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Personal profile

Research Interests

  1. Environmental Microbiology
  2. Eco-toxicology
  3. Soil & Water Quality
  4. Antibiotic resistance in the environment

Microorganisms are omnipresent and capable of impacting the entire biosphere. They, especially the bacteria, are highly diverse in terms of structure and function, and they can play a major role in cycling of nutrients, remediation of contamination, and public health. My research interest involves the integration of state-of-the-art microbiological measurement technologies and ecological principles into the realm of environmental protection and sustainability.

Some on-going projects: 

Team DAGGAR - Dangerous and Growing Globally, Antimicrobial Resistance. 

Work related to antimicrobial resistance evolved from pharmaceutical eco-toxicology with the development of microbial-community endpoints. This work resulted in international exposure and award-winning publications. International collaborations include researchers and government/policy agencies in Australia, UK, USA, Canada, Cuba, Denmark and The Netherlands. Research focus has been to quantitatively measure resistance genes and antibiotics in the environment; it extends previous qualitative observations to a predictive level aimed at solving practical problems.  The investigations of PEC (pollutants of emerging concern) continue, as it remains a contemporary international problem.

Team ARMOR – Antimicrobial Resistance May Offer Resilience? (stability and resilience of microbial communities and performance during pollution stress). 

Microbial community dynamics are examined in response to contaminant exposure in engineered bioreactors. The research endeavours to find processes that are ecologically resilient and economically robust to avoid major investment in a new (or upgraded) treatment process as new regulations emerge.

GR-AMS - Greco-Roman Antimicrobial Minerals.  Multi-disciplinary, collaborative project.

Frack ET - Unconventional oil & gas (hydraulic Fracturing) Eco-Toxicology. 

We investigate the environmental risks associated with hydraulic fracturing. The project does not infer that operations and their fluids are hazardous; rather, we aim to determine whether any potential hazards do exist, and if so, provide quantitative measures and to aid engineers and risk assessors to make accurate evaluations and decisions. In collaboration with Prof. Shipton. 

FrankenSoil - rehabilitation and restoration of formerly contaminated lands. 

In the UK, there are still over 100,000 land sites, with an estimated economic value in £billions, but with the economic downturn, capturing the economic value of these sites in an economically and environmentally sustainable manner is now more elusive than ever. Contamination and aggressive remediation strategies often leave barren landscapes, devoid of aesthetic and economic value. Supplementation of organisms and plants  is often employed to these Brownfield sites; while effective, these strategies are relatively short-term, as maintaining the persistence of desired populations or the ecological conditions is often difficult and-or costly.

An understanding of terrestrial succession and the dynamics of plant-microbe interaction underpins any strategy to best optimise the recovery process. Succession is defined as the underlying development process creating a robust community. It has been extensively studied in plant communities, but little is known about bacterial succession, particularly in harsh environments such as contaminated or aggressively remediated soils. 

The aim of this project is to understand community dynamics during ecosystem recovery in previously harsh, or highly disturbed, environments. In collaboration with Dr Christine Switzer.

Sticky MESS - Microbially enhanced soil stabilisation by microbial biofilms. 

Multi-disciplinary project seeking the development of novel bio-technologies for low-carbon design of remedial measures for geotechnical infrastructure. We explore 'biogenic/microbial methods' which involves the use of microbes to improve soil properties. These microbial geo-technologies have shown great potential in improving soil properties with ease, less cost, and enhanced environmental sustainability. In collaboration with Prof. Alessandro Tarantino.

Teaching Interests

Programme Coordinator of MSc in Environmental Engineering

Courses taught:

  • Environmental Engineering (CL328)
  • Water & Wastewater Treatment Design (CL447 + CL978)
  • Principles of Environmental Microbiology (CL430 + CL948)
  • Pollution and the Rehabilitation of Degraded Ecosystems (EV908)
  • MSc Projects in Environmental Engineering (CL944)
  • Independent Study in Collaboration with Industry (CL973, contributor)


  • 2018 - Teaching Excellence Awards, nominated (award TBD, May 2018)
  • 2016 - Teaching Excellence Awards, shortlisted Best in Faculty.
  • 2015 - Teaching Excellence Awards, shortlisted Best in Faculty.
  • 2015 - Fellow of the Higher Education Academy (FHEA)
  • 2014 - Teaching Excellence Awards, shortlisted Overall Best Supportive Teacher

International courses

  • Microbiology for Engineers, Gdansk University of Technology (Poland, TBD 2018)
  • Microbiology for Engineers, Indian Institute of Technology-Bombay (India, 2017)
  • Restoration of contaminated land, Gdansk University of Technology (Poland, 2015)
  • Ecotoxicology, Gdansk University of Technology (Poland, 2014)

Academic / Professional qualifications

Work Experience

Additional Qualifications:

  • 2015 - Fellow of the Higher Education Academy (FHEA) 

Expertise & Capabilities

Research themes:

  • Antibiotic resistance in the environment
  • Antimicrobial resistance
  • Susceptibility assays
  • Biological indicators of environmental pollution
  • Microbiological community stability in engineered and natural systems
  • Eco-toxicology, bioremediation
  • Outdoor, microcosm/mesocosm experimental systems

Routine research services

  • DNA/RNA analyses
  • PCR (polymerase chain reaction)
  • Genetic probe design (primer design)
  • Community analysis (sequencing, DGGE)
  • Biological assessments of soil, sediment and water
  • Molecular and microbiological techniques
  • Phytoplankton, algae
  • Bacteria
  • Micro-invertebrates
  • Water quality monitoring
  • Soil quality determinations
  • Wastewater analysis

Advance Statistics

  • Descriptor / inferential 
  • Multi-parametric analyses
  • Non-parametric analyses
  • Community analyses

Personal Statement

Dr. Knapp is Course Coordinator of MSc Environmental Engineering and active researcher in the "Water, Environment, Sustainability and Public Health" (WESP) research centre.

Think you can live without microbes?  Wanna take that challenge?

Microorganisms are omnipresent and capable of impacting the entire biosphere. They, especially the bacteria, are highly diverse in terms of structure and function, and they can play a major role in cycling of nutrients, remediation of contamination, and public health. Unfortunately, many people often overlook the ecological interactions within the microbial communities that support the process. Understanding these interactions require knowledge of the distribution and abundance of organisms and their interactions in an environmental setting. Further, it requires analytical tools to examine microbial organisms in an effective and timely fashion. Fortunately, high throughput culture-independent molecular methods are allowing researchers to quantitatively monitor these interactions. My research interest involves the integration of state-of-the-art microbiological measurement technologies and ecological principles into the realm of environmental protection and sustainability.

Education/Academic qualification

Doctor of Philosophy, University of Kansas

Master of Science, University of Kansas

Bachelor of Science, University of Kansas

External positions

Research Associate - EU Marie Curie funded, Newcastle University

1 Oct 200631 Jan 2009

Research Associate, University of Kansas

1 Sep 200230 Sep 2006


  • wastewater treatment
  • bioremediation
  • pollution control
  • pharmaceutical contamination
  • lagoon
  • constructed wetland
  • microbiology
  • molecular ecology
  • microbial ecology
  • limnology
  • water quality
  • molecular biology
  • DNA analysis
  • RNA analysis
  • genomic
  • bioinformatics

Fingerprint Fingerprint is based on mining the text of the person's scientific documents to create an index of weighted terms, which defines the key subjects of each individual researcher.

Genes Chemical Compounds
antibiotic resistance Earth & Environmental Sciences
Anti-Bacterial Agents Chemical Compounds
Microbial Drug Resistance Medicine & Life Sciences
gene Earth & Environmental Sciences
Probiotics Medicine & Life Sciences
bacterium Earth & Environmental Sciences
Bacteria Medicine & Life Sciences

Network Recent external collaboration on country level. Dive into details by clicking on the dots.

Projects 2009 2020

Research Output 2003 2018

Can the legacy of industrial pollution influence antimicrobial resistance in estuarine sediments?

Rodgers, K., McLellan, I., Peshkur, T., Williams, R., Tonner, R., Hursthouse, A. S., Knapp, C. W. & Henriquez, F. L., 13 Oct 2018, In : Environmental Chemistry Letters. 13 p.

Research output: Contribution to journalArticle

Open Access
estuarine sediment
Anti-Bacterial Agents
Crude oil


Nitrogen and phosphorous removal from groundwater using waste materials

Author: Gkiouzepas, S., 1 Feb 2015

Supervisor: Kalin, R. (Supervisor) & Knapp, C. (Supervisor)

Student thesis: Doctoral Thesis

The role of water distribution systems in the enrichment of antimicrobial resistance

Author: Khan, S., 1 Oct 2016

Supervisor: Knapp, C. (Supervisor) & Beattie, T. (Supervisor)

Student thesis: Doctoral Thesis

Activities 2008 2019

Aligarh Muslim University

Charles Knapp (Visiting researcher), Tatyana Peshkur (Visiting researcher)
3 Feb 201916 Feb 2019

Activity: Visiting an external institution typesVisiting an external academic institution

Antimicrobial resistance: what does the environment have to say

Charles Knapp (Speaker)
5 Feb 2019

Activity: Talk or presentation typesInvited talk