Environmental DNA metabarcoding reveals the effects of seafloor litter and trawling on marine biodiversity

Environmental DNA (eDNA) techniques are emerging as promising tools for monitoring marine communities. However, they have not been applied to study the integrated effects of anthropogenic pressures on marine biodiversity. This study examined the relationships between demersal community species composition, key environmental features, and anthropogenic impacts such as fishing effort and seafloor litter using eDNA data in the central Tyrrhenian Sea. The results indicated that both fishing effort and seafloor litter influenced species composition and diversity. The adaptive traits of marine species played a critical role in their response to debris accumulation and fishing. Mobile species appeared to use relocation strategies, while sessile species showed flexibility in the face of disturbance. Epibiotic species relied on passive transport. The use of eDNA-based methods is a valuable resource for monitoring anthropogenic impacts during scientific surveys, enhancing our ability to monitor marine ecosystems and more effectively assess the effects of pollution

Spatial analysis of demersal food webs through integration of eDNA metabarcoding with fishing activities

The evaluation of the status of marine communities, and especially the monitoring of those heavily exploited by fisheries, is a key, challenging task in marine sciences. Fishing activities are a major source of disruption to marine food webs, both directly, by selectively removing components at specific trophic levels (TL), and indirectly, by altering habitats and production cycles. Food web analysis can be very useful in the context of an Ecosystem Approach to Fisheries, but food web reconstructions demand large and expensive data sets, which are typically available only for a small fraction of marine ecosystems. Recently, new technologies have been developed to easily, quickly and cost-effectively collect environmental DNA (eDNA) during fishing activities. By generating large, multi-marker metabarcoding data from eDNA samples obtained from commercial trawlers, it is possible to produce exhaustive taxonomic inventories for the exploited ecosystems, which are suitable for food-web reconstructions. Here, we integrate and re-analyse the data of a recent study in which the α diversity was investigated using the eDNA opportunistically collected during fishing operations. Indeed, we collect highly resolved information on species feeding relationships to reconstruct the food webs at different sites in the Strait of Sicily (Mediterranean Sea) from eDNA and catch data. After observing that the trophic networks obtained from eDNA metabarcoding data are more consistent with the available knowledge, a set of food web indicators (species richness, number of links, direct connectance and generality) is computed and analysed to unravel differences in food webs structure through different areas (spatial variations). Species richness, number of links and generality (positively) and direct connectance (negatively) are correlated with increasing distance from the coast and fishing effort intensity. The combined effects of environmental gradients and fishing effort on food web structure at different study sites are then examined and modelled. Taken together, these findings indicate the suitability of eDNA metabarcoding to assist and food web analysis, obtain several food web-related ecological indicators, and tease out the effect of fishing intensity from the environmental gradients of marine ecosystems

Development of label-free biophysical markers in osteogenic maturation

The spatial and temporal changes of morphological and mechanical properties of living cells reflect complex functionally-associated processes. Monitoring these modifications could provide a direct information on the cellular functional state. Here we present an integrated biophysical approach to the quantification of the morphological and mechanical phenotype of single cells along a maturation pathway. Specifically, quantitative phase microscopy and single cell biomechanical testing were applied to the characterization of the maturation of human foetal osteoblasts, demonstrating the ability to identify effective label-free biomarkers along this fundamental biological process

Spatial analysis of demersal food webs through integration of eDNA metabarcoding with fishing activities

The evaluation of the status of marine communities, and especially the monitoring of those heavily exploited by fisheries, is a key, challenging task in marine sciences. Fishing activities are a major source of disruption to marine food webs, both directly, by selectively removing components at specific trophic levels (TL), and indirectly, by altering habitats and production cycles. Food web analysis can be very useful in the context of an Ecosystem Approach to Fisheries, but food web reconstructions demand large and expensive data sets, which are typically available only for a small fraction of marine ecosystems. Recently, new technologies have been developed to easily, quickly and cost-effectively collect environmental DNA (eDNA) during fishing activities. By generating large, multi-marker metabarcoding data from eDNA samples obtained from commercial trawlers, it is possible to produce exhaustive taxonomic inventories for the exploited ecosystems, which are suitable for food-web reconstructions. Here, we integrate and re-analyse the data of a recent study in which the α diversity was investigated using the eDNA opportunistically collected during fishing operations. Indeed, we collect highly resolved information on species feeding relationships to reconstruct the food webs at different sites in the Strait of Sicily (Mediterranean Sea) from eDNA and catch data. After observing that the trophic networks obtained from eDNA metabarcoding data are more consistent with the available knowledge, a set of food web indicators (species richness, number of links, direct connectance and generality) is computed and analysed to unravel differences in food webs structure through different areas (spatial variations). Species richness, number of links and generality (positively) and direct connectance (negatively) are correlated with increasing distance from the coast and fishing effort intensity. The combined effects of environmental gradients and fishing effort on food web structure at different study sites are then examined and modelled. Taken together, these findings indicate the suitability of eDNA metabarcoding to assist and food web analysis, obtain several food web-related ecological indicators, and tease out the effect of fishing intensity from the environmental gradients of marine ecosystems

Impact of two Erwinia sp. on the response of diverse Pisum sativum genotypes under salt stress

The current study reveals that two non-pathogenic strains of Erwinia sp. are diferent in their PGP traits. By using an integrated approach, a picture of the pea plant status in three genotypes subjected to a salt stress condition was obtained and the role of the two bacterial considered Erwinia sp. strains has been highlighted. Results showed the relevance of plant genotype in determining the response to bacterial inoculants as well as the diferences in the plant mechanisms activated to cope with the stress in the diferent plant/strain combination. Overall, this study emphasizes the importance of understanding the molecular and biochemical processes occurring in plant–microbe interactions at genotype level, and the influence on plant responses to environmental stresses. Further analyses are needed to clarify the behaviour of the three genotypes, such as the leaf water potential, and to verify the efects of the bacterial inoculation in feld conditions, subjectd by an increased environmental unpredictability due to the climate change scenarioCurrently, salinization is impacting more than 50% of arable land, posing a significant challenge to agriculture globally. Salt causes osmotic and ionic stress, determining cell dehydration, ion homeostasis, and metabolic process alteration, thus negatively influencing plant development. A promising sustainable approach to improve plant tolerance to salinity is the use of plant growth-promoting bacteria (PGPB). This work aimed to characterize two bacterial strains, that have been isolated from pea root nodules, initially called PG1 and PG2, and assess their impact on growth, physiological, biochemical, and molecular parameters in three pea genotypes (Merveille de Kelvedon, Lincoln, Meraviglia d'Italia) under salinity. Bacterial strains were molecularly identified, and characterized by in vitro assays to evaluate the plant growth promoting abilities. Both strains were identified as Erwinia sp., demonstrating in vitro biosynthesis of IAA, ACC deaminase activity, as well as the capacity to grow in presence of NaCl and PEG. Considering the inoculation of plants, pea biometric parameters were unaffected by the presence of the bacteria, independently by the considered genotype. Conversely, the three pea genotypes differed in the regulation of antioxidant genes coding for catalase (PsCAT) and superoxide dismutase (PsSOD). The highest proline levels (212.88 μmol g-1) were detected in salt-stressed Lincoln plants inoculated with PG1, along with the up-regulation of PsSOD and PsCAT. Conversely, PG2 inoculation resulted in the lowest proline levels that were observed in Lincoln and Meraviglia d'Italia (35.39 and 23.67 μmol g-1, respectively). Overall, this study highlights the potential of these two strains as beneficial plant growth-promoting bacteria in saline environments, showing that their inoculation modulates responses in pea plants, affecting antioxidant gene expression and proline accumulation

Gestire l'edilizia sociale. Intervento di riqualificazione del quartiere di San Vito, Lucca.

La gestione del patrimonio di edilizia residenziale pubblica rappresenta una priorità per gli Enti gestori: i fabbricati destinati all'edilizia sociale nella maggior parte dei casi sono datati, spesso risalenti al secondo dopoguerra, ed è quindi necessario provvedere a un monitoraggio continuo che consenta di garantire la funzionalità degli edifici stessi. La conoscenza completa e sempre aggiornata del patrimonio rappresenta il primo passo verso un'organizzazione più efficiente, finalizzata al miglioramento della qualità dei servizi offerti agli utenti, per rispondere tempestivamente alle loro richieste e garantire il monitoraggio costante delle attività sul territorio dal punto di vista manutentivo e gestionale. In quest'ottica la tesi analizzando il quartiere popolare di San Vito a Lucca, è finalizzata all'elaborazione di un sistema informativo territoriale, cioè uno strumento di supporto alle attività dell'ente gestore (ERP Lucca srl), spaziando dal monitoraggio degli edifici e degli aspetti relativi alla loro manutenzione, alla gestione dei rapporti con gli utenti; attraverso l'utilizzo di questo strumento si vuole inoltre evidenziare come sia possibile elaborare un cronoprogramma degli interventi sul patrimonio edilizio di San Vito, per proporre infine, un intervento di riqualificazione urbanistica e il progetto di un centro polivalente

DNA metabarcoding of trawling bycatch reveals diversity and distribution patterns of sharks and rays in the central Tyrrhenian Sea

Conservation and management of chondrichthyans are becoming increasingly important, as many species are particularly vulnerable to fishing activities, primarily as bycatch, which leads to incomplete catch reporting, potentially hiding the impact on these organisms. Here, we aimed at implementing an eDNA metabarcoding approach to reconstruct shark and ray bycatch composition from 24 hauls of a bottom trawl fishing vessel in the central Mediterranean. eDNA samples were collected through the passive filtration of seawater by simple gauze rolls encapsulated in a probe (the “metaprobe”), which already showed great efficiency in detecting marine species from trace DNA in the environment. To improve molecular taxonomic detection, we enhanced the 12S target marker reference library by generating sequences for 14 Mediterranean chondrichthyans previously unrepresented in public repositories. DNA metabarcoding data correctly identifies almost all bycaught species and detected five additional species not present in the net, highlighting the potential of this method to detect rare species. Chondrichthyan diversity showed significant association with some key environmental variables (depth and distance from the coast) and the fishing effort, which are known to influence demersal communities. As DNA metabarcoding progressively positions itself as a staple tool for biodiversity monitoring, we expect that its melding with opportunistic, fishery-dependent surveys could reveal additional distribution features of threatened and elusive megafauna

Macrobenthos of the Tortolì Lagoon: A Peculiar Case of High Benthic Biodiversity among Mediterranean Lagoons

Coastal lagoons and brackish ponds are extremely dynamic and temporary ecosystems that follow natural changes throughout their geological history. The correct management of the lagoons ensures their integrity and proper functioning. For this reason, their ecological status should be surveyed for assessing the most appropriate strategies of use. In the present study, historical datasets collected in 2003–2004 are used to investigate the spatiotemporal variation in the species composition and community structure of the macrobenthos of the Tortolì Lagoon (Sardinia, Italy) and to assess their relationship with key environmental variables. Owing to the presence of a riverine runoff at a site and confined areas at some distance from the sea inlet, we hypothesize the marked spatiotemporal changes of the macrobenthic community consistent with the high environmental variability typical of coastal lagoons. The results show a surprisingly high benthic biodiversity for a medium-sized lagoon (250 ha), with 101 species unevenly distributed across the lagoon. The environmental variables did not explain the zonation of the macrobenthic community as that typically found along a lagoonal gradient, due to a marked marine influence. The sampling sites were in fact discriminated by the species distribution according to their ecological affinity; in particular, the most distinctive characteristics of the Tortolì Lagoon emerged from the strictly marine species that represented the most abundant group, consistently with the high marinization of the lagoon. Our results show that the Tortolì Lagoon constitutes a peculiar ecosystem within Mediterranean lagoons, departing from the classic confinement theory

Ecological implications beyond the ecotoxicity of plastic debris on marine phytoplankton assemblage structure and functioning

Plastic pollution is a global issue posing a threat to marine biota with ecological implications on ecosystem functioning. Micro and nanoplastic impact on phytoplankton autotrophic species (e.g., cell growth inhibition, decrease in chlorophyll a and photosynthetic efficiency and hetero-aggregates formation) have been largely documented. However, the heterogeneity of data makes rather difficult a comparison based on size (i.e. micro vs nano). In addition, knowledge gaps on the ecological impact on phytoplankton assemblage structure and functioning are evident. A new virtual meta-analysis on cause-effect relationships of micro and nanoplastics on phytoplankton species revealed the significant effect posed by polymer type on reducing cell density for tested PVC, PS and PE plastics. Linked with autotrophic phytoplankton role in atmospheric CO2 fixation, a potential impact of plastics on marine carbon pump is discussed. The understanding of the effects of microplastics and nanoplastics on the phytoplankton functioning is fundamental to raise awareness on the overall impact on the first level of marine food web. Interactions between micro and nanoplastics and phytoplankton assemblages have been quite documented by in vitro examinations; but, further studies considering natural plankton assemblages and/or large mesocosm experiments should be performed to evaluate and try predicting ecological impacts on primary producers

Food preference determines the best suitable digestion protocol for analysing microplastic ingestion by fish

Microplastic presence in the marine environment has generated considerable concern. Many procedures for microplastics detection in fish gastrointestinal tract have been recently developed. In this study, we compared efficiencies of two common procedures applied for the digestion of organic matter (10% KOH; 15% H2O2) with a new proposal (mixture of 5% HNO3 and 15% H2O2). We considered ecological diversity among species and differences in their diet compositions as factors that could affect the efficiency and feasibility of analytical approaches. Our aim was to understand whether either one of the three protocols might be suitable for all species or it might be more advisable to select a method according to the gut content determined by different food preferences. The results showed that the trophic level and feeding habits should be considered for protocol selection. Finally, we applied the best protocols on samples from the Tyrrhenian sea