Thursday, February 9, 2017

New Position: Charles River Swimming Water Quality Monitoring and Assessment

We are looking for a graduate research assistant to do water quality sampling and analysis at a future swimming site on the Charles River ...STARTING MAY 1, 2017!

Planning efforts are currently under way to open a permanent swimming location on the Charles River. A solid database of water quality observations is needed to support the management of the site. This position is for a Masters student to perform water quality monitoring and assessment. Specific tasks include sample collection and analysis for E. coli and total cyanobacteria cell counts in the laboratory, analysis and interpretation of the results, and summary and communication to stakeholders. Sampling and analysis will need to be performed on a daily basis during the swimming season (Memorial Day to Labor Day), with other times dedicated to data analysis and communication and coursework. This research project is a collaboration of the Charles River Conservancy ( and Northeastern University ( The dates of the position are May 1, 2017 through April 31, 2019. The student is expected to enroll in the Masters program at Northeastern University in the Department of Civil & Environmental Engineering or Marine & Environmental Sciences, advised by Prof. Ferdi Hellweger. The position provides a stipend, benefits and tuition. For more information see the Charles River Conservancy’s swimming site at or contact Ferdi Hellweger at

This is an exciting project. We are looking for a student that is enthusiastic about the idea of swimming in the Charles River and a desire to do research in the urban environmental arena.

Image credit: Charles River Conservancy

Saturday, February 4, 2017

IWA Dipcon 2017 in LA - Abstracts due March 1

We hope you will be able to join us for the 18th IWA International Conference on Diffuse Pollution & Eutrophication held August 13-17, 2017 in Los Angeles. Abstracts are due March 1. Here is the website:

Friday, January 6, 2017


I am pleased to announce the publication of “75 years since Monod: It is time to increase the complexity of our predictive ecosystem models”. This opinion paper contributes to the debate about the level of complexity in ecological modeling. I have been developing relatively complex models for some time now and often the complexity is the subject of criticism (as part of the Q&A part of talks and seminars and the journal and proposal peer review process). Over time I have come to develop counterarguments and I am now at a point where I feel it would be useful to share these with a larger audience. This paper is my attempt to deliver a broadside salvo at the critics of complex ecological models.

A bit of a personal perspective: With this paper I am questioning some of the long-standing principles of ecological modeling, i.e. that models should be as simple as possible. Writing this paper made me think of the movie “Jerry McGuire”, where he writes an assay “The Things we Think but Do Not Say” criticising how things are done in his business. He ends up getting fired…

Paper link:

Saturday, December 17, 2016

Saturday, December 3, 2016

Ocean currents and temperature selection

I am pleased to announce our latest paper on agent-based modeling of ocean microbes. Microbe biogeography studies typically assume that the microbes are affected only by local conditions. However, in areas with substantial advection (e.g. ocean currents), upstream conditions may play a stronger role in shaping the local community. Here we explore this effect for temperature selection in surface ocean microbes. We develop a novel agent-based model and perform simulations to quantify the effect of advection at the global scale. Our results show that advection by currents can change the effective selection temperature of microbes by several degrees Celsius, and therefore should be considered in microbe biogeography studies. We then apply our results to three global datasets and for all we can better explain observations when currents are considered. We make our results accessible to the broader community by providing an atlas of temperature corrections.

I think this is an interesting study with some important conclusions. In terms of my research program, this model also represents a stepping stone for a more complex global microbe agent-based model. Specifically, we are now working on integrating a gene-level model of Synechococcus I developed previously (see link below) into this model. We will then make predictions of gene, transcript and protein levels at the global scale. Pretty exciting!





Tuesday, August 23, 2016

ISME Conference Report

I am in Montreal at ISME16 (16th International Symposium on Microbial Ecology). Yesterday I presented a poster on our Anabaena - nitrogen interaction model. This is a very exciting meeting with many presentations that are very close to my research area. I listened to talks about the role of uncultured bacteria that live in symbiosis with eukaryotes and fix N in the ocean and “cable bacteria" that move electrons over distances of centimeters in sediments. There are so many interesting ecological problems where our modeling approach can make a contribution. The list of “future projects” continues to grow...

Wednesday, August 17, 2016

Special Issue in Frontiers in Microbiology

In collaboration with Frontiers in Microbiology, section Systems Microbiology, we are organizing a Research Topic titled "The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling", hosted by Weiwen Zhang, Johan Leveau, Clara Prats, Jan-Ulrich Kreft, Ferdi L Hellweger. We would like to encourage you to contribute to this topic. Please find more information at the homepage we have created on the Frontiers website, which defines the focus of the topic, and where all published articles will appear.

Please note the submission deadline for this Research Topic: Apr 30, 2017