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