Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5

Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

In-depth characterization of the genetic diversity and population structure of wild relatives is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we sampled the Alpine plum (Briançon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 24 nuclear simple sequence repeat (microsatellite) markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model–based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. Similar to previous studies, dendrograms and networks placed P. brigantina closer to the Armeniaca section than to the Prunus section. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies.ADAPTATION DES CULTURES FRUITIÈRES AU CHANGEMENT CLIMATIQUE DANS LE BASSIN MÉDITERRANÉE

Genetic diversity and population structure analyses in the Alpine plum ( Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

In-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briançon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex-situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums ( P. cerasifera ) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placed P. brigantina closer to Armeniaca species than to Prunus species. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies

Impact de la durée de stockage au froid des oeufs embryonnés de truite arc-en-ciel

International audienceL’objectif général du projet EpiCOOL est d’étudier les conséquences du stockage au froid (3°C) des œufs embryonnés de truite arc-en-ciel, l’espèce piscicole majeure de la filière française. En effet, des études récentes ont montré que l’exposition précoce à des stimuli environnementaux (tels que l’hypoxie ou la température) pouvait avoir un impact sur la physiologie, la croissance, le métabolisme et la nutrition des poissons à plus ou moins long terme. Plusieurs mécanismes peuvent être sous-jacents à cette programmation, parmi eux les modifications des patrons d’expression de gènes et les régulations épigénétiques comme par exemple la méthylation de l’ADN. Dans ce projet, nous testerons donc l’effet d’un passage des œufs au stade oeillé à basse température (3°C au lieu de 11°C) pendant 15 jours sur plusieurs caractères d’intérêt aquacole, à savoir les performances zootechniques (survie, croissance et malformations), le métabolisme intermédiaire, le développement du muscle et les qualités, ainsi que la résistance à des stress ultérieurs. Nous essaierons également de comprendre par quels mécanismes moléculaires l’exposition précoce au froid peut impacter la physiologie des poissons ultérieurement, en analysant les patrons d’expression génique et la méthylation de l’ADN (approches LUMA et RRBS). La finalité est d’utiliser la programmation précoce comme levier pour mieux maîtriser les performances des animaux à long terme. Ce projet se basera sur l’utilisation d’un modèle biologique tout à fait pertinent, deux lignées expérimentales divergentes pour la teneur en lipides du muscle : lignée grasse (LG) et lignée maigre (LM). En effet, elles ont montré une utilisation différente des aliments et possèdent un métabolisme intermédiaire et énergétique bien différencié. Il est donc possible qu’elles réagissent différemment à l’effet du froid pendant l’incubation. L’utilisation de ces deux lignées divergentes permettra de tester l’impact du fond génétique sur les réponses observées, et ainsi d’aboutir à une compréhension plus fine des mécanismes sous-jacents.Financement : FEAMP (Fonds Européen pour les Affaires Maritimes et la Pêche) – projet EpiCOOL numéro PFEA470018FA100001

Assessing methane emissions for northern peatlands in ORCHIDEE-PEAT revision 7020

Abstract. In the global methane budget, the largest natural source is attributed to wetlands that encompass all ecosystems composed of waterlogged or inundated ground, capable of methane production. Among them, northern peatlands that store large amounts of soil organic carbon have been functioning, since the end of the last glaciation period, as long-term sources of methane (CH4) and are one of the most significant methane sources among wetlands. To reduce global methane budget uncertainties, it is of significance to understand processes driving methane production and fluxes in northern peatlands. A methane model that features methane production and transport by plants, ebullition process and diffusion in soil, oxidation to CO2 and CH4 fluxes to the atmosphere has been embedded in the ORCHIDEE-PEAT land surface model which includes an explicit representation of northern peatlands. This model, ORCHIDEE-PCH4 was calibrated and evaluated on 14 peatland sites distributed on both Eurasian and American continents in the northern boreal and temperate regions. Data assimilation approaches were employed to optimized parameters at each site and at all sites simultaneously. Results show that, in ORCHIDEE-PCH4, methanogenesis is sensitive to temperature and substrate availability over the top 75 cm of soil depth. Methane emissions estimated using single site optimization (SSO) of model parameters are underestimated by 9 g CH4 m−2 year−1 on average (i.e. 50 % higher than the site average of yearly methane emissions). While using the multi-sites optimization (MSO), methane emissions are overestimated by 5 g CH4 m−2 year−1 on average across all investigated sites (i.e. 37 % lower than the site average of yearly methane emissions)

Assessing methane emissions for northern peatlands in ORCHIDEE-PEAT revision 7020

International audienceIn the global methane budget, the largest natural source is attributed to wetlands, which encompass all ecosystems composed of waterlogged or inundated ground, capable of methane production. Among them, northern peatlands that store large amounts of soil organic carbon have been functioning, since the end of the last glaciation period, as long-term sources of methane (CH4) and are one of the most significant methane sources among wetlands. To reduce uncertainty of quantifying methane flux in the global methane budget, it is of significance to understand the underlying processes for methane production and fluxes in northern peatlands. A methane model that features methane production and transport by plants, ebullition process and diffusion in soil, oxidation to CO2, and CH4 fluxes to the atmosphere has been embedded in the ORCHIDEE-PEAT land surface model that includes an explicit representation of northern peatlands. ORCHIDEE-PCH4 was calibrated and evaluated on 14 peatland sites distributed on both the Eurasian and American continents in the northern boreal and temperate regions. Data assimilation approaches were employed to optimized parameters at each site and at all sites simultaneously. Results show that methanogenesis is sensitive to temperature and substrate availability over the top 75 cm of soil depth. Methane emissions estimated using single site optimization (SSO) of model parameters are underestimated by 9 g CH4 m−2 yr−1 on average (i.e., 50 % higher than the site average of yearly methane emissions). While using the multi-site optimization (MSO), methane emissions are overestimated by 5 g CH4 m−2 yr−1 on average across all investigated sites (i.e., 37 % lower than the site average of yearly methane emissions)

Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA.

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition