Friday, August 4, 2017

Congratulations and thanks to YSPs Olivia and Isabel

Congratulations and thanks to Olivia Hanna and Isabel Koran on a nice summer project investigating the water quality at the future Charles River swimming site. Olivia and Isabel are high school students that joined our research group this summer through Northeastern’s Young Scholars Program (see link below). They were supervised and worked closely with PhD student Max Rome. Olivia and Isabel went out and measured E. coli and cyanobacteria at a number of sites and found some very interesting spatial and temporal patterns, like hotspots of E. coli at certain locations. Here is a picture I took during their final presentation.

Wednesday, July 19, 2017

Congratulations to Scott & Ryan for a successful defense

Scott Simpson and Ryan Shae successfully defended their MS theses as part of the Gordon Engineering Leadership program. Scott’s thesis -Modeling and Analysis of Forecast-Integrated Stormwater Discharge Control Systems - focused on developing automated control of stormwater infrastructure based on weather forecasts. The idea is that retention ponds release their stored water ahead of a storm to increase the storage volume and decrease runoff and damage to downstream infrastructure. Ryan’s project - Eliminating Unaccounted for Water in the Dedham-Westwood Water District - dealt with combating water loss in distribution systems. By isolating parts of a system and combining various sources of data, Ryan was able to get a better estimate of the losses and their likely cause.
Image from Scott Simpson thesis.

Saturday, July 8, 2017

CBAD: Community Biological Ammonium Demand

I am pleased to announce our recent publication in ES&T under the leadership of Wayne Gardner from the University of Texas. In this paper we present the concept of CBAD (community biological ammonium demand) to help understand CyanoHAB ecology. (C)BAD is similar to BOD (biochemical oxygen demand), a well-known and proven concept in environmental engineering and we hope BAD will be useful for advancing understanding and managing lakes plagued by CyanoHABs.

Monday, June 5, 2017

ASM Microbe 17 Conference Report

I am at ASM in New Orleans. Today, I will make a presentation about our work on individual-based, genome-scale modeling of microbe ecology and evolution. I also attended several very interesting presentations. Obviously there is a lot of focus on the human microbiome and the effect on health and disease. On Friday I attended a very interesting presentation by Eran Segal of the Weizmann Institute. His work showed that a lot of the differences in how people respond to nutrients is due to differences in the gut flora. So we are all different, but not because of our genes, but because of our microbiomes. This is why a general approach to nutrition (“cholesterol is bad”) doesnt work. He was able to make predictions about what constitutes a healthy diet for each individual. Fascinating! I always try to relate this surface water quality. Maybe the reason why our lakes often behave in unexpected ways is because of our general management approach (“phosphorus is bad”). Should we be thinking about “personalized diets” for each lake?!/4358/presentation/1452

Friday, May 19, 2017

Upcoming Talk: ASM Microbe 17 in New Orleans

If you are going to be in New Orleans for ASM Microbe 17, I hope to see you at my presentation:

"Individual-Based, Genome-Scale Modeling of Microbe Ecology & Evolution"

June 5, 2017, 11:00 - 11:30 AM
Room 346
Session 474 - Ecology of the Individual Microbe!/4358/presentation/1452

Wednesday, March 29, 2017

Thursday, March 16, 2017

Neutral Biogeography of Lake Systems

I am pleased to announce the publication of Sahar Shirani’s paper “Neutral evolution and dispersal limitation produce biogeographic patterns in Microcystis aeruginosa populations of lake systems” in Microbial Ecology

Compared to higher organisms, microbes have large population sizes and high dispersal rates. Consequently, their populations are often assumed to be well connected in space, and any spatial patterns are attributed to environmental differences. In this paper, we explore the role of dispersal limitation and neutral evolution in the biogeography of cyanobacteria in lake systems using an agent-based model (ABM) that simulates individual cells, including their transport, growth, death and mutation. Biogeographic patterns, quantified as nucleotide divergence and computed from the genomes of the model cells, can be substantial in some cases. These results contradict the common notion of no dispersal limitation for microbes, provide a benchmark for future biogeography studies and have implications for how lakes may respond to change.

In this project, we used a novel modeling methodology. We simulate 20k individual cells, each with a full Microcystis genome, for up to 20k years. Then we analyze the evolved genomes from the model using BLAST and MAFFT/Bio-Phylo. Application of these bioinformatics tools to models is new and opens new concepts, like a dynamic phylogeny tree (see movie below) and this synergy with observations highlights the realism of the model

Some interesting future applications of this model may include applying it to the human microbiome (see this paper or bacterial dispersal by ship balast water (see this paper The code is available at the link below and I am available to help and/or collaborate.

Image source: NASA WorldView




Enough about simple!

One of the goals of my research program is to bring modern biology into the models we use to manage our waterbodies. When learning about the science in a certain area I am always impressed by how much we know about certain topics. On the other hand I feel that there is an obsession with finding simple solutions to complex systems, which limits the utility of biological research. In this blog post at “On Biology” I argue that biologists should be more like modern car mechanics and delegate understanding (not just number crunching) to computers.

Regular visitors to this blog may realize I am a bit on a crusade here. I have been writing papers criticising our community (of ecosystem modelers) with titles “100 Years since Streeter and Phelps: It Is Time To Update the Biology in Our Water Quality Models” and “75 years since Monod: it is time to increase the complexity of our predictive ecosystem models” and now “Biology 2.0: It is time to delegate understanding to computers”. And I am writing another one as we speak. I guess it is a phase I am going through...


SASM HOMEPAGE (hasn’t been updated for a while)

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: