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

Wednesday, July 13, 2016

SIAM Conference Report

I am at the SIAM (Society of Industrial and Applied Mathematics) Life Sciences conference here in Boston. This morning I made a presentation about our Anabaena model and listened to many interesting talks about modeling microbes.

Here is a link to the program and abstract:

Monday, June 27, 2016

Gordon Research Conference Report

I am at the Gordon Research Conference on Environmental Sciences - Water in New Hampshire. Today I gave a talk about our research. In some ways this conference marks a 10 year anniversary for me. In 2006 I was here and presented my first poster on agent-based modeling (ABM) of phytoplankton. That was a real milestone, because since then this has been the defining theme of my research. In fact, that poster is still prominently displayed in my office :) 

A main goal of my presentation was to start a discussion about updating the biology in our water quality models. One reason for doing this is to bring models up to the level of modern observations (see figure below). When we first developed water quality models in the 1970s, people were measuring total phosphorus and chlorophyll a, and those were adopted as state variables in our model. Since then, observations have evolved and now observations include DNA, RNA, etc. However, our models have not kept up. This disconnect really limits the utility of our models, and I think it is leading to the extinction of a specialty: water quality modelers. A big problem, because most of our waterbodies are polluted and models are important tools for management and research in this area :(

Here is a link to the program:

Thursday, June 9, 2016

IAGLR Conference Report

I am in beautiful Guelph, Ontario, Canada for IAGLR's 59th annual Conference on Great Lakes Research. I was not planning on coming here, but my graduate student, Sahar Shirani, was not able to get a visa, so here I am. Today I presented Sahar’s research on the role of neutral evolution and dispersal limitation in the biogeography of Microcystis in the Great Lakes. Here are links to our abstract and the conference:

Monday, June 6, 2016

The journey continues: NRM paper is out

I am glad to announce that our latest review/opinion paper on agent-based modeling for microbes, written under the leadership of Jan Kreft, is now out in Nature Reviews Microbiology. This is the latest installment of “ABM for microbes” review papers, a journey that now spans almost a decade from Hellweger (2007) to Hellweger and Bucci (2009) to Kreft et al (2013) and now Hellweger et al (2016). Judging from the Impact Factor of the journals these papers were published in, the importance of this subject is increasingly being recognized (see figure below). If you are still using concepts from chemistry to model biology or ecology - STOP. Join the revolution!

Hellweger et al. (2016)

Kreft et al. (2013)

Hellweger and Bucci (2009)

Hellweger (2007)

Monday, May 16, 2016

Capstone Group Wins NEWEA Design Competition

Congratulations to Alston Potts, Greg Coyle, Andrew Gillen and Meghan Bruckman, and their mentor Annalisa Onnis-Hayden, for winning the New England Water Environment Association (NEWEA) student design competition. Their project “Restoring the cycle: Northeastern University On-site Wastewater Reclamation and Reuse” combined the design, construction and operation of a wastewater treatment pilot plant, as well as a web site – all in one semester! You can read more about these news here:

Thursday, April 28, 2016

Anabaena Paper Published

I am pleased to report that the Anabaena model paper is now published in Environmental Microbiology.

In this paper we present a dynamic, mechanistic, gene level model of Anabaena – nitrogen interaction. This model is unique and constitutes a significant step in the area of microbial ecology, where models are typically based on concepts developed over 50 years ago (i.e., Monod kinetics), do not include modern biology and do not make predictions commensurate with modern observational technologies (e.g., transcript levels). The model development process is also novel in the context of microbial ecology. It builds on a large database of empirical observations, data from 55 papers (269 experiments) were digitized and used for model-data comparison (i.e. a meta-analysis). The model helps to interpret the observations. For example, application to isotope tracing experiments suggests a role for an N storage pool, consistent with recent observations. We use the model to explore an important question about the efficacy of reducing nitrogen to control lake eutrophication. Beyond these results we propose that our approach constitutes a way to summarize observations that has significant advantages over the traditional review paper when the amount of observations is large. We believe this paper makes a significant contribution to the biology and ecology of Anabaena and presents a novel approach that is of interest to researchers in other areas of microbiology and ecology.

I want to use this post to lay out some of the thoughts I have about possible follow-on projects for this model. The overall “master plan” for the Anabaena model is shown in the figure below, and some more details follow. Please contact me, if you are interested in collaborating on any of these projects.

Anabaena Lab: This is done now. To give you some idea of the effort involved: The Anabaena Lab model took much of my time over the course of a year. I think on average about 4h/day.

Anabaena Lab Validation: This is a validation exercise. It would involve taking additional papers that were not used in the model development and comparing the model to those. The present model was developed and compared to experiments from 55 papers. This exercise may include about 10 papers. I already have these papers identified. This would be a good MS thesis project for a student. Along with this paper, I would like to publish the source code and user guide of the model as well.

Anabaena Field: The present model can be applied to a real lake. Since it only includes Anabaena, this lake would have to be dominated by Anabaena. If everything goes smoothly, this could also be a good MS thesis project.

Microcystis Toxin Lab: This would involve taking the present model and adapting it to Microcystis. The basic structure would be the same, except that Microcystis does not fix N. This is easily handled in the model by “knocking out” nifH and associated genes. Then the model would need to be calibrated to observations of Microcystis. Then, the toxin production genes and pathways would have to be programmed and calibrated/validated. This will require more work, comparable to the Anabaena Lab project, and a good PhD thesis topic.

Anabaena Energy Lab: The present model does not explicitly track intracellular energy (i.e. in terms of ATP or equivalent) and tie it to growth. For example, the cost of fixing one N2 vs. taking up and reducing one NO3 is not explicitly considered in the model. I could, for example, simply increase the NifH rate and then the cells would grow faster on N2 than NO3. This change would make the model more mechanistically detailed and correct. This will require more work, comparable to the Anabaena Lab project, again a good PhD topic.

Microcystis Field: Once the Microcystis model is coded we could apply it to a real lake. Again, this would require that the lake is dominated by Microcystis. Of course, it is unlikely that we would find such a system anywhere [this is a Taihu insider joke].

Anabaena/Microcystis Lab Competition: This came out of some discussion and ideas we had about light energy and competition between these species.

Anabaena/Microcystis Competition Field: Finally, the whole model can be used to explore the competition between these two species in the field.

Link to the paper:

Link to the YouTUBE movie:

Friday, April 15, 2016

Environmental Capstones

It’s that time of year again... Capstones! Please join us for the 2016 Environmental Capstone student presentations. This year, we have a variety of interesting projects, including designing refugee camps in Haiti and Greece, a floodwall to protect the Logan Airport power station from hurricanes, a water management system at the Blue Hills Ski Area, a dam on the Charles River, an off-the-grid home, a solar system for an industrial client, a food waste composting system for the Town of Melrose and a wastewater treatment plant for the Northeastern University campus. Nine Capstone teams have been working hard all semester and now it’s time to see what they came up with. Please join us! A flyer with more details is posted here:

Tuesday, April 5, 2016

Freeman Lecture

Please join us for the annual John R Freeman Lecture, which will be held at Northeastern this year. This year’s speaker will be Prof. John H Lienhard V from MIT and he will be talking about desalination. The problem of freshwater availability is growing with the increase in population across the globe, and desalination is one important solution. The event will be on April 11 in room 20 WVF. It starts with a reception (free food) at 6pm and then the lecture at 7pm.

Sunday, March 20, 2016

@ASM Conference Report

I am at DCA on my way back to Boston. We just finished a conference on single-cell analyses and agent-based modeling at the ASM headquarters in Washington DC. This is an excellent venue. It was great to be among so many like-minded people and I really enjoyed the presentations and discussions. Here are the slides from my opening remarks and presentation and a copy of the program.

Intro Slides
Anabaena Slides
Conference Program