Access profile

The doctoral programme in Marine Sciences is aimed at students with a strong background at the bachelor’s and master's level, in accordance with the provisions of Royal Decree 99/2011, in marine sciences or a related field.

It is therefore also aimed at students who have completed degrees in biology, geology, environmental sciences, physics, chemistry, mathematics, geography or related fields. It is also a programme conceived and designed by and for engineers, preferably those who have completed a degree in civil or naval engineering. The doctoral course is also open to graduates of industrial engineering, telecommunications and architecture programmes. Students who hold equivalent degrees from foreign universities are also welcomed.

Output profile

Doctoral candidates who complete a doctoral degree will have acquired the following competencies, which are needed to carry out quality research (Royal Decree 99/2011, of 28 January, which regulates official doctoral studies):

a) A systematic understanding of the field of study and a mastery of the research skills and methods related to the field.
b) An ability to conceive, design or create, put into practice and adopt a substantial process of research or creation.
c) An ability to contribute to pushing back the frontiers of knowledge through original research.
d) A capacity for critical analysis and an ability to assess and summarise new and complex ideas.
e) An ability to communicate with the academic and scientific community and with society in general as regards their fields of knowledge in the manner and languages that are typical of the international scientific community to which they belong.
f) An ability to foster scientific, technological, social, artistic and cultural progress in academic and professional contexts within a knowledge-based society.

The award of a doctoral degree must equip the graduate for work in a variety of settings, especially those requiring creativity and innovation. Doctoral graduates must have at least acquired the personal skills needed to:

a) Develop in contexts in which there is little specific information.
b) Find the key questions that must be answered to solve a complex problem.
c) Design, create, develop and undertake original, innovative projects in their field.
d) Work as part of a team and independently in an international or multidisciplinary context.
e) Integrate knowledge, deal with complexity and make judgements with limited information.
f) Offer criticism on and intellectually defend solutions.

Finally, with respect to competencies, doctoral students must:
a) have acquired advanced knowledge at the frontier of their discipline and demonstrated, in the context of internationally recognised scientific research, a deep, detailed and well-grounded understanding of theoretical and practical issues and scientific methodology in one or more research fields;
b) have made an original and significant contribution to scientific research in their field of expertise that has been recognised as such by the international scientific community;
c) have demonstrated that they are capable of designing a research project that serves as a framework for carrying out a critical analysis and assessment of imprecise situations, in which they are able to apply their contributions, expertise and working method to synthesise new and complex ideas that yield a deeper knowledge of the research context in which they work;
d) have developed sufficient autonomy to set up, manage and lead innovative research teams and projects and scientific collaborations (both national and international) within their subject area, in multidisciplinary contexts and, where appropriate, with a substantial element of knowledge transfer;
e) have demonstrated that they are able to carry out their research activity in a socially responsible manner and with scientific integrity;
f) have demonstrated, within their specific scientific context, that they are able to make cultural, social or technological advances and promote innovation in all areas within a knowledge-based society;
g) have demonstrated that they are able to participate in scientific discussions at the international level in their field of expertise and disseminate the results of their research activity to audiences of all kinds.

Number of places

10

Duration of studies and dedication regime

Duration
The maximum period of study for full-time doctoral studies is three years, counted from the date of admission to the programme to the date of submission of the doctoral thesis. The academic committee of the doctoral programme may authorise a doctoral candidate to pursue doctoral studies on a part-time basis. In this case, the maximum period of study is five years, counting from the date of admission to the programme to the date of submission of the doctoral thesis. For calculating these periods, the date of admission is considered to be the date of the first enrolment for tutorials, and the date of submission the moment in which the Doctoral School officially deposits the doctoral thesis.

For full-time doctoral candidates, the minimum period of study is two years, counted from the date of an applicant's admission to the programme until the date on which the doctoral thesis is deposited; for part-time doctoral candidates it is four years. When there are justified grounds for doing so, and the thesis supervisor and academic tutor have given their authorisation, doctoral candidates may request that the academic committee of their doctoral programme exempt them from the minimum period of study requirement.

The calculation of periods of study will not include periods of absence due to illness, pregnancy or any other reason provided for in the regulations in force. Students who find themselves in any of these circumstances must notify the academic committee of the doctoral programme, which, where appropriate, must inform the Doctoral School. Doctoral candidates may also temporarily withdraw from the programme for up to one year, and this period may be extended for an additional year. Doctoral candidates who wish to interrupt their studies must submit a justified request to the academic committee of the doctoral programme, which will decide whether or not to approve the request. Each programme will establish conditions for readmission to doctoral studies.

Extension
If full-time doctoral candidates have not applied to deposit their thesis by the end of the three-year period of study, the academic committee of the programme may authorise an extension of up to one year. In exceptional circumstances, a further one-year extension may be granted, subject to the conditions established by the corresponding doctoral programme. In the case of part-time doctoral candidates, an extension of two years may be authorised. In both cases, in exceptional circumstances a further one-year extension may be granted by the Doctoral School's Standing Committee, upon the submission of a reasoned application by the academic committee of the doctoral programme.

Dismissal from the doctoral programme
A doctoral candidate may be dismissed from a doctoral programme for the following reasons:

• The doctoral candidate submitting a justified application to withdraw from the programme.
• The maximum period of study and of extensions thereof ending.
• The doctoral candidate not having enrolled every academic year (unless he or she has been authorised to temporarily withdraw).
• The doctoral candidate failing two consecutive assessments.
• The doctoral candidate having disciplinary proceedings filed against him or her that rule that he or she must be dismissed from the UPC.

Dismissal from the programme implies that doctoral candidates cannot continue studying at the UPC and the closing of their academic record. This notwithstanding, they may apply to the academic committee of the programme for readmission and the committee must reevaluate them in accordance with the criteria established in the regulations.

Organization

• Sanchez-Arcilla Conejo, Agustin

• Espino Infantes, Manolo
• Gironella i Cobos, Xavi
• Jimenez Quintana, Jose Antonio
• Mösso Aranda, Cesar
• Sanchez-Arcilla Conejo, Agustin
• Sierra Pedrico, Juan Pablo

University of Barcelona

• Department of Civil and Environmental Engineering (PROMOTORA)
• (ENG)Laboratori d'Enginyeria Marítima

Office 202 – Building C2 (North Campus)
Tel.: 934 016 497
E-mail: doctorat.CMAR.camins@upc.edu

Agreements with other institutions

Convenio colaboración_UB_UPC Ciencias del Mar.pdf

Access profile

The doctoral programme in Marine Sciences is aimed at students with a strong background at the bachelor’s and master's level, in accordance with the provisions of Royal Decree 99/2011, in marine sciences or a related field.

It is therefore also aimed at students who have completed degrees in biology, geology, environmental sciences, physics, chemistry, mathematics, geography or related fields. It is also a programme conceived and designed by and for engineers, preferably those who have completed a degree in civil or naval engineering. The doctoral course is also open to graduates of industrial engineering, telecommunications and architecture programmes. Students who hold equivalent degrees from foreign universities are also welcomed.

Access requirements

Applicants must hold a Spanish bachelor’s degree or equivalent and a Spanish master’s degree or equivalent, provided they have completed a minimum of 300 ECTS credits on the two degrees (Royal Decree 43/2015, of 2 February)

In addition, the following may apply:

• Holders of an official degree awarded by a university in Spain or any other country in the European Higher Education Area, pursuant to the provisions of Article 16 of Royal Decree 1393/2007, of 29 October, which establishes official university course regulations, who have completed a minimum of 300 ECTS credits on official university degrees, of which at least 60 must be at the master's degree level.
• Holders of an official Spanish bachelor’s degree comprising at least 300 credits, as provided for by EU regulations. Holder of degrees of this kind must complete bridging courses unless the curriculum of the bachelor’s degree in question included research training credits equivalent in value to those which would be earned on a master's degree.
• Holders of an official university qualification who, having passed the entrance examination for specialised medical training, have completed at least two years of a training course leading to an official degree in a health-sciences specialisation.
• Holders of a degree issued under a foreign education system. In these cases, homologation is not required, but the UPC must verify that the degree certifies a level of training equivalent to an official Spanish master's degree and qualifies the holder for admission to doctoral studies in the country where it was issued. Admission on this basis does not imply homologation of the foreign degree or its recognition for any purpose other than admission to doctoral studies.
• Holders of a Spanish doctoral qualification issued under previous university regulations.

Note 1: Doctoral studies entrance regulations for holders of an undergraduate degree awarded before the introduction of the EHEA (CG 47/02 2014)

Note 2: Governing Council Decision 64/2014, which approves the procedure and criteria for assessing the fulfilment of academic admission requirements for doctoral studies by holders of non-homologated foreign degrees (CG 25/03 2014)

Admission criteria and merits assessment

The main admission criterion is training within the framework of an official Spanish bachelor's degree (or equivalent) and a master's degree (or equivalent), that prepares the student to undertake and benefit from the research training provided on the doctoral programme in Marine Sciences.

Therefore, the following points will be given particular consideration:

• Master’s level or equivalent qualifications held by applicants (and corresponding course plans)
• Bachelor’s level or equivalent qualifications held by applicants (and corresponding course plans)
• Other merits for which the applicant has provided documentary proof, such as periods of mobility spent at marine science research centres, publications and professional experience

The admission process involves the following steps:

I. Applicants’ entrance qualifications are assessed. Those who hold degrees that are fully compatible with the doctoral programme are automatically pre-admitted. This applies in the case of degrees in:

a) Marine sciences and oceanography
b) Civil and naval engineering
c) Biology, geology, chemistry, physics, environmental sciences and mathematics

For other studies, the Programme Committee reviews the curriculum for the degree completed by the applicant and submits a proposal to the university where they plan to enrol if accepted.

In all cases, the secretary for the doctoral programme in Marine Sciences will verify that the curriculum includes the subjects most closely related to the four basic branches of marine sciences. This verification process may point to the need for a student to complete bridging courses. Relevant details will be discussed in an interview with the student concerned.

II. For pre-admitted students, an order of priority will be established based on the following factors (weighting in parentheses):

a) Marks for previous studies (55%).
b) Projects that introduce students to research (e.g. on master’s programmes), publications and contributions to conferences and scientific meetings mentioned on the applicant’s CV (30%).
c) Grants, scholarships or financial aid received (10%).
d) Other merits (5%).

Training complements

The academic committee for the programme may require that doctoral students pass specific bridging courses, which will be linked to research training credits. These credits will be compulsory for students who have completed a bachelor’s degree that carries 300 or more ECTS credits and qualifies them for admission to the doctoral programme but does not include credits of this type. In such cases, the committee will keep track of the bridging courses completed and establish appropriate criteria to limit their duration.

Bridging courses will provide research training. In no case may doctoral students be required to enrol for 60 or more ECTS credits. (The academic regulations for UPC doctoral courses state that bridging courses may also provide cross-disciplinary training, but it is anticipated that this point will be changed so that bridging courses are associated only with research training credits, particularly in the case of students admitted to a doctoral programme with a bachelor’s degree that carries 300 ECTS credits.)

Taking into account the doctoral student activity report, the academic committee may propose measures that complement those specified in the regulations and which result in doctoral students who do not meet the specified requirements being excluded from the programme.

For the doctoral programme in Marine Sciences, decisions concerning any bridging courses required will be based on the recommendations of tutors, with the approval of the interuniversity committee for the programme. Every effort will be made to ensure that students admitted from the interuniversity master's degree in Marine Science: Oceanography and Marine Management (a joint UB-UPC programme) or similar degrees are not required to take any bridging courses.

When a student's academic background leads their tutor to conclude that additional training is needed, the student concerned will be required to complete credits based on the joint master’s degree in Marine Science: Oceanography and Marine Management. As a general rule, tutors will select specialisation modules from the master’s programme that provide added value for the student’s training. For example, students admitted to the doctoral programme in Marine Sciences who have gaps in their knowledge of chemistry or engineering will be recommended to complete the corresponding training modules.

Enrolment period for new doctoral students

From around mid-September to mid-October of each academic year.

February (extraordinary enrolment), mainly for students awaiting visas and/or grants

More information at the registration section for new doctoral students

Enrolment period

From around mid-September to mid-October of each academic year.

More information at the general registration section

Procedure for the preparation and defense of the research plan

Doctoral candidates must submit a research plan, which will be included in their doctoral student activity report, before the end of the first year. The plan may be improved over the course of the doctoral degree. It must be endorsed by the tutor and the supervisor, and it must include the method that is to be followed and the aims of the research.

At least one of these annual assessments will include a public presentation and defence of the research plan and work done before a committee composed of three doctoral degree holders, which will be conducted in the manner determined by each academic committee. The examination committee awards a Pass or Fail mark. A Pass mark is a prerequisite for continuing on the doctoral programme. Doctoral candidates awarded a Fail mark must submit a new research plan for assessment by the academic committee of the doctoral programme within six months.

The committee assesses the research plan every year, in addition to all of the other activities in the doctoral student activity report. Doctoral candidates who are awarded two consecutive Fail marks for the research plan will be obliged to definitely withdraw from the programme.

If they change the subject of their thesis, they must submit a new research plan.

Formation activities

- Activity: Tutorial.

Hours: 432.

Type: compulsory.

- Activity: Courses.

Hours: 72.

Type: optional.

- Activity: Seminars.

Hours: 25.

Type: optional.

- Activity: Workshops.

Hours: 10.

Type: optional.

- Activity: Research stays.

Hours: 480.

Type: optional.

- Activity: Training in information skills.

Hours: 8.

Type: optional.

- Activity: Research methodology.

Hours: 12.

Type: optional.

- Activity: Innovation and creativity.

Hours: 8.

Type: optional.

- Activity: Language and communication skills.

Hours: 18.

Type: optional.

- Activity: Assessment based on doctoral student activity report (DAD) and research plan.

Hours: 4.

Type: compulsory.

Procedure for assignment of tutor and thesis director

The academic committee of the doctoral programme assigns a thesis supervisor to each doctoral candidate when they are admitted or enrol for the first time, taking account of the thesis supervision commitment referred to in the admission decision.

The thesis supervisor will ensure that training activities carried out by the doctoral candidate are coherent and suitable, and that the topic of the candidate’s doctoral thesis will have an impact and make a novel contribution to knowledge in the relevant field. The thesis supervisor will also guide the doctoral candidate in planning the thesis and, if necessary, tailoring it to any other projects or activities undertaken. The thesis supervisor will generally be a UPC professor or researcher who holds a doctoral degree and has documented research experience. This includes PhD-holding staff at associated schools (as determined by the Governing Council) and UPC-affiliated research institutes (in accordance with corresponding collaboration and affiliation agreements). When thesis supervisors are UPC staff members, they also act as the doctoral candidate’s tutor.

PhD holders who do not meet these criteria (as a result of their contractual relationship or the nature of the institution to which they are attached) must be approved by the UPC Doctoral School's Standing Committee in order to participate in a doctoral programme as researchers with documented research experience.

The academic committee of the doctoral programme may approve the appointment of a PhD-holding expert who is not a UPC staff member as a candidate’s thesis supervisor. In such cases, the prior authorisation of the UPC Doctoral School's Standing Committee is required. A UPC staff member who holds a doctoral degree and has documented research experience must also be proposed to act as a co-supervisor, or as the doctoral candidate’s tutor if one has not been assigned.

A thesis supervisor may step down from this role if there are justified reasons (recognised as valid by the committee) for doing so. If this occurs, the academic committee of the doctoral programme will assign the doctoral candidate a new thesis supervisor.

Provided there are justified reasons for doing so, and after hearing any relevant input from the doctoral candidate, the academic committee of the doctoral programme may assign a new thesis supervisor at any time during the period of doctoral study.

If there are academic reasons for doing so (an interdisciplinary topic, joint or international programmes, etc.) and the academic committee of the programme gives its approval, an additional thesis supervisor may be assigned. Supervisors and co-supervisors have the same responsibilities and academic recognition.

The maximum number of supervisors of a doctoral thesis is two: a supervisor and a co-supervisor.

For theses carried out under a cotutelle agreement or as part of an Industrial Doctorate, if necessary and if the agreement foresees it this maximum number of supervisors may not apply. This notwithstanding, the maximum number of supervisors belonging to the UPC is two.

More information at the PhD theses section

Permanence

The academic committee of the programme may authorise an extension of up to one year for full-time doctoral candidates who have not applied to deposit their thesis by the end of the three-year period of study, in the terms outlined in the Academic Regulations for Doctoral Studies of the Universitat Politècnica de Catalunya. In the case of part-time candidates, an extension of two years may be authorised. In both cases, in exceptional circumstances a further one-year extension may be granted by the Doctoral School's Standing Committee, upon the submission of a reasoned application by the academic committee of the doctoral programme.

A doctoral candidate may be dismissed from a doctoral programme for the following reasons:

• The doctoral candidate submitting a justified application to withdraw from the programme.
• The maximum period of study and of extensions thereof ending.
• The doctoral candidate not having enrolled every academic year (unless he or she has been authorised to temporarily withdraw).
• The doctoral candidate failing two consecutive assessments.
• The doctoral candidate having disciplinary proceedings filed against him or her that rule that he or she must be dismissed from the UPC.

Dismissal from the programme implies that doctoral candidates cannot continue studying at the UPC and the closing of their academic record. This notwithstanding, they may apply to the academic committee of the programme for readmission and the committee must reevaluate them in accordance with the criteria established in the regulations.

International Mention

The doctoral degree certificate may include International Doctorate mention. In this case, the doctoral candidate must meet the following requirements:

a) During the period of study leading to the award of the doctoral degree, the doctoral candidate must have spent at least three months at a respected higher education institution or research centre outside Spain to complete courses or do research work. The stays and activities carried out must be endorsed by the thesis supervisor and authorised by the academic committee of the programme. The candidate must provide a certifying document issued by the person responsible for the research group of the body or bodies where the stay or activity was completed. This information will be added to the doctoral student’s activity report.
b) Part of the thesis (at least the summary and conclusions) must be written and presented in one of the languages commonly used for science communication in the relevant field of knowledge, which must not be an official language of Spain. This rule does not apply to stays and reports in Spanish or to experts from Spanish-speaking countries.
c) At least two PhD-holding experts belonging to a higher education institution or research centre outside Spain must have issued officially certified reports on the thesis.
d) The thesis examination committee must have included at least one PhD-holding expert from a higher education or research institution outside Spain who was not responsible for the candidate’s stay abroad (point a) above).
e) The thesis defence must have taken place on UPC premises or, in the case of joint programmes, at the location specified in the collaboration agreement.

List of authorized thesis for defense

• MARÍN VINDAS, CAROLINA ALEXANDRA: Patrones de conectividad de comunidades microbianes marinas.
  
  Author: MARÍN VINDAS, CAROLINA ALEXANDRA
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN MARINE SCIENCES
  Department: (DECA)
  Mode: Normal
  Deposit date: 14/04/2023
  Reading date: 06/09/2023
  Reading time: 11:00
  Reading place: Institut de Ciències del Mar (ICM)-Sala d'Actes Ramón Margalef-Passeig Marítim de la Barceloneta, 37-49 08003 Barcelona
  Thesis director: GASOL PIQUÉ, JOSEP MARIA | SEBASTIÁN CAUMEL, MARTA
  Committee:
       PRESIDENT: MASSANA MOLERA, RAMON
       SECRETARI: ORTEGA RETUERTA, EVA
       VOCAL NO PRESENCIAL: SÁNCHEZ MARTÍNEZ, OLGA
  Thesis abstract: Marine microorganisms are fundamental for life on Earth. For example, they have produced most of the oxygen existing in our planet and are essential in biogeochemical cycles and energy flow to different trophic levels. One of the critical aspects of microbial ecology is the distribution of microorganisms at spatial and temporal scales since it allows us to understand the effect of environmental factors on the structure of microbial communities. In this thesis, the aim was to determine the structure of microbial communities at three spatial scales: In the first chapter, a study was conducted on the spatiotemporal dynamics of bacterioplankton communities in a tropical estuary strongly impacted by the discharge of the Tempisque River during the rainy season. The results show high spatial heterogeneity in the communities, and represent the first report on the spatial and temporal patterns in which the bacterioplankton of the Gulf of Nicoya is structured. The second chapter determined the effect of environmental gradients on the horizontal distribution of bacterioplankton in the northwestern Mediterranean. The samples were taken along cross-shore transects so that the gradients would presumably be due to the change in environmental parameters along the transect and a dilution of the anthropogenic and terrestrial effect. Community structure was observed to vary depending on the sites, but a large fraction of the microorganisms were shared in all sampled areas, reflecting a relatively high connectivity of the communities. The third chapter presents the vertical distribution of prokaryotic and eukaryotic microorganisms within the Deep Chlorophyll Maxima (DCM) in the NW Mediterranean sea, as determined by high-resolution sampling and separating two microbial size fractions (0.2-3 and 2-20 µm). The results show that the DCM acts as a transition zone (ecotone), but despite the drastic changes observed in the relative abundance of taxa in this layer both prokaryotic and eukaryotic communities below the DCM were dominated (~70% of the sequences) by taxa already detected at the ocean surface.
  

Last update: 10/06/2023 04:45:36.

List of lodged theses

Last update: 10/06/2023 04:30:26.

List of defended theses by year

• BALLESTEROS MASCARELL, AINARA: Pelagia noctiluca (Cnidaria: Scyphozoa) como un modelo de investigación industrial: Mejoras en las técnicas de acuicultura y medidas preventivas contra sus picaduras.
  
  Author: BALLESTEROS MASCARELL, AINARA
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN MARINE SCIENCES
  Department: (DECA)
  Mode: Normal
  Reading date: 13/01/2023
  Thesis director: GILI SARDÁ, JOSEP MARIA | JOURDAN RENE, ERIC
  

  Committee:
       PRESIDENT: MILISENDA, GIACOMO
       SECRETARI: SALVO, VANESSA-SARAH
       VOCAL NO PRESENCIAL: BOSCH BELMAR, MARIA DEL MAR
  Thesis abstract: Jellyfish stings cause discomfort to users of the marine environment, who sometimes require medical assistance. Although jellyfish stings are common today, the scientific community remains in disagreement on how to act in first-aid protocols. Most of the recommended compounds are based on empirical knowledge, and they are difficult to transfer to the cosmetic or pharmaceutical industry due to the lack of knowledge of their mechanisms of action.In the Mediterranean Sea, the mauve stinger Pelagia noctiluca (Cnidaria: Scyphozoa) is the most important jellyfish due to its high frequency, abundance, wide distribution and severity of its sting. This jellyfish is the cause of a high number of stings, which is why it is considered a target species in the development of tools for the prevention and mitigation of jellyfish stings. P. noctiluca is one of the few jellyfish with a holoplanktonic life cycle, a peculiarity that has limited its study in different areas of knowledge under controlled conditions.The main objective of this PhD thesis was to inhibit the discharge of P. noctiluca stinging cells (cnidocytes) through active ingredients that could be incorporated into cosmetic products intended to prevent and mitigate the effects of jellyfish stings. As secondary objectives highlighted: expanding knowledge in the biology of P. noctiluca, its aquaculture techniques, and the implication of topical solutions in first-aid protocols.In Chapter 1, the morphological and anatomical characteristics of P. noctiluca were described, including the first cnidome description ¿ set of stinging cells ¿ through growth in aquaculture. Cnidocytes were classified into four nematocyst types: a-isorhiza, A-isorhiza, O-isorhiza, and eurytele; being the types a-isorhiza and eurytele the most important throughout the life cycle, and O-isorhiza and eurytele the main ones involved in its sting.In Chapter 2, the life cycle of P. noctiluca was optimized in aquaculture. Total body diameter, instantaneous growth rate, and survival rate were monitored in the presence of different feeding regimens. For the first time, the third generation of individuals was obtained in the presence and absence of gelatinous prey (Aurelia sp.). In order to improve jellyfish aquaculture techniques, in Chapter 3, the design of an aquarium for the growth of the early life cycle stages in flow-through or closed systems was presented. Its configuration allows changing the mesh screen in situ, adjusting the size of the mesh according to the stages of the cycle, as well as the prey offered.The use of vinegar, a compound widely used as a rinse solution after jellyfish stings, was contraindicated in Chapter 4. This compound triggered the discharge of all types of nematocysts by the tentacle solution assay (TSA). In addition, vinegar did not decrease the hemolytic areas produced after inoculation of the venom in the tentacle skin blood agarose assay (TSBAA). Finally, in Chapter 5, the discharge of P. noctiluca nematocysts was inhibited with hydroxyacetophenone and Symsitive¿ in combination with butylene glycol, two active ingredients widely used in the cosmetics sector. Furthermore, hemolytic areas decreased after the stinging event compared to seawater, a non-inhibitory compound. These compounds were considered of high value because they are also beneficial for treating skin damage, relieving pain and burning sensations; clinical signs and symptoms typical of jellyfish stings.Overall, this PhD thesis provided significant advances in the area of knowledge of the biology of P. noctiluca, aquaculture and management of jellyfish stings.
  

• LATORRE PÉREZ, FRANCISCO: Population dynamics, interactions and evolution of marine microbes using genomic approaches.
  
  Author: LATORRE PÉREZ, FRANCISCO
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN MARINE SCIENCES
  Department: (DECA)
  Mode: Normal
  Reading date: 03/02/2023
  Thesis director: LOGARES HAURIE, RAMIRO ERNESTO | JAILLON, OLIVIER
  

  Committee:
       PRESIDENT: GONZÁLEZ HERNÁNDEZ, JOSÉ MANUEL
       SECRETARI: GONZÁLEZ ACINAS, SILVIA
       VOCAL NO PRESENCIAL: DELMONT, TOM
  Thesis abstract: There is a myriad of microorganisms on Earth contributing to global biogeochemical cycles. In the surface ocean, the smallest microbes (picoplankton) are responsible for an important fraction of the total atmospheric carbon and nitrogen fixation. The ocean picoplankton encompasses both prokaryotes (bacteria and archaea) and tiny unicellular eukaryotes (protists). Despite their overall importance for the functioning of the biosphere, many questions remain unanswered on their biogeography, population dynamics, interactions, and evolution. Answering these questions is essential in the context of global change, as alterations of the ocean microbiome could impact the function of multiple ecosystems. In this thesis, we aim at reducing the knowledge gap on the above topics through the application of High-Throughput Sequencing (HTS) and genomic approaches, using data collected during the circumglobal Tara Oceans and Malaspina-2010 expeditions, as well as at the Gulf of Maine (North Atlantic), and two Northwestern Mediterranean coastal microbial observatories (BBMO and SOLA stations). Chapters 1 and 2 are dedicated to a small protistan group of heterotrophic flagellates (HF): the Marine Stramenopiles (MAST)-4, relevant during picoplankton grazing and nutrient remineralization. Due to its widespread distribution and relatively high abundance, MAST-4 has become a target group of microbes to study HF. Unfortunately, MAST-4 remains uncultured. We investigated four evolutionary-related species of MAST-4 (species A, B, C, and E) by reconstructing their genomes with Single-Cell genomics data. In chapter 1, co-occurrence and biogeographic analyses in the surface global ocean indicated contrasting patterns driven by temperature. Although MAST-4 species were similar in terms of broad metabolic functions, they differed in the set of genes related to the food degradation machinery. We proposed that differential niche adaptation to temperature and prey type has promoted the evolutionary diversification in MAST-4. In chapter 2, we explore the intraspecies genomic divergence within each MAST-4 in the surface global ocean using metagenomic data. We found highly-differentiated populations among MAST-4A and C but lowly-differentiated populations in species B and E. Nevertheless, positive selection in specific genes pointed to niche adaptation to different ocean basins driven by fluctuating temperature and salinity conditions.Environmental factors also oscillate over time, but the effect they have over population remains a mystery. In chapter 3, we compared the genomic differentiation of 495 abundant prokaryotic metagenome-assembled genomes (MAGs) over 12 and 7 years in BBMO and SOLA stations, and across the surface global ocean. Our results suggested a stronger population differentiation at large-spatial scales, modulated by temperature and salinity, compared to long-temporal scales. However, underlying population structure was still detected in both time-series, with differential patterns of positive selection within the same genes. Although protists and prokaryotes are very different in terms of cellular structure, feeding, diversity, and reproduction, they are interconnected through biogeochemical and food web networks. In chapter 4, we developed an approach to infer potential interactions between these two groups based on the annotation of functional genes within Single-Amplified Genomes (SAGs). From a collection of over 3,000 SAGs, we corroborated associations (potential interactions) reported in previous works and inferred new ones involving uncultured marine protists that may hold important roles in ecosystem functioning.This thesis not only contributes to a better understanding of the biogeography, population dynamics, interactions, and evolution of marine microorganisms, but it also constitutes an expandable resource to test future hypotheses involving the ocean microbiome.
  

• OBIOL PLANA, ALEIX: Return of the marine heterotrophic flagellates: diversity, distribution and gene expression patterns.
  
  Author: OBIOL PLANA, ALEIX
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN MARINE SCIENCES
  Department: (DECA)
  Mode: Article-based thesis
  Reading date: 27/01/2023
  Thesis director: MASSANA MOLERA, RAMON
  

  Committee:
       PRESIDENT: ARNDT, HARTMUT
       SECRETARI: RICHTER, DANIEL
       VOCAL: ALONSO SAEZ, LAURA
  Thesis abstract: Marine heterotrophic flagellates (HF) are very small (2-5 µm) unpigmented protists that are dominant bacterial grazers in the ocean, where they link the transfer of carbon from bacterial cells to higher trophic levels. Through their bacterivorous activity, they also act as nutrient recyclers that allow for regenerated primary production, and they are partially responsible of keeping bacterial abundances in the ocean fairly constant. HFs are widespread throughout the eukaryotic tree of life, ubiquitous in the plankton and display a high functional diversity. During the last decades of the twentieth century, a growing interest in this functional group occurred, and studies were performed to characterize their ecological role. However, this initial attention diminished due to the difficulty to study natural HF species, as they possess few morphological traits for identification and generally remain uncultured.Consequently, HFs have been often neglected in marine surveys, to the extent of becoming one of the most understudied components of the marine microbiome. With the advent of high-throughput sequencing and the reduction of sequencing costs, studying these protists at a high-resolution level became feasible. This thesis represents areturn to the study of HFs using these newly developed tools. We first investigated the distribution patterns of eukaryotic diversity along the water column of the ocean by metagenomics and compared the results with metabarcodingapproaches. This analysis revealed a clear separation of taxonomic groups between pico- (0.2-3 µm) and nanoplanktonic (3-20 µm) fractions, as well as between photic (0-200 m) and aphotic (>200 m) regions. While some groups were not well represented by metabarcoding approaches due to technical biases, HFs were generally notaffected by them. We then studied the diversity and distribution of HFs in the ocean using global metabarcoding datasets. With this, we identified a few dozens of HF species, most of them uncultured, as the dominant in surface and deep ocean regions. Many of these dominant species were present at relatively constant abundances, while others were influenced by temperature or displayed patchy distributions. Finally, we jumped from global patterns to study the gene expression of HFs in natural assemblages growing by bacterivory in unamended incubations. Theobtained results using metatranscriptomics sequencing showed similar functional dynamics between experiments done at different times of a seasonal cycle, with marked differences between incubation times. Genes related to cysteine peptidases as well as some glycoside hydrolases emerged as key components involved in the process of bacterivory. Overall, this thesis returns HFs back to the spotlight and creates a solid foundation on which to perform renewed research on the ecology and functional role of this group.
  

• RODERO GARCÍA, CARLOS: Citizen sciences technologies for operational monitoring of aquatic ecosystems.
  
  Author: RODERO GARCÍA, CARLOS
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN MARINE SCIENCES
  Department: (DECA)
  Mode: Article-based thesis
  Reading date: 29/05/2023
  Thesis director: PIERA FERNANDEZ, JAIME | OLMEDO CASAL, ESTRELLA
  

  Committee:
       PRESIDENT: ESPINOSA DURO, VIRGINIA
       SECRETARI: DEL RIO FERNANDEZ, JOAQUIN
       VOCAL: GONZALEZ BLANCO, SUSANA
  Thesis abstract: Light attenuation is a critical factor in aquatic ecosystems for many physical and biological processes. Water transparency plays an essential role in understanding the variations of the ecological environment in water, especially in coastal and continental areas. Monitoring the transparency of the water serves as an indicator of the water quality and reports on the concentrations of phytoplankton, the levels of dissolved organic compounds, or particulate matter.The traditional method for measuring water transparency is the Secchi disk. However, some limitations exist in this method. In shallow and transparent waters, the Secchi disk can reach the bottom without disappearing. In addition, the quality of the Secchi disk distance observations has an error associated with each person¿s vision. Furthermore, it is not possible to include this measurement as an operational oceanography measurement due to the measurement¿s difficulty in quantifying its uncertainty. These issues contrast with the objectivity of technological equipment, which can provide accurate and complete measurements that help with long-term evaluations. The main goal of this thesis is to assess the feasibility of an operational water quality monitoring system based on low-cost optical technologies that ensure a high density of measurement stations (completeness) and, at the same time, an automated system to control the quality of the observations (accuracy). For this reason, we plan to validate the concept of Operational Marine Optics (OMO): Towards systematic and long-term routine measurements of the optical properties of the water and their rapid interpretation and dissemination. First, a low-cost operational monitoring device, the KduPRO, has been developed for coastal and inland waters. This device estimates the Kd (the diffuse attenuation coefficient, which describes the concept of light extinction with depth) with an automated quality control system. The measurements have been compared with the ones provided by other reference instruments in Loch Leven (Scotland). Besides an estimate of the measurement uncertainty is provided. A co-design exercise has been carried out by volunteers in the Lobo Reservoir (Brazil). The recommendations and outcomes of this exercise will be integrated into the new phase of the development of KduPRO.Secondly, we designed a new device: The KnuSTICK. It consists of a watertight transparent tube with light measurement sensors inside. It is easy to use, maintain, and connect to the Internet of Things (IoT) networks, making KnuSTICK suited for observations based on citizen science. To fit with the design requirements, a new annular-shaped irradiance measurement concept, Ea, is introduced. This new concept is assessed by using a radiative transfer model (Hydrolight). The theoretical annular-shaped irradiance can be measured by setting the sensors at different orientation angles. We have evaluated several configurations and selected the one which provides the best performance. The robustness of the corresponding diffuse attenuation coefficient, Ka, has been analysed in different conditions of water types, solar angles, cloudiness levels, as well as bottom types and depths.Finally, to ensure the high density of the measurements, we evaluated the coverage of an IoT network to demonstrate that the low-cost deployment of this technology is feasible to carry out operational monitoring in a specific territory, such as the coast of Catalonia. Different prototypes developed during the European H2020 MONOCLE project have been tested to check network connectivity, such as the KnuSTICK and the KduMIC (a professional multiparametric modular device with multispectral detectors and temperature sensors), sending data in real-time.The study carried out in this thesis represents an important contribution that can help in the management of water quality by policymakers and governmental institutions.
  

• SANZ LANZAS, CLAUDIA: Assessment of the biological risks associated to the use of biosolids and wastewater.
  
  Author: SANZ LANZAS, CLAUDIA
  Thesis file: (contact the Doctoral School to confirm you have a valid doctoral degree and to get the link to the thesis)
  Programme: DOCTORAL DEGREE IN MARINE SCIENCES
  Department: (DECA)
  Mode: Article-based thesis
  Reading date: 26/05/2023
  Thesis director: PIÑA CAPÓ, BENJAMIN | NAVARRO MARTÍN, LAIA
  

  Committee:
       PRESIDENT: TORREBLANCA TAMARIT, AMPARO
       SECRETARI: SUBIRATS MEDINA, JESSICA
       VOCAL: PROIA, LORENZO
  Thesis abstract: The circular economy is an emerging concept presented as a solution to counteract the damage caused by the linear economic scheme followed in the past decades. It is based on the principle of "closing the life cycle" and seeks, through reuse and revaluation, to extend the value of products, materials, and resources, such as water and energy, minimizing the generation of waste. In this context, the European Union (EU) aims to build a food system that could work under all circumstances, ensuring a safe and sustainable food and water supply for all citizens by applying circularity. Ensuring the availability of water and fertilizers for agriculture is probably the major challenge for achieving this goal. In this respect, the EU contemplates the use of effluents collected from water treatment plants (WWTP) for irrigation or aquifer recovery. Similarly, the use of solid waste such as sludge from WWTPs, the organic fraction of urban solid waste (OFMSW), or livestock waste, at different processing levels, is a promising alternative to mineral/chemical fertilization, promoting a self-sustainable, circular food system. However, the use of these recycled materials is not free from risks. They contain hazards of emerging concern including Contaminants of Emerging Concern (CECs) (like prescription drugs, endocrine disruptors and antibiotics) as well as different microbial hazards (not only pathogens, which are legally regulated and tested, but also antibiotic resistant bacteria known to spread the resistance to different antibiotics to the microbiomes from waterbodies, soils, and crops). Upcoming legislations that aim to promote and regulate their use agree on the fact that the main challenge relies on correctly assessing their associated risks for environmental and human health. This thesis aims to evaluate the biological activities associated to livestock wastes, OFMSW and WWTP effluents and associated biosolids in order to determine their potential hazards and the level of exposure for the environment and for the general population in the context of their use. For this purpose, we specifically evaluated the impact of organic fertilization on agroecosystems through ABs, ARGs and ARBs transmission and microbiome modulation monitoring. Moreover, we assessed the impact linked to WWTP effluents through the screening of ARGs and ARBs and associated toxic activities. Consequently, we developed an environmental risk analysis framework associated to biosolids and wastewater reuse considering the occurrence of the monitored hazards and their potential impacts on exposed environments. In the studies included in this thesis we observed that the selective pressure posed by the analyzed organic fertilizers was enough to favor the soil colonization by antibiotic-resistant bacteria and to increase horizontal gene transfer (HGT) in both target soils and crops. The fact that this impact appeared transient highlights the importance of respecting fertilization rates and the time elapsing from fertilization to harvest. Moreover, the processing of wastes favoring bacterial succession appeared as a valuable tool to reduce this risk. On the other hand, we detected high loads of both chemical and microbial hazards in WWTP effluents, underscoring the need of tertiary treatments able to reduce them in order to ensure a safe reuse of wastewater. In this regard, Soil Aquifer Treatment (SAT) technologies appeared in our studies as cost-effective alternatives to other tertiary treatments given their efficiency on removing biological (particularly ARG loads) and chemical hazards and their potential ability to promote the displacement of gut-related, copiotrophic bacteria by groundwater-like microbiomes, enhancing in this way the removal of ARGs, CECs and toxic activities.
  

Last update: 10/06/2023 05:01:04.

Research groups

• LIM/UPC-Maritime Engineering Laboratory

- Institute of Marine Sciences – Barcelona (ICM-CSIC)

- Institute of Environmental Assessment and Water Research (IDAEA-CSIC)

- Oceans Catalonia International S.L.

- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)

- Blanes Centre for Advanced Studies (CEAB-CSIC)

- International Centre for Coastal Resources Research

- Spanish Institute of Oceanography (IEO)

- Benthic Ecology and Biology Research Group (Bentonic)

- Research and Development Centre (CID)

- Research Group on Marine Geosciences (Geociema)

Research areas:

• Physical and chemical oceanography
• Marine geosciences
• Marine biology
• Marine ecology
• Maritime engineering
• Coastal and marine area management

Teachers

• Andre Sanchez, Michel
• Caceres Rabionet, Ivan
• Calvete Manrique, Daniel
• del Rio Fernandez, Joaquin
• Espino Infantes, Manolo
• Garcia Serrano, Joan
• Gironella i Cobos, Xavi
• Gonzalez Marco, Daniel
• Gracia Garcia, Vicente
• Grifoll Colls, Manuel
• Jimenez Quintana, Jose Antonio
• Mestres Ridge, Marc
• Mösso Aranda, Cesar
• Sanchez-Arcilla Conejo, Agustin
• Sierra Pedrico, Juan Pablo
• Valdemoro Garcia, Herminia