{"id":14,"date":"2016-04-05T21:59:11","date_gmt":"2016-04-05T21:59:11","guid":{"rendered":"http:\/\/projects.nib.si\/diavir\/?page_id=14"},"modified":"2022-11-15T10:10:27","modified_gmt":"2022-11-15T09:10:27","slug":"summary","status":"publish","type":"page","link":"https:\/\/projects.nib.si\/diavir\/summary\/","title":{"rendered":"Project overview"},"content":{"rendered":"

Viruses are important elements of marine pelagic ecosystems. They actively participate in marine microbial communities through infections of bacteria and archaea and phytoplankton. The principal effect of viral infection of phytoplankton is the so-called ‘viral shunt’, whereby the particulate organic matter in the form of living cells as well as cell debris is transformed into the dissolved form, providing a substrate for heterotrophic prokaryotes. This has profound effects on the biological carbon pump (BCP) that are not straightforward however. By returning organic matter that has accumulated in primary producers back to its dissolved form it cuts the transport of carbon through the trophic chain, while simultaneously enabling further phytoplankton growth in the photic zone.<\/p>\n

The majority of studied marine viruses are prokaryotic. Viruses infecting eukaryotic phytoplankton are far less known, and diatom viruses, of one of the most abundant and diverse phytoplankton groups, were first described only in 2004. To date, roughly 20 different diatom viruses infecting 7 different genera have been described and characterized. They are all small, around 30nm big, and host either ssRNA or ssDNA genomes. The impact of viral infection on diatom populations can be substantial and can match that of zooplankton grazing in terms of biomass loss. However, the lack of data and research prevents the integration of viral lysis into phytoplankton community structure and function studies and the subsequent generation of robust carbon and production models. There is thus an urgent need to expand the known universe of diatom viruses, particularly for keystone taxa. Diatoms from the Pseudo-nitzschia genus are globally spread, bloom-forming and can cause disturbances in food safety and ecosystem health due to the production of the neurotoxin domoic acid. Viruses infecting these diatoms have been so far hypothesized from cross-infection studies with mixed viral communities isolated from natural samples and from preliminary investigation conducted by me where a strong indication of viral presence was recorded by transmission electron microscopy (TEM) in a culture of Pseudo-nitzschia calliantha.<\/p>\n

\u200b<\/span>The overall objective of the proposed research is to develop study systems and protocols for diatom virus investigation, which will present a new layer of understanding of plankton ecology, organic matter turnover, diatom life cycles and infection mechanisms.<\/p>\n

\"virus\"<\/p>\n

Graphical Summary<\/strong><\/span><\/p>\n

\"workflow\"<\/p>\n

\"virus\"<\/p>\n

Main Objectives<\/strong><\/p>\n

    \n
  1. Establish a propagating Pseudo-nitzschia<\/em> virus-host system with native Pseudo-nitzschia<\/em> cultures of different species and strains from the Gulf of Trieste.\u00a0\"virus-yellow\"<\/li>\n
  2. Characterization of the virus with TEM and state-of-the-art genomic tools, encompassing the assembly of the viral genome from shotgun sequencing of culture viromes, and the mining of existing transcriptomic libraries for viral cues.\"virus-yellow\"<\/li>\n
  3. Determination of functional characteristics of the virus such as the virus-host growth dynamic, viral titers and burst sizes and the establishment of host-ranges for different strains and species.\"\"<\/li>\n
  4. Design of a qPCR assay to track the virus in the environment and culture.\"\"<\/li>\n<\/ol>\n

    \n

    \"virus-green\"\u00a0Task completed\u00a0\"virus-yellow\"\u00a0Task partially completed\u00a0\"virus-red\"\u00a0Task incomplete<\/p>\n","protected":false},"excerpt":{"rendered":"

    Viruses are important elements of marine pelagic ecosystems. They actively participate in marine microbial communities through infections of bacteria and archaea and phytoplankton. The principal effect of viral infection of phytoplankton is the so-called ‘viral shunt’, whereby the particulate organic matter in the form of living cells as well as cell debris is transformed into … Continue reading “Project overview”<\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"page-fullwidth.php","meta":{"footnotes":""},"class_list":["post-14","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P7OqMV-e","jetpack-related-posts":[{"id":30,"url":"https:\/\/projects.nib.si\/diavir\/references\/","url_meta":{"origin":14,"position":0},"title":"Publications","author":"ablejec","date":"05\/04\/2016","format":false,"excerpt":"Our first paper is out in Harmful Algae!","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/projects.nib.si\/diavir\/wp-content\/uploads\/sites\/51\/2024\/10\/capture.jpg?resize=350%2C200","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/projects.nib.si\/diavir\/wp-content\/uploads\/sites\/51\/2024\/10\/capture.jpg?resize=350%2C200 1x, https:\/\/i0.wp.com\/projects.nib.si\/diavir\/wp-content\/uploads\/sites\/51\/2024\/10\/capture.jpg?resize=525%2C300 1.5x, https:\/\/i0.wp.com\/projects.nib.si\/diavir\/wp-content\/uploads\/sites\/51\/2024\/10\/capture.jpg?resize=700%2C400 2x"},"classes":[]},{"id":484,"url":"https:\/\/projects.nib.si\/diavir\/2022\/11\/23\/preamplification-of-samples\/","url_meta":{"origin":14,"position":1},"title":"Preamplification of samples","author":"timtd","date":"23\/11\/2022","format":false,"excerpt":"On Thursday, 17.11.2022, we have successfully preamplified RNA from a series of diatom cultures lysates that could stem from viral infection. This RNA will be subsequently sequenced and viromes will be constructed. \u00a0 The experiment showing controls and flasks infected with viruses","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/projects.nib.si\/diavir\/wp-content\/uploads\/sites\/51\/2022\/11\/IMG_20221117_170052.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":40,"url":"https:\/\/projects.nib.si\/diavir\/","url_meta":{"origin":14,"position":2},"title":"Short description","author":"ablejec","date":"05\/04\/2016","format":false,"excerpt":"The main aim of this project is to study and understand the role of diatom viruses in organic matter cycling in coastal seas. This will be performed on a novel host-virus model system based on the potentially toxic diatom\u00a0Pseudo-nitzschia, which is a globally distributed genus, with an important ecological role.\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"arrs-logo-en","src":"https:\/\/i0.wp.com\/projects.nib.si\/alge\/wp-content\/uploads\/sites\/33\/2016\/04\/ARRS_logo_small-300x166.png?resize=350%2C200","width":350,"height":200},"classes":[]}],"_links":{"self":[{"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/pages\/14","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/comments?post=14"}],"version-history":[{"count":41,"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/pages\/14\/revisions"}],"predecessor-version":[{"id":463,"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/pages\/14\/revisions\/463"}],"wp:attachment":[{"href":"https:\/\/projects.nib.si\/diavir\/wp-json\/wp\/v2\/media?parent=14"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}