Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)

11openInternationalInternational coauthor/editorMonitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.openLeontidou, Kleopatra; Vokou, Despoina; Sandionigi, Anna; Bruno, Antonia; Lazarina, Maria; De Groeve, Johannes; Li, Mingai; Varotto, Claudio; Girardi, Matteo; Casiraghi, Maurizio; Cristofori, AntonellaLeontidou, K.; Vokou, D.; Sandionigi, A.; Bruno, A.; Lazarina, M.; De Groeve, J.; Li, M.; Varotto, C.; Girardi, M.; Casiraghi, M.; Cristofori, A

Πρότυπα αερομεταφερόμενης γύρης κατά μήκος μιας υψομετρικής διαβάθμισης στις Ιταλικές Άλπεις: εφαρμογή αλληλούχισης νέας γενιάς σε περιβαλλοντικό DNA και κλασικών μεθόδων ταυτοποίησης γύρης

The aim of the study was (i) the development of an efficient method for pollen taxonomic identification from complex environmental samples by use of molecular approaches, and (ii) the application of this method for the detection of spatio-temporal patterns of airborne pollen in a mountainous area and the evaluation of the potential of metabarcoding to be used for monitoring vegetation changes. We developed an optimal protocol for processing samples of different type and complexity for DNA extraction, further applied Sanger and next generation sequencing (NGS), and compared results to those taken by classical microscopy. We applied this protocol in combination with NGS to environmental samples from six habitats along the altitudinal gradient of the Italian Alps (National Park of Paneveggio–Pale di San Martino). Providing high resolution taxonomic results, metabarcoding can be used for biodiversity assessments and floral surveys and for monitoring vegetation changes, particularly those expressed in species composition rather than in species abundance.Σκοπός της διατριβής ήταν (α) η ανάπτυξη κατάλληλης μεθοδολογίας ανίχνευσης και ταυτοποίησης γύρης σε περιβαλλοντικά δείγματα με εφαρμογή μοριακών προσεγγίσεων και (β) η εφαρμογή αυτής της μεθοδολογίας για την ανίχνευση χωρικών και χρονικών προτύπων της αερομεταφερόμενης γύρης σε μια υψομετρική διαβάθμιση και τη διερεύνηση της δυνατότητας να χρησιμοποιηθεί η προσέγγιση metabarcoding για την βιοπαρακολούθηση των αλλαγών της βλάστησης. Αναπτύχθηκε κατάλληλο πρωτόκολλο επεξεργασίας δειγμάτων διαφορετικού τύπου και πολυπλοκότητας προς απομόνωση του DNA γύρης, χρησιμοποιήθηκαν οι μέθοδοι αλληλούχισης Sanger και νέας γενιάς (NGS) και συγκρίθηκαν τα αποτελέσματα που προέκυψαν με τα προερχόμενα από την κλασική μέθοδο ταυτοποίησης γύρης με μικροσκόπιο. Το πρωτόκολλο αυτό σε συνδυασμό με τη μέθοδο NGS εφαρμόστηκε σε περιβαλλοντικά δείγματα από έξι οικοτόπους των Ιταλικών Άλπεων (εθνικό πάρκο Paneveggio–Pale di San Martino) ενώ κατασκευάστηκε μια τοπική βάση δεδομένων με αλληλουχίες DNA για τα taxa γύρης της περιοχής. Παρέχοντας υψηλής ανάλυσης αποτελέσματα, η προσέγγιση metabarcoding μπορεί να εφαρμοστεί για εκτίμηση της φυτικής βιοποικιλότητας και για την παρακολούθηση αλλαγών στη βλάστησης, κυρίως αυτών που αφορούν στη σύνθεση παρά στην αφθονία των ειδών

Script from "Comparing Quantile Regression Spline analyses and Supervised Machine Learning for environmental quality assessment at coastal marine aquaculture installations"

This zip archive contains data and R code used in the manuscript 'Comparing Quantile Regression Spline analyses and Supervised Machine Learning for environmental quality assessment at coastal marine aquaculture installations' by Kleopatra Leontidou, Verena Rubel, Thorsten Stoeck. It contains a data folder with the datasets used for Quantile Regression Spline analyses and Supervised Machine Learning, R code for the Quantile Regression Splines Analysis and for the production of the figures shown in the results section and R code for the Supervised Machine Learning analysis. Description of data files: Two 'asv table' datasets were used (Norway_asvtable.csv, Scotland_asvtable.csv), one of which included all samples from seven Norwegian salmon farms (n = 138) and one including all samples (n=92) from seven Scottish salmon farms. The 'asv table' datasets include as rows the Amplicon Sequence Variants (ASVs), as columns the samples (corresponding to the Sample column in the 'metadata' datasets) and as cell values the number of sequence reads. The 'metadata' datasets (Norway_metadata.csv, Scotland_metadata.csv) include as rows the samples and as columns information about the samples.  The data folder includes also data from Supervised Machine Learning analysis (table_of_predictions_relab_norway.csv, table_of_predictions_relab_scotland.csv,  varimp_mean_nor.csv, varimp_mean_sco.csv). </p

Comparative Transcriptomics and Metabolomics Reveal an Intricate Priming Mechanism Involved in PGPR-Mediated Salt Tolerance in Tomato

Plant-associated beneficial strains inhabiting plants grown under harsh ecosystems can help them cope with abiotic stress factors by positively influencing plant physiology, development, and environmental adaptation. Previously, we isolated a potential plant growth promoting strain (AXSa06) identified as Pseudomonas oryzihabitans, possessing 1-aminocyclopropane-1-carboxylate deaminase activity, producing indole-3-acetic acid and siderophores, as well as solubilizing inorganic phosphorus. In this study, we aimed to further evaluate the effects of AXSa06 seed inoculation on the growth of tomato seedlings under excess salt (200 mM NaCl) by deciphering their transcriptomic and metabolomic profiles. Differences in transcript levels and metabolites following AXSa06 inoculation seem likely to have contributed to the observed difference in salt adaptation of inoculated plants. In particular, inoculations exerted a positive effect on plant growth and photosynthetic parameters, imposing plants to a primed state, at which they were able to respond more robustly to salt stress probably by efficiently activating antioxidant metabolism, by dampening stress signals, by detoxifying Na+, as well as by effectively assimilating carbon and nitrogen. The primed state of AXSa06-inoculated plants is supported by the increased leaf lipid peroxidation, ascorbate content, as well as the enhanced activities of antioxidant enzymes, prior to stress treatment. The identified signatory molecules of AXSa06-mediated salt tolerance included the amino acids aspartate, threonine, serine, and glutamate, as well as key genes related to ethylene or abscisic acid homeostasis and perception, and ion antiporters. Our findings represent a promising sustainable solution to improve agricultural production under the forthcoming climate change conditions.&lt;/p&gt