Doctoral student (Innosuisse) in environmental DNA and autonomous biodiversity monitoring

Introduction

UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility.

unil.ch/work

Presentation

The Group of Prof. Nadir Alvarez is proposing a Doctoral Student (Innosuisse) position in museomics, environmental genomics and molecular ecology at the Department of Ecology and Evolution, University of Lausanne, Switzerland. The PhD Student will join a dynamic team working mainly on environmental DNA (eDNA) methods for biodiversity and pathogen monitoring, in the framework of the Innosuisse-funded AquaDecode project, in partnership with the EPFL-based startup Decode NAture. For more information, see https://applicationspub.unil.ch/interpub/noauth/php/Un/UnPers.php?PerNum=1107109&LanCode=37&menu=coord

The Alvarez group has a strong track record in museomics and environmental genomics. Pioneering work on hybridisation capture from historical and ancient specimens has enabled genomic studies on degraded DNA from historical collections, including butterfly population genomics across the 20th century among other topics. In conservation genomics, the group integrates population genomic data with species conservation, and actively contributes to strengthening partnerships between researchers and conservation practitioners across Switzerland and Europe

More recently, the group has expanded into environmental DNA (eDNA) population genomics, developing an enrichment-based nuclear eDNA capture method that opens new avenues for population-level studies directly from water samples, while advocating the use of natural history collections for improved eDNA reference databases and developing a roadmap on scaling up aquatic eDNA population genetics.

Job information

Expected start date in position:    01.06.2026

Contract length:                           1 year, This contract can be renewed until the end of the grant, that is to say 28.02.2029

Activity rate:                                 100%

Workplace:                                   Lausanne Dorigny

Annual gross salary: (According to SNSF standard salary scales).

Your responsibilities

AquaDecode aims to build the first fully autonomous eDNA monitoring station, integrating water sampling, molecular amplification (and possibly DNA capture), nanopore sequencing, and cloud-based reporting into a single field-deployable device. A functional autonomous water sampler (CoWaS) already exists; the main challenge is to integrate the complete molecular workflow on board, from Recombinase Polymerase Amplification (RPA) through to batch nanopore sequencing with real-time data transmission. Environmental DNA technologies offer the potential for universal and standardised biodiversity monitoring; AquaDecode aims to make this operational through continuous, autonomous surveillance. The applied conservation dimension is significant: the platform can enable early detection of invasive species, monitoring of pathogen loads in aquaculture and agricultural irrigation systems, and wastewater surveillance for public health.

Doctoral Research (85%)

Working alongside a postdoctoral researcher who leads the advanced molecular and system-integration developments, the doctoral student will focus on designing, conducting, and interpreting proof-of-concept monitoring campaigns that demonstrate the ecological relevance of the AquaDecode platform. Core responsibilities include: i) Design and execute field-based eDNA monitoring campaigns across diverse aquatic environments (lakes, rivers, torrents, and potentially groundwater), generating the datasets that validate the platform's ecological performance ; ii) Benchmark detection sensitivity, specificity, and reproducibility of the AquaDecode workflows against conventional laboratory-based eDNA approaches ; iii) Assess the influence of sampling strategies, environmental conditions, and molecular markers (COI, 16S, 18S, etc.) on biodiversity detection and ecological interpretation ; iv) Compare and evaluate complementary enrichment approaches (eg, hybridization capture) ; v) Analyse spatio-temporal biodiversity patterns from autonomous monitoring data, contributing ecological insights to conservation and environmental management ; vi) Publish results in peer-reviewed journals

The thesis will not only contribute to molecular method validation, but will deliver ecological insights from field deployments — including early detection of invasive species, pathogen surveillance in agricultural irrigation systems, and microbial communities monitoring.

The successful candidate will be based at the Department of Ecology and Evolution under the supervision of Prof. Nadir Alvarez, who is also the Director of the Naturéum (Muséum cantonal des sciences naturelles, Lausanne), and will work in close interaction with Decode NAture.

Teaching Activities (15%)

The doctoral student will participate in teaching activities within the department, including assistance in practical courses and student supervision.

Your qualifications

In order to complete our team, we are looking for someone with the following skills : 

Essential:

• Master’s degree in molecular biology, ecology, environmental sciences, microengineering, bioengineering, bioinformatics, biotechnology or a related field


• Strong interest in applied systems and interdisciplinary research


• Hands-on experience with molecular biology techniques and/or microengineering


• Strong interest in aquatic biodiversity monitoring, conservation biology, or environmental genomics


• Skills using bioinformatics tools and programming


• Good spoken and written English proficiency

Desirable:

• Experience with environmental DNA (eDNA) metabarcoding, metagenomics, or isothermal amplification


• Experience with Oxford Nanopore Technologies (ONT) sequencing platforms


• Knowledge of aquatic ecology, freshwater biodiversity, or conservation biology


• Interest in fieldwork and willingness to participate in autonomous monitoring deployments across Swiss aquatic environments

Interpersonal skills

• Strong motivation, intellectual curiosity, and willingness to explore new methods


• Ability to work both independently and collaboratively in an interdisciplinary team


• Good organizational skills and ability to meet project deadlines


• Interest in connecting fundamental research with real-world environmental applications

What the position offers you

• Work at the interface of academic research and startup innovation, contributing to a real-world environmental genomics platform with direct societal impact


• Be part of a dynamic and interdisciplinary team combining molecular biology, engineering, and data science, in close collaboration with DecodeNAture and Swiss environmental partners


• An inspiring setting at the University of Lausanne, on the shores of Lake Geneva with views of the Alps, in a department where research activities and seminars are conducted in English


• Direct involvement in a project connected to real ecosystems, with opportunities for fieldwork across Swiss aquatic environments


• Access to state-of-the-art molecular biology and sequencing facilities, and a strong network across academia, industry, and environmental stakeholders

• Being part of a campus offering a broad range of topics, producing a rich intellectual and social life. Although French is the common language in Lausanne region, the department research activities and seminars are conducted in English. The campus is located on the shore of the Geneva Lake, with the view on the Alps.

Contact for further information

For further information please contact Prof. Nadir Alvarez: E-Mail schreiben

Your application

Deadline: 27.04.2026 

Formal applications should include:

• a cover letter containing a short description of your research interests and research experience explaining why you reply to this job offer


• Your CV


• A copy of your master certificate,


• Master’s thesis summary (max. one page)


• The contact details of 2-3 referees

To receive full consideration, application documents should be uploaded online through the University of Lausanne recruitment platform.

Additional information

UNIL is committed to:
•    equality, diversity and inclusion within its community;
•    ensuring an open and respectful environment that is conducive to personal development;
•    offering working conditions that facilitate work-life balance;
•    supporting early career researchers.
 

unil.ch/equality
unil.ch/families
unil.ch/graduatecampus