ILRI PhD Graduate Fellowship: Fate of Antibiotic Residues and Antibiotic Resistant Bacteria in Livestock Manure and their Effects on Greenhouse Gas Emissions and Nutrient Cycling

December 12, 2021

The International Livestock Research Institute (ILRI) seeks to recruit a PhD graduate fellow to work on fate of antibiotic residues and antibiotic resistant bacteria in livestock manure and their effects on greenhouse gas emissions and nutrient cycling. The successful fellow will be co-hosted under ILRI’s One Health Research and Education Center for Africa (OHRECA) and Mazingira Center for Environmental Research and Education.

ILRI works to improve food and nutritional security and reduce poverty in developing countries through research for efficient, safe and sustainable use of livestock. It is the only one of 15 CGIAR research centers dedicated entirely to animal agriculture research for the developing world. Co-hosted by Kenya and Ethiopia, it has regional or country offices in East, South and Southern Asia as well as Central, East, Southern and West Africa. www.ilri.org

OHRECA seeks to improve the health of humans, animals and ecosystems through capacity building, strengthening of local, regional and global networks and provision of evidence-based policy advice on One Health in sub-Saharan Africa. The center has four thematic areas: control of neglected tropical zoonotic diseases; emerging infectious diseases; food safety and informal markets; and prevention and control of antimicrobial resistance. https://www.ilri.org/research/facilities/one-health-centre

The Mazingira Centre is an environmental research and educational facility established by ILRI in Nairobi. Research at the Mazingira Centre focuses on understanding and managing the environmental footprint of livestock systems without hampering productivity. https://mazingira.ilri.org/

About the position

Imprudent use of antibiotics is increasing in livestock production systems in low- and middle-income countries, with potentially severe consequences for human, animal, and environmental health. However, little is known about the fate of antibiotic residues in livestock manure in smallholder farm settings under traditional manure management systems. Bacteria that are resistant to antibiotics can spread into and across the environment through livestock manure, posing a health hazard that needs to be addressed. In addition, livestock manure is a source of greenhouse gas (GHG) emissions that contribute to global warming. To achieve sustainable livestock development pathways in East Africa, it is important to understand the impact of livestock production on the environment (GHG emissions as well as animal and human health impacts).

Despite potentially negative aspects of livestock manure, it is an important resource for smallholder farmers. It can be used as crop fertilizer, thereby reducing the need for expensive synthetic fertilizer, and is beneficial for soil fertility and stability. Understanding if and how antibiotic residues and antibiotic-resistant bacteria affect nutrient cycling during manure storage and field application is critical. Because GHGs are formed during microbially-mediated processes, the presence of antibiotic residues and resistant organisms can influence the magnitude of GHG emissions and the fertilizer quality of the manure. Manure management practices that both reduce antibiotic resistance and GHG emissions and are practical for smallholder farmers are urgently needed to stop the spread of AMR and to mitigate climate change.

To address these research gaps, ILRI seeks to recruit a PhD graduate fellow to investigate how the presence of antibiotic residues and antibiotic resistant bacteria affect GHG emissions and nutrient cycling in manure in different livestock production systems in Kenya, and how manure management interventions can help to reduce both GHG emissions and antibiotic resistance. To answer these research questions, the candidate will conduct a series of lab and on-farm experiments. The gained knowledge will help to prioritize good livestock adaptation and mitigation options in relevant livestock systems and help to build capacity in decision support and planning in East Africa.

ILRI Program: The fellow will be associated with Animal and Human Health & Sustainable Livestock Systems Programs at ILRI.

ILRI fellowship project title: Fate of antibiotic residues and antibiotic resistant bacteria in livestock manure and their effects on greenhouse gas emissions and nutrient cycling.

Responsibilities of the fellow:

Study decomposition rates and half lives of the most important antibiotics used in livestock production during simulated manure storage.
Measure GHG emissions (CH4, N2O, CO2) during manure storage and from manure applied to soils and how these emissions are affected by concentrations of antibiotic residues.
Measure leaching of nutrients, antibiotic residues, and antibiotic resistant bacteria from manure.
Evaluate the microbiome structure of livestock manure with and without antibiotic residues, and how microbial functionality is affected through changes in nutrient cycling processes (e.g., decomposition rates, respiration, nitrification/denitrification, methanogenesis/methane oxidation).
Test the influence of manure management interventions (e.g., covering, compacting, composting, biogas digestion, use of additives) on antibiotic residue concentrations and antibiotic resistance as well as fertilizer quality.
Write scientific papers and prepare conference/workshop presentations describing results and their implications for antibiotic resistance transmission risks, livestock productivity, GHG and nutrient management.
Communicate findings to relevant stakeholders (ministries, extension officers, farmers, etc.).
Provide supervision and guidance to field support staff and research assistants.

Minimum requirements for the ideal candidate

MSc in Environmental Microbiology, Environmental Sciences, Agricultural Sciences, or any other relevant discipline.
Experience with GHG measurements, soil and water measurements, and environmental microbiology.
Knowledge on livestock production systems in developing countries.
Experience in handling diverse datasets, data processing and statistical software such as R, SPSS, Matlab or Python.
Ability to jointly work in a multinational team of scientists and technicians from other disciplines (biogeochemistry, agricultural sciences, social sciences, economics, veterinary medicine etc.).
Ability to apply necessary steps to ensure data quality assurance and data quality control.
Ability to supervise and guide research assistants and junior graduate students e.g., Bachelor or master’s level.
Excellent communication skills.

Location: ILRI, Nairobi, Kenya.

Duration: 3 years

Terms of appointment and benefits: This is a 3-year appointment subject to satisfactory performance. ILRI will offer a competitive stipend to cover living expenses in the project location, medical cover, and meet all research expenses. ILRI will also meet tuition fees at the fellow’s university of admission. The successful candidate will be supervised jointly by an ILRI scientist and the university/academic supervisor and will receive capacity development opportunities from ILRI.

How to apply: All applications MUST include the following (applications not containing these documents will not be considered):

a cover letter addressed to Head of Capacity Development, expressing interest in the fellowship position and the motivation. The position title and reference number (REF: GF/ILRI/OHRECA-SLS/12/2021) should be clearly marked on the subject line of the cover letter.
CV including names and addresses (including telephone and email) of three referees who are knowledgeable about the candidate’s professional qualifications and work experience.
academic qualification certificates/transcripts.

Applications must be submitted by clicking on the tab “APPLY NOW” on or before 31st January 2022.

Due to the volume of applications, only shortlisted candidates will be contacted.

ILRI does not charge a fee at any stage of the recruitment process (application, interview meeting, processing or training). ILRI also does not concern itself with information on applicants’ bank accounts.

To find out more visit https://www.ilri.org/jobs