Tree-microbe interactions are essential for forest ecosystem functioning. Most plant-microbe research has focused on the rhizosphere, while composition of microbial communities in the phyllosphere remains underexplored. Here, we use 16S rRNA gene sequencing to explore differences between beech and Scots pine phyllospheric microbiomes at the European continental scale, map their functional profiles, and elucidate the role of host trees, forest features, and environmental factors such as climate and atmospheric deposition in phyllosphere microbiota assembly. We identified tree species and the associated foliar trait (specifically carbon:nitrogen ratio) as primary drivers of the bacterial communities. We characterized taxonomical and functional composition of epiphytic bacteria in the phyllosphere of beech and Scots pine across an environmental gradient from Fennoscandia to the Mediterranean area, with major changes in temperature and nitrogen deposition. We also showed that temperature and nitrogen deposition played a crucial role in affecting their assembly for both tree species. This study contributes to advancing our understanding on factors shaping phyllosphere microbial communities in beech and Scots pine at the European continental scale, highlighting the need of broad-scale comparative studies (covering a wide range of foliar traits and environmental conditions) to elucidate how phyllosphere microbiota mediates ecosystem responses to global change. Phyllosphere microbiota of beech and Scots pine at European continental scale is influenced by the host species and associated foliar traits, as well as by temperature and nitrogen deposition, according to 16S rRNA gene sequencing analyses on leaf epiphytic microbes.

Elicited pumpkin was evaluated as a potential daily consumption product able to modulate the gut microbiota. An in vitro dynamic colonic fermentation performance with microbiota from obese volunteers was used. Prebiotic effects were observed after the pumpkin treatment. Bifidobacterium abundance was maintained during the treatment period whereas Lactobacillus increased in the transversal and descending colon. Conversely, Enterobacteriaceae and Clostridium groups were more stable, although scarce decreasing trends were observed for same species. Increments of Lactobacillus acidophilus and Limosilactobacillus fermentum (old Lactobacillus fermentum) were observed in the whole colonic tract after the treatment period. However, modulatory effects were mainly observed in the transversal and descending colon. Diverse bacteria species were increased, such as Akkermansia muciniphila, Bacteroides dorei, Cloacibacillus porcorum, Clostridium lactatifermentans, Ruminococcus albus, Ruminococcus lactaris, Coprococcus catus, Alistipes shahii or Bacteroides vulgatus. The prebiotic effect of the elicited pumpkin was provided by the fiber of the pumpkin, suggesting a release of pectin molecules in the transversal and distal colonic tract through low cellulosic fiber degradation, explaining the increases in the total propionic and butyric acid in these colonic sections. Also, a possible modulatory role of carotenoids from the sample was suggested since carotenes were found in the descending colon. Hence, the results of this research highlighted pumpkin as a natural product able to modulate the microbiota towards a healthier profile.

Sourdough bread enriched with soluble fiber (by in-situ exopolysaccharides production) and insoluble fiber (by gazpacho by-products addition) showed prebiotic effects an in vitro dynamic colonic fermentation performance with obese volunteer's microbiota. Bifidobacterium population was maintained whereas Lactobacillus increased throughout the colonic sections. Conversely, Enterobacteriaceae and Clostridium groups clearly decreased.Specific bacteria associated with beneficial effects increased in the ascending colon (Lactobacillus fermentum, Lactobacillus paracasei, Bifidobacterium longum and Bifidobacterium adolescentis) whereas Eubacterium eligens, Alistipes senegalensis, Prevotella copri and Eubacterium desmolans increased in the transversal and descending colon. Additionally, Blautia faecis and Ruminococcus albus increased in the transversal colon, and Bifidobacterium longum, Roseburia faecis and Victivallis vadensis in the descending colon.Bifidobacterium and Lactobacillus fermented the in-situ exopolysaccharides and released pectins from gazpacho by-products, as well as cellulosic degraded bacteria. This increased the short and medium chain fatty acids. Acetic acid, as well as butyric acid, increased throughout the colonic tract, which showed greater increases only in the transversal and descending colonic segments. Conversely, propionic acid was slightly affected by the colonic fermentation.These results show that sourdough bread is a useful food matrix for the enrichment of vegetable by-products (or other fibers) in order to formulate products with microbiota modulatory capacities.

Human activities have greatly increased the reactive nitrogen in the biosphere, thus profoundly altering global nitrogen cycling. The large increase in nitrogen deposition over the past few decades has led to eutrophication in natural ecosystems, with negative effects on forest health and biodiversity. Recent studies, however, have reported oligotrophication in forest ecosystems, constraining their capacity as carbon sinks. Here we demonstrate the widespread biological transformation of atmospheric reactive nitrogen in the canopies of European forests by combining nitrogen deposition quantification with measurements of the stable isotopes in nitrate and molecular analyses across ten forests through August–October 2016. We estimate that up to 80% of the nitrate reaching the soil via throughfall was derived from canopy nitrification, equivalent to a flux of up to 5.76 kg N ha −1 yr −1 . We also document the presence of autotrophic nitrifiers on foliar surfaces throughout European forests. Canopy nitrification thus consumes deposited ammonium and increases nitrate inputs to the soil. The results of this study highlight widespread canopy nitrification in European forests and its important contribution to forest nitrogen cycling.

Abstract Hidradenitis suppurativa (HS) is a chronic inflammatory skin disorder characterized by nodules, abscesses, and tunnels. Understanding the role of the skin microbiome in HS pathogenesis is crucial for developing targeted therapies. Previous studies have reported dysbiosis in HS-affected skin. This study aimed to investigate the microbiome in lesional skin biopsies of HS patients compared to perilesional healthy skin and healthy controls. Additionally, we sought to identify potential differences in the microbiome based on disease endotype, clinical variables, and lesion type. We collected skin samples from 30 HS patients and 20 healthy controls. Participants were categorized into follicular and inflammatory endotypes. Skin biopsies were obtained from lesional and perilesional areas of patients, and from anatomically matched areas in healthy controls. The microbiome was characterized using 16S rRNA gene sequencing. Clinical variables were recorded, including age, sex, body mass index, smoking habit, age of disease onset, family history, and lesion type. The microbiome composition differed significantly between lesional, perilesional, and healthy skin. Lesional skin showed higher abundance of Mycoplasma (P = 0,013) and Bacillus (p < 0,01), while Propionibacterium was more prevalent in healthy controls (p < 0,01). No significant differences were observed in the microbiome composition based on endotypes or lesion types. However, the severity of HS was associated with decreased Propionibacterium abundance. Our study provides novel insights into the microbiome variations in HS-affected skin in a Mediterranean population. The dysbiosis observed, particularly the higher abundance of Mycoplasma, may play a role in the inflammatory process of HS. Understanding the microbiome's impact on HS pathogenesis could lead to innovative treatments aimed at restoring microbiological balance and controlling inflammation. Propionibacterium's lower abundance in severe HS suggests its potential as a therapeutic target. Further investigations into microbiome manipulation as a potential therapeutic approach are warranted, particularly in early-stage lesions with potential for reversibility.

The main goal of the present work is to investigate the modulatory effect of Brassica oleracea italica x alboglabra (Bimi (R)) on gut microbiota composition through an in vitro digester and an in vivo trial. The digester simulates the entire gastrointestinal digestive process. The maintenance of the microbial population during the stabilization and treatment period was checked by bacteria plate counts The human trial included 15 Spanish adults who included 90 g of Bimi (R) every two days into their habitual diet. Plate counts showed that the treatment with Bimi (R) elicits eubiosis, favouring the growth of health promoting gut microbes, as seen on the total anaerobic values In vitro results showed many short chain fatty acids (SCFAs)-producing bacteria favoured by synergetic effects of the fibres, resistant starch and polyphenols present in Bimi (R). The human intervention confirmed some of these results and evidenced an increase in beneficial bacteria such as the genus Lactobacillus, and the species Chistensenella minuta, and Ruminococcus bromii, suggesting that Bimi (R) is capable of modulating gut microbiota towards a healthier status, with great potential in the management of human disorders related to microbiota dysbiosis.

The gut microbiota profile is determined by diet composition, and therefore this interaction is crucial for promoting specific bacterial growth and enhancing the health status. Red radish (Raphanus sativusL.) contains several secondary plant metabolites that can exert a protective effect on human health. Recent studies have shown that radish leaves have a higher content of major nutrients, minerals, and fiber than roots, and they have garnered attention as a healthy food or supplement. Therefore, the consumption of the whole plant should be considered, as its nutritional value may be of greater interest. The aim of this work is to evaluate the effects of glucosinolate (GSL)-enriched radish with elicitors on the intestinal microbiota and metabolic syndrome-related functionalities by using an in vitro dynamic gastrointestinal system and several cellular models developed to study the GSL impact on different health indicators such as blood pressure, cholesterol metabolism, insulin resistance, adipogenesis, and reactive oxygen species (ROS). The treatment with red radish had an influence on short-chain fatty acids (SCFA) production, especially on acetic and propionic acid and many butyrate-producing bacteria, suggesting that consumption of the entire red radish plant (leaves and roots) could modify the human gut microbiota profile toward a healthier one. The evaluation of the metabolic syndrome-related functionalities showed a significant decrease in the gene expression of endothelin, interleukin IL-6, and cholesterol transporter-associated biomarkers (ABCA1 and ABCG5), suggesting an improvement of three risk factors associated with metabolic syndrome. The results support the idea that the use of elicitors on red radish crops and its further consumption (the entire plant) may contribute to improving the general health status and gut microbiota profile.

The gut microbiota plays a key role in gastrointestinal immune and metabolic functions and is influenced by dietary composition. An in vitro protocol simulating the physiological conditions of the digestive system helps to study the effects of foods/biocompounds on gut microbiome and metabolome. The Dynamic-Colonic Gastrointestinal Digester consists of five interconnected compartments, double jacket vessels that simulate the physiological conditions of the stomach, the small intestine and the three colonic sections, which are the ascending colon, transverse colon and descending colon. Human faeces are required to reproduce the conditions and culture medium of the human colon, allowing the growth of the intestinal microbiota. After a stabilization period of 12 days, a food/biocompound can be introduced to study its modulatory effects during the next 14 days (treatment period). At the end of the stabilization and treatment period, samples taken from the colon compartments are analysed. The 16S rRNA gene analysis reveals the microbiota composition. The untargeted metabolomics analysis gives more than 10,000 features (metabolites/compounds). The present protocol allows in vitro testing of the modulatory effects of foods or biocompounds on gut microbiota composition and metabolic activity.

The MD (Mediterranean diet) is recognized as one of the healthiest diets worldwide and is associated with the prevention of cardiovascular and metabolic diseases. Dietary habits are considered one of the strongest modulators of gut microbiota, which seem to play a significant role in health status of the host. The purpose of the present study was to evaluate interactive associations between gut microbiota composition and habitual dietary intake in 360 Spanish adults from the Obekit cohort (normal weight, overweight, and obese participants). Dietary intake and adherence to the MD tests were administered and fecal samples were collected from each participant. Fecal 16S rRNA (ribosomal Ribonucleic Acid) gene sequencing was performed and checked against the dietary habits. MetagenomeSeq was the statistical tool applied to analyze data at the species taxonomic level. Results from this study identified several beneficial bacteria that were more abundant in the individuals with higher adherence to the MD. Bifidobacterium animalis was the species with the strongest association with the MD. Some SCFA (Short Chain Fatty Acids) -producing bacteria were also associated with MD. In conclusion, this study showed that MD, fiber, legumes, vegetable, fruit, and nut intake are associated with an increase in butyrate-producing taxa such as Roseburia faecis, Ruminococcus bromii, and Oscillospira (Flavonifractor) plautii.

There is mounting evidence demonstrating that fluxes and chemical composition of precipitation is substantially changed after passing through tree canopies, particularly in the case of atmospheric nitrogen (N) compounds, with important implications on forest N cycling. However, the processes underpinning those changes – beyond the leaf retention and/or leaching of N compounds - have been less investigated. In a previous study we provided isotopic evidence that biological nitrification in tree canopies was responsible for significant changes in the amount of NO3- from rainfall to throughfall across two UK forests at high nitrogen (N) deposition. This finding strongly suggested that forest canopies are not just passive filters for precipitation water and dissolved nutrients, and that the microbial life hidden within them can be responsible for transforming atmospheric N before it reaches the soil. We extended the isotopic approach at the European scale, and combined it to next-generation sequence analyses with the aim of elucidating canopy nitrification and identify phyllosphere microbes responsible for it. Specifically, in this study we: 1) estimated the relative contribution of NO3- derived from biological canopy nitrification vs. atmospheric deposition by using δ18O and δ17O of NO3- in rainfall and throughfall water; 2) quantified the functional genes related to nitrification, and finally 3) characterized the microbial communities harboured in tree canopies (i.e., phyllosphere) and in the underlying soils for two dominant tree species in Europe (Fagus sylvatica L. and Pinus sylvestris L.) using metabarcoding techniques. We considered twelve sites included in the European ICP Forests monitoring network, chosen along climate and N deposition gradients, spanning from Fennoscandia to the Mediterranean. We will show that presence of nitrifying microbes (as assessed through qPCR) and their activity (as derived from δ18O and δ17O) were detected in the tree canopies across most of the sites, and that canopy nitrification was significantly correlated with atmospheric N deposition. Finally, we will discuss differences in microbial community structure and composition across phyllosphere (and between the two tree species considered), water and soil samples in the investigated forests. Our study demonstrates the potential of integrating stable isotopes with microbial analyses to advance our understanding on canopy-atmosphere interactions and their contribution to N cycling.

The Mediterranean diet (MD) is recognised as one of the healthiest diets worldwide and is associated with the prevention of cardiovascular and metabolic diseases, among others. Dietary habits are considered one of the strongest modulators of the gut microbiota, which seems to play a significant role in the health and disease of the host. The purpose of the present study was to evaluate interactive associations between gut microbiota composition and habitual dietary intake in 360 Spanish adults of the Obekit cohort (normal weight, overweight and obese subjects). Dietary intake and adherence to the MD tests together with faecal samples were collected from each subject. Faecal 16S rRNA sequencing was performed and checked against the dietary habits. MetagenomeSeq was the statistical tool applied to analyse at the species taxonomic level. Results from this study confirm that a strong adherence to the MD increases the population of some beneficial bacteria, improving microbiota status towards a healthier pattern. Bifidobacterium animalis is the species with the strongest association with the MD. One of the highlights is the positive association between several SCFA-producing bacteria and high adherence to the MD. In conclusion, this study shows that MD, fibre, legumes, vegetables, fruit and nuts intakes are associated with an increase in butyrate-producing taxa such as Roseburia faecis, Ruminococcus bromii and Oscillospira (Flavonifractor) plautii.

Microbial activity plays a central role in nitrogen (N) cycling, with effects on forest productivity. Although N biotransformations, such as nitrification, are known to occur in the soil, here we investigate whether nitrifiers are present in tree canopies and actively process atmospheric N. This study was conducted in a Mediterranean holm oak (Quercus ilex L.) forest in Spain during the transition from hot dry summer to cool wet winter. We quantified NH4+ —N and NO3- —N fluxes for rainfall (RF) and throughfall (TF) and used δ15N, δ18O and Δ17O to elucidate sources of NO3- . Finally, we characterized microbial communities and abundance of nitrifiers on foliage, RF and TF water through metabarcoding and quantitative polymerase chain reaction respectively. NO3—N fluxes at the site were larger in TF than RF, suggesting a contribution from dry deposition, as also supported by δ15N and δ18O. However, Δ17O indicated that about 20% of NO3- in TF derived from canopies nitrification in August, after a severe drought, with a lower proportion in September (≈8%). This seasonal partitioning between biologically and atmospherically derived NO3- coincided with a decreasing trend of the abundance of archaeal nitrifiers. Tree canopies and TF had more diverse microbial communities than RF. Yet, RF showed higher variability in microbial composition, likely associated with the origin of air masses. Synthesis. Atmospheric N deposition is significantly altered after passing through tree canopies. While nitrification has been proposed as one of the mechanisms responsible for these changes, very few studies directly investigate its occurrence. Here, we showed that nitrification by epiphytic leaf microbes contributed to increasing NO3 in TF and that nitrifiers' activity was reduced going from the dry and hot summer to the cool winter. Overall, these results highlight the power of coupling microbial community analysis, functional gene amplification and stable isotope approaches to examine ecosystem‐scale processes.

A study aimed at defining population structure of Italian tomato spotted wilt virus (TSWV) isolates was performed. Full genome sequencing of six TSWV isolates found in two Italian regions (two from Latium: Lazio 17 and Tarquinia; and four from Calabria: PepCal 10, 12, 22 and 24) were assembled. Identity percentages in nucleotide sequence among these TSWV isolates are here provided. The six full length genome sequences were compared with other two Italian isolates (p105 and p202/3WT) already fully sequenced, as well as full TSWV genomes that could be retrieved from GenBank. Phylogenetic analysis, performed in concatenated sequences and for each gene of each genome segment (L, M and S), confirmed the presence of two clades, namely A-like and D-like. In particular, the phylogenetic tree based on segment L grouped all the newly sequenced TSWV isolates in D-like clade. In the M segment phylogenetic tree, all our TSWV isolates shifted in the A-like clade. Isolates separation was not correlated to their geographical origin in phylogenetic study of distinct ORFs encoded by the RNA S segment. In fact, in nucleocapsid-encoding phylogenetic tree, PepCal 10 and 22 grouped in an A-like clade with p105, PepCal 12 and 24 in a D-like clade with p202/3WT, whereas Lazio 17 and Tarquinia in a third well distinct group. NSs tree displayed only PepCal 10 with p105 in A-like clade, whereas PepCal 12, 22, 24 with p202/3WT in D-like subclade; and isolates from Latium grouped a separated clade adjacent to D-like isolates. Additional analysis on putative reassortment events showed that TSWV Calabrian isolates likely originated from a reassortment event in M RNA and other in S RNA with p105 as major parent. Recombination events were detected in isolates from Latium in L and S RNAs with Chinese isolates as putative major parent.

1 Centre for Ecological Research and Forestry Applications, CREAF, c/o Universidad Autonoma de Barcelona, Edificio C, 08290 Cerdanyola, Barcelona (Spain); Servei de Genòmica i Bioinformàtica, IBB-Parc de Recerca UAB Mòdul B, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain); Centre of Advanced Studies of Blanes, CEAB-CSIC, Spanish Council for Scientific Research (Spain); Universidad de Navarra, Laboratorio Integrado de Calidad Ambiental (LICA), Campus Universitario, 31080, Pamplona (Spain); IVL Swedish Environmental Research Institute, P.O. Box 5302, SE-400 14 Göteborg, Sweden; CNR-ISAFOM, Via Patacca, 85, 80056 Ercolano, Napoli, Italy; Natural Resources Institute Finland (Luke), Oulu, P.O. Box 413, 90570 Oulu, Finland; Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, 550 Stadium Mell Drive, West Lafayette, IN 47907, USA; ONF, Office National des Forêts, Departement Recherche et Developpement, Bâtiment B, Boulevard de Constance, F-77300 Fontainebleau, France; Centre for Ecosystem, Society and Biosecurity, Forest Research, Alice Holt, UK;Research Institute for Nature and Forest, Gaverstraat 4, 9500 Geraardsbergen (Belgium);WSL, Swiss Federal Institute for Forest, Snow and Landscape Research, Zürcherstrasse 111, CH-8903 Birmensdorf (Switzerland); National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan; CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Barcelona (Spain)

V. M. E. was evacuated when he was a young boy in 1939. He left an aunt and cousins in Spain (G. E. family). He was adopted in Belgium by the D. family and thus his new name became V. D. He has been unable to remember his childhood before his adoption, a symptomatology compatible with amnesia for personal identity, presumably because he may have suffered a head contusion before or during his exodus. Identification tests were performed on blood samples from V. D. and V. G. E., a mitochondrial cousin of the missing boy. V. G. E. and the missing boy have a common mitochondrial ancestor, their maternal grandmother. The mitochondrial profile of both samples turned out to be highly specific, which allowed the genetic identification of V. D. as V. M. E. As a result, V. D. has reclaimed his past and reunited with his former family in Spain after more than seven decades. As far as we know, this is the first report describing the application of mitochondrial DNA in the identification of a person evacuated during the Spanish Civil War suffering from amnesia for personal identity.

Background: Biopsies extracted from brain cancer patients often display degraded ribosomal RNA, which makes them unusable in transcriptomic experiments. This has not been properly documented in previous works aimed at refining the molecular classification of brain cancer. Objective: To determine RNA integrity in a large cohort of human brain cancer biopsies and to evaluate different factors that may influence RNA integrity in both a murine model of glioblastoma and in additional subsets of patient biopsies. Methods: Total RNA was isolated from 255 biopsies of various human brain tumors (HBTs) and processed on a Bioanalyzer. Correct RNA integrity was considered for samples showing either the ribosomal 28S/18S peak ratio ≥1.2 or RNA integrity number ≥6. The time-dependent effect of ex vivo ischemia was evaluated in a murine model, whose results were tested in a new collection of 27 human biopsies. Multiple biopsy sampling was considered in a further set comprising 32 biopsies. Results: The 255 human biopsies revealed a substantial percentage of samples displaying degraded RNA (27.5%). The murine model confirmed the known relevance of ex vivo ischemia time in increased RNA degradation. Human biopsies extracted immediately after cauterization showed a trend toward less RNA degradation. Combining snap freezing and multiple sampling of biopsies, the percentage of patients with degraded RNA was reduced by twofold (15.6%). Conclusions: We provide a first concise study of factors influencing RNA degradation in HBT biopsies. Immediate biopsy removal after cauterization of the tumor area, snap freezing, and multiple sampling improve RNA quality.

Lack of the yeast Ptc1 Ser/Thr protein phosphatase results in numerous phenotypic defects. A parallel search for high-copy number suppressors of three of these phenotypes (sensitivity to Calcofluor White, rapamycin and alkaline pH), allowed the isolation of 25 suppressor genes, which could be assigned to three main functional categories: maintenance of cell wall integrity (CWI), vacuolar function and protein sorting, and cell cycle regulation. The characterization of these genetic interactions strengthens the relevant role of Ptc1 in downregulating the Slt2-mediated CWI pathway. We show that under stress conditions activating the CWI pathway the ptc1 mutant displays hyperphosphorylated Cdc28 kinase and that these cells accumulate with duplicated DNA content, indicative of a G2-M arrest. Clb2-associated Cdc28 activity was also reduced in ptc1 cells. These alterations are attenuated by mutation of the MKK1 gene, encoding a MAP kinase kinase upstream Slt2. Therefore, our data show that Ptc1 is required for proper G2-M cell cycle transition after activation of the CWI pathway.