High-frequency automated imaging to capture phytoplankton morpho-functional traits
Dr. Diana Sarno, Stazione Zoologica Anton Dohrn, Napoli
Phytoplankton diversity is a main descriptor of the ecological status of marine ecosystems. Its assessment is fundamental in monitoring programs aimed at understanding how marine systems respond to environmental changes. Traditionally, plankton diversity is assessed through cell counting in microscopy, but this is time- consuming and requires broad taxonomic expertise. High-throughput methods such as DNA metabarcoding and imaging flow cytometry are gradually integrating microscopy routine analysis for a rapid characterization of plankton communities.
All these methods are implemented at the Long-Term Ecological Research site in the Gulf of Naples, where SZN staff studies plankton diversity and dynamics (LTER-MC and NEREA Observatory). Environmental data gathering and modelling concur to integrate the collected biodiversity data into a spatiotemporal framework. Since recently, an Imaging FlowCytoBot (IFCB) has been implemented, enabling automated imaging, and identification and processing of thousands of images from live plankton. The main aim of the proposed PhD project is to apply a trait-based approach, exploiting the IFCB’s images to measure morpho-functional traits (size, shape, chain-forms), and to compare results with environmental factors, cell counts and metabarcode data. Lab experiments on cultured strains have uncovered remarkable morphological responses of phytoplankton organisms to environmental conditions. Do these occur likewise in situ? This question can be pursued interdisciplinary at SZN because the LTERs provide the contextual data needed to enable comparison with results of the trait-based analyses.
The classification of the IFCB images using trait-based criteria represents an original way of gathering ecological relevant data on plankton community. Occurrence patterns of different morpho-functional groups, as well as changes in morpho-functional traits in response to changing environmental pressures will contribute to our understanding of costs, benefits, and evolutionary constraints of these traits. Results enable predicting effects of climate change on the structure and functioning of the phytoplankton.
The project will deliver elements towards development of standards for phytoplankton diversity assessment, including morpho-functional groups as indicators of environmental status. Results will integrate classical and molecular assessments of plankton diversity, thus contributing to the design of more effective marine observatories. The IFCB is also a marvellous tool for outreach activities, showing the diversity and beauty of planktonic organisms. Last but not least, the project will deliver a young expert in phytoplankton diversity who has acquired all the practical and state-of-the-art skills to pursue a successful research career.
Students are expected to complete their thesis within three years, with the possibility of a fourth year without salary, to write up the thesis (should this be necessary). The gross salary is € 16.000,00 per year for three years from which taxes (approximately 18%) will be subtracted. Students are liable to an annual registration fee to be paid to the Open University (not to the Stazione Zoologica). The Stazione Zoologica will cover the registration fee for three years
Thesis Supervision Each student is assigned a Supervision Team before the start of the internship, whose appointment is proposed by the direct supervisor (Director of Studies) and approved by the Open University. The Supervision Team is composed at least by: – one direct supervisor (Director of Studies), who will guide the student during the whole thesis work and will supervise the student on a daily basis; – one external supervisor, (not belonging to SZN staff), appointed at the beginning of the internship, who will offer an independent assessment of the student progress annually. It is possible to appoint additional members of the supervision team, as Internal (SZN staff), External (nonSZN staff) Supervisors or Advisors. Courses and Training PhD-level training is offered annually (2-3 courses per year) on scientific topics and complementary skills, together with specialized seminars (12-14 per year) offered by scientists invited by the SZN on different topics. Attendance to courses, seminars and all PhD Program’s events is mandatory. Students are required to follow all training events as well as the seminars and the tutorials before the seminars in order to qualify for the degree. All courses, seminars and tutorials are held in English. Selection procedure Applicants must specify the chosen project in the application form, also providing a second preference option. A selection Commission appointed by the President will evaluates the candidates’ applications on the basis of the CV, the quality of the application and the reference letters and selects a short list of candidates to be interviewed, in a number not exceeding the double of the published projects in the call; Candidates will be notified of this first pre-selection and will have two weeks to contact the Director of Studies of the two projects they had indicated in the application, to support their candidacy. The Directors of Studies, at the end of the interviews with the candidates referred to in the previous paragraph, may send the Commission a letter of interest for the candidate they consider to be the best among those interviewed. The presence of at least one letter of interest is binding for the selection of the candidate. After two weeks from the communication above, the Commission interviews the candidates who have received a letter of interest, confirms or not their suitability and draws up a merit ranking of the suitable candidates. During the interview candidates must also present their chosen project, demonstrating their knowledge on the subject. Proficiency in English will be also tested. The interviews will be held in English and will be conducted, except for restrictions for serious and/or health reasons, by the commission meeting in attendance at the Stazione Zoologica Anton Dohrn in Naples and with the participation of candidates in remote session. Scholarships will be awarded to candidates usefully placed in the ranking, until exhaustion of the available scholarships, to carry out the project they have chosen. In the event that several candidates placed at the top of the list have chosen the same project, the project will be assigned to the first in the list. Subsequent students will be able to choose from published projects not yet assigned to another student. In this case, they must first be interviewed by the Director of Studies, who will eventually have to express his/her interest in the candidate. In case of refusal of a candidate awarded a scholarship, this will be assigned to the first candidate placed successively among those deemed suitable and not awarded a scholarship, to carry out the project chosen by he/she in the application. In the event that the two projects indicated by the candidate have already been assigned, they will be able to choose from the projects published and not yet assigned to another student and the procedure will proceed as per the previous paragraph. The titles, provided according to the procedures indicated in the announcement, include the academic and professional qualifications consistent with the proposed project, the letters of reference, the letter of motivation. The selected students, subject to the approval of the OU, will be admitted to the PhD Programme with President’s Decree approving the selection documents and subsequently summoned to sign the contract. The contract, signed for the Stazione Zoologica by the Director General, will be drawn up in Italian and English. Final candidates are expected to start their internship on October 1st 2023. If you have any question regarding the application process, please, contact Gabriella Grossi at phdszn(at)szn.it. Special needs Candidates with disabilities should please detail in the application form, any eventual facility they require to participate in the interview. Every effort will be made to ensure that they can participate on an equal basis with other candidates and all reasonable arrangements requested by disabled candidates will be adopted. Practical information The SZN does not offer lodging or financial support for moving expenses, neither parental support. Students are offered practical support for their settling in Naples through the Higher Education & University Liaison Office that can be contacted at phdszn(at)szn.it.
- Job Type: PhD
- Application deadline: 06/21/2023
- Organization: Open University - Stazione Zoologica Anton Dohrn
- Qualifications: Applicants must hold or be in the process of receiving (within July 14th 2023): 1. an advanced degree such as a Master of Science (M.Sc.) or its equivalent in a scientific area coherent with the project proposed; and, where English is not the applicant’s first language, 2. an IELTS certificate (dated within the last two years) with scores that meet the minimum requirements of 6.5 overall score, and no less than 6.0 in any of the four elements (reading, writing, listening and speaking). Alternative language certificate accepted: - a degree completed either in the UK or in one of the majority English speaking countries listed listed below is also considered a proof of English proficiency: • Antigua and Barbuda • Australia • The Bahamas • Barbados • Belize • Dominica • Grenada • Guyana • Ireland • Jamaica • Malta • New Zealand • St Kitts and Nevis • St Lucia • St Vincent and the Grenadines • Trinidad and Tobago • United States of America The PhD Program is in English. Where English is not the applicant’s first language, he/she must demonstrate sufficient proficiency in the English language to support successful study at research degree standard. Fluency in spoken English will be assessed during the interview and is a strict requirement
- How to apply: Apply at website: https://szn.it/index.php/en/education/doctorate--international-phd-iii-level/positions-on-offer-phd/call-for-phd-students-n-1-2023-phd-programme-ou-szn-xxv-cycle
- Location: Naples, Italy
- Web address: https://szn.it/index.php/en/education/doctorate-%E2%80%93-international-phd-iii-level/positions-on-offer-phd/call-for-phd-students-n-1-2023-phd-programme-ou-szn-xxv-cycle