Observing microbial processes at the microscale with in situ technology
MetadataShow full item record
KeywordMicroorganisms; Bacteria; Marine ecology; Scientific apparatus and instruments; Plankton; Plankton--Growth; Phytoplankton; Chemical oceanography; Antarctic Ocean
Marine microbes are key drivers of biogeochemical transformations within the world’s oceans. Although seawater appears uniform at scales that humans often interact with and sample, the world that marine microbes inhabit can be highly heterogeneous, with numerous biological and physical processes giving rise to resource hotspots where nutrient concentrations exceed background levels by orders of magnitude. While the impact of this microscale heterogeneity has been investigated in the laboratory with microbial isolates and theoretical models, microbial ecologists have lacked adequate tools to interrogate microscale processes directly in the natural environment. Within this thesis I introduce three new technologies that enable interrogation of microbial processes at the microscale in natural marine communities. The IFCB-Sorter acquires images and sorts individual phytoplankton cells, directly from seawater, allowing studies exploring connections between the diversity of forms present in the plankton and genetic variability at the single-cell level. The In Situ Chemotaxis Assay (ISCA) is a field-going microfluidic device designed to probe the distribution and role of motility behavior among microbes in aquatic environments. By creating microscale hotspots that simulate naturally occurring ones, the ISCA makes it possible to examine the role of microbial chemotaxis in resource acquisition, phytoplankton-bacteria interactions, and host-symbiont systems. Finally, the Millifluidic In Situ Enrichment (MISE) is an instrument that enables the study of rapid shifts in gene expression that permit microbial communities to exploit chemical hotspots in the ocean. The MISE subjects natural microbial communities to a chemical amendment and preserves their RNA in a minute-scale time series. Leveraging an array of milliliter-volume wells, the MISE allows comparison of community gene expression in response to a chemical stimulus to that of a control, enabling elucidation of the strategies employed by marine microbes to survive and thrive in fluctuating environments. Together, this suite of instruments enables culture-independent examination of microbial life at the microscale and will empower microbial ecologists to develop a more holistic understanding of how interactions at the scale of individual microbes impact processes in marine ecosystems at a global scale.
Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2019.
Suggested CitationThesis: Lambert, Bennett, "Observing microbial processes at the microscale with in situ technology", 2019-02, DOI:10.1575/1912/10810, https://hdl.handle.net/1912/10810
Showing items related by title, author, creator and subject.
Caron, David A. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1984-06)The distribution and feeding behavior of bacterivorous micro flagellates (2-20 μm protozoa) and their ingestion by copepods were examined in an attempt to assess the importance of these protozoa as a trophic link ...
Sutherland, Kelly R. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2010-02)Trade-offs between filtration rate and swimming performance among several salp species with distinct morphologies and swimming styles were compared. Small-scale particle encounter at the salp filtering apparatus was also ...
The distribution, abundance and ecology of mixotrophic algae in marine and freshwater plankton communities Arenovski, Andrea L. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1994-09)Mixotrophic algae are algae that combine photosynthesis with phagotrophy to satisfy nutritional requirements. Mixotrophic algae have been found to dominate the nanoplankton assemblage in some aquatic environments, and ...