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Microbial Resource Management and Engineering in the Urban Water Cycle

Final Report Summary - MERMAID (Microbial Resource Management and Engineering in the Urban Water Cycle)

Mermaid is a European network formed to train promising young researchers to describe and control the microbial communities that are central to the treatment of residual water and the production and distribution of drinking water. The ambition is to strongly establish the emergent discipline of Microbial Resource Management & Engineering, which we define as managing and engineering open microbial communities to attain specific services for the benefit of society and the environment.

Motivation & Goals
Water is at the foundation of our lives, which tend to be more and more urbanized. As water resources are limited, water needs to be purified and redistributed after use to close the urban water cycle. Microbial communities have a central role in closing the urban cycle in a safe and sustainable way. Microbes can either be valuable actors, for example by removing pollutants in an energy efficient manner, or be a nuisance, as is the case if pathogenic bacteria establish themselves in water distribution systems. Managing microbial resources in the urban water cycle is thus crucial, yet presents major challenges as we lack some of the conceptual foundations and practical tools to understand and control the massively diverse microbial communities present in these open systems. These challenges can only be met by a trans-disciplinary research effort complemented by a training program designed to educate promising young researchers to solve current and upcoming problems in the urban water cycle using innovative technologies based on microbial communities.

MERMAID aims to:
• Prepare young researchers to solve tomorrow’s technical and environmental challenges in the water sector using Microbial Resource Management;
• Pose and answer central questions on the behavior, activity, and composition of open microbial communities, to solve specific and broader problems in science and industry;
• Support the development of novel, science-based, water engineering biotechnologies;
• Reach out to the general audience to share the scientific basis and discoveries at the core of Mermaid.

Work performed and achievements
The first achievement of the Network was to assemble a team of talented young researcher. We recruited 13 PhD students and one postdoctoral researcher with diverse expertise and origin (11 nationalities represented) and were able to instill a true collaborative spirit in this group. The Network organized six training events (typically one week long) specifically tailored to equip the Mermaid fellows with scientific and technical skills (e.g. high throughput methods to describe microbial communities, modelling of biosystems) and complementary skills (conducting PhD studies, grantsmanship). These events were highly successful and also contributed to strengthening the collaboration across the project partners.
The individual projects conducted by the fellows and organized in five complementary workpackages have been initiated, refined, and have provided important findings upon conclusion. Significant scientific milestones attained include:
o The identification and physiological and biokinetic characterization of a bacterium that degrades the persistent antibiotic sulfamethoxazole more efficiently than communities typically present in wastewater treatment plants.
o The description of the considerable abundance of antibiotic resistant bacteria and antibiotic resistance genes across the urban water system and the demonstration of the role of integrons in the mobility of these genes.
o The clarification of the ecological processes and controlling factors that govern invasion in microbial communities, highlighting the role of invader density for invasion success.
o The demonstration that community evenness decreases invasiveness and that coliform bacteria can invade in a system treating shower water designed for usage in space stations.
o The development of a novel concept to utilize ammonia from waste water to produce valuable microbial protein by growing hydrogen oxidizing bacteria, and the description and genomic characterization of an efficient strain selected during operation.
o The demonstration that most pharmaceuticals in wastewater are removed more efficiently by thicker nitrifying biofilms, that support more diverse microbial communities.
o The identification of stochastic processes as key contributors to the assembly of microbes on filters treating surface water for potable water production and the quantification of the effect of filter material on the filtration efficiency of various potential pathogenic groups.
o The discovery and genomic analysis of novel bacteria that completely oxidize ammonia to nitrate in biofilters treating groundwater for potable water production and the description of their major functional role in these systems.
o The description of the positive association of microbial community diversity in wastewater treatment plants with most of their biokinetic parameters but also with the abundance and expression of genes associated with antimicrobial resistance genes.
o The identification of optimal operational conditions for concurrent bioplastic production and ammonium removal from residual waters while maintaining aeration cost low.
o The development of novel amplicon sequencing approaches to describe nitrifying communities and the identification of the mechanisms behind performance improvement in biofilters for drinking water production induced by Copper supplementation.
o The identification and quantification of ammonia oxidizing bacteria that are performant under low oxygen concentration and have an unusually high biomass yield.
o The description of microbial colonization of pipes as affected by pipe material and the quantification of the potential for cell detachment from these biofilms, both of which affect water quality.
o The development and validation of a bioinformatics tool to infer microbial guild composition from metagenome sequencing data.

The network has put high emphasis on disseminating its research results and sharing its field of research. All fellows participated to scientific conferences, in many cases as oral presenter. ‘Mermaid’ articles have been published in the best journals of the field. The fellows have engaged in outreach activities towards school children, high school students, senior citizen, directly sharing the excitement of environmental biotechnology with more than 250 persons in five countries. Digital communication was also used, with an official website ( a twitter account (@MermaidITN) and a blog ( both run by the fellows.

We are confident that the Network’s efforts will have a significant and lasting impact on the fellows’ career; on the technological developments in the way our wastewaters and drinking waters are treated, produced, and managed; and on the public’s awareness of the role of microbial services in the urban water cycle.

Prof. Barth F. Smets; DTU Environment
+45 45 25 22 30