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!




PAPER

YOUTUBE MOVIE

CODE AT GITHUB

SYNCHOCOCCUS MODEL PAPER


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... 


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

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.

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


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



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

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:

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

http://iaglr.org/iaglr2016/

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)
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