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

none7noPlastic 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.openCasabianca Silvia, Bellingeri Arianna, Capellacci Samuela, Sbrana Alice, Russo Tommaso, Corsi Ilaria, Penna AntonellaCasabianca, Silvia; Bellingeri, Arianna; Capellacci, Samuela; Sbrana, Alice; Russo, Tommaso; Corsi, Ilaria; Penna, Antonell

Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis

Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. CFS were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression.Comment: 18 pages, accepted for publication in BMC Bioinformatic

Gene expression in Rhizoglomus irregulare at two different time points of mycorrhiza establishment in Helianthus annuus roots, as revealed by RNA-seq analysis

Arbuscular mycorrhizal fungi (AMF) play a fundamental role in plant growth and nutrition in natural and agricultural ecosystems. Despite the importance of such symbionts, the different developmental changes occurring during the AMF life cycle have not been fully elucidated at the molecular level. Here, the RNA-seq approach was used to investigate Rhizoglomus irregulare specific and common transcripts at two different time points of mycorrhizal establishment in Helianthus annuus in vivo. Four days after inoculation, transcripts related to cellular remodeling (actin and tubulin), cellular signaling (calmodulin, serine/threonine protein kinase, 14-3-3 protein, and calcium transporting ATPase), lipid metabolism (fatty acid desaturation, steroid hormone, and glycerophospholipid biosynthesis), and biosynthetic processes were detected. In addition to such transcripts, 16 days after inoculation, expressed genes linked to binding and catalytic activities; ion (K+, Ca2+, Fe2+, Zn2+, Mn2+, Pi, ammonia), sugar, and lipid transport; and those involved in vacuolar polyphosphate accumulation were found. Knowledge of transcriptomic changes required for symbiosis establishment and performance is of great importance to understand the functional role of AMF symbionts in food crop nutrition and health, and in plant diversity in natural ecosystems

Net gain: Low-cost, trawl-associated eDNA samplers upscale ecological assessment of marine demersal communities

Marine biodiversity stewardship requires costly and time-consuming capture-based monitoring techniques, which limit our understanding of the distribution and status of marine populations. Here, we reconstruct catch and demersal community compo- sition in a set of 24 fishing sites in the central Tyrrhenian Sea by gathering environ- mental DNA (eDNA) aboard commercial bottom-trawl fishing vessels. We collected genetic material from two sources: the water draining from the net after the end of hauling operations (“slush”), and custom-made rolls of gauze tied to a hollow perfo- rated sphere placed inside the fishing net (“metaprobe”). Species inventories were generated using a combination of fish-specific (Tele02 12S) and universal metazoan (COI) molecular markers. DNA metabarcoding data recovered over 90% of the caught taxa and accurately reconstructed the overall structure of the assemblages of the examined sites, reflecting expected differences linked to major drivers of community structure in Mediterranean demersal ecosystems, such as depth, distance from the coast, and fishing effort. eDNA also returned a “biodiversity bonus” mostly consisting of pelagic species not catchable by bottom trawl but present in the surrounding en- vironment. Overall, the “metaprobe” gauzes showed a greater biodiversity detection power as compared to “slush” water, both qualitatively and quantitatively, strengthen- ing the idea that these low-cost sampling devices can play a major role in upscaling the gathering of data on both catch composition and the broader ecological charac- teristics of marine communities sustaining trawling activities. This approach has the potential to drastically expand the reach of ecological monitoring, whereby fishing vessels operating across the oceans may serve as opportunistic scientific platforms to increase the strength and granularity of marine biodiversity data

Application of a multi-species bio-economic modelling approach to explore fishing traits within eligible cetacean conservation areas in the Northern Ionian Sea (Central Mediterranean Sea)

The assessment of the spatial overlap between eligible cetacean conservation areas (CCAs) and fishing grounds could be a strategic element in the implementation of effective conservation measures in the pelagic offshore areas. A multi-species bio-economic modelling approach has been applied to estimate the fishing traits in eligible CCAs in the Northern Ionian Sea (NIS, Central Mediterranean Sea) between 10-800 m of depth, adopting the Spatial MAnagement of demersal Resources for Trawl fisheries model (SMART). Four possible CCAs were defined according to the distribution of cetacean species, their bio-ecological needs, as well as socio-economic needs of human activities, identifying a Blue, Red, Orange and Green CCAs in the NIS. SMART spatial domain was a grid with 500 square cells (15x15 NM). The analysis was conducted for the period 2016-2019, considering the Otter Trawl Bottom (OTB) fleet activities in the study areas through the Vessel Monitoring System. The spatial extension of fishing activities, hourly fishing effort (h), landings (tons) and economic value (euros) for each CCA and the NIS were estimated as yearly median values. Fishing activities were absent in the Blue CCA, where the presence of the submarine canyon head does not offer accessible fishing grounds. The hourly fishing effort in the Green area accounted for about 22% (3443 h) of the total hourly effort of the NIS, while the Orange and Red areas were about 8% (1226 h) and 2% (295 h), respectively. The Green CCA corresponded to about 14% (36 tons) of the total landings in the NIS, whereas the Orange and Red areas represented about 9% (22 tons) and 6% (16 tons), respectively. The Green CCA accounted for about 13% (156 thousand euros) of the total economic value of the NIS, while the Orange and Red areas represented about 6% (69 thousand euros) and 4% (44thousand euros), respectively. Results showed no or negligible negative effects on trawl activities by potential spatial restrictions due to the establishment of CCAs highlighting the importance to consider spatially integrated information during the establishment process of conservation areas for cetacean biodiversity according to the principles of Ecosystem Based Management

Technical measures without enforcement tools: is there any sense? A methodological approach for the estimation of passive net length in small scale fisheries

Passive nets are currently among the most important fishing gears largely used along the Mediterranean coasts by the small scale fisheries sector. The fishing effort exerted by this sector is strongly correlated with net dimensions. Therefore, the use of passive nets is worldwide managed by defining net length and net drop. The EC Reg. 1967/2006 reports that the length of bottom-set and drifting nets may be also defined considering their weight or volume; however, no practical suggestions for fisheries inspectors are yet available. Consequently,  even if such technical measures are reasonable from a theoretical viewpoint, they are hardly suitable as a management tool, due to the difficulties in harbour control. The overall objective of this paper is to provide a quick methodological approach for the gross estimation of passive net length (by net type) on the basis of net volume. The final goal is to support fisheries managers with suitable advice for enforcement and control purposes. The results obtained are important for the management of the fishing effort exerted by small scale fisheries. The methodology developed in this study should be considered as a first attempt to tackle the tangled problem of net length estimation that can be easily applied in other fisheries and areas in order to improve the precision of the models developed herein

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

Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots

Arbuscular mycorrhizal (AM) fungi are essential elements of soil fertility, plant nutrition and productivity, facilitating soil mineral nutrient uptake. Helianthus annuus is a non-model, widely cultivated species. Here we used an RNA-seq approach for evaluating gene expression variation at early and late stages of mycorrhizal establishment in sunflower roots colonized by the arbuscular fungus Rhizoglomus irregulare. mRNA was isolated from roots of plantlets at 4 and 16 days after inoculation with the fungus. cDNA libraries were built and sequenced with Illumina technology. Differential expression analysis was performed between control and inoculated plants. Overall 726 differentially expressed genes (DEGs) between inoculated and control plants were retrieved. The number of upregulated DEGs greatly exceeded the number of down-regulated DEGs and this difference increased in later stages of colonization. Several DEGs were specifically involved in known mycorrhizal processes, such as membrane transport, cell wall shaping, and other. We also found previously unidentified mycorrhizal-induced transcripts. The most important DEGs were carefully described in order to hypothesize their roles in AM symbiosis. Our data add a valuable contribution for deciphering biological processes related to beneficial fungi and plant symbiosis, adding an Asteraceae, non-model species for future comparative functional genomics studies

Synthesis of CdS and CdSe nanocrystallites using a novel single-molecule precursors approach

The synthesis of CdS and CdSe nanocrystallites using the thermolysis of several dithioor diselenocarbamato complexes of cadmium in trioctylphosphine oxide (TOPO) is reported. The nanodispersed materials obtained show quantum size effects in their optical spectra and exhibit near band-edge luminescence. The influence of experimental parameters on the properties of the nanocrystallites is discussed. HRTEM images of these materials show well-defined, crystalline nanosized particles. Standard size fractionation procedures can be performed in order to narrow the size dispersion of the samples. The TOPO-capped CdS and CdSe nanocrystallites and simple organic bridging ligands, such as 2,2¢-bipyrimidine, are used as the starting materials for the preparation of novel nanocomposites. The optical properties shown by these new nanocomposites are compared with those of the starting nanodispersed materials