Wednesday, December 18, 2013

Living the dream: Desperately Seeking Agent 5503216

Our latest project involves modeling individual microbes, each with a full genome, in the global ocean over 10k+ years. This is a really exciting problem and I wake up every day thinking about it. We are currently in the model development phase and are struggling with keeping track of the microbes in the model. Microbe 5503216 shows up in the population at time 317.34 years, but not at time 318.35, yet it doesn't register as dying in between these two times. Where did it go? In my experience, and those of my students, this is common problem and there is no alternative, but to hunt the cell down. So thats what I am working on these days. Its the same thing I did many years ago when I developed my first agent-based model of phytoplankton. So my life hasn't changed a bit... I love it!

Friday, November 22, 2013

Muddy River Restoration Project Visit

Last week our Hydro class visited the Muddy River Restoration Project construction site. This project includes “daylighting” of a previously buried section of the river. These types of projects are happening across the country and they highlight a change in our attitude towards urban water systems. In the old days, we polluted rivers and hid them under the ground. Now we protect, cherish and enjoy them as part of our urban environment. This visit was very interesting to me because, this project has been the subject of a previous Senior Design Capstone class (which helped inform some of the design) and also research (see link to paper below). Here is a picture of Mike Andryuk, a former student and now an engineer with the US Army Corps of Engineers, telling us about the site.

Wednesday, November 6, 2013

Vision: Microbial Individual-Based Ecology (µIBE)

I am pleased to announce the publication of our opinion article in PNAS. This paper represents a milestone in our continuing crusade to change modeling of microbial ecology. You know, we used to (and often still do) model microbes as if they are chemical molecules. This approach does not allow us to account for their heterogeneity and it limits how much complexity we can include. Also, and this is the main point of this specific paper, it prohibits us from using any of the individual-based observations (IBOs) generated using novel single-cell observational and experimental techniques. Microbial ecologists are drowning in a flood of IBOs and, just as with systems biology years ago, new analysis tools are needed. Individual-based models (IBMs) to the rescue! This paper lays out our vision for combining IBMs and IBOs, which leads to microbial individual-based ecology (µIBE). Here are links to the paper and a couple of news coverages:

Wednesday, October 9, 2013

Prof. Vanni Bucci Seminar

My former PhD student Vanni Bucci, now Assistant Professor in Biology at U. Mass. Dartmouth, will be back on campus to give a seminar about his research. The talk will be October 10th - 6:15-7:30pm - 346 Curry Student Center. This event is organized by the NU NEWEA (New England Water Environment Association) student group. PIZZA WILL BE SERVED!! Title and abstract are below.

Ecological modeling from metagenomics: predicting multi-species microbial dynamics relevant to Clostridium di fficile infection

The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. In this talk I will present recent work to infer microbiota ecology directly from time-resolved metagenomics and predict its temporal dynamics. Data from recent experiments on antibiotic-mediated Clostridium diffi cile infection are analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Numerical simulations and linear stability analysis confirm that the microbiota is multistable and that antibiotic perturbations and C. di fficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, we identify a subnetwork of bacterial groups implicated in protection against C. diffi cile, which is common to mice as well as hospitalized cancer patients.

Thursday, September 19, 2013

UMass Dartmouth SMAST Visit

Last week Neil Fredrick and I visited the School of Marine Science and Technology (SMAST) at U. Mass. Dartmouth. I gave a seminar and we had some very good discussions about science and research with SMAST faculty. One thing we were very excited about was meeting Dr. Changsheng Chen, who is the developer of the FVCOM model, which we are using for our Lake Taihu project. Dr. Chen gave us some useful advice on our model and also showed us his  Northeast Coastal Ocean Forecast System (NECOFS). I spent a couple of hours playing with this system today. For someone interested in surface water quality, its really interesting technology. I made the plot below, which shows the currents at 8am today, outgoing tide. A while back, Boston discharged its wastewater at Moon Island (red circle). Then, they constructed two treatment plants, at Nut Island (green circle) and Deer Island (yellow circle). Seems like a good (or better) choice considering the currents. Now Boston has just one treatment plant at Deer Island, but the outfall is 9 miles offshore. Here is the link to the system:

Monday, September 2, 2013

New paper: Mechanisms of Heterogeneity in Phytoplankton

I am pleased to announce the publication of our paper “Use of Agent-Based Modeling To Explore the Mechanisms of Intracellular Phosphorus Heterogeneity in Cultured Phytoplankton“ by Neil Fredrick et al. in Applied & Environmental Microbiology. I want to use this post to highlight an important point that has real consequences for our biogeochemical models. This paper is related to a previous one where we looked at the nutrient content heterogeneity in a field population. One of the main conclusions from that research was that microscale patchiness leads to large heterogeneity. This process is related to zooplankton excretion and thus does not operate in laboratory experiments. This means the heterogeneity in laboratory experiments is much lower than in the field, and that, considering the effect of heterogeneity, means that parameters estimated from the lab are not applicable to the field. Specifically, the maximum growth rate in the Droop quota model should be reduced by a factor of about 0.7. Here is a side-by-side comparison of the laboratory and field results:
Here are links to the “lab” and “field” papers.
And if you want to try the model, here it is:

Tuesday, August 20, 2013

Lake Taihu Field Report

Earlier this month, PhD student Neil Fredrick and I were in China for a meeting on our Lake Taihu project. The picture below is me standing on the dock at the Taihu Laboratory for Lake Ecosystem Research (TLLER) during a bloom. Despite the rather challenging conditions (107dF & high humidity), the trip was enjoyable and very productive. Specifically, we connected with a hydrodynamic modeler (Li Wei) and started combining her hydrodynamic model with Neil’s N cycle model. This will allow us to predict spatial patterns in the N cycle processes.

Saturday, August 17, 2013

Summer Research Wraps Up

This year, our summer research focused on understanding the role of N fixation on the N cycle and export of N from lakes. The team was led by PhD student Xiaodan Ruan and included PhD student Frank Schellenger, RET Bruce Brender and YSPs Garlyn Colas and Janice Tso. Janice and Garlyn made a very nice oral presentation at the wrap-up meeting on August 2. Here is a picture of the team.

Thursday, August 1, 2013

Antibiotic Resistance Modeling Lecture NOW AVAILABLE

I published a lecture video entitled “Modeling antibiotic resistance in the ambient aquatic environment”. This 1-hour lecture is suitable as an advanced topic in graduate-level surface water quality modeling courses. The lecture provides an introduction to antibiotics, antibiotic resistance (AR) and AR in the ambient environment. It presents a mathematical model (MAQUIS) and application to tetracyclines in the Poudre River, as well as a hands-on tutorial and homework assignment. If you are teaching surface water quality modeling, you may find this lecture to be a valuable addition to your course. Please contact me if you have any questions or comments. Here is the link to the lecture:

Wednesday, July 24, 2013

FEMS Conference Report

I am at the Congress of European Microbiologists (FEMS 2013) in Leipzig I helped organize a session on modeling, and presented a poster on intraspecific internal nutrient heterogeneity and a talk on bet hedging in yeast. This is a very interesting meeting and I am learning a lot about microbiology. Let me tell you about one thing that stands out to me. You know, there is now a lot of realization on the role of the gut bacteria (microbiome) on human health. A couple of people presented research linking (pretty conclusively in my mind) the biodiversity in the gut to obesity and infection risk. Those are important and interesting problems, but I am not a medical person so my interests are more in the tools they are using. In one experiment they took germ-free mice and inoculated them with various bacteria. Wow! I wish we could do this with our environmental systems. I mean, can I have a few sterile Charles Rivers that I can inoculate with different bacteria? Please? Of course, we can make lab experiments, but those don’t include any of the complexities of the real system. Whole lake experiments can be and are done (e.g. at the Experimental Lake Area in Canada), but there we are limited to simple perturbations – we don’t have direct control of the microbe population. I think because of these types of experimental capabilities (and also availability of funding in the medical area), some of the most exciting advances in microbial ecology in the near future will come from the medical arena. Next stop: Shanghai and Lake Taihu.

Tuesday, July 16, 2013

Victory for the Charles!

This Saturday, the Charles River opened for swimming! For the first time in over 50 years we had public swimming. This event was organized by the Charles River Conservancy, who also led the effort to bring swimming back to the river over the past years. My research group has helped out by doing some water quality monitoring at potential (ahem actual!) swimming sites. Of course I had to participate. And you know what? It was wonderfully refreshing! And surprisingly so! I didn’t even realize and I wonder if all those people on the Esplanade realize that there is a cool and refreshing (and swimmable) river just a few feet from where we sweat in the sun. The plan is to do more of this, and I think this would significantly improve the quality of life in Boston!

See the article on the NU news blog here:

Read the article in the Boston Globe here:

Visit the swimming page at the Charles River Conservancy here:

Tuesday, July 9, 2013

Microbe Ecology and Water Engineering (MEWE) Workshop Report

I am at DTW on my way back from MEWE in Ann Arbor, which was a very interesting meeting. There are many areas where people study microbial ecology, including the ocean and the human gut, but also wastewater treatment plants (the “gut of the city”, Tong Zhang). It is interesting to see so many of the same problems (e.g. diversity) and tools (e.g. metagenomics) applied to these different environments. I participated in a session on antibiotic resistance and presented some of my modeling work on the Poudre River (see my post of June 16, 2013) and adaptation to the cost of resistance (see post of November 15, 2012). In this session, there were many very interesting data sets presented from treatment plants and ambient (“receiving”) water systems. Unfortunately they were all from different locations, which limits their utility for modeling. When I was developing my model I was able to take advantage of the large and comprehensive database developed for the Poudre River, and I think we need more of these concerted efforts - testbeds. It brings to mind a recent effort of the environmental engineering community to establish a network of testbed systems across the US (known initially as CLEANER, then WATERS). This effort did not succeed, maybe because it was too big, but it would have been really useful for developing models. Maybe a smaller-scale effort, focused on pharmaceuticals and personal care products (PPCPs) and antibiotic resistance, in one watershed could happen, and it should be pursued! Next stop: FEMS in Leipzig.

Friday, July 5, 2013

Edinburgh Workshop Report

Earlier this week I was in Edinburgh for a workshop on microbe modeling. The meeting focused on biofilms and included many presentations of experimental and modeling research. My work is not directly focused on biofilms per se, but there are a lot of the same tools/methods/questions/problems, so I found it very useful. I felt like I got a good overview of where the state-of-the-science is in this area. There is an interesting story about the use of modeling in biofilm science, which I want to briefly outline. It has to do with social conflict in biofilms. Specifically, bacteria in biofilms produce a sort of glue (extracellular polymer substance, EPS), which helps to hold the biofilm together. This is believed to be a public good (i.e. it benefits all cells in the biofilm), but the production is carried out by individual cells. This raises the question why individual cells produce this substance. In other words, why do they not evolve to not produce EPS and grow faster, while taking advantage of the EPS produced by other cells (i.e. why do “cheaters” not evolve). A few years ago, Xavier and Foster (PNAS, 2007) explored this question using a model. They found that, EPS is not a public good, but that it helps the cells that produce it to push up into the high oxygen regions. Subsequently, there have been a number of experimental investigations that have explored this hypothesis, and indeed, confirmed it. For more information see the workshop outline below. I think its an interesting story which illustrates the role of models in moving science forward, at a time scale greater than an individual paper or project.

Sunday, June 16, 2013

Antibiotic Resistance in the Aquatic Environment Trilogy & Off to Edinburgh

Hi Everyone:

I am pleased to announce the publication of our latest paper on modeling antibiotic resistance in the ambient aquatic environment. I want to use this post to try to put this paper into a larger context. You see, mathematical models are useful tools for managing and understanding environmental systems, and they have an established track record in environmental engineering and science. Water quality models can be used to relate discharges to ambient conditions, interpret field observations and test hypotheses. The first water quality model focused on the depletion of dissolved oxygen downstream of a wastewater discharge (Streeter-Phelps model).  Since then, models have continuously evolved to address changing societal needs, including pathogens (e.g. E. coli), eutrophication, toxics (e.g. PCBs), heavy metals and harmful algae (e.g. cyanobacteria). Antibiotic resistance in the aquatic environment is an emerging concern, and it makes sense for us to develop mathematical water quality models for this problem as well.

We are currently developing a model for this problem, and this latest paper includes the mechanism of co-selection by metals. Here are some results from the final model. The figure shows the Poudre River study area with WWTP inputs and urban land use.  The stream segments are shaded based on simulated tetracycline antibiotic resistance for the zinc co-selection case (Model H3\Zn, see paper). The data are from Pei et al. 2006.

Here are the links to the three papers, the newest one is listed last:

Next I am off to Edinburgh, Scotland to participate in a modeling workshop.

Guid cheerio the nou! (Good bye in Scots),


Sunday, May 12, 2013

Columbia & CDM Smith visits done, many coming up

Hi Everyone:

Just a brief note today. Last month I was at Columbia U for a seminar visit. It was nice to see some old friends, including my PhD advisor Manu Lall. Earlier this month a group of faculty from Northeastern went over to CDM Smith ( to learn about each others work and explore possibilities for collaborations. Its always good to get a reality check of what the “real” problems are faced by practicing engineers and scientists.

Now (Tuesday) I am off to Turkey, where I will be for a month on a mix of personal and business things. I will give a research seminar at Middle East Technical University [Orta Doğu Teknik Universitesi (ODTÜ) in Turkish], the top technical university in Turkey. After that I have quite a busy summer, including a workshop in Edinburgh, a meeting in Ann Arbor, the FEMS conference in Leipzig, and then to China for project meetings and an IWA conference. Here are some links for these:

Maybe we will meet in one of these places!

Güle Güle ("bye bye" in Turkish)

Sunday, April 14, 2013

Capstone Final Presentations & Columbia Seminar & Freeman Lecture

Hi again,

It’s that time of year again... Capstones! Please join us for the 2013 Environmental Capstone student presentations. This year, the course is focusing on nonpoint source phosphorus inputs to the Charles River - one of the most important contemporary problems in the Boston area (and worldwide). Four Capstone teams have been working with communities (Boston, Brookline, Cambridge and Newton) and professional mentors (from CDM Smith, Kleinfelder, CRWA and MWH) to design site-specific, tailored solutions. Please join us and learn about the solutions they came up with. A flyer with more details is posted here:

On April 26 I will be at Columbia University for a seminar visit. If you are in the area and interested in learning more about my work, please come. Here is the advertisement:

Finally, I would like to invite you to the 2013 Freeman Lecture, which this year focuses on hurricane barrier design (motived by Hurricane Sandy). The details are below.

Best regards,

2013 John R. Freeman Lecture
Hurricane Storm Barrier Design and Operation


Lawrence J. Murphy, P.E.
CDM Smith/New York, NY

Michael Bachand, P.E.

Around the world numerous hurricane or storm surge barriers have been
constructed to protect areas deemed to be critical. With the recent impacts to the
Northeast United States from Hurricane Sandy and to a lesser extent Hurricane Irene
which made landfall a year earlier, concepts for providing flood protection to storm
prone areas have been a national focus. This lecture will present a concept design of
a barrier to protect a portion of Lower Manhattan, as well as provide information on
the operation of two storm barriers that currently exist in the northeast. Various
types of barricades utilized around the world and their effectiveness will also be

DATE: Thursday, April 18th, 2013
TIME: Reception: 6 p.m./ Lecture: 7 p.m.
LOCATION: MIT’s Tang Center (E51)
70 Memorial Drive
Cambridge, MA 02139

Friday, March 15, 2013

DIMENSIONS Project Kick-Off

Hi Everyone:

Earlier this month I was in Morehead City at the UNC Institute of Marine Sciences for the kick-off meeting for our project on cyanobacteria in Lake Taihu (see my September 2012 post). It was a very productive visit. From a modeler’s perspective this project is exciting because it includes a lot of relevant and exciting observations not commonly available (e.g., ammonia regeneration, nifH gene expression, 14/15N isotope tracing, etc.). These will be a challenge to integrate in the model, but that is the fun part. It is also exciting to work on such an important problem, affecting the drinking water of millions of people. Here is a picture (from Paerl et al., 2011):

This project will keep us busy for a while!

Besides that, chairing a faculty search and teaching two classes is keeping me pretty busy this semester...

Best regards,

Saturday, February 16, 2013

Bigelow Visit & ASLO Talk & Charles River Workshop

Hello Friends,

Last week I was at the Bigelow Lab ( for a seminar. My visit was hosted by Ben Twining and Ramunas Stepanauskas. I really enjoyed the visit. One thing that stuck with me is the single cell genomics work Ramunas is doing. It turns out that cells of the same species (judged by 16S rRNA similarity) and from the same drop of water, typically (actually, apparently always) have different DNA. I always thought they would be the same, except for a rare mutation here and there. So are microbes as different as people? Have to do some more thinking about this... but - of course - as an individual-based modeler, I see a lot of opportunity for using IBMs here. “Single cell genomics is to metagenomics what individual-based modeling is to population-level modeling”?

Visit our presentations at ASLO! Neil Fredrick will present a talk entitled “EXPLORING MECHANISMS OF P CONTENT HETEROGENEITY IN CULTURED PHYTOPLANKTON USING AGENT-BASED MODELING” in session GS08A Plankton Ecology - Phytoplankton on Feb. 19. Here is a link:
And John Berges will present “DIVERSE CAUSES OF CELL DEATH IN PHYTOPLANKTON IN SMALL FRESHWATER ECOSYSTEMS” in session SS79 Phytoplankton interactions in aquatic ecosystems. Here is a link:

We had our 3rd Charles River Water Quality Workshop last week, which was attended by 30 people. This is an annual event where we bring together people doing research on the river and share results in an informal setting. The agenda and presentation slides are available online here:

Best regards,

Friday, January 11, 2013

Happy New Year, Water Management on Steroids & Spring Semester Starts & Charles River Workshop

Hello Everyone:

First: Happy New Year!

Second: The news:

As mentioned in last month’s blog, I was in Israel as part of a delegation focusing on water technologies. The trip was very interesting and productive. I found water management in Israel quite fascinating. The country has experienced so many different phases including mostly dry land, water transfer/distribution, conservation, wastewater reuse and now desalination. One problem motivating the use of desalination is the concern over hormones in the wastewater (e.g., reduced sperm count and motility in males). Each of these phases are very strong, and I would characterize it as “water management on steroids”. I also had the opportunity to meet with other researchers at Technion, which may lead to some interesting collaborations. Here is a picture of me and my colleague, Auroop Ganguly at the Hadera Desalination Plant:

The Spring Semester is starting. I am teaching two classes. (1) The environmental section of the senior design capstone class. This year we are focusing on “community-scale solutions for reducing phosphorus inputs to the Charles River”. (2) The surface water quality modeling graduate class.

On behalf of the Charles River Conservancy (CRC) and the Civil & Environmental Engineering Department at Northeastern University (NU), I would like to invite you you to attend the Third Annual Charles River Water Quality Workshop on February 5, 2013 from 8 AM - Noon at NU.  Charles River Water Quality Workshops were held in 2010 and 2011 and, similar to previous years, this workshop will focus on sharing water quality data gathered by a variety of skateholders, including US EPA Region 1, the Massachusetts Department of Public Health, and Charles River Watershed Association, and others during the 2012 season.  Following the presentations, there will be time for a broader group discussion on work and experiences during 2012 and plans for the coming year.  
Below is additional meeting information.  Please RSVP by January 30th (see RSVP info below).
Location: Northeastern University Snell Library Room 90SL
Date and Time: February 5, 2013 | 8 AM - Noon
RSVP: Please RSVP by email to to Be sure to include your name, title/position, organization, and phone number in your email.

Best regards,