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  • 1
    Online Resource
    Online Resource
    Supplementary material 2 from: Parisy B, Schmidt NM, Wirta H, Stewart L, Pellissier L, Holben WE, Pannoni S, Somervuo P, Jones MM, Siren J, Vesterinen E, Ovaskainen O, Roslin T (2023) Ecological signals of arctic plant-microbe associations are consistent across eDNA and vegetation surveys. Metabarcoding and Metagenomics 7: e99979. https://doi.org/10.3897/mbmg.7.99979
    Pensoft Publishers ; 2023
    In:  Metabarcoding and Metagenomics Vol. 7 ( 2023-08-09)
    Details
    In: Metabarcoding and Metagenomics, Pensoft Publishers, Vol. 7 ( 2023-08-09)
    Abstract: Understanding how different taxa respond to abiotic characteristics of the environment is of key interest for understanding the assembly of communities. Yet, whether eDNA data will suffice to accurately capture environmental imprints has been the topic of some debate. In this study, we characterised patterns of species occurrences and co-occurrences in Zackenberg in northeast Greenland using environmental DNA. To explore the potential for extracting ecological signals from eDNA data alone, we compared two approaches (visual vegetation surveys and soil eDNA metabarcoding) to describing plant communities and their responses to abiotic conditions. We then examined plant associations with microbes using a joint species distribution model. We found that most (68%) of plant genera were detectable by both vegetation surveys and eDNA signatures. Species-specific occurrence data revealed how plants, bacteria and fungi responded to their abiotic environment – with plants, bacteria and fungi all responding similarly to soil moisture. Nonetheless, a large proportion of fungi decreased in occurrences with increasing soil temperature. Regarding biotic associations, the nature and proportion of the plant-microbe associations detected were consistent between plant data identified via vegetation surveys and eDNA. Of pairs of plants and microbe genera showing statistically supported associations (while accounting for joint responses to the environment), plants and bacteria mainly showed negative associations, whereas plants and fungi mainly showed positive associations. Ample ecological signals detected by both vegetation surveys and by eDNA-based methods and a general correspondence in biotic associations inferred by both methods, suggested that purely eDNA-based approaches constitute a promising and easily applicable tool for studying plant-soil microbial associations in the Arctic and elsewhere.
    Type of Medium: Online Resource
    ISSN: 2534-9708
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3897/mbmg.7.99979
    DOI: 10.3897/mbmg.7.99979.suppl1
    DOI: 10.3897/mbmg.7.99979.suppl2
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2023
    detail.hit.zdb_id: 2913203-4
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  • 2
    Online Resource
    Online Resource
    Figure 1 from: Jaquier M, Albouy C, Bach W, Waldock C, Marques V, Maire E, Andrello M, Valentini A, Manel S, Dejean T, Mouillot D, Pellissier L (2021) Environmental DNA diffusion of reef fishes along a distance gradient from four isolated islands of the Western Indian Ocean. ARPHA Conference Abstracts 4: e65060. https://doi.org/10.3897/aca.4.e65060
    Pensoft Publishers ; 2021
    In:  ARPHA Conference Abstracts Vol. 4 ( 2021-03-04)
    Details
    In: ARPHA Conference Abstracts, Pensoft Publishers, Vol. 4 ( 2021-03-04)
    Abstract: Islands have traditionally served as model systems to study ecological and evolutionary processes (Warren et al. 2015) and could also represent a relevant system to study environmental DNA (eDNA). Isolated island reefs that are affected by climatic threats would particularly benefit from cost- and time-efficient biodiversity surveys to set priorities for their conservation. Among time efficiency methods, eDNA has emerged as a novel molecular metabarcoding technique to detect biodiversity from simple environmental samples even in remote marine environments. However, eDNA monitoring techniques for marine environments are at a developmental phase, with a few remaining unknowns related to DNA residence time and movement. In particular, the redistribution of eDNA, via ocean currents, could blur the composition signal and its association with local environmental conditions (Goldberg et al. 2016). Here, we investigated the detection variation of eDNA along a distance gradient across four islands in the French Scattered Islands. We collected 30 L of surface water per filter at an increasing distance from the islands reefs (0m, 250m, 500m, 750m). Using a metabarcoding protocol, we used the teleo primers to target a fraction of 12S mitochondrial DNA to detect Actinopterygii and Elasmobranchii. We then applied a sequence clustering approach to generate Molecular Taxonomic Units (MOTUs), which were assigned to a taxonomic group using a reference database. By assigning eDNA sequences to species using a public reference database, we classified species according to their preferred habitat types between benthic/demersal and pelagic. Our results show no significant relationship between distance and MOTUs richness for both habitat types. By using a Joint Species Distribution Modelling approach (JSDM, Hierarchical Modelling of Species Communities), we retained the multidimensional information captured by eDNA and detect species- and family-specific responses to distance (Fig. 1). We showed that benthic MOTUs were found in closer proximity to the reef, while typical pelagic MOTUs were found at greater distances from the reef. Hence, MOTU-level analyses coupled with JSDM were more informative that when aggregating it into coarser richness. Altogether, our eDNA distance sampling gradient detected an ecological signal of habitat selection by fish species, which suggest that eDNA could help understand the behavior of species and their distribution in marine environments at a fine spatial scale.
    Type of Medium: Online Resource
    ISSN: 2603-3925
    URL: Article
    URL: Article
    DOI: 10.3897/aca.4.e65060
    DOI: 10.3897/aca.4.e65060.figure1
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2021
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  • 3
    Online Resource
    Online Resource
    A landscape‐scale assessment of the relationship between grassland functioning, community diversity, and functional traits
    Wiley ; 2020
    In:  Ecology and Evolution Vol. 10, No. 18 ( 2020-09), p. 9906-9919
    Details
    In: Ecology and Evolution, Wiley, Vol. 10, No. 18 ( 2020-09), p. 9906-9919
    Abstract: Livestock farmers rely on a high and stable grassland productivity for fodder production to sustain their livelihoods. Future drought events related to climate change, however, threaten grassland functionality in many regions across the globe. The introduction of sustainable grassland management could buffer these negative effects. According to the biodiversity–productivity hypothesis, productivity positively associates with local biodiversity. The biodiversity–insurance hypothesis states that higher biodiversity enhances the temporal stability of productivity. To date, these hypotheses have mostly been tested through experimental studies under restricted environmental conditions, hereby neglecting climatic variations at a landscape‐scale. Here, we provide a landscape‐scale assessment of the contribution of species richness, functional composition, temperature, and precipitation on grassland productivity. We found that the variation in grassland productivity during the growing season was best explained by functional trait composition. The community mean of plant preference for nutrients explained 24.8% of the variation in productivity and the community mean of specific leaf area explained 18.6%, while species richness explained only 2.4%. Temperature and precipitation explained an additional 22.1% of the variation in productivity. Our results indicate that functional trait composition is an important predictor of landscape‐scale grassland productivity.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.v10.18
    DOI: 10.1002/ece3.6650
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2635675-2
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  • 4
    Online Resource
    Online Resource
    Comparing spatial diversification and meta-population models in the Indo-Australian Archipelago
    The Royal Society ; 2018
    In:  Royal Society Open Science Vol. 5, No. 3 ( 2018-03), p. 171366-
    Details
    In: Royal Society Open Science, The Royal Society, Vol. 5, No. 3 ( 2018-03), p. 171366-
    Abstract: Reconstructing the processes that have shaped the emergence of biodiversity gradients is critical to understand the dynamics of diversification of life on Earth. Islands have traditionally been used as model systems to unravel the processes shaping biological diversity. MacArthur and Wilson's island biogeographic model predicts diversity to be based on dynamic interactions between colonization and extinction rates, while treating islands themselves as geologically static entities. The current spatial configuration of islands should influence meta-population dynamics, but long-term geological changes within archipelagos are also expected to have shaped island biodiversity, in part by driving diversification. Here, we compare two mechanistic models providing inferences on species richness at a biogeographic scale: a mechanistic spatial-temporal model of species diversification and a spatial meta-population model. While the meta-population model operates over a static landscape, the diversification model is driven by changes in the size and spatial configuration of islands through time. We compare the inferences of both models to floristic diversity patterns among land patches of the Indo-Australian Archipelago. Simulation results from the diversification model better matched observed diversity than a meta-population model constrained only by the contemporary landscape. The diversification model suggests that the dynamic re-positioning of islands promoting land disconnection and reconnection induced an accumulation of particularly high species diversity on Borneo, which is central within the island network. By contrast, the meta-population model predicts a higher diversity on the mainlands, which is less compatible with empirical data. Our analyses highlight that, by comparing models with contrasting assumptions, we can pinpoint the processes that are most compatible with extant biodiversity patterns.
    Type of Medium: Online Resource
    ISSN: 2054-5703
    URL: Article
    DOI: 10.1098/rsos.171366
    Language: English
    Publisher: The Royal Society
    Publication Date: 2018
    detail.hit.zdb_id: 2787755-3
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  • 5
    Online Resource
    Online Resource
    Growth‐competition‐herbivore resistance trade‐offs and the responses of alpine plant communities to climate change
    Wiley ; 2018
    In:  Functional Ecology Vol. 32, No. 7 ( 2018-07), p. 1693-1703
    Details
    In: Functional Ecology, Wiley, Vol. 32, No. 7 ( 2018-07), p. 1693-1703
    Abstract: Climate change is expected to modify current ecological conditions sustaining the coexistence of species within cold‐adapted plant communities. It will primarily act upon the existing structure of communities, whose response should depend on the functional differences governing coexistence among alpine species. We postulated that a possible trade‐off between (1) plant growth in response to temperature, (2) plant competition and (3) resistance to herbivory, modulates the rate of plant community turnover under climate change. We reviewed the literature investigating functional traits variability within communities along elevation gradients. Despite environmental filtering, our review indicates that interspecific plant functional variation within communities does not necessarily decrease with elevation. While the diversity of traits related to abiotic affinities or competition are well documented, the variability in species resistance to herbivory within communities is poorly known. Using a Lotka–Volterra‐based model, we simulated the impact of climate change on plant communities through (1) a direct effect on plant growth and competition and (2) an indirect effect via an increase in herbivore pressure. We showed that different shapes of trade‐offs between temperature‐related growth, competition and resistance to herbivory modulate community turnover under climate change. We documented the existence of two independent trade‐offs axes using a detailed dataset of functional traits within two alpine grasslands in the European Alps. Plant competitive traits (i.e. leaf area and height) where negatively associated to cold tolerance, whereas traits of the leaf economic spectrum were associated to traits related to the physical resistance to herbivory. We propose that the immediate effect of climate change on alpine plant communities will depend on existing functional variability and how functional axes trade‐off with each other. Documenting ecological constraints between plant functional axes should provide indications to anticipate winners and losers in alpine plant communities. A plain language summary is available for this article.
    Type of Medium: Online Resource
    ISSN: 0269-8463 , 1365-2435
    URL: Issue
    URL: Article
    DOI: 10.1111/fec.2018.32.issue-7
    DOI: 10.1111/1365-2435.13075
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2020307-X
    detail.hit.zdb_id: 619313-4
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Species pool distributions along functional trade-offs shape plant productivity–diversity relationships
    Springer Science and Business Media LLC ; 2017
    In:  Scientific Reports Vol. 7, No. 1 ( 2017-11-13)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2017-11-13)
    Abstract: Grasslands deliver the resources for food production and are among the most biologically diverse ecosystems. These characteristics are often in conflict as increasing yield through fertilization can lead to biodiversity loss. Thus, the challenge in grassland management is to sustain both yield and diversity. Biodiversity–ecosystem functioning experiments typically reveal a positive relationship between manipulated species diversity and productivity. In contrast, observations of the effect of increasing productivity via fertilization suggest a negative association with biodiversity. Using a mathematical model simulating species co-existence along a resource gradient, we show that trade-offs and species pool structure (size and trait distribution) determines the shape of the productivity-diversity relationship. At a constant resource level, over-yielding drives a positive relationship between biodiversity and productivity. In contrast, along a resource gradient, the shape of the productivity-diversity relationship is determined by the distribution of species along trade-off axes and often resulted in a bell-shaped relationship. In accordance to this theoretical result, we then explain the general trend of plant biodiversity loss with fertilisation in the European flora, by showing empirical evidence that trait distribution of plant species pools throughout Europe is biased toward species preferring poorer soils.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-017-15334-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2615211-3
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  • 7
    Online Resource
    Online Resource
    Lags in the response of mountain plant communities to climate change
    Wiley ; 2018
    In:  Global Change Biology Vol. 24, No. 2 ( 2018-02), p. 563-579
    Details
    In: Global Change Biology, Wiley, Vol. 24, No. 2 ( 2018-02), p. 563-579
    Abstract: Rapid climatic changes and increasing human influence at high elevations around the world will have profound impacts on mountain biodiversity. However, forecasts from statistical models (e.g. species distribution models) rarely consider that plant community changes could substantially lag behind climatic changes, hindering our ability to make temporally realistic projections for the coming century. Indeed, the magnitudes of lags, and the relative importance of the different factors giving rise to them, remain poorly understood. We review evidence for three types of lag: “dispersal lags” affecting plant species’ spread along elevational gradients, “establishment lags” following their arrival in recipient communities, and “extinction lags” of resident species. Variation in lags is explained by variation among species in physiological and demographic responses, by effects of altered biotic interactions, and by aspects of the physical environment. Of these, altered biotic interactions could contribute substantially to establishment and extinction lags, yet impacts of biotic interactions on range dynamics are poorly understood. We develop a mechanistic community model to illustrate how species turnover in future communities might lag behind simple expectations based on species’ range shifts with unlimited dispersal. The model shows a combined contribution of altered biotic interactions and dispersal lags to plant community turnover along an elevational gradient following climate warming. Our review and simulation support the view that accounting for disequilibrium range dynamics will be essential for realistic forecasts of patterns of biodiversity under climate change, with implications for the conservation of mountain species and the ecosystem functions they provide.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    URL: Article
    DOI: 10.1111/gcb.2018.24.issue-2
    DOI: 10.1111/gcb.13976
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2020313-5
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Linking functional traits and demography to model species-rich communities
    Springer Science and Business Media LLC ; 2021
    In:  Nature Communications Vol. 12, No. 1 ( 2021-05-11)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-05-11)
    Abstract: It has long been anticipated that relating functional traits to species demography would be a cornerstone for achieving large-scale predictability of ecological systems. If such a relationship existed, species demography could be modeled only by measuring functional traits, transforming our ability to predict states and dynamics of species-rich communities with process-based community models. Here, we introduce a new method that links empirical functional traits with the demographic parameters of a process-based model by calibrating a transfer function through inverse modeling. As a case study, we parameterize a modified Lotka–Volterra model of a high-diversity mountain grassland with static plant community and functional trait data only. The calibrated trait–demography relationships are amenable to ecological interpretation, and lead to species abundances that fit well to the observed community structure. We conclude that our new method offers a general solution to bridge the divide between trait data and process-based models in species-rich ecosystems.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-021-22630-1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2553671-0
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  • 9
    Online Resource
    Online Resource
    Loss of connectivity among island-dwelling Peary caribou following sea ice decline
    The Royal Society ; 2016
    In:  Biology Letters Vol. 12, No. 9 ( 2016-09), p. 20160235-
    Details
    In: Biology Letters, The Royal Society, Vol. 12, No. 9 ( 2016-09), p. 20160235-
    Abstract: Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both continental and Peary caribou, even after accounting for the possible effect of sea surface. Sea ice has thus been an effective corridor for Peary caribou, promoting inter-island connectivity and population mixing. Using a time series of remote sensing sea-ice data, we show that landscape resistance in the Canadian Arctic Archipelago has increased by approximately 15% since 1979 and may further increase by 20–77% by 2086 under a high-emission scenario (RCP8.5). Under the persistent increase in greenhouse gas concentrations, reduced connectivity may isolate island-dwelling caribou with potentially significant consequences for population viability.
    Type of Medium: Online Resource
    ISSN: 1744-9561 , 1744-957X
    URL: Article
    DOI: 10.1098/rsbl.2016.0235
    Language: English
    Publisher: The Royal Society
    Publication Date: 2016
    detail.hit.zdb_id: 2103283-X
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices
    American Society for Microbiology ; 2016
    In:  Applied and Environmental Microbiology Vol. 82, No. 7 ( 2016-04), p. 2121-2131
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 82, No. 7 ( 2016-04), p. 2121-2131
    Abstract: Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km 2 along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO 3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.03336-15
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2016
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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