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We believe that the contribution of volunteers could play a fundamental role in monitoring and protecting the environment. People at sea sighting pollution caused by oil or hydrocarbon spillages can now immediately report this using a freely downloadable mobile application. At the Signals and Images Laboratory (SI-LAB) of the Institute of Information Science and Technology of the National Research Council of Pisa (ISTI-CNR), we have developed a Marine Information System (MIS) for monitoring vessel traffic and oil spills within the Mediterranean basin. The MIS collects and integrates geotagged data related to safety and health issues of the sea from various sources (satellites, optical sensors, electronic noses, autonomous underwater vehicle systems) and provides predictive models to assist the authorities in the management of emergencies at sea. An integrant part of the MIS is represented by the data that can be collected and shared by volunteers who want to collaborate in monitoring the status of the sea. For this purpose, we have developed ARGO Sentinel, a free application for smartphones with a Geolocation System.

An array of fluid flow sensors can be used to detect and track underwater objects via the fluid flow field these objects create. The sensed flows combine to a spatio-temporal velocity profile, which can be used to solve the inverse problem; determining the relative position and orientation of a moving source via a trained model. In this study, two training strategies are used: simulated data resulting from continuous motion in a path and from vibratory motion at discrete locations on a grid. Furthermore, we investigate two sensing modalities found in literature: 1D and 2D sensitive flow sensors; all while varying the sensor detection threshold via a noise level. Results show that arrays with 2D sensors outperform those with 1D sensors, especially near and next to the sensor array. On average, the path method outperforms the grid method with respect to estimating the location and orientation of a source.

Microbial mats are phylogenetically and functionally diverse benthic microbial communities, which can be sometimes calcified (i.e. microbialites). Fossil microbial mats constitute the oldest traces of life on Earth and their modern representatives are thus used as analogues of those primordial ecosystems to gain insights into their functioning. I have studied the microbial communities (archaea, bacteria and eukaryotes) of several microbialites (lake Alchichica, Mexico) and microbial mats (in a small pond in the salar de Llamara, Chile). The main objectives of my PhD were to finely characterize their phylogenetic structure and to improve our understanding of the functioning of these complex ecosystems. To do so, I have applied a multi-disciplinary approach combining molecular approaches (metabarcoding, metagenomics) to environmental data (physico-chemical parameters of the water column or mineral composition of the microbialites).The results presented in this thesis allowed refining our model of microbialite formation in Lake Alchichica. We showed that, in addition to cyanobacterial photosynthesis, both eukaryotic and, particularly, anoxygenic photosyntheses were potentially important to promote carbonate precipitation. Llamara mat communities were characterised by the presence of numerous novel archaeal and bacterial lineages, some of which were identified for the first time in this work. Our analyses have also highlighted the diversity of organisms involved in both sulphur and nitrogen cycles in these mats and identified potential biotic interactions between poorly known prokaryotic lineages. Finally, we showed that the composition of the microbial communities associated to these microbialites and microbial mats was strongly influenced by environmental parameters. Overall, these results represent a substantial contribution to our understanding of the ecology of these systems as well as of the factors that influence their phylogenetic and functional structures.; Les tapis microbiens sont des communautés benthiques, calcifiées (i.e. microbialites) ou non, diverses à la fois phylogénétiquement et métaboliquement. Les tapis microbiens fossiles constituent les plus anciennes traces de vie sur Terre et leurs représentants modernes peuvent donc être utilisés pour comprendre le fonctionnement de ces écosystèmes anciens. J'ai étudié les communautés microbiennes (archées, bactéries et eucaryotes) de plusieurs microbialites (lac Alchichica, Mexique) et tapis microbiens (dans une mare du salar de Llamara, Chili) afin de caractériser finement leur structure phylogénétique et d'améliorer notre compréhension de leur fonctionnement. J'ai pour cela utilisé une approche combinant des outils moléculaires (métabarcoding, métagénomique) à des données environnementales (paramètres physico-chimiques de la colonne d'eau ou composition minérale des microbialites). Mon travail de thèse a permis d'affiner le modèle de formation des microbialites d'Alchichica, en montrant notamment que, en plus de la photosynthèse oxygénique cyanobactérienne, le potentiel à précipiter des carbonates de la photosynthèse eucaryote et, surtout, de la photosynthèse anoxygénique est important. Les communautés des tapis de Llamara étaient quant à elles caractérisées par la présence de nombreuses lignées d'archées et de bactéries très divergentes, dont certaines ont été identifiées pour la première fois dans ce travail. Nos analyses ont aussi souligné la diversité des organismes impliqués dans les cycles du soufre et de l'azote au sein de ces systèmes et permis d'identifier de potentielles interactions biotiques entre des lignées procaryotes dont l'écologie est peu connue. Enfin, nous avons mis en évidence que les paramètres environnementaux influencent fortement la composition des communautés associées à ces microbialites et à ces tapis microbiens. L'ensemble de ces résultats permet de mieux comprendre le fonctionnement de ces systèmes ainsi que les facteurs qui influencent leur structure phylogénétique et fonctionnelle.

Fungal symbionts of terrestrial plants are among the most widespread and well-studied symbioses, relatively little is known about fungi that are associated with macroalgae. To fill the gap in marine fungal taxonomy, we combined simple culture methods with amplicon sequencing to characterize the fungal communities associated with three brown (Sargassum muticum, Pelvetia canaliculata, and Himanthalia elongata) and two red (Mastocarpus stellatus and Chondrus crispus) macroalgae from one intertidal zone. In addition to characterizing novel fungal diversity, we tested three hypotheses: fungal diversity and community composition vary (i) among species distributed at different tidal heights, (ii) among tissue types (apices, mid-thallus, and stipe), and (iii) among "isomorphic" C. crispus life cycle stages. Almost 70% of our reads were classified as Ascomycota, 29% as Basidiomycota, and 1% that could not be classified to a phylum. Thirty fungal isolates were obtained, 18 of which were also detected with amplicon sequencing. Fungal communities differed by host and tissue type. Interestingly, P. canaliculata, a fucoid at the extreme high intertidal, did not show differences in fungal diversity across the thallus. As found in filamentous algal endophytes, fungal diversity varied among the three life cycle stages in C. crispus. Female gametophytes were also compositionally more dispersed as compared to the fewer variable tetrasporophytes and male gametophytes. We demonstrate the utility of combining relatively simple cultivation and sequencing approaches to characterize and study macroalgal-fungal associations and highlight the need to understand the role of fungi in near-shore marine ecosystems.

Operational MSI/NM(T&P) service

The size and shape of snow grains directly impacts the reflection by a snowpack. In this article, different approaches to retrieve the optical-equivalent snow grain size (ropt) or, alternatively, the specific surface area (SSA) using satellite, airborne, and ground-based observations are compared and used to evaluate ICON-ART (ICOsahedral Nonhydrostatic—Aerosols and Reactive Trace gases) simulations. The retrieval methods are based on optical measurements and rely on the ropt-dependent absorption of solar radiation in snow. The measurement data were taken during a three-week campaign that was conducted in the North of Greenland in March/April 2018, such that the retrieval methods and radiation measurements are affected by enhanced uncertainties under these low-Sun conditions. An adjusted airborne retrieval method is applied which uses the albedo at 1700 nm wavelength and combines an atmospheric and snow radiative transfer model to account for the direct-to-global fraction of the solar radiation incident on the snow. From this approach, we achieved a significantly improved uncertainty (ropt of 15 µm within a five-day period after a snowfall event which is small compared to previous observations under similar temperature regimes. ICON-ART captured the observed change of ropt during snowfall events, but systematically overestimated the subsequent snow grain growth by about 100%. Adjusting the growth rate factor to 0.012 µm2 s−1 minimized the difference between model and observations. Satellite-based and airborne retrieval methods showed higher ropt over sea ice (<300 µm) than over land surfaces (<100 µm) which was reduced by data filtering of surface roughness features. Moderate-Resolution Imaging Spectroradiometer (MODIS) retrievals revealed a large spread within a series of subsequent individual overpasses, indicating their limitations in observing the snow grain size evolution in early spring conditions with low Sun.

B hromozomi predstavljaju prekobrojne hromozome koji nisu neophodni za normalan rast i razviće. Ovi prekobrojni hromozomi se javljaju kod svih višećelijskih eukariotskih grupa, osim kod ptica, i različiti su po poreklu, morfologiji, veličini, broju, genetičkoj strukturi i efektima na fenotip. Njihova prisutnost u živom svetu procenjuje se na 3% kariotipski analiziranih vrsta. Karakteriše ih nasleđivanje koje ne prati Mendelova pravila, kao i izostanak rekombinacije sa hromozomima osnovnog A seta. Glavna pitanja koja se postavljaju u savremenim istraživanjima B hromozoma se odnose na njihovo poreklo, mehanizme nastanka i održavanja. Poznavanje genetičkog sadržaja, transkripcionog statusa i efekata prekobrojnih hromozoma, omogućuje rasvetljavanje njihovog biološkog značaja. Glodari su najbrojniji nosioci B hromozoma među sisarima. Rod Apodemus broji ukupno 20 vrsta, od kojih je kod šest zabeleženo prisustvo B hromozoma. U ovoj studiji izučavani su B hromozomi na jedinkama vrste žutogrli miš, Apodemus flavicollis. Nosioci imaju najčešće jedan ili dva B, dok je maksimalan zabeležen broj osam B hromozoma. Prekobrojni hromozomi se kod ove vrste javljaju u svim do sada proučavanim populacijama na teritoriji Republike Srbije, sa različitom učestalošću. Brojne populacione studije na ovoj vrsti pokazuju da jedinke sa B hromozomima imaju višu adaptivnu vrednost u poređenju sa jedinkama bez prekobrojnih hromozoma. Cilj ove studije bio je utvrđivanje sekvence, proučavanje porekla, kao i analiza transkripcione aktivnosti pojedinih sekvenci B hromozoma vrste A. flavicollis. U istraživanje su uključene životinje sa lokaliteta u Republici Srbiji, Ruskoj federaciji i Republici Belorusiji. Metodom mikrodisekcije iz kariotipa tri jedinke su izolovani B hromozomi koji su potom umnoženi u lančanoj reakciji polimeraze (PCR). Proizvedene su fluorescentne B-specifične probe. Procena homologije između B-specifičnih proba i hromozoma osnovnog kariotipa iste vrste izvršena je putem fluorescentne in situ hibridizacije (FISH). Utvrđena je homologija između sekvence B hromozoma i: a) pericentromernog regiona (PR) polnih hromozoma, b) subtelomernih regiona dva para malih autozoma, kao i c) slabija homologija sa distalnim regionom Y hromozoma B chromosomes (Bs) are supernumerary chromosomes in a standard karyotype, unnecessary for normal growth and development. Bs are present in all main groups of multicellular eukaryotes, except birds, and extremely variable considering origin, morphology, size, number, molecular structure, and phenotypic effects. 3% of all analyzed species have B chromosomes. The Bs do not follow rules of Mendelian segregation law and do not recombine with members of the basic A chromosome complement. The main questions considered in contemporary studies of Bs are surrounding their origin, mechanisms of formation and maintenance. Knowledge of their molecular structure, transcriptional activity, and phenotypic effects, will allow a deeper understanding of their biological importance. Within mammals, the most frequent carriers of Bs are rodents. The genus Apodemus includes 20 species, six of which carry Bs, in addition to A chromosome set. In this study, B chromosomes were analyzed in specimens of the yellow-necked mouse, Apodemus flavicollis. Carriers usually have one or two Bs, and the highest recorded number in this species is eight B chromosomes. In different frequencies, supernumeraries are present in all studied populations of A. flavicollis in the territory of the Republic of Serbia. Numerous population studies of this species are indicating that B carriers have a higher fitness compared to individuals without B chromosomes. The aim of this study was to define sequence, origin and transcriptional activity of selected B regions in species A. flavicollis. Specimens were collected from different localities in the Republic of Serbia, Russian Federation and the Republic of Belarus. B chromosomes have been isolated by microdissection from the karyotype of three individuals and amplified in the polymerase chain reaction (PCR). B-specific fluorescent probes were synthesized. Estimation of homology between B-specific probes and chromosomes of A set had been obtained by fluorescent in situ hybridization (FISH). Homology was shown between the B chromosome and: a) pericentromeric region (PR) of sex chromosomes b) subtelomeric region of the two pairs of small chromosomes and c) lower homology with the distal region of the Y chromosome.

A massive diatom bloom is observed each year in the surface waters of the naturally Fe-fertilized Kerguelen Plateau (Southern Ocean). We measured biogenic silica production and dissolution fluxes (ρSi and ρDiss, respectively) in the mixed layer in the vicinity of the Kerguelen Plateau during austral spring 2011 (KEOPS-2 cruise). We compare results from a high-nutrient low-chlorophyll reference station and stations with different degrees of iron enrichment and bloom conditions. Above the plateau biogenic ρSi are among the highest reported so far in the Southern Ocean (up to 47.9 mmol m−2 d−1). Although significant (10.2 mmol m−2 d−1 on average), ρDiss were generally much lower than production rates. Uptake ratios (ρSi : ρC and ρSi : ρN) confirm that diatoms strongly dominate primary production in this area. At the bloom onset, decreasing dissolution-to-production ratios (D : P) indicate that the remineralization of silica could sustain most of the low silicon uptake and that the system progressively shifts toward a silica production regime which must be mainly supported by new source of silicic acid. Moreover, by comparing results from the two KEOPS expeditions (spring 2011 and summer 2005), we suggest that there is a seasonal evolution of the processes decoupling Si and N cycles in the area. Indeed, the consumption of H4SiO4 standing stocks occurs only during the growing stage of the bloom when strong net silica production is observed, contributing to higher H4SiO4 depletion relative to NO3−. Then, the decoupling of H4SiO4 and NO3− is mainly controlled by the more efficient nitrogen recycling relative to Si. Gross Si : N uptake ratios were higher in the Fe-rich regions compared to the high-nutrient low-chlorophyll (HNLC) area, likely due to different diatom communities. This suggests that the diatom responses to natural Fe fertilization are more complex than previously thought, and that natural iron fertilization over long timescales does not necessarily decrease Si : N uptake ratios as suggested by the silicic acid leakage hypothesis. Finally, we propose the first seasonal estimate of the Si biogeochemical budget above the Kerguelen Plateau based on direct measurements. This study points out that naturally iron-fertilized areas of the Southern Ocean could sustain very high regimes of biogenic silica production, similar to those observed in highly productive upwelling systems.

Urban areas are the primary habitat for a majority of the global population. The development of cities not only entails a fundamental change in human settlement patterns but also a dramatic transformation of the physical environment. Thus, urban areas and their development are at the centre of all discussions on sustainability and/or sustainable development. This review essay introduces the notion of Urban Metabolism (UM), a term that provides a conceptual framework to study how a city functions, and hence, a way to address the sustainability issue of a city. Due to the significance and scope of the subject, the notion of UM is interpreted and thus approached differently across diverse disciplines from both the natural and social science fields. In order to comprehend the commonalities and controversies between them, the present review also briefly introduces the historical roots of the term. This review reveals the increasing significance of a rich and rapidly evolving field of research on the metabolism of urban areas.