Is there chaos out there? : analysis of complex dynamics in plankton communities

Species often show irregular fluctuations in their population abundances. Traditionally, ecologists have thought that external processes (e.g., variability in weather conditions) are the main drivers of these ups and downs. However, recent theoretical work suggests that fluctuations in natural populations may also be driven by internal mechanisms (e.g., the interplay between species). In this thesis I use a combination of time series analysis and modeling to provide more insight into the question to which extent such internally generated chaos might drive the population dynamics of plankton communities under controlled as well as natural conditions. In short, this thesis demonstrates in theory and experiment that species in plankton communities may rise and fall forever in a chaotic way. This result challenges the traditional view that nature is at equilibrium and that only externally driven processes may disturb this equilibrium

Bacterial cell cycle dynamics: size regulation during exponential growth and role of polyphosphate during starvation response

Bacteria are the most diverse and abundant kingdom of life and have adapted to survive and thrive in habitats around the globe. When provided with ample nutrients they grow and divide at staggering rates, increasing their population exponentially. Upon nutrient depletion on the other hand, they quickly adapt by drastically altering their metabolism, halting growth to survive for a very long time. Since bacteria are tiny -about a few micrometers-, visualizing these processes requires microscopy. To measure the dynamics of their shape and inner structures precisely, one needs to choose a technique that balances spatial resolution, temporal resolution and photo-toxicity. In this thesis, I present two projects using advanced dynamic microscopy, first to study cell size regulation during exponential growth in the abundance of nutrients and then to elucidate the role and positioning of polyphosphate granules during cell cycle exit in response to nutrient starvation. During exponential growth, bacteria balance growth and division to regulate their size, resulting in a narrow size distribution, referred to as cell size homeostasis. Recent work tried to uncover what cells sense to decide to divide in order to achieve size homeostasis: time, size, growth or a combination of those. Control of cell division is often equated to control of constriction onset; however, the constriction period still accounts for up to 40% of cell growth and could thus contribute significantly to cell size regulation. We used SIM microscopy to measure constriction kinetics and their impact on cell size regulation in Caulobacter crescentus. We found that constriction rate regulation can determine cell size. Moreover, constriction rate modulation compensates for variability in elongation before constriction, allowing a higher fidelity cell size homeostasis. We suggest a parsimonious model where excess cell wall precursors accumulate proportionally to elongation before constriction and set the rate of constriction. This is the first direct demonstration that constriction rate can contribute to cell size control and homeostasis in bacteria. Upon nutrient starvation, bacteria exit their cell cycle to preserve energy and nutrients. In many bacteria, such as Pseudomonas aeruginosa, this is associated with the accumulation of polyphosphate (polyP) in intracellular granules. PolyP is created by polyphosphate kinases (ppkâs), which are required for successful cell cycle exit and survival of and recovery from long-term starvation. Interestingly, these polyP granules are regularly spaced within the nucleoid. To date, it is not known during which stage polyP is required for cell cycle exit, and what causes the spacing of the granules. Here, we use fluorescence microscopy to probe the cell cycle stage of Îppk cells arrested during nutrient starvation as well as the localization and dynamics of ppkâs. We show that a majority of Îppk cells are arrested with open replication forks. Furthermore, we find that ppkâs localize in distinct patterns, already prior to starvation and polyP granule production, which could be responsible for the positioning of polyP granules. To this end, we developed a background subtraction algorithm to remove cytoplasmic fluorescence, improving accuracy of spot detection and localization

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Geomicrobiology of the ocean crust : the phylogenetic diversity, abundance, and distribution of microbial communities inhabiting basalt and implications for rock alteration processes

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2007Basaltic ocean crust has the potential to host one of the largest endolithic communities on Earth. This portion of the biosphere, however, remains largely unexplored. In this study, we utilize molecular biological, microscopic, and geochemical tools to gain a better understanding of the geomicrobiology of the ocean crust. Specifically, we examine the phylogenetic diversity of microorganisms inhabiting basaltic lavas, the activities and abundances of these microorganisms, the spatial extent of the biosphere, and the potential effect that microbial activity has on the geochemistry of the ocean crust and overlying water column. Our study demonstrates that young, fresh volcanic lavas near mid-ocean ridges host an incredibly diverse and dense population of microorganisms dominated by Bacteria, quite distinct from the microbial communities found in surrounding deep seawater and hydrothermal vents. Furthermore, these communities may contribute to the elemental cycling of Fe, S, Mn, N, and C in this environment. The inability to definitively identify microorganisms in drill-cores of old (> 15 Ma) ocean crust, however, implies that these once prolific communities may become scarce as the crust ages and moves further away from the ridge axis. Finally, we provide evidence suggesting that these communities are fueled by oxidative alteration reactions occurring in the basaltic crust.Funding for this project came from: RIDGE 2000 Grant #OCE-0241791 awarded to Katrina J. Edwards and Wolfgang Bach, the NASA Astrobiology Institute - Cycle 3 CAN-02-OSS-02 awarded to Katrina J. Edwards, USSSP ODP Post-cruise funding Grant #TX A&M F001724 awarded to Cara M. Santelli and Katrina J. Edwards, and a Schlanger Ocean Drilling Fellowship awarded to Cara M. Santelli

Pathways to Water Sector Decarbonization, Carbon Capture and Utilization

The water sector is in the middle of a paradigm shift from focusing on treatment and meeting discharge permit limits to integrated operation that also enables a circular water economy via water reuse, resource recovery, and system level planning and operation. While the sector has gone through different stages of such revolution, from improving energy efficiency to recovering renewable energy and resources, when it comes to the next step of achieving carbon neutrality or negative emission, it falls behind other infrastructure sectors such as energy and transportation. The water sector carries tremendous potential to decarbonize, from technological advancements, to operational optimization, to policy and behavioural changes. This book aims to fill an important gap for different stakeholders to gain knowledge and skills in this area and equip the water community to further decarbonize the industry and build a carbon-free society and economy. The book goes beyond technology overviews, rather it aims to provide a system level blueprint for decarbonization. It can be a reference book and textbook for graduate students, researchers, practitioners, consultants and policy makers, and it will provide practical guidance for stakeholders to analyse and implement decarbonization measures in their professions