Bioprocess Engineer II – Fermentation & Downstream Processing

Dakota BioWorx; Brookings, Northern (SD, KY); Hybrid; USD 85,000 - 120,000; Full time

Job summary

Dakota BioWorx in Brookings, SD seeks a bioprocess engineer to lead client fermentation and downstream operations. You will operate bioreactors, centrifuges, and filtration systems, while applying process data to improve yield and scale-up performance.

The role requires hands-on processing experience, strong communication, and the ability to troubleshoot and document procedures for clients and colleagues.

Qualifications

• Bachelor's degree in chemical/biochemical/biological engineering or related field.
• Over two years of bioprocessing/fermentation/process development experience with equipment handling.
• Hands-on bioreactor operation including microbial cultivation and aseptic technique.
• Experience with at least one downstream operation (centrifugation, filtration, drying).
• Apply engineering fundamentals to scale-up and process performance.
• Strong problem-solving and data interpretation with documentation.
• Clear technical communication and organized project work.

Responsibilities

• Plan and execute client fermentation and downstream work, coordinating equipment, materials, staffing needs, and timelines with the team.
• Review client processes, identify operating constraints, and develop run plans and protocols with clients and colleagues.
• Set up, operate, monitor, and clean bioreactors, centrifuges, filtration systems, homogenizers, and spray dryers within your demonstrated proficiency.
• Apply engineering calculations and data to select operating conditions and improve yield and reproducibility.
• Investigate deviations and equipment problems, identify causes, and implement corrective actions.
• Assess equipment readiness and perform routine checks and maintenance; coordinate repairs with specialists.
• Write and improve procedures, batch records, and protocols; prepare client reports and recommendations.
• Train junior scientists, engineers, and operators in equipment use and documentation practices.
• Communicate progress and risks, and follow safety procedures for biological materials and equipment.

Skills

Bioprocessing

Fermentation

Aseptic technique

Process development

Scale-up

Data interpretation

Documentation

Education

Bachelor's degree in chemical/biochemical/biological engineering

Tools

Spreadsheet software

Job description

Position Overview

Dakota BioWorx (dakotabiowork.org) helps biotechnology companies develop and scale the processes that turn microbiological innovation into useful products. Based in the Research Park at South Dakota State University, we provide fermentation and downstream processing services from laboratory scale through 3,000-liter pilot scale.

Reports to the Director of Operations

Required Qualifications

• A bachelor’s degree in chemical engineering, biochemical engineering, biological engineering, bioengineering, or a related engineering discipline.
• More than two years of relevant experience in bioprocessing, fermentation, process development, or bio-manufacturing, gained through industry or applied research with substantial equipment operation responsibilities.
• Hands‑on experience preparing, operating, monitoring, and cleaning bioreactors, including microbial cultivation, aseptic technique, sampling, and process control.
• Practical experience with at least one downstream unit operation, such as centrifugation, tangential flow filtration, homogenization, or drying.
• Ability to apply engineering fundamentals, including material balances, fluid flow, heat transfer, and gas–liquid mass transfer, to process performance and scale‑up questions.
• Demonstrated ability to troubleshoot equipment and process problems, interpret operating data, and execute established procedures independently while recognizing when to seek specialist support.
• Clear technical communication, accurate documentation, and the ability to organize project work and analyze data using spreadsheets or other relevant software.

Desirable Qualifications

• Experience across every equipment type is not required.
• Experience operating pilot‑scale bioreactors and steam‑in‑place or clean‑in‑place systems.
• Experience with continuous‑flow or disc‑stack centrifugation, microfiltration or ultrafiltration, high‑pressure homogenization, and spray drying.
• Experience with process scale‑up or technology transfer, including adapting operating parameters and preparing transfer documentation.
• Experience with equipment commissioning, instrumentation, calibration, process control systems, or reading process flow diagrams and piping and instrumentation diagrams.
• Experience with experimental design, statistical analysis, root cause investigation, or training colleagues in equipment operation.
• Experience working with clients, equipment vendors, or service providers in a contract development or pilot facility.

Responsibilities

• Plan and execute client fermentation and downstream work, coordinating equipment, materials, staffing needs, and timelines with the team.
• Review client processes, identify operating constraints, and develop run plans and protocols with clients and colleagues.
• Set up, operate, monitor, and clean bioreactors, centrifuges, filtration systems, homogenizers, and spray dryers within your demonstrated proficiency.
• Apply engineering calculations and process data to select operating conditions, evaluate scale‑up constraints, and improve yield, reproducibility, and resource use.
• Investigate process deviations and equipment problems, identify likely causes, and implement and document corrective actions within approved procedures.
• Assess equipment readiness, perform routine checks and maintenance within your training, and coordinate repairs or specialist support when needed.
• Write and improve operating procedures, batch records, and protocols; prepare client reports and recommendations.
• Train and guide junior scientists, engineers, and operators in equipment use, troubleshooting, and sound documentation practices.
• Communicate project progress and technical risks promptly, and follow safety procedures for biological materials, chemicals, steam, pressure, and moving equipment.