Bio-Mineralogy: the influence of the mineral composition of hard substrates on marine benthic organisms and communities distribution.

Studying the interactions between environmental variables and marine organisms is fundamental to understanding these delicate dynamic balances at different space-time scales. These processes are in constant mutual influence since the biotic compartment undergoes abiotic factors but simultaneously modifies the environmental parameters through their own physiological activities. Nevertheless, each of these drivers, taken individually, is the result of precise balances involving single organisms, communities or entire ecosystems, and multiple environmental parameters can be directly correlated with each other. In an age of climate change such as the one we live in, a multidisciplinary approach to the study of the environments and marine organisms appears essential to understand the potential effect of a single part of the system on the others and, consequently, to try to relate to each other, all of these, to optimally manage ecosystems and safeguarding habitats. Benthic marine species, both sessile for the entire duration of their life cycle or linked to the seabed only for part of it, undergo the effect of physic-chemical changes in the water column and through their adaptations can oppose or support them, sometimes exploiting them to advantage, thanks to their resilience and resistance. On the other hand, the same substrate can be modified by different processes of various nature (mechanical, physical, chemical, biological), thus becoming an essential element that can influence the phases of colonization and consequent larval settlement, on the development of the single organism, and the entire benthic community, up to the point of characterizing the submerged landscape. Furthermore, all these aspects have both a very different spatial and temporal scale; therefore, the observation of the interaction phenomena between organisms and environmental variables requires very different approaches, often conducted step by step, to isolate the effect of a single factor and, where this is not possible, mitigate the interaction. The substrate characteristics have already been considered in many scientific fields, ranging from engineering to ecology, highlighting innovative aspects and conflicting conclusions. Furthermore, the interest in bio-mineralogy, i.e., the study of the interaction between the organism and the mineralogical composition of the substrate, began to emerge at the end of the last century, focusing on the toxic effect of the quartz present in the dissolved sediment on colonization phase of the associated fauna. Since then, numerous studies have deepened this area of research, investigating the hard substrates of various kinds and the structure of the communities settled there. Here, the continuation of this research has attempted to define what effects the substrate can have at different ecological scales (from the single organism to the community, up to the landscape), examining different types of rocks and highlighting affinities between similar lithotypes. Due to their natural geological conformation, the Ligurian coast and the Sardinian context of the Tavolara Marine Protected Area - P.ta Coda Cavallo have been investigated. Particularly, this last locality presents, on a reduced spatial scale, the variability of substrates as well as environments of great environmental value. These contexts have proved to be optimal for expanding knowledge on the effect of the mineralogical composition of lithotypes on the distribution and abundance of benthic organisms, pointing out the crucial role of encrusting coralline algae in stabilising substrates. In a second analysis, the survey made it possible to characterize ecologically and deepen the knowledge on the distribution and the state of health and conservation of priority habitats of great environmental value, currently under-valued and subject to substantial impacts by fisheries, indicating new more suitable for the management of these by the competent Bodies

The influence of the rock mineralogy on population density of Chthamalus (Crustacea: Cirripedia) in the Ligurian Sea (NW Mediterranean Sea)

Settlement, recruitment and survival of sessile marine species are driven by many biotic and abiotic factors. Among them, substrate mineral composition is generally a neglected topic, despite it proved to be a relevant contributing variable in driving the structure of benthic communities. Thanks to their ecology, Chthamalus species are a good proxy to test the role of substrate in affecting settlement and final population density on exposed rocky shores. Differences in the number of individuals were analysed in eight localities along the Eastern Ligurian Riviera (north-western Mediterranean Sea), from Portovenere to Manara Cape. In this sector of the Ligurian littoral, the coast is constituted by different rocks characterised by variable concentrations of calcite, silicates and quartz. This situation constitutes an ideal setting to evaluate the influence of mineral composition of the rocks in structuring the epilithic macrobiota communities in energetic splash zones and under similar physical pressures. Rocks rich in calcites turned out to be more suitable for Chthamalus species than substrates containing high amounts of silicates, and of quartz in particular. Additionally, also the grain size of the main mineral component of the rocks, determining in turn the surface roughness seemed to influence barnacle densities, with a significant preference for finer-grained substrates

Thirty year ecosystem trajectories in a submerged marine cave under changing pressure regime

Marine caves are unique and vulnerable habitats exhibiting high biodiversity and heterogeneity, but threatened by multiple global and local disturbances. Marine caves, although widely distributed along the Mediterranean coast, suffer for the lack of quantitative data on their structure and function, which hinder their conservation status assessment. Thanks to the availability of a nearly 30-year-long series of data (1986-2013), we evaluated ecosystem change in the Bergeggi marine cave (Ligurian Sea, NW Mediterranean), a cave with a complex shape and high habitat heterogeneity. Non-taxonomic descriptors were adopted, namely growth forms (GF) and trophic guilds (TG), which are informative about ecosystem structure and functioning, respectively. The cave experienced a general trend of change during the last three decades, mainly due to the decline in the cover of sessile organisms (especially 3-dimensional forms) matched by an increase of turf and sediment, thus causing the structural and functional homogenization of the cave community. While change before 2004 had been attributed to climatic factors (especially to the summer heat waves of 1999 and 2003), the most important rate of change was observed between 2009 and 2013, coinciding with recent major beach nourishments and the extension of the neighbouring Vado Ligure harbour, thus providing evidences on the importance of local disturbances deriving from coastal interventions. Monitoring the status of cave ecosystems is urgently needed, and the use of effective indicators, such as the specific traits here adopted (morphology and feeding strategy), could provide effective tools to assist marine cave conservation

Realtime PCR Is More Sensitive than Multiplex PCR for Diagnosis and Serotyping in Children with Culture Negative Pneumococcal Invasive Disease

Background: Pneumococcal serotyping is usually performed by Quellung reaction, considered the gold standard test. However the method cannot be used on culture-negative samples. Molecular methods can be a useful alternative. The aim of the study was to evaluate the use of Multiplex-sequential-PCR (MS-PCR) or Realtime-PCR on blood samples for diagnosis and serotyping of invasive pneumococcal disease (IPD) in a pediatric clinical setting. Methodology/Principal Findings: Sensitivity and specificity of MS-PCR and Realtime-PCR have been evaluated both on 46 well characterized pneumococcal isolates and on 67 clinical samples from children with culture-negative IPD. No difference in sensitivity and specificity between MS-PCR and Realtime PCR was found when the methods were used on isolates: both methods could type 100 % isolates and the results were always consistent with culture-based methods. On the contrary, when used on clinical samples 43/67 (64.2%) were typeable by MS-PCR and 61/67 (91.0%) by Realtime-PCR (p = 0.0004,K Cohen 0.3, McNemar’s p,0.001). Non-typeability by MS-PCR was associated in 18/20 cases (90.0%) with low bacterial load. The difference between the two methods was present both when they were used on normally sterile fluids (respectively 31/ 33 (93.9%) typeable samples for Realtime-PCR and 24/33 (72.7%) for MS-PCR, p = 0.047, 95%CL 0.03–0.98; K Cohen 0.3; McNemar’s p = 0.0016) and when they were used on nasopharyngeal swabs (respectively 30/34 (88.2%) typeable samples for Realtime-PCR and 19/34 (55.9%) for MS-PCR, p = 0.007, 95%CL 0.04–0.66); the presence of multiple pneumococca

Pneumococcal DNA is not detectable in the blood of healthy carrier children by real-time PCR targeting the lytA gene

The diagnosis of invasive pneumococcal disease (IPD) is currently based on culture methods, which lack sensitivity, especially after antibiotic therapy. Molecular methods have improved sensitivity and do not require viable bacteria; however, their use is complicated by reports of low specificity with some assays. The present study investigated the specificity of a real-time PCR targeting lytA for the detection of IPD. A group of 147 healthy children, aged 6 months to 16 years (mean 6.4 years, median 4.9 years, interquartile range 6.4 years), who were in hospital for routine examinations, were tested for pneumococcal carrier status and for the presence of detectable pneumococcal DNA in their blood by real-time PCR targeting the pneumococcal lytA gene. In addition, 35 culture-positive biological samples were analysed. Urine was examined for the presence of pneumococcal DNA and C-polysaccharide antigen. Carriage was detected in 77 of the 147 subjects (52.4 %); however, regardless of carrier status, none of the subjects had a positive result from blood. Analysis of the culture-positive biological samples yielded positive results in 100 % (15/15) of cerebrospinal fluid samples and 95 % (19/20) of blood samples. All urine samples from healthy carriers were negative for DNA, whilst antigenuria was detected in 44/77 carriers (57.1 %). In conclusion, real-time PCR is both sensitive and specific and can be a useful tool in the routine diagnosis of IPD. Its sensitivity, which surpasses that of other methods for this purpose, does not come at the cost of reduced specificity

Differential diagnosis of neurodegenerative dementias with the explainable MRI based machine learning algorithm MUQUBIA

Biomarker-based differential diagnosis of the most common forms of dementia is becoming increasingly important. Machine learning (ML) may be able to address this challenge. The aim of this study was to develop and interpret a ML algorithm capable of differentiating Alzheimer's dementia, frontotemporal dementia, dementia with Lewy bodies and cognitively normal control subjects based on sociodemographic, clinical, and magnetic resonance imaging (MRI) variables. 506 subjects from 5 databases were included. MRI images were processed with FreeSurfer, LPA, and TRACULA to obtain brain volumes and thicknesses, white matter lesions and diffusion metrics. MRI metrics were used in conjunction with clinical and demographic data to perform differential diagnosis based on a Support Vector Machine model called MUQUBIA (Multimodal Quantification of Brain whIte matter biomArkers). Age, gender, Clinical Dementia Rating (CDR) Dementia Staging Instrument, and 19 imaging features formed the best set of discriminative features. The predictive model performed with an overall Area Under the Curve of 98%, high overall precision (88%), recall (88%), and F1 scores (88%) in the test group, and good Label Ranking Average Precision score (0.95) in a subset of neuropathologically assessed patients. The results of MUQUBIA were explained by the SHapley Additive exPlanations (SHAP) method. The MUQUBIA algorithm successfully classified various dementias with good performance using cost-effective clinical and MRI information, and with independent validation, has the potential to assist physicians in their clinical diagnosis

The Red Coral Community in the Messina Strait: New Findings from the 1700s Lazzaro Spallanzani Collection

The precious red coral (Corallium rubrum L.) represents one of the most fascinating marine species of the Mediterranean Sea. Several samples, including red coral together with its accompanying species, were found in the zoological collection of the Italian pioneer biologist Lazzaro Spallanzani (1729–1799), collected in the Messina Strait during his voyage in Sicily (1788). The study of these samples allowed the inclusion of numerous additional species in the traditional red coral facies as the large oyster Neopycnodonte cochlear, the giant barnacle Pachylasma giganteum, the mesophotic scleractinian Caryophyllia (Caryophyllia) cyathus. These specimens proved to be very useful in describing the diversity of the paleo-community including red coral, shedding light on its formation processes. In particular, some specimens are composed of red coral rubble consolidated and cemented with other carbonatic remains Probably, these peculiar specimens have a similar origin to those of the Sciacca Banks already known from the Sicily Channel. In fact, the two areas are prone to intense seismic activity that periodically causes mass mortalities of red coral from nearby rocky reliefs and the formation of biogenic detritus, while the resulting chemical environment of the water and the sediments allows the consolidation of the carbonatic remains

The Red Coral Community in the Messina Strait: New Findings from the 1700s Lazzaro Spallanzani Collection

The precious red coral (Corallium rubrum L.) represents one of the most fascinating marine species of the Mediterranean Sea. Several samples, including red coral together with its accompanying species, were found in the zoological collection of the Italian pioneer biologist Lazzaro Spallanzani (1729–1799), collected in the Messina Strait during his voyage in Sicily (1788). The study of these samples allowed the inclusion of numerous additional species in the traditional red coral facies as the large oyster Neopycnodonte cochlear, the giant barnacle Pachylasma giganteum, the mesophotic scleractinian Caryophyllia (Caryophyllia) cyathus. These specimens proved to be very useful in describing the diversity of the paleo-community including red coral, shedding light on its formation processes. In particular, some specimens are composed of red coral rubble consolidated and cemented with other carbonatic remains Probably, these peculiar specimens have a similar origin to those of the Sciacca Banks already known from the Sicily Channel. In fact, the two areas are prone to intense seismic activity that periodically causes mass mortalities of red coral from nearby rocky reliefs and the formation of biogenic detritus, while the resulting chemical environment of the water and the sediments allows the consolidation of the carbonatic remains

Filling a Gap: A Population of <i>Eunicella verrucosa</i> (Pallas, 1766) (Anthozoa, Alcyonacea) in the Tavolara-Punta Coda Cavallo Marine Protected Area (NE Sardinia, Italy)

Among Mediterranean habitat-forming alcyonaceans, the sea fan Eunicella verrucosa is known to form dense forests at circalittoral depths, providing seascape complexity and sustaining a rich associated fauna. Its occurrence in the Tavolara–Punta Coda Cavallo Marine Protected Area (NE Sardinia) has never been deeply investigated despite this area being well known from a biocoenotic point of view. This study provides new information on the size of the colonies settled between 35 and 59 m depth on granitic outcrops and represents a contribution to highlighting the hotspot of megabenthic diversity enclosed in the protected area. The presence of 100 colonies was assessed by photographic samplings performed between 2015 and 2020, in a small area characterized by peculiar ecological conditions. The morphometric descriptions and age estimation showed a persistently isolated population probably derived from a stochastic event of settling of larvae presumably coming from the Tuscany Archipelago. A richly associated epibiotic community, composed of 18 species/OTUs, showed how branched bryozoans, particularly Turbicellepora avicularis, and the parasitic octocoral Alcyonium coralloides, affected the colonies’ branches, suggesting a putative anthropogenic impact related to fishing activity. This study indicates that proper protection and management strategies are mandatory for the Marine Protected Area, in order to conserve this unique population and the whole associated benthic assemblage