show a strong trait‐specific shift in latitudinal abundance through time, as ECM species have become more abundant relative to saprotrophic species in the north. Along precipitation gradients, phenology was important, in that species with shorter fruiting seasons have declined markedly in abundance in oceanic regions, whereas species with longer seasons have become relatively more common overall. These changes in fruit body distributions are correlated with temperature and rainfall, which act directly on both saprotrophic and ECM fungi, and also indirectly on ECM fungi, through altered photosynthate allocation from their hosts. If these distributional changes reflect fungal activity, there will be important consequences for the responses of forest ecosystems to changing climate, through effects on primary production and nutrient cycling.

• Büntgen, Ulf; Greuter, Lucie; Bollmann, Kurt; Jenny, Hannes; Liebhold, Andrew & Galván, J. Diego [Show all 9 contributors for this article] (2017). Elevational range shifts in four mountain ungulate species from the Swiss Alps. Ecosphere. 8(4), p. 1–15. doi: 10.1002/ecs2.1761. Full text in Research Archive Show summary

  Warming-induced range shifts along elevational and latitudinal gradients have been observed in several species from various taxa. The mobility and behavioral plasticity of large endothermic mammals, however, complicate the detection of climatic effects on their spatial distributions. Here, we analyzed 230,565 hunting locations of the four most abundant ungulate species in the European Alps: ibex, chamois, red deer, and roe deer. Year-to-year and inter-decadal range shifts toward higher elevations in Switzerland coincided with warmer, snow-free, and thus more favorable autumn conditions in the same area. The average harvest elevation of ibex, chamois, and red deer significantly increased between 1991 and 2013. Although this trend is anticipated to continue, behavioral plasticity may allow the Alpine ibex and other mountain ungulates to buffer some of the associated consequences of climate change. Our results demonstrate the utility of well-replicated hunting archives to supplement shorter but more precise monitoring data. This study also provides independent evidence of animal range shifts in response to environmental change at interannual and multi-decadal time-scales.

• Andrew, Carrie Joy; Heegaard, Einar; Kirk, Paul M.; Bässler, Claus; Heilmann-Clausen, Jacob & Krisai-Greilhuber, Irmgard [Show all 18 contributors for this article] (2017). Big data integration: Pan-European fungal species observations' assembly for addressing contemporary questions in ecology and global change biology. Fungal Biology Reviews. ISSN 1749-4613. 31(2), p. 88–98. doi: 10.1016/j.fbr.2017.01.001. Full text in Research Archive Show summary

  Species occurrence observations are increasingly available for scientific analyses through citizen science projects and digitization of museum records, representing a largely untapped ecological resource. When combined with open-source data, there is unparalleled potential for understanding many aspects of the ecology and biogeography of organisms. Here we describe the process of assembling a pan-European mycological meta-database (ClimFun) and integrating it with open-source data to advance the fields of macroecology and biogeography against a backdrop of global change. Initially 7.3 million unique fungal species fruit body records, spanning nine countries, were processed and assembled into 6 million records of more than 10,000 species. This is an extraordinary amount of fungal data to address macro-ecological questions. We provide two examples of fungal species with different life histories, one ectomycorrhizal and one wood decaying, to demonstrate how such continental-scale meta-databases can offer unique insights into climate change effects on fungal phenology and fruiting patterns in recent decades. Keywords Biogeography; Citizen science; Fungi; Global change; Meta-database; Open-source

• Andrew, Carrie Joy; Heegaard, Einar; Halvorsen, Rune; Martinez-Pena, Fernando; Egli, Simon & Kirk, Paul M. [Show all 12 contributors for this article] (2016). Climate impacts on fungal community and trait dynamics. Fungal ecology. ISSN 1754-5048. 22, p. 17–25. doi: 10.1016/j.funeco.2016.03.005. Full text in Research Archive
• Heegaard, Einar; Boddy, Lynne; Diez, Jefferey M.; Halvorsen, Rune; Kauserud, Håvard & Kuyper, Thomas W. [Show all 15 contributors for this article] (2016). Fine-scale spatiotemporal dynamics of fungal fruiting: prevalence, amplitude, range and continuity. Ecography. ISSN 0906-7590. 40(8), p. 947–959. doi: 10.1111/ecog.02256. Full text in Research Archive Show summary

  Despite the critical importance of fungi as symbionts with plants, resources for animals, and drivers of ecosystem function, the spatiotemporal distributions of fungi remain poorly understood. The belowground life cycle of fungi makes it difficult to assess spatial patterns and dynamic processes even with recent molecular techniques. Here we offer an explicit spatiotemporal Bayesian inference of the drivers behind spatial distributions from investigation of a Swiss inventory of fungal fruit bodies. The unique inventory includes three temperate forest sites in which a total of 73 952 fungal fruit bodies were recorded systematically in a spatially explicit design between 1992 and 2006. Our motivation is to understand how broad-scale climate factors may influence spatiotemporal dynamics of fungal fruiting within forests, and if any such effects vary between two functional groups, ectomycorrhizal (ECM) and saprotrophic fungi. For both groups we asked: 1) how consistent are the locations of fruiting patches, the sizes of patches, the quantities of fruit bodies, and of prevalence (occupancy)? 2) Do the annual spatial characteristics of fungal fruiting change systematically over time? 3) Are spatial characteristics of fungal fruiting driven by climatic variation? We found high inter-annual continuity in fruiting for both functional groups. The saprotrophic species were characterised by small patches with variable fruit body counts. In contrast, ECM species were present in larger, but more distinctly delimited patches. The spatial characteristics of the fungal community were only indirectly influenced by climate. However, climate variability influenced overall yields and prevalence, which again links to spatial structure of fruit bodies. Both yield and prevalence were correlated with the amplitudes of occurrence and of fruit body counts, but only prevalence influenced the spatial range. Summarizing, climatic variability affects forest-stand fungal distributions via its influence on yield (amount) and prevalence (occupancy), whereas fungal life-history strategies dictate fine-scale spatial characteristics.

• Andrew, Carrie Joy & Lilleskov, Erik (2014). Elevated CO2 and O3 effects on ectomycorrhizal fungal root tip communities in consideration of a post-agricultural soil nutrient gradient legacy. Mycorrhiza. ISSN 0940-6360. 24, p. 581–593. doi: 10.1007/s00572-014-0577-4. Full text in Research Archive

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• Chala, Desalegn; Kusch, Erik; Rossi, Tuomas; Juottonen, Heli; Weiland, Claus & Grieb, Jonas [Show all 11 contributors for this article] (2025). BioDT uc-CWR: Crop Wild Relative Digital Twin. doi: 10.5281/ZENODO.15696971. Full text in Research Archive Show summary

  BioDT: Crop Wild Relative prototype Digital Twin (CWR pDT). The prototype digital twin (pDT) aids in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance the resilience of various crops against diverse stress factors.

• Chala, Desalegn; Kusch, Erik; Andrew, Carrie; Torma, Michal; Johaadien, Rukaya Sarah & Kehel, Zakaria [Show all 9 contributors for this article] (2024). BioDT Hackathon: Second End-Users Workshop, January 2024. Full text in Research Archive Show summary

  Three-day hackathon titled Harnessing Digital Twinning for Sustainable Agriculture: Predictive Characterisation and Conservation of Crop Wild Relatives, takes place from January 23rd to 25th, 2024 in Oslo, Norway. The event, promises to unravel the immense potential of digital twinning in revolutionizing global agricultural practices.

• Islam, Sharif; Gordillo, Julian Lopez; Endresen, Dag & Andrew, Carrie (2024). Bridging Data Standards and FAIR Principles in Biodiversity Digital Twinning: Prototyping, Challenges, Lessons Learned, and Future Plans. Biodiversity Information Science and Standards (BISS). 8. doi: 10.3897/biss.8.133089. Full text in Research Archive Show summary

  Digital twins combine modelling, domain knowledge, computing power, and multiple datasets to offer the potential to unlock new insights into biodiversity (de Koning et al. 2023). The Biodiversity Digital Twin (BioDT) project pioneers this approach to aid in understanding biodiversity through prototyping digital twins (Golivets et al. 2024). However, working with biodiversity data presents challenges due to their dynamic and diverse nature as well as the need for having to deal with incompleteness, uncertainties (Rocchini et al. 2011), disproportionate representation patterns in global studies from wealthier economies (Hughes et al. 2024), and issues with data aggregation and integration (Wüest et al. 2020). Similar to BioDT, there are also plans for creating a Digital Twin of the Ocean (DTO). DTO-Bioflow project addresses these data challenges in the marine domain, where studies show that although European seas host 48,000 marine species (75% described), the data are not yet FAIR (Findable, Accessible, Interoperable, and Reusable) (Ramírez et al. 2022). These challenges hamper the modelling capabilities needed for effective predictions and conservation prioritisation. The adaptability of digital twins across temporal and spatial scales and their ability to model dynamic ecosystems make them ideal for biodiversity research and real-time conservation efforts. However, their success hinges on the consistent integration and alignment of data from disparate sources (Trantas et al. 2023). This integration involves standardising terms used to describe datasets, such as temporal coverage or controlled vocabularies like "Forest" for targetHabitatScope. Thus, adopting data standards is essential. Additionally, challenges such as model bias (Lewers 2023), research context, and data provenance must be considered, adding complexity to metadata capture and alignment. BioDT addresses these challenges with modular building blocks for data integration, model deployment, and workflow management. This approach facilitates the gradual adoption of data standards and FAIR principles, which need to encompass not just data, but also models and software. As automation, ease of reproducibility, and deployability are critical for digital twinning success, data integration and interoperability issues may arise due to missing or insufficient parameter descriptions in the model, incomplete information on data selection, and the unavailability of required software package details. Thus, data standardisation provides a pathway for a consistent approach that can be adopted for different use cases. Common data sources in BioDT, like species occurrences and environmental variables, benefit from standards such as Darwin Core (Wieczorek et al. 2012) and the Ecological Metadata Language (Jones et al. 2019). While valuable, these standards may not fully encompass the complexity needed for comprehensive biodiversity digital twins. Additionally, differing familiarity with these standards and FAIR principles among communities pose challenges. Continuous adoption of data standards, alongside exploring complementary approaches like schema.org or bioschemas.org for capturing diverse (meta)data, is essential. Collaboration with data providers, modellers, and various research infrastructures is also crucial (Andrew et al. 2024).

• Weiland, Claus; Grieb, Jonas; Bauer, Daniel; Gelete, Desalegn Chala; Kusch, Erik & Andrew, Carrie [Show all 7 contributors for this article] (2024). Dataspace Integration for Agrobiodiversity Digital Twins with RO-Crate. Biodiversity Information Science and Standards (BISS). 8. doi: 10.3897/biss.8.134479. Full text in Research Archive Show summary

  A severe impact of human-induced climate change is the global decrease in crop yields, threatening the United Nations sustainable development goal (SDG) to end hunger, achieve food security, improve nutrition, and promote sustainable agriculture (SDG 2: “Zero Hunger Goal”). Decision-making on appropriate mitigation strategies requires data integration from heterogeneous data-rich contexts including Earth observation (EO), biodiversity monitoring, gene banks as well as socio-economic data. Accordingly, large-scale initiatives for thematic data spaces, such as the European projects Destination Earth (DestinE) and the Green Deal Data Space, have been launched. Underutilized crops and crop wild relatives (CWR) can contribute to mitigating the impacts of climate change since their greater genetic diversity allows adaptation of agro-food sources to extreme weather events such as flooding and drought or emerging crop pests. Within the framework of Biodiversity Digital Twin (BioDT), a prototype digital twin for crop genetic resources modeling is under development. This prototype combines the scanning of genetic resources of CWRs and traditional cultivars for promising pest resistance and abiotic tolerance traits with advanced species distribution modeling and actual climate scenarios from EO. The aim is to generate habitat suitability maps and identify potential areas where relevant populations are potentially growing (Chala et al. 2024). The talk gives an overview of data models used to facilitate the required interoperability of both Earth models and environmental data within and across different data spaces such as the DestinE Data Lake (Duatis Juarez et al. 2023). Based on our findings from the use case of agrobiodiversity digital twins, we will discuss approaches for processing machine-actionable digital objects (Fig. 1) containing workflow information (i.e., in the Common Workflow Language format, Crusoe et al. 2022), and for sharing resulting research data in a FAIR (Findable, Accessible, Interoperable, and Reusable) manner by leveraging on so-called webby FAIR Digital Objects involving Research Object Crate (RO-Crate, Soiland-Reyes et al. 2022), FAIR Signposting (Soiland-Reyes et al. 2024) and schema.org and its Bioschemas extension respectively (Castro et al. 2020),

• Rechsteiner, Aud Helen Halbritter; Grainger, Matthew; Telford, Richard James; Kusch, Erik; Nilsen, Erlend Birkeland & Andrew, Carrie [Show all 9 contributors for this article] (2023). Living Norway Course on Open, Reproducible and Transparent Science in Ecology. Full text in Research Archive Show summary

  Universities, journals, and funding bodies increasingly demand open and reproducible research practices across the scientific community. Research data needs to be FAIR (findable, accessible, interoperable, and reusable), workflows need to be reproducible, and science needs to be transparent. This aims to improve the efficiency and quality of research and thus to increase the credibility of science. This course offers hands-on training on methods and technologies to make research more open, reproducible and transparent. The course is centred around the life-cycle of data from planning, managing, collecting, curating, analysing, publishing, storing, sharing and reusing data. It is aimed at PhD students (will be prioritised) as well as early-career researchers in ecology, who produce their own data (i.e. collect data in the field/lab), use data from others (i.e. databases) or both.

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