Presentations for NIMBioS Investigative Workshop:
Individual-based Ecology of Microbes, June 8-10, 2011

Introduction

• Introduction to NIMBioS, Lou Gross
• Introduction to workshop, Ferdi Hellweger

Interactions among populations

• The evolution of co-occuring protozoa species in response to competition and predation in natural microcosms (leaves of Sarracenia purpurea), Tom Miller
• Functional traits, trade-offs and community structure in phytoplankton and other microbes, Elena Litchman (discussion leader)
• Stochastic colonization and extinction of microbial species on marine aggregates, Drew Kramer

Interactions within populations

• Mathematical model of infection control on medical implants, Alicia Prieto L
• Individual-based models of social evolution in biofilms, Sara Mitri (discussion leader)
• Invasive amphibian fungal skin disease dynamics, Gabriela Rios-Sotelo
• Within-biofilm interactions between alternative phenotypes with altered expression of extracellular "public goods", Will Driscoll

Interactions with the environment

• Using IBM's to predict substrate use preference from pyrosequencing data in permafrost soils, Jessica Ernakovich
• Individual-based modeling of marine biogeochemistry, James Clark (discussion leader)
• Elucidating the bacteria responsible for utilization of dissolved organic matter in streams, Philips Akinwole
• Evolutionary response of microbes to fluctuating environment: an mechanistic account, Xiao Yi

Intracellular biochemical networks

• Linking genes to ecosystems using systems bioecology, Ferdi Hellweger
• Single cell analysis on microfluidic platforms, Alexandra Ros (discussion leader)
• Variability in yeast sporulation, Colin Maxwell

Heterogeneity, diversity and structure

• Continuum models of biofilms, Isaac Klapper
• Activated sludge floc modeling: structure formation and scale up, Dana Ofiteru (discussion leader)
• Individual-based microbial ecology of agricultural rhizosphere and phyllosphere populations with a focus on horizontal gene transfer and the ecology and evolution of plant pathogens, Andrea Vu

Microscopy based methods

• Persistence of microbial communities (including aquatic pathogens) in marine snow-like organic aggregates, Maille Lyons
• Individual-based microbial ecology of plant leaf surface colonization, Johan Leveau (discussion leader)
• Extracting ecological information from complex biofilm spatial structures, Nabil Mabrouk

Flow cytometry, microfluidics, and other single cell methods

• Analysis of cell-cell and cell-environment interaction by integration of microfluidic devices and agent-based modeling, Andre Levchenko
• Importance of variation in elemental composition of marine protists to oceanic biogeochemical cycles and foodweb dynamics, Stephen Baines (discussion leader)
• Cyst germination and emergence flux of Alexandrium fundyense cells in shelf sea and coastal sediments, Emil Vahtera

Community: Physiology and Sequencing

• Enhanced generation of biogenic methane from coal, Lisa Gallagher
• Syntrophic interactions in anoxic aquatic communities, Caroline Plugge (discussion leader)
• Cyanobacterial growth rate response to varying experimental environments, RajReni Kaul

Model development and frameworks

• Agent-based modeling with Repast Simphony, Jonathan Ozik
• Individual-based modeling using the Lagrangian Ensemble Metamodel, Tony Field (discussion leader)
• Mechanistic prediction of fermentation by rumen microbes, Chris Topping
• Individual Based Modeling of rodlike bacteria in microfluidic device, Kami Koleva

Model application

• Integrating experimental soil community ecology and modeling techniques, Kirstin Holfelder
• Individual-based modeling: the role of patterns and standards, Volker Grimm (discussion leader)
• Individual-based modeling of interactions between microbes in biofilms and the effect of spatial structure, Jan Kreft

Modeling methods

• Essential community interactions supporting organohalide respiration by Dehalococcoides, Kirsti Ritalahti
• Individual based modeling of Toxoplasma gondii, Xiaopeng Zhao (discussion leader)
• The impact of bacterial dispersal networks on biodegradation performance, Thomas Banitz

Summing up

• Report of session groups
• Synthesis, Caroline Plugge & Andre Levchenko
• Future directions discussion, Jan Kreft

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From 2008 until early 2021, NIMBioS was supported by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.