A new chapter in my life: TU Berlin

Dear Friends and Colleagues:

On 1. January 2018 I started at the Technical University of Berlin as Chair of Water Quality Engineering (Wasserreinhaltung). This web site www.SystemsBioEcology.org will not be updated anymore in the foreseeable future. To find out whats new with me you can visit my web site at TU Berlin: http://www.wrh.tu-berlin.de.

Sincerely,
Ferdi Hellweger

Lichthof mit Nike-Statue im TU-Hauptgebäude

© TU Berlin/Böck

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.

https://stem.neu.edu/summer/ysp/
http://www.thecharles.org/swim-park-project/
www.systemsbioecology.org

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.

http://www.northeastern.edu/gordonleadership/

www.systemsbioecology.org

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.

http://pubs.acs.org/doi/full/10.1021/acs.est.6b06296

www.systemsbioecology.org

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?

http://www.abstractsonline.com/pp8/#!/4358/presentation/1452
http://www.asm.org/index.php/asm-microbe-2017

https://omegavia.com

 www.systemsbioecology.org

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
http://www.abstractsonline.com/pp8/#!/4358/presentation/1452
http://www.asm.org/index.php/asm-microbe-2017

www.systemsbioecology.org

Freeman Lecture: Lake Erie's Death, Resurrection, Re-Death, and the role of Models in Guiding a Re-Resurrection

I hope you will be able to join us for this year’s Freeman Lecture, which will be presented by Prof. Don Scavia of the University of Michigan. 

http://www.bsces.org/events/2017-john-r-freeman-lecture-496
http://files.bsces.org/file/2017-Freeman-Flyer.pdf

Picture:www.ibtimes.com

www.systemsbioecology.org

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 http://science.sciencemag.org/content/326/5960/1694) or bacterial dispersal by ship balast water (see this paper http://pubs.acs.org/doi/pdf/10.1021/acs.est.6b03108). The code is available at the link below and I am available to help and/or collaborate.

Image source: NASA WorldView

PAPER:
https://link.springer.com/article/10.1007/s00248-017-0963-5

MOVIE: 
https://youtu.be/LV8th6TfALo

CODE:
https://github.com/fhellweger/LargeLakes

www.systemsbioecology.org

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...

BLOG POST LINK
http://blogs.biomedcentral.com/on-biology/2017/03/16/biology-2-0-it-is-time-to-delegate-understanding-to-computers/

SASM HOMEPAGE (hasn’t been updated for a while)
http://www.systemsbioecology.org/sasm.htm

www.systemsbioecology.org

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 (www.thecharles.org) and Northeastern University (www.neu.edu). 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 http://www.thecharles.org/projects-and-programs/swim-park/ or contact Ferdi Hellweger at ferdi@coe.neu.edu.

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

www.systemsbioecology.org

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: http://www.iwadipcon2017.org/

THE THINGS WE THINK AND DO NOT SAY

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:

http://www.sciencedirect.com/science/article/pii/S0304380016303209

Charles River Bathymetry Map Updated

There is a nice article in the Boston Globe about mapping the Charles River bathymetry. You can read it here:
http://www.bostonglobe.com/business/2016/12/16/charting-project-reveals-charles-river-depths/FMTKuYABfzHSLxggV0sXkK/story.html

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!

PAPER

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167010

YOUTUBE MOVIE

https://youtu.be/CGvGNskYgTU

CODE AT GITHUB

https://github.com/fhellweger/GlobalTemp

SYNCHOCOCCUS MODEL PAPER

http://www.sciencedirect.com/science/article/pii/S0304380010001602

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... 

http://www.isme-microbes.org/isme16

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.

http://frontiersin.org/Systems_Microbiology/researchtopics/The_Individual_Microbe_Single-Cell_Analysis_and_Agent-Based_Modelling/5193

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

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:
http://www.siam.org/meetings/ls16/
http://meetings.siam.org/sess/dsp_talk.cfm?p=78264

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:
https://www.grc.org/programs.aspx?id=11255

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:

http://iaglr.org/conference/abstracts/pub_abstract_view.php?abstract_id=1454097536

http://iaglr.org/iaglr2016/

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)
http://www.nature.com/nrmicro/journal/vaop/ncurrent/full/nrmicro.2016.62.html

Kreft et al. (2013)
http://www.pnas.org/content/110/45/18027.short

Hellweger and Bucci (2009)
http://www.sciencedirect.com/science/article/pii/S0304380008004390

Hellweger (2007)
http://www.ingentaconnect.com/content/wef/wefproc/2007/00002007/00000012/art00001