Postdoctoral Research Associate: Soil Metagenome Research

Urbana, Illinois
Salary will be commensurate with experience.
February 19 2018
Position Type
Full Time
Organization Type
Job Type

Postdoctoral Research Associate: Soil Metagenome Research

A Post-doctoral Research Associate position on Soil Metagenome Research is available in the Department of Crop Sciences at the University of Illinois at Urbana-Champaign.

The position is available within Dr. Villamil’s lab to study the impacts of the inclusion of cover cropping into long-term agricultural trials on the soil microbiome and health. Cover cropping has been identified in Illinois as the most promising in-field strategy to help achieve the goal of decreasing the N load to the Mississippi River by 15% by 2025. The main goal of this three-year grant-funded collaborative project is to study cover cropping as an ecological intensification tool, an approach to enhance agricultural sustainability through the promotion of biodiversity and targeted management of soil community composition. Our long-term goal is to identify specific microbes or microbial communities that help characterize and affect soil health status within typical Illinois production systems, while advancing our understanding of the relationships between soil health and soil microbiome with agroecosystem services of carbon and N cycling and crop productivity.


  • Development of bioinformatics automated pipelines, workflows, and visualization tools, along with preparation of reports and publication of research papers in peer reviewed journals.
  • Interrogation and interpretation of soil microbial metagenome datasets in two major areas: i) the impact of agricultural practices on microbial diversity and function, and ii) the nitrogen cycling role of microbes in agroecosystems (microbe-environment interactions).
  • Perform large-scale analysis of soil genome sequence data, analyze amplicon sequences, and perform comparative analyses using bioinformatics tools.
  • Help mentor graduate students conducting relevant research.
  • Elaborate on existing hypotheses and develop new research directions based on own interests
  • Present findings at relevant conferences at least once per year


To join our group, we are looking for highly motivated individuals that have demonstrated scientific productivity, excellent communication skills, and the capacity to conduct independent research. The successful candidate will have a strong background in statistical modelling, with significant experience in linux/unix command line scripting, Perl, Python, R, or other scripting language; be deeply familiar with metagenomics analysis paradigms and tool-sets, and proven record in data interpretation and visualization. Domain knowledge in molecular biology and microbiology or microbial ecology is required as is a familiarity with current research in the microbiome field, preferably of soils. The ideal candidate enjoys new challenges and learning new things with a good balance of innovative and practical methods to get things done in a timely manner.

Required Skills and Experiences

  • A Ph.D. in Computational Biology, Microbiology, Bioinformatics, Bioengineering, Microbial Genetics/Genomics, Molecular Biology, or a related field and relevant experience. Experience with bioinformatics is required. Candidates must be within five years of receiving their PhD.
  • Must be familiar with publicly available bioinformatics tools, algorithms, and data repositories.
  • Advanced scripting and programming skills in R and Python.
  • Experience with microbiome analysis tools, such as mothur, QIIME, UPARSE, Swarm, vegan, metagenomeSeq, phyloseq.
  • Experience in NGS data analysis, including model development and testing, machine learning algorithm development, microbial community profiling using 16S, archaea, and ITS amplicon data, and development of statistical reporting tools.
  • Additional experience in cloud computing, paralellization, databases (relational and graph based), and higher-level programming, such as C/C++/C# would be desirable.
  • Ability to exercise judgment within broadly defined practices and policies in selecting methods, techniques, and evaluation criteria for obtaining results.
  • Strong experience in analysis of microbial metagenomes is essential with a proven record of accomplishment in this area reflected in recent or pending publications.
  • Experience in the field of Microbiology, Molecular Biology, and or Microbial Ecology, particularly focused on C and N cycles.
  • Knowledge and understanding of key and complex biological concepts (genes, pathways, microbial phylogeny, nitrogen cycling in agroecosystems).
  • Ability to carry out independent and creative research of the highest quality standards.
  • Must be a team player and a focused individual with a strong work ethic and great attention to detail.
  • Must exhibit excellent communication skills and relay complex scientific concepts to a variety of members within the team.
  • Excellent organizational, analytical, and record-keeping skills with the ability to organize and present technical reports to collaborators, management, and sponsors.

Appointment and Salary

The anticipated start date for this position is August 16th, 2018. There is possibility to start earlier. The posting shall remain open until the position is filled, however for full consideration, please apply by close of business on March 30th, 2018.

This is a 100% full time, 3 year, postdoctoral appointment renewable annually, based upon satisfactory job performance. An extension beyond that 3-year period is contingent on availability of funds and ongoing operational needs.  Salary will be commensurate with experience.

To Apply

Interested individuals should submit a single PDF application file including: 1) a letter of interest, 2) curriculum vitae, 3) a recent publication in a peer-reviewed journal relevant to the position (please explain the relevance in your letter of interest), 4) a sample code notebook (R markdown, jupyter, or other), or link to a code repository (github,  bitbucket, etc), and 5) contact information for three professional references to Dr. Villamil ( Please put “postdoc application” in the subject line of the email. Applications received by March 30th will be given priority.

All requested information must be submitted for your application to be considered. Individuals with diverse backgrounds are strongly encouraged to apply.

The University of Illinois conducts criminal background checks on all job candidates upon acceptance of a contingent offer.

The University of Illinois is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans and individuals with disabilities are encouraged to apply. For more information, visit To learn more about the University’s commitment to diversity, please visit