Observing microbial processes at the microscale with in situ technology

• Main Author: Lambert, Bennett
• Format: Thesis
• Language: English
• Published: Massachusetts Institute of Technology and Woods Hole Oceanographic Institution 2019
• Subjects: Microorganisms; Bacteria; Marine ecology; Scientific apparatus and instruments; Plankton; Plankton > Growth; Phytoplankton; Chemical oceanography; Antarctic Ocean; Antarctic; Antarc*
• Online Access: https://hdl.handle.net/1912/10810

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. 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 ...