M-AMBI revisited: looking inside a widely-used benthic index

M-AMBI is a multimetric index for assessing the ecological quality status of marine and transitional waters. It is based on benthic macroinver- tebrates and integrates AMBI, a biotic index based on species sensitivity/tolerance, with diversity and rich- ness, making it compliant with the European Water Framework Directive. The success of AMBI paved the way for the introduction of M-AMBI, which was subsequently incorporated into the regulations of several European countries. The M-AMBI algorithm integrates the metrics by means of factor analysis (FA). In this paper, we first reproduced the algorithm using the open source R software. This enabled us to point out that FA is not functional to M-AMBI, and its omission does not appreciably change the results. We then enhanced the applicability of the index, making it independent of the number of samples. In this way, M-AMBI is closely approximated by the simple mean of the normalised metrics with no need for multivar- iate techniques. Finally, we further simplified the approach, presenting a bivariate version that is still highly correlated with M-AMBI, in which the consti- tutive metrics are reduced to a diversity measure and a species sensitivity index. The properties of this bivariate version include simplicity, transparency, robustness, and openness

Open Nomenclature in the biodiversity era

Summary The uncertainty or the provisional status of a taxonomic identification can be expressed by a set of terms and abbreviations known as Open Nomenclature (ON) qualifiers. This approach is widely applied across biological disciplines, and a high amount of biodiversity data left in ON can be found in literature and data bases. However, there is no consensus about ON qualifiers and their meaning. The use of ON qualifiers has been reviewed in order to provide a summary and guide to current practice in zoology. Some recommendation is given to avoid inconsistencies or vagueness. A flow chart is proposed to clarify the sources of uncertainties during identification and to facilitate the application of ON qualifiers. This review provides a guide for taxonomists and ecologists currently involved in biomonitoring and biodiversity programmes, as well as for researchers dealing with biodiversity data infrastructures and tools, offering a starting point for a methodological harmonization

Modeling the inter-annual variability of salinity in the lagoon of Venice in relation to the water framework directive typologies

The Water Framework Directive (2000/60/EC) requires member states to classify and enhance the ecological quality of water bodies in accordance with their type. To estimate the effect on type of the natural variability of lagoons, we applied a two-dimensional hydrodynamic model to the lagoon of Venice. The model calculated the mean annual spatial distributions of two variables: salinity and residence time. The standard deviation of salinity was also included, in order to estimate the variation of salinity values around the mean, which is associated with the instability of the mean salinity value. A highly detailed numerical grid was calibrated and high-frequency tributary discharge data were used. The simulations, under realistic forcing conditions, are based on the years 2003 and 2005. The former was characterized by low precipitation, around 30% less than the typical value. A comparison of model results and measurements shows the high reliability of the model in reproducing the spatial distribution and temporal evolution of salinity. We found strong inter-annual variation in salinity, standard deviation of salinity and residence time. The effect on the typing process is that the most representative types shift from one category to another. On the basis of the spatial patterns of the variables and their superposition, we identi fi ed types that described the bulk of the lagoon. This numerical tool offers support for lagoon management on various levels, in terms of both WFD requirements and other applications, by: (1) providing unbiased and objective zoning indications for the basin; (2) evaluating the response of water quality elements; (3) establishing the reference status of a water body; and (4) establishing a hierarchical division of a lagoon that can be used to select an appropriate number of sampling stations for monitoring

Evaluation of seabed mapping methods for fine-scale classification of extremely shallow benthic habitats – application to the Venice Lagoon, Italy

Recent technological developments of multibeam echosounder systems (MBES) allow mapping of benthic habitats with unprecedented detail. MBES can now be employed in extremely shallow waters, challenging data acquisition (as these instruments were often designed for deeper waters) and data interpretation (honed on datasets with resolution sometimes orders of magnitude lower). With extremely high-resolution bathymetry and colocated backscatter data, it is now possible to map the spatial distribution of fine scale benthic habitats, even identifying the acoustic signatures of single sponges. In this context, it isnecessary to understand which of the commonly used segmentation methods is best suited to account for such level of detail. At the same time, new sampling protocols for precisely georeferenced ground truth data need to be developed to validate the benthic environmental classification. This study focuses on a dataset collected in a shallow (2–10 m deep) tidal channel of the Lagoon of Venice, Italy. Using 0.05-m and 0.2-m raster grids, we compared a range of classifications, both pixel- based and object-based approaches, including manual, Maximum Likelihood Classifier, Jenks Optimization clustering, textural analysis and ObjectBased Image Analysis. Through a comprehensive and accurately geo-referenced ground truth dataset, we were able to identify five different classes of the substrate composition, including sponges, mixed submerged aquatic vegetation, mixed detritic bottom (fine and coarse) and unconsolidated bare sediment. We computed estimates of accuracy (namely Overall, User and Producer Accuracies) by cross tabulating predicted and reference instances. Overall, pixel based segmentations produced the highest accuracies and that the accuracy assessment is strongly dependent on the choice of classes for the segmentation. Tidal channels in the Venice Lagoon are extremely important in terms of habitats and sediment distribution, particularly within the context of the new tidal barrier being built. However, they had remained largely unexplored until now, because of the surveying challenges. The application of this remote sensing approach, combined with targeted sampling, opens a new perspective in the monitoring of benthic habitats in view of a knowledge-based management of natural resources in shallow coastal areas

A widespread picornavirus affects the hemocytes of the noble pen shell (Pinna nobilis), leading to its immunosuppression

IntroductionThe widespread mass mortality of the noble pen shell (Pinna nobilis) has occurred in several Mediterranean countries in the past 7 years. Single-stranded RNA viruses affecting immune cells and leading to immune dysfunction have been widely reported in human and animal species. Here, we present data linking P. nobilis mass mortality events (MMEs) to hemocyte picornavirus (PV) infection. This study was performed on specimens from wild and captive populations.MethodsWe sampled P. nobilis from two regions of Spain [Catalonia (24 animals) and Murcia (four animals)] and one region in Italy [Venice (6 animals)]. Each of them were analyzed using transmission electron microscopy (TEM) to describe the morphology and self-assembly of virions. Illumina sequencing coupled to qPCR was performed to describe the identified virus and part of its genome.Results and discussionIn 100% of our samples, ultrastructure revealed the presence of a virus (20 nm diameter) capable of replicating within granulocytes and hyalinocytes, leading to the accumulation of complex vesicles of different dimensions within the cytoplasm. As the PV infection progressed, dead hemocytes, infectious exosomes, and budding of extracellular vesicles were visible, along with endocytic vesicles entering other cells. The THC (total hemocyte count) values observed in both captive (eight animals) (3.5 × 104–1.60 × 105 ml−1 cells) and wild animals (14 samples) (1.90–2.42 × 105 ml−1 cells) were lower than those reported before MMEs. Sequencing of P. nobilis (six animals) hemocyte cDNA libraries revealed the presence of two main sequences of Picornavirales, family Marnaviridae. The highest number of reads belonged to animals that exhibited active replication phases and abundant viral particles from transmission electron microscopy (TEM) observations. These sequences correspond to the genus Sogarnavirus—a picornavirus identified in the marine diatom Chaetoceros tenuissimus (named C. tenuissimus RNA virus type II). Real-time PCR performed on the two most abundant RNA viruses previously identified by in silico analysis revealed positive results only for sequences similar to the C. tenuissimus RNA virus. These results may not conclusively identify picornavirus in noble pen shell hemocytes; therefore, further study is required. Our findings suggest that picornavirus infection likely causes immunosuppression, making individuals prone to opportunistic infections, which is a potential cause for the MMEs observed in the Mediterranean

The Italian long-term ecosystem research (LTER-Italy) network: results, opportunities, and challenges for coastal transitional ecosystems

1 - The Long-Term Ecosystem Research (LTER) network, now a global reality, was founded on a combination of long-term ecological studies, short-term experiments, and comparisons among sites and eco-domains. 2 - The LTER-Italy network was officially established as a formal member of the LTER international network in 2006, following a wider on-going process in Europe; it currently consists of 22 sites representing the main ecosystem typologies of Italy. Four coastal transitional ecosystem sites are included in the LTER-Italy network: on the northern Peninsula, these include the Venice Lagoon and the lagoons of the Po River Delta, which are characterized by a temperate climate and the influence of tides; and in the southern sector, these include the coastal ecosystems of Sardinia and the Mar Piccolo of Taranto, which are characterized by a Mediterranean climate and the absence of sensible tides. 3 - In this paper, we present and discuss three main issues: the LTER-International and LTER-Europe context, emphasising the most practical issues and activities that must be addressed for the effective organization and maintenance of LTER networks; the history, structure, and perspectives of the national LTER-Italy network; and the opportunities, strengths, and weaknesses related to participation of the LTER-Italy network in the study of coastal transitional ecosystems

The fingerprint of chemosymbiosis: origin and preservation of isotopic biosignatures in the nonseep bivalve Loripes lacteus compared with Venerupis aurea

Endosymbionts in marine bivalves leave characteristic biosignatures in their host organisms. Two nonseep bivalve species collected in Mediterranean lagoons, thiotrophic symbiotic Loripes lacteus and filter-feeding nonsymbiotic Venerupis aurea, were studied in detail with respect to generation and presence of such signatures in living animals, and the preservation of these signals in subfossil (late Pleistocene) sedimentary shells. Three key enzymes from sulfur oxidation (APS-reductase), CO2 fixation (RubisCO) and assimilation of nitrogen [glutamine synthetase (GS)] were detected by immunofluorescence in the bacterial symbionts of Loripes. In Loripes, major activity was derived from GS of the symbionts whereas in Venerupis the host GS is active. In search of geologically stable biosignatures for thiotrophic chemosymbiosis that might be suitable to detect such associations in ancient bivalves, we analyzed the isotopic composition of shell lipids (d 13C ) and the bulk organic matrix of the shell (d 13C , d 15N , d 34S ). In the thiotrophic Loripes, d 13C values were depleted compared with the filter-feeding Venerupis by as much as 8.5 parts per thousand for individual fatty acids, and 4.4 parts per thousand for bulk organic carbon. Likewise, bulk d 15N and d 34S values were more depleted in recent thiotrophic Loripes. Whereas d 34S values were found to be unstable over time, the combined d 15N and d 13C values in organic shell extracts revealed a specific signature for chemosymbiosis in recent and subfossil specimens

Biological Resistance of Acetylated Radiata Pine, European Beech, and MDF against Marine Borers at Three Italian Sites after Five Years Immersion

The aim of this research was to determine the resistance of acetylated wood against marine biodeterioration in use class 5 for use in temperate waters. The resistance of acetylated radiata pine (Pinus radiata D. Don) on solid and medium-density fiberboard (MDF) panels was compared with untreated wood of European species, such as European beech (Fagus sylvatica L.), sweet chestnut (Castanea sativa Mill.), European oak (Quercus robur L.), and marine plywood. As a reference control, untreated Scots pine (Pinus sylvestris L.) sapwood was used. The field tests were carried out in accordance with EN 275, and started in April 2015. The three Italian exposure sites were Marine of Scarlino private harbor, Port of Genoa, and the Venice Lagoon. Final evaluation in 2021 showed a greater resistance to marine borers of acetylated wood, radiata pine, and beech and MDF panels. However, the untreated European species showed low resistance against marine organisms, with complete decay after the first year of exposure

Biological Resistance of Acetylated Radiata Pine, European Beech, and MDF against Marine Borers at Three Italian Sites after Five Years Immersion

The aim of this research was to determine the resistance of acetylated wood against marine biodeterioration in use class 5 for use in temperate waters. The resistance of acetylated radiata pine (Pinus radiata D. Don) on solid and medium-density fiberboard (MDF) panels was compared with untreated wood of European species, such as European beech (Fagus sylvatica L.), sweet chestnut (Castanea sativa Mill.), European oak (Quercus robur L.), and marine plywood. As a reference control, untreated Scots pine (Pinus sylvestris L.) sapwood was used. The field tests were carried out in accordance with EN 275, and started in April 2015. The three Italian exposure sites were Marine of Scarlino private harbor, Port of Genoa, and the Venice Lagoon. Final evaluation in 2021 showed a greater resistance to marine borers of acetylated wood, radiata pine, and beech and MDF panels. However, the untreated European species showed low resistance against marine organisms, with complete decay after the first year of exposure