Depth-driven patterns in lytic viral diversity, auxiliary metabolic gene content, and productivity in offshore oligotrophic waters

IntroductionMarine viruses regulate microbial population dynamics and biogeochemical cycling in the oceans. The ability of viruses to manipulate hosts’ metabolism through the expression of viral auxiliary metabolic genes (AMGs) was recently highlighted, having important implications in energy production and flow in various aquatic environments. Up to now, the presence and diversity of viral AMGs is studied using -omics data, and rarely using quantitative measures of viral activity alongside.MethodsIn the present study, four depth layers (5, 50, 75, and 1,000 m) with discrete hydrographic features were sampled in the Eastern Mediterranean Sea; we studied lytic viral community composition and AMG content through metagenomics, and lytic production rates through the viral reduction approach in the ultra-oligotrophic Levantine basin where knowledge regarding viral actions is rather limited.Results and DiscussionOur results demonstrate depth-dependent patterns in viral diversity and AMG content, related to differences in temperature, nutrients availability, and host bacterial productivity and abundance. Although lytic viral production rates were similar along the water column, the virus-to-bacteria ratio was higher and the particular set of AMGs was more diverse in the bathypelagic (1,000 m) than the shallow epipelagic (5, 50, and 75 m) layers, revealing that the quantitative effect of viruses on their hosts may be the same along the water column through the intervention of different AMGs. In the resource- and energy-limited bathypelagic waters of the Eastern Mediterranean, the detected AMGs could divert hosts’ metabolism toward energy production, through a boost in gluconeogenesis, fatty-acid and glycan biosynthesis and metabolism, and sulfur relay. Near the deep-chlorophyll maximum depth, an exceptionally high percentage of AMGs related to photosynthesis was noticed. Taken together our findings suggest that the roles of viruses in the deep sea might be even more important than previously thought as they seem to orchestrate energy acquisition and microbial community dynamics, and thus, biogeochemical turnover in the oceans

Microplastics increase the marine production of particulate forms of organic matter

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Ιδιότητες και δυναμική της χρωμοφόρου διαλυτής οργανικής ύλης (CDOM) σε υδάτινα οικοσυστήματα της Ανατολικής Μεσογείου

The purpose of this study is to investigate the optical properties of Dissolved Organic Matter (DOM) and to gain information regarding the nature and transformation processes of DOM in a large region of the Eastern Mediterranean Sea covering the Marmara Sea, the North-Central and South Aegean Sea, the Ionian Trench and Northwestern Levantine Sea as well as Sperchios River and Maliakos Gulf. A secondary purpose of this study is to get insights into autochtonous CDOM production. Chromophoric Dissolved Organic Matter(CDOM) and Fluorescent Dissolved Organic Matter (FDOM) are used for the characterization of the optical properties of DOM but they can also provide information about DOM composition and track transformation processes. CDOM is the fraction of DOM that has the ability to absorb light in the UV-visible region of the electromagnetic spectrum. FDOM is the fraction of CDOM that additionally has the ability to fluorescence upon excitation. CDOM is of significant ecological importance as is a major factor in the light attenuation in the sea impacting the primary production. In order to achieve the purposes of this study, absorption spectra in the UV-visible region and fluorescence Excitation and Emission Matrices (EEMs) were obtained while Parallel Factor Analysis (PARAFAC) was applied for the identification of the fluorescent components. Our results show the distinct optical print of rivers and that their influence in the coastal waters is better tracked through fluorescence analysis. CDOM/FDOM dynamics at the surface of Marmara Sea deviate from the observed summer pattern in open seas while Black Sea Water (BSW) outflowing the Dardanelles introduce significant amounts of CDOM, aminoacid-like and humic-like substances in North Aegean Sea (NAS). The influence of BSW and the established optical properties in NAS presents seasonal variations. Photodegradation appears to be a major sink of CDOM and humic substances at the surface layer of the Aegean Sea. Contrary in mesopelagic and bathypelagic layers microbial activity seems to leed to the depletion of amino acid-like substances and the production of humic nature DOM. Overall our results suggest that CDOM and FDOM can provide important information regarding DOM composition and its dynamics (sources and sinks) in various water bodies.Ο σκοπός της εργασίας είναι η διερεύνηση των οπτικών ιδιοτήτων της Διαλυτής Οργανικής Ύλης, DOM, σε μια μεγάλη περιοχή της Ανατολικής Μεσογείου η οποία καλύπτει τη Θάλασσα του Μαρμαρά, το Βόρειο-Κεντρικό και Νότιο Αιγαίο, το Νότιο Ιόνιο, τη Βορειοδυτική Θάλασσα της Λεβαντίνης καθώς και το Σπερχειό Ποταμό. Δευτερέυων στόχος της διατριβής είναι να μελετήσει την αυτόχθονη παραγωγή της CDOM. Για τον χαρακτηρισμό των οπτικών ιδιοτήτων της DOM καθώς και στη διερεύνηση της χημική σύνθεσης της DOM και στον προσδιορισμό διεργασιών μετασχηματισμού χρησιμοποιούνται η Χρωμοφόρα Διαλυτή Οργανική Ύλη (CDOM) και η Φθορίζουσα Διαλυτή Οργανική Ύλη (FDOM). Η CDOM είναι το τμήμα της DOM που έχει την ικανότητα να απορροφά ακτινοβολία στο υπεριώδες και ορατό τμήμα του ηλεκτρομαγνητικού φάσματος. Η FDOM είναι το τμήμα της CDOM που επιπλέον παρουσιάζει φθορισμό. Η CDOM παρουσιάζει μεγάλη οικολογική σημασία καθώς είναι από τους κυριότερους παράγοντες που ευθύνονται για την απορρόφηση της ηλιακής ακτινοβολίας στα φυσικά ύδατα επηρεάζοντας τις φωτοσυνθετικές διεργασίες. Για το σκοπό της εργασίας λήφθηκαν φάσματα απορρόφησης καθώς και φάσματα φθορισμού Excitation Emission Matrices. Για την ταυτοποίηση των φθοριζόντων στοιχείων πραγματοποιήθηκε ανάλυση Parallel FactorAnalysis, PARAFAC. Τα αποτελέσματά μας δείχνουν ότι τα ιδιαίτερα οπτικά χαρακτηριστικά των ποταμών και η επίδρασή τoυς στα παράκτια ύδατα μπορούν να προσδιοριστούν καλύτερα μέσω του φθορισμού. Η επιφάνεια της Θάλασσας του Μαρμαρά παρουσιάζει οπτικές ιδιότητες οι οποίες αποκλίνουν από τις παρατηρούμενες στις ανοικτές θάλασσες. Η Μαύρη Θάλασσα φαίνεται να εισάγει σημαντικές ποσότητες CDOM καιFDOM πρωτεϊνικής και χουμικής φύσεως στο Βόρειο Αιγαίο επηρεάζοντας τις οπτικές ιδιότητες της περιοχής και παρουσιάζοντας ταυτόχρονα εποχιακές διακυμάνσεις. Η φωτοδιάσπαση φαίνεται να είναι καθοριστικός παράγοντας αποικοδόμησης της CDOM και της FDOM χουμικής φύσεως στην επιφάνεια του Αιγαίου. Αντίθετα σε μεσοπελαγικά και βαθυπελαγικά νερά η μικροβιακή δραστηριότητα φαίνεται να οδηγεί σε εξάντληση των φθοριζόντων ουσιών πρωτεϊνικής φύσεως και στην παραγωγή χουμικών ενώσεων.Συνολικά η παρούσα εργασία δείχνει ότι η ανάλυση της CDOM και FDOM μπορεί να παρέχει χρήσιμες πληροφορίες σχετικά με τη σύνθεση της DOM και να παρακολουθήσει χημικές διεργασίες αλλοίωσης στις οποίες υπόκειται

Increase in marine POM related to the presence of microplastic beads in a mesocosm experiment

This dataset supports the recent publication "Microplastics increase the marine production of particulate forms of organic matter" by L. Galgani et al (2019) in ERL. It comprises all data presented in the manuscript and Supplementary Information. In the file, Control = mesocosm without plastic addition (1,2,3) and MP = mesocosm with plastic addition (1,2,3). The data proceed from the MESO-Plastic experiment in 2017 conducted at the Hellenic Center for Marine Research, a member of the European Aquacosm network of mesocosm facilities

Seawater physics and chemistry along the Med-SHIP transects in the Mediterranean Sea in 2016

The Mediterranean Sea has been sampled irregularly by research vessels in the past, mostly by national expeditions in regional waters. To monitor the hydrographic, biogeochemical and circulation changes in the Mediterranean Sea, a systematic repeat oceanographic survey programme called Med-SHIP was recommended by the Mediterranean Science Commission (CIESM) in 2011, as part of the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). Med-SHIP consists of zonal and meridional surveys with different frequencies, where comprehensive physical and biogeochemical properties are measured with the highest international standards. The first zonal survey was done in 2011 and repeated in 2018. In addition, a network of meridional (and other key) hydrographic sections were designed: the first cycle of these sections was completed in 2016, with three cruises funded by the EU project EUROFLEETS2. This paper presents the physical and chemical data of the meridional and key transects in the Western and Eastern Mediterranean Sea collected during those cruises