Post-doctoral fellow in Raman spectroscopy of soil microbes

Subject description

Soils are the base of our society and our food security, but they are one of the last domains of our modern life to be technologized. Soil microbes are essential as symbionts, pathogens and drivers of nutrient cycles, but it has been difficult to study them in their natural habitats. We want to use and develop a novel way to investigate soil microbial communities and species over space and time: with help of microfluidic soil chips and an advanced access system for microscopy and spectroscopy we will access natural soil microbial communities to answer questions about their temporal dynamics over weeks and seasons, their interactions such as predator-prey relations and their spatial extent over time.

As part of this Swedish Research Council funded interdisciplinary research environment project, we will develop automated species and community recognition, particularly focusing on pathogenic soil fungi, with help of deep-learning algorithms fed with microscopic image and Raman spectroscopy data, benchmarked against classical DNA profiling. For this, we are now looking for a postdoc who will assemble a database of Raman spectra describing different microbial species, both in bulk and at single-cell scale in microfluidics-based soil chips, in different conditions, representing those encountered in real soils. The postdoc will collaborate with other participants within the project to enable microbial species detection and recognition in situ, using a sensor system that will eventually be deployed in agricultural fields for soil monitoring in space and time.  

Work duties

The main duties involved in the post-doctoral posistion is to conduct research, consisting of assembling a library of Raman spectra of laboratory-grown and field-recovered soil pathogenic fungal cultures and other microorganisms, and developing of spectral collection and analysis protocols that will allow this biochemical data to be effectively used to support optical microscopy-based deep-learning algorithms for species identification and characterization.

Teaching may also be included to promote career development, but up to no more than 20% of working hours. The position shall also include the opportunity for three weeks of training in higher education teaching and learning.

Detailed description of the work duties:

• Preparing samples and recording Raman spectra of bulk mycelia of laboratory-grown soil pathogenic fungi
• Preparing samples and recording Raman spectra of the fungi and other soil microorganisms at single-cell scale in microfluidics-based soil chips
• Developing sampling and data collection protocols for the collection of representative spectral database/library that can be implemented, together with optical microscopy data, to train deep-learning algorithms for microbial identification and characterization in real soils.
• Analysing the produced spectral data.
• Scientific writing

Qualification requirements

Appointment to a post-doctoral position requires that the applicant has a PhD, or an international degree deemed equivalent to a PhD, within the subject of the position, completed no more than three years before the date of employment decision. Under special circumstances, the doctoral degree can have been completed earlier. Special emphasis will be placed on scientific ability in the subject areas of analytical chemistry (especially Raman microspectroscopy approaches) and soil microbiology, but other subject areas may also be considered if they are deemed relevant to the project. 

Additional requirements:

• Experience in working with spectroscopy methods, particularly Raman (micro)spectroscopy
• Experience in spectral data analysis in general and multivariate methods in particular
• Very good oral and written proficiency in English.

Assessment criteria and other qualifications

This is a career development position primarily focused on research. The position is intended as an initial step in a career, and the assessment of the applicants will primarily be based on their research qualifications and potential as researchers.

Particular emphasis will be placed on research skills within the subject.

For appointments to a post-doctoral position, the following shall form the assessment criteria:

• A good ability to develop and conduct high quality research.
• Teaching skills.
• Fulfilment of the requirements above.

Additional assessment criteria

• Experience in handling and analysing biological, particularly microbial, samples
• Experience in machine learning approaches.

Consideration will also be given to good collaborative skills, drive and independence, and how the applicant’s experience and skills complement and strengthen ongoing research within the department, and how they stand to contribute to its future development.

Terms of employment
This is a full-time, fixed-term employment of 2 years. The period of employment is determined in accordance with the agreement “Avtal om tidsbegränsad anställning som postdoktor” (“Agreement on fixed-term employment as a post-doctoral fellow”) between Lund University, SACO-S and OFR/S, dated 1st February 2022.

Instructions on how to apply

Applications shall be written in English and be compiled into a PDF-file containing:

• résumé/CV, including a list of publications,
• cover letter, including a general description of past research and future research interests (no more than two pages)
• contact information of at least two references,
• copy of the doctoral degree certificate, and other certificates/grades that you wish to be considered.