Seminar day: Single cell technologies for microbial community characterization

Post date: Tuesday, 18 September, 2018 - 17:16

We will  be organizing a special seminar on single-cell technologies for microbial community characterization. Specifically we will focus on the applications of flow cytometry and Raman Spectroscopy with a selected panel of 6 national and international speakers from industry and academia.


  • Prof. Susann Müller / Helmholtz Centre for Environmental Research (UFZ) – Leizpig (DE)

Can microbial communities be controlled in managed systems?

  • Prof. Hyun-Dong Chang / Deutsches Rheuma-Forschungszentrum (DRFZ) – Berlin (DE)

Flow Cytometry and Cell Sorting of a Defined Intestinal Microbiota

  • Prof. Wei Huang / Synthetic biology & single-cell biotechnology, University of Oxford (UK)

Raman activated cell sorting and metagenomics sequencing reveals carbon-fixing bacteria in the ocean.

  • Dr. Michael Besmer (CEO) / OnCyt microbiology AG, Zürich (CH)

On-line/Real-time Flow Cytometry for Microbial Monitoring

  • Dr. Björn Biederman / rqmicro AG, Schlieren (CH)

Rapid & reliable detection of pathogens

  • Prof. Frank Delvigne / Université de Liège (BE)

Phenotypic heterogeneity in bioprocess monitoring

  • Q&A session: Practical flow cytometry

Set-up and design considerations for routine flow cytometric monitoring of microbial populations

Event location: Campus Dunant, building 24.01 – Dunant 2, Ghent University, 9000 Ghent
Event date: Tuesday, 16 October, 2018 - 09:00 to 17:00

Microbial population and community dynamics in natural and managed freshwater systems: from methodology development to mechanistic insights

Post date: Tuesday, 18 September, 2018 - 17:04

Abstract of the doctoral research:

Freshwater ecosystems are hotspots of biodiversity, biogeochemical processes, and provide numerous societal services (e.g., drinking water production, wastewater treatment). The microbial communities that inhabit these systems form complex networks of interacting populations, for which the structure and function are not yet fully understood. This PhD research presents new insights into the microbial community ecology of both natural (i.e., lakes) and managed (i.e., cooling and drinking water) freshwater systems by developing and validating new technologies to study them and by investigating the genomic adaptations to their freshwater habitat.

A novel flow cytometric fingerprinting method for measuring microbial diversity was developed that correlated strongly with the benchmark marker gene sequencing approach typically used in diversity surveys. This new approach was applied in the monitoring of cooling water systems, the detection of microbial disturbances in drinking water, and the tracking of lake microbial diversity during exposure to invasive species. In parallel, the genomic adaptations of the prevalent microbial populations which shape the diversity in these managed and natural freshwater communities were investigated. We found that positive selection on nutrient scavenging genes and morphological plasticity may be adaptations to phosphate-limited environments commonly found in managed systems. In natural freshwater systems, our results indicated that small genetic or expression differences between populations can facilitate adaptation to steep temperature gradients, while larger genetic and expression differences underpin adaptation to nutrient gradients.

Dissertation Supervisors:

Prof. Dr. Ir. Nico Boon, Prof. Dr. Ir. Vincent Denef & Dr. Ir. Pieter Monsieurs

Event location: Conference Center "Het Pand", Onderbergen 1, Gent
Event date: Monday, 15 October, 2018 - 17:00

Cold anammox for energy-positive sewage treatment: impact of temperature and organic carbon on performance and microbiota.

Post date: Tuesday, 15 May, 2018 - 17:08

Abstract of the doctoral research:

The development of mainstream partial nitritation/anammox (PN/A) processes is a crucial step towards reaching a more sustainable, energy neutral or even energy positive wastewater treatment. However, mainstream conditions e.g. low temperatures and ammonium concentrations as well as the presence of residual organic carbon can impact the kinetics in the system and disturb the balance between different (desired/undesired) bacterial groups implicated in the process, rendering it unstable and inefficient. This PhD focused on the short and long-term impact of low temperature on the performance, enrichment and adaptation of anammox bacteria (AnAOB), as well as their ability to compete with heterotrophic bacteria (HB) in the presence of organic carbon.
Short-term activity tests on different biomass types allowed to obtain more accurate modelling parameters and provided insights on factors influencing the temperature sensitivity. The operation of two lab-scale reactors, at constant (30°C) and decreasing temperature (down to 10°C), showed the long-term impact of temperature on anammox performance, microbial community dynamics and granulation. Very high removal rates were observed at 10°C due to enrichment and adaptation. Finally, the reactor influent was modified to gain new insights on the impact of slowly biodegradable organic carbon on the competition between AnAOB and HB at 30°C and 10°C. The findings from this research project show the potential of ‘cold anammox’ and provided insights that can contribute to the development of a suitable microbial resource management strategy for the implementation of mainstream PN/A applications.

More information click here

Dissertation Supervisors:

Prof. Dr. Ir. Siegfried Vlaeminck & Prof. dr. ir. Mathieu Sperandio

Event location: Coupure Links 653, Gent
Event date: Friday, 25 May, 2018 - 15:00

Kraks@dekrook: Unlimited Energy use due to New Technologies?

Post date: Thursday, 5 April, 2018 - 13:09

Dr Marjolein Vanoppen from PaInT will discuss the topic of "Energy Generation: the Power of Mixing Salt and Fresh Water" during a seminar series in the public library of Ghent entitled Kraks@DeKrook. More info and registration can be found here.

Event location: Public Library De Krook, Gent
Event date: Tuesday, 24 April, 2018 - 19:00

Combination of ion exchange and coagulation for removal of natural organic matter

Post date: Monday, 12 March, 2018 - 14:40

Dr. Klaas Schoutteten of the research group on Particle and Interfacial Technology (PaInT) explains his postdoctoral research on the use of ion exchange and coagulation for removal of natural organic matter in drinking water production processes. This research is conducted in the framework of an Interreg-2-Seas funded project DOC2C's.The video is available here.

Recently Defended PhD theses

Post date: Sunday, 11 March, 2018 - 16:30
  • Single-cell optical fingerprinting for microbial community characterization [download] (Benjamin Buysschaert, promoter Nico Boon, Bart De Gusseme)
  • Towards innovative technologies for nutrient recovery from human urine [download] (Sebastiaan Derese, promoter Arne Verliefde)
  • Surrogate-based online monitoring and control framework for trace organic contaminant removal during ozonation of secondary wastewater effluent: from lab-scale to practical application [download] (Michael Chys, promoter Stijn Van Hulle, Kristof Demeestere, Ingmar Nopens)
  • Impact of speciation on the removal and recovery of trace elements from aqueous streams, [download] (Karel Folens, promoter Gijs Du Laing and Frank Vanhaecke)
  • The interaction of bacteria with volcanic rocks on Earth and in space [download] (Bo Byloos, promoter Nico Boon, Natalie Leys and Rob Van Houdt)
  • Innovative strategies to maximize carbon and energy recovery from domestic wastewater, [download] (Cristina Cagnetta, promoter Korneel Rabaey and Arne Verliefde)
  • Production of lactic acid and derivatives from grass using mixed populations[download] (Way Cern Khor, promoter Korneel Rabaey and Han Vervaeren)
  • Advanced reduction and adsorption for trace organic contaminant removal from water, [download] (Klaas Schoutteten, promoter Arne Verliefde)

Yearly Advisory board and Showcase

Post date: Friday, 9 March, 2018 - 16:03

The yearly Advisory board and Showcase of the R2T consortium was a great succes.

Almost all (except for 2) industrial partners were present to discuss the latest developments within the Consortium both at an organizational and scientific level. This led to nice and critical interactions during the presentations, breaks and dinner, showing that the members really get to know each other.

For the partners that want to revisit the event, all seminars have been recorded and can be accesssed after log-in.

Please find below the program overview:

Welcome and event introduction

R2T: looking back and forward (advisory board; can be accessed after log-in)

  • Intro R2T & CAPTURE-water
  • Short overview per academic staff member
  • Introduction new academics
  • New Company introductions
  • Activities manager 
  • Interaction opportunities
  • Upcoming Events

Showcase presentations on various topics (can be accessed after log-in)

  • Metals
  • Water fit for Use
  • Modelling/ DSS
  • Energy & Organics
  • Waste Water Treatment of the Future
  • N(utrients)

R2T Reception + R2T researchers & Posters

Walking dinner

Event location: Coupure Links 653, Gent
Event date: Thursday, 1 February, 2018 - 13:00

Flux analysis in microbial communities

Post date: Friday, 9 March, 2018 - 15:06

You are kindly invited to the seminar given by Robbert Kleerebezem, assistant professor from TUDelft. Robbert has years of experience in biotechnology and he is going to share his opinion in the molecular techniques that are used in understanding bioprocesses.

“Using basic redox chemistry, thermodynamics, mass balances, simple kinetic expressions, and fundamental transport terms, the essence of the functional behaviour of microbial ecosystems can be captured and analyzed. I try to convey this approach from an engineering perspective and an ecological perspective. Thermodynamic state analysis of microbial ecosystems provides a firm foundation and first generalization of microbial processes and is often overlooked. “

Event location: Auditorium A1.1 formerly known as A1.095, Coupure Links 653, Gent
Event date: Monday, 12 March, 2018 - 16:00

Exopolymers & eDNA

Post date: Friday, 9 March, 2018 - 15:04

While exopolymer function across a range of environmental and clinical biofilms has been studied extensively, there is still much ambiguity regarding which exopolymers are important and how they contribute. Thomas will present a description of how they managed to assign eDNA as most fundamental cross-linking unit and hence foundation structure of the model biofilm producer and pathogen Pseudomonas aeruginosa. By elucidating at a molecular level how eDNA was assembled, they could thus begin to address the question of how DNA transforms from the chromosomal form to that present in the biofilm matrix. While the seminar will focus on P. aeruginosa many of the principles discussed can also be applied to understanding the composition and function of matrices in other biofilms.

By Dr Thomas Seviour

Event location: Coupure Links 653, Gent
Event date: Friday, 23 March, 2018 - 11:00

Introduction to WATEC (water technology) and CBIO (Circular Bioeconomy) Research centres at Aarhus University

Post date: Friday, 9 March, 2018 - 14:48
  • Introduction to the new engineering investment at the Science and Technology faculty at Aarhus University, and establishment of the cross disciplinary centres WATEC (water technology) and CBIO (Circular Bioeconomy). (Lars DM Ottosen)
  • Centre for water technology (WATEC) research and short announcement of open positions. (Niels Peter Revsbech)
  • Ambitions and research for the new sensor technology laboratory under WATEC. (Klaus Koren)
  • Ambitions for waste water technology under WATEC and CBIO. (Lars DM Ottosen)

Lars DM Ottosen is Head of the Biological and Chemical Engineering at Aarhus University. Lars has a mixed industry and academia background. His research area is in environmental biotechnology, i.e. anaerobic digestion and biological waste water treatment.

Niels Peter Revsbech is professor at department of Bioscience, and head of the WATEC centre. Niels Peter is the pioneer of development and application of microsensors in microbial ecology, and co-founder of Unisense A/S.

Klaus Koren is head of the new sensor development laboratory under WATEC, and assistant professor at Bioscience. Klaus Koren has extended experience in optical sensor development and application from positions at Copenhagen University and University Graz, Austria.

Event location: Auditorium A2, Coupure Links 653
Event date: Wednesday, 14 March, 2018 - 09:00


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