Dr Charles Knapp

Senior Lecturer

Civil and Environmental Engineering

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.


Has expertise in:

    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

Prizes and awards

Researcher Development Programme Supervisor, 2017-18 - Nominated
Teaching Excellence Awards - Nominated
Teaching Excellence Awards - Shortlisted "Best in Faculty"
Teaching Excellence Awards - Shortlisted "Best in Faculty"
Teaching Excellence Awards (2014) -- Shortlisted "Best Overall Supportive Teacher"
“Best Environmental Science Paper of 2009”, Runner-up; Environmental Science and Technology 

more prizes and awards


Work Experience

Additional Qualifications:

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


Rapid selection of antimicrobial resistant bacteria in complex water systems by chlorine and pipe materials
Khan Sadia, Beattie Tara K, Knapp Charles W
Environmental Chemistry Letters (2019)
Greco-Roman mineral (litho)therapeutics and their relationship to their microbiome : the case of the red pigment miltos
Photos-Jones E, Knapp CW, Venieri D, Christidis GE, Elgy C, Valsami-Jones E, Gounaki I, Andriopoulou NC
Journal of Archaeological Science: Reports Vol 22, pp. 179-192 (2018)
Can the legacy of industrial pollution influence antimicrobial resistance in estuarine sediments?
Rodgers Kiri, McLellan Ian, Peshkur Tatyana, Williams Roderick, Tonner Rebecca, Hursthouse Andrew S, Knapp Charles W, Henriquez Fiona L
Environmental Chemistry Letters (2018)
Deciphering resistome and virulome diversity in a porcine slaughterhouse and pork products through its production chain
Campos Calero Guillermo, Benomar Nabil, Pérez Montoro Beatriz, Knapp Charles W, Gálvez Antonio, Abriouel Hikmate, Gómez Natacha Cabellero
Frontiers in Microbiology, pp. 1-13 (2018)
Inputs, source apportionment, and transboundary transport of pesticides and other polar organic contaminants along the lower Red River, Manitoba, Canada
Challis Jonathan K, Cuscito Leah D, Joudan Shira, Luong Kim H, Knapp Charles W, Hanson Mark L, Wong Charles S
Science of the Total Environment Vol 635, pp. 803-816 (2018)
Proteomic analysis of Lactobacillus pentosus for the identification of potential markers of adhesion and other probiotic features
Pérez Montoro Beatriz, Benomar Nabil, Gomez Natacha Cabellero, Ennahar Said, Horvatovich Peter, Knapp Charles, Alonso Esther, Gálvez Antonio, Abriouel Hikmate
Food Research International Vol 111, pp. 58-66 (2018)

more publications


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)

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.

Professional activities

Antimicrobial resistance: what does the environment have to say
Aligarh Muslim University
Visiting researcher
Environmental Geotechnics (Journal)
Editorial board member
NERC Standard Grant Panel (Event)
Gdańsk University of Technology
Visiting lecturer
Society for Applied Microbiology Annual Conference

more professional activities


Monitoring of PAHs and heavy metals in sediments industrial estuaries
Knapp, Charles (Principal Investigator)
01-Jan-2018 - 31-Jan-2020
EPSRC Centre for Doctoral Training in Wind & Marine Energy Systems | Hall, Rebecca
João, Elsa (Principal Investigator) Knapp, Charles (Co-investigator) Hall, Rebecca (Research Co-investigator)
01-Jan-2017 - 01-Jan-2021
Doctoral Training Partnership (DTP 2016-2017 University of Strathclyde) | Tonner, Rebecca
Knapp, Charles (Principal Investigator) Phoenix, Vernon (Co-investigator) Tonner, Rebecca (Research Co-investigator)
01-Jan-2017 - 01-Jan-2020
Robust Decentralised Low Energy Faecal Sludge Dewatering leading to Sanitation, Clean Water and Sustainable Energy Resource - Natural Synergies
Lord, Richard (Principal Investigator) João, Elsa (Co-investigator) Knapp, Charles (Co-investigator)
"The project concerns dewatering/treatment of faecal sludge (black waters). Natural Synergies Ltd's (NS) aims are to develop a stand-alone dewatering process for rural areas of the UK/EU, reducing transport costs and carbon footprint and in developing countries as a low cost decentralised/localised sanitation system. The developed system can be also be used as a pre/post-cursor to a small scale anaerobic digestion (a follow-on proposal) or thermal unit, leading to closed loop decentralised, localised sanitation and off-grid energy generation. The dewatering process being developed will incorporate ultrasound to make available free, interstitial and cell water, together with electrokinetics to drive/separate water from faecal sludge via filter mesh. Preliminary work has shown potential for high levels of dewatering (15 - 40 % DM) and pathogen reduction (incl. helminths) at low energy inputs. System design will aim at non-specialised component manufacture, where possible, using local industries.

Our vision is to develop an entire new system of treating pit latrine wastes in developing countries, which not only generates renewable energy, but also a safe, useable fertilizer. In theory, this could be achieved now using conventional process technology. What is lacking, however, is a small scale robust system at relatively lower cost that can be operated with ease in remote areas. Our research contribution to delivering this is focussing on two specific challenges: Firstly, how to destroy human parasitic worms or their eggs, so as to allow safe reuse of the solidified material for agricultural fertilizer; Secondly, can we use locally available plant material to simultaneously increase the amount of energy, as biogas, which can be produced. The systems that Natural Synergies Ltd have been developing are highly effective but also highly innovative. We need to be sure of the overall environmental performance and social benefits of any new system, as well as its cost effectiveness. If successful this technology could also offer significant cost-savings and environmental benefits in developed countries at small-scale wastewater treatment plants in remote locations (e.g. Scottish Highlands), reducing road-tanker traffic, transport fuels and carbon emissions."
01-Jan-2017 - 31-Jan-2018
Genes of past, present and future: does legacy pollution contribute to antibiotic resistance in industrialised estuaries?
Knapp, Charles (Principal Investigator)
01-Jan-2016 - 31-Jan-2018
Quantifying Spatial AMR Patterns across Urban and Rural Landscapes
Knapp, Charles (Principal Investigator)
"Antimicrobial resistance is increasing in nature and threatens the effectiveness of our drug therapies and infection control. However, it remains difficult to distinguish what originates from human activities or what is natural. Therefore, we must extend the scale and depth monitoring efforts to better understand what is driving the increases in resistance traits.

This project will use two collections of previously characterised soils to compare and contrast distributions of AR genes under widely varying conditions, ranging from urban, agriculture, legacy mining, and pristine rural environments. The project will utilise DNA extractions and new genetic technology to quantify over 230 AR genes in the samples. Soil inventories provide us well-characterised soils and the wealth of information that describes both the soils and the impacts at source locations.

The project will generate an astonishing 120,000 AR-related data points (400 locations x 300 genes), each with extended background information on environmental conditions-creating among the largest geographic representation of AR gene distribution across landscapes ever created; sufficiently detailed to make cross-cutting observations of landscape effects on acquired vs innate AR levels. With advanced multi-parametric statistics, we will relate specific environmental conditions and factors with observed AR genes levels in soils to identify risk factors associated resistance development and impacts on human and agricultural health."
01-Jan-2016 - 31-Jan-2018

more projects


Civil and Environmental Engineering
James Weir Building

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