Simulating Microbial Ecosystems
Chapter 1 Clustering on Human Microbiome Sequencing Data: A Distance-Based Unsupervised Learning Model.............................................................................................................................1 Dongyang Yang and Wei Xu Chapter 2 The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale..................................................................................................................................................19 Daniel Craig Zielinski, Arjun Patel and Bernhard O. Palsson Chapter 3 Photorespiration and Rate Synchronization in a Phototroph-Heterotroph Microbial Consortium..........................................................................................................................................37 Fadoua El Moustaid, Ross P. Carlson, Federica Villa and Isaac Klapper Chapter 4 An Integrated Mathematical Model of Microbial Fuel Cell Processes: Bioelectrochemical and Microbiologic Aspects†...........................................................................77 Andrea G. Capodaglio, Daniele Cecconet and Daniele Molognoni Chapter 5 Stoichiometric Network Analysis of Cyanobacterial Acclimation to Photosynthesis-Associated Stresses Identifies Heterotrophic Niches........................................................91 Ashley E. Beck, Hans C. Bernstein and Ross P. Carlson Chapter 6 In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi..................................................................................................................................................122 St. Elmo Wilken, Mohan Saxena, Linda R. Petzold and Michelle A. O’Malley Chapter 7 Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function...................................................................................................................................136 Emily B. Graham and James C. Stegen Chapter 8 Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists........................................................................................................................154 Marco Zaccaria, Sandra Dedrick and Babak Momeni Chapter 9 Individual-Based Modelling of Invasion in Bioaugmented Sand Filter Communities.............................................................................................................................................173 Aisling J. Daly, Jan M. Baetens, Johanna Vandermaesen, Nico Boon, Dirk Springael and Bernard De Baets Chapter 10 Modeling Biofilms: From Genes to Communities........................................................................................194 Tianyu Zhang Chapter 11 Dynamics of the Bacterial Community Associated with Phaeodactylum tricornutum Cultures..............................................................................................................210 Fiona Wanjiku Moejes, Antonella Succurro, Ovidiu Popa, Julie Maguire and Oliver Ebenhöh Permissions List of Contributors Index IV Contents