Research Studentships for PhD students - IST/2025/BL2

Organisation/Company Instituto Superior Técnico Department Direção de Recursos Humanos Research Field Other Researcher Profile First Stage Researcher (R1) Positions Master Positions Country Portugal Application Deadline 3 Dec 2025 - 23:59 (Europe/Lisbon) Type of Contract Not Applicable Job Status Not Applicable Offer Starting Date 26 Nov 2025 Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

Objective 1: Review and synthesis of current knowledge

• Task 1. 1: Comprehensive literature review on traditional and emerging microbial indicators, analytical techniques and pathogens (bacteria, viruses, fungi).
• Task 1. 2: Identify knowledge gaps to refine research questions and hypotheses.

Timeline: Months 1–6

Output: Literature review chapter, annotated bibliography, updated objectives.

Objective 2: Method development and optimization

• Task 2. 1: Optimize laboratory protocols for DNA/RNA extraction.
• Task 2. 2: Select and implement molecular and analytical methods (q
  PCR, d
  PCR, HT-PCR assays, NGS pipelines) for pathogen detection delineated in task 1 and perform a comparative evaluation of these methods to determine the most robust and sensitive technique.
• Task 2. 3: Establish QA/QC procedures.

Timeline: Months 4–12 (overlapping with literature review)

Output: Validated laboratory protocols, SOPs, performance metrics reports, calibration curves.

Objective 3: Normalization Marker

• Task 3. 1: Common normalization markers implementation (cr
  Assphage, PPMo
  V, 16S r
  RNA).
• Task 3. 2: Selection of new viruses (indigenous virus) detected in high concentration in raw wastewater to be tested against cr
  Assphage, PPMo
  V for viruses and normalization fungi markers (chosen in task 1) in wastewater.
• Task 3. 3: Validation of new normalization markers by statistical analysis.

Timeline: Months 8-15 (overlapping with Method development and optimization)

Output: Validated new normalization markers, performance metrics reports.

Objective 4: Field sampling and data collection

• Task 4. 1: Identify and characterize sampling sites (rural vs urban catchments, WWTPs, recreational waters).
• Task 4. 2: Conduct regular sampling campaigns across seasons.
• Task 4. 3: Record environmental parameters (flow, temperature, rainfall, land use context).

Timeline: Months 8–24

Output: Sample database, environmental metadata.

Objective 5: Laboratory analyses and detection of markers

• Task 5. 1: Perform traditional indicator of contamination assays (e. g. , E. coli).
• Task 5. 2: Quantify novel genetic viral and fungi markers identified in task 3.
• Task 5. 3: Conduct NGS/metagenomic analysis to characterize microbial communities (microbiome, pathobiome, antimicrobial resistance genes).
• Task 5. 4: Evaluation of the presence of the pathogens chosen from task 1 in raw wastewater from different countries and sources (hospital, wastewater treatment plants, and planes).

Timeline: Months 10–28

Output: Marker concentration datasets, sequencing data, databases.

Objective 6: Data integration, interpretation, and risk implications

• Task 6. 1: Integrate and process data.
• Task 6. 2: Assess correlations with environmental drivers and pollution events.
• Task 6. 3: Discuss implications for health risk assessment and monitoring.
• Task 6. 4: Model to infer pathogen risk based in their circulation in wastewater.

Timeline: Months 20–34

Output: Draft chapters on results & discussion.

Objective 7: Dissemination and recommendations

• Task 7. 1: Develop practical recommendations for water managers and policymakers.
• Task 7. 2: Prepare manuscripts for peer‑reviewed journals.
• Task 7. 3: Present findings at conferences and stakeholder workshops.

Timeline: Months 28–36

Output: Publications, conference presentations, policy briefs.

Contest Procedure

Applications must be exclusively submitted on the admissions platform of the Instituto Superior Técnico at https://fenix. tecnico. ulisboa. pt/fenixedu-admissions and requires registration and validation of the candidate's identity. Applications are only accepted when the form available in the platform is correctly filled, submitted and locked without any validation errors.

Required documentation to submit in the scholarship application includes:

• Curriculum Vitae
• Proof of Qualifications (or declaration of honour in case you do not yet have the certificate)
• Proof of Registration/Enrolment
• Motivation Letter

The application submission deadlines can be viewed in the admissions platform. The results of the contest will be made available in the same admissions platform.

Must be registered in a doctoral programme. Knowledge in molecular biology techniques, including q
PCR, conventional PCR, digital PCR, and sequencing. Interest in microbiology and environmental surveillance. Must have a Master’s degree in microbiology, clinical microbiology and similar areas.

Additional Information

Must be registered in a doctoral programme. Knowledge in molecular biology techniques, including q
PCR, conventional PCR, digital PCR, and sequencing. Interest in microbiology and environmental surveillance. Must have a Master’s degree in microbiology, clinical microbiology and similar areas.

Contest Evaluation Method(s)

• Curricular evaluation weighted to 60% on a scale of 12 points.
• Individual interview weighted to 40% on a scale of 8 points.

The minimum final grade needed for admission is 16 points.

Conditions for the Contest Evaluation

Curriculum Evaluation

The curriculum evaluation will focus on academic background, professional experience, and technical skills relevant to the development and validation of new techniques and markers for microbial water quality assessment. The following criteria will be considered:

Academic background: Master’s degree in Applied Microbiology, with emphasis on coursework and projects related to environmental microbiology, molecular techniques, and water analysis.

Laboratory experience: Proficiency in DNA/RNA extraction methods, PCR techniques (q
PCR, d
PCR),
- generation sequencing (NG