UC Berkeley

Abstract

Interconnections at the microbial and societal scales: The response of hypersaline microbial communities to environmental perturbations and a situated exercise in the democratization of science

by

Karen Andrade

Doctor of Philosophy in Environmental Science, Policy, and Management

University of California, Berkeley

Professor Jillian F. Banfield, Co-Chair

Professor Alastair T. Iles, Co-Chair

Regardless of the scale at which it is defined, at the core of a community is the interdependence and connection of organisms. It is from the connections between organisms that a community emerges. This interdisciplinary dissertation is an investigation of, and an engagement with, both microbial and human communities from the point of view of several disciplines and methods. Microorganisms and humans both exist in and form close communities with each other. The methods and theoretical frameworks used in each chapter vary widely, providing different lenses through which to understand these communities and their networks of interactions. Furthermore, in all chapters the results of community-wide approaches highlight the phenomena that emerge from the interconnections within, and with the environmental context in which the community exists.

The first part of this dissertation analyzes the ecology, function and response of the microbial community of a hypersaline lake. Lake Tyrell (NW, Victoria, Australia) is a thalassohaline lake whose microbial community we propose is a model for understanding the response of microbes and their communities to short time scale environmental perturbations. Cultivation-independent methods were used to study the dynamics and metabolic profile of the planktonic microbial community. Cultivation-independent methods allow the study of the whole community, including organisms that cannot be grown in the laboratory. In chapter 1 metagenomics, lipidomics and microscopy methods demonstrated the operation of a strong community-level diel (day-night) cycle, likely driven by the interconnection of nutrient fluxes, temperature, light abundance and oxygen concentrations. Lipidomic and statistical analyses demonstrated striking and significant shifts in the proportions of bacterial and archaeal lipids across the diel cycle in a 3-day and 2-night time series experiment. Bacterial lipids increase during the day and decrease during the night and archaeal lipids show the opposite trend. Metagenomic analysis revealed the day-night behavior of specific types of organisms and resolved community composition. The community includes two bacteria in the phylum Bacteroidetes, eight archaea members of the Halobacteriaceae family and six different nanohaloarchaeal types, three of which have not been identified previously. Metagenomic analyses support the finding of an overall preference in Archaea for nighttime, relative to Bacteria, which increase during the daytime. The nanohaloarchaea showed a particularly strong diel cycle, with a pronounced increase in relative abundance over the night periods The Nanohaloarchea are nano-sized archaea that were first identified at Lake Tyrrell by previous studies. They are part of a recently described group of archaea that tend to have small genomes (~1.2Mb) and cell size (~<500 nm in diameter). The combining of multi-‘omic methods and microscopy allowed the detection of a diel cycle in relative abundances of bacteria and archaea, resolved the behavior of the Nanohaloarchaea, which opened a window into their ecology and possible associations with other organisms in the community.

Chapter 2 further investigated the ecology of Lake Tyrrell’s microbial community during the 3-day and 2-night time series experiment mentioned above. Metagenomic and metaproteomic methods allowed the study of how the community’s function is impacted by evaporative concentration as it is modulated by variations in temperature and solar radiation during the diel cycle. An in-depth characterization of the physiological changes of Haloquadratum, the dominant organisms in the lake, showed increased expression of proteins involved in stress response, cell division, and the biosynthesis of vitamin B cofactors. The expression of proteins that biosynthesize vitamin B12 adds to recent findings that underlie the importance of B vitamins in natural environments. Metaproteomics showed that evaporative concentration was a major driver of shifts in the Haloquadratum proteome and that a physiological diel cycle might be suppressed as environmental stress increases. Analysis of nanohaloarchaeal genomes suggests that they are anaerobic fermenters that overall have limited metabolic capacity. Given that they lack many core biosynthetic pathways, they likely depend on abundant archaea such as Haloquadratum for many basic metabolic substrates, possibly including membrane lipids as well as nucleotides and amino acids. . Results provide new insight into the response of hypersaline microbial communities to the interrelated environmental factors that track the diel cycle, including evaporative concentration.

Chapter 3 is an interdisciplinary essay that brings microbial ecology into conversation with Science and Technology studies. Partly ethnography of science, I discuss the recent technological changes that have taken place in the field of microbiology. Further I highlight their contribution to a shifting perception of microbes as individual threats to a view that emphasizes our co-dependence and collaboration with microbial communities. By shedding light on the complex and mutually affecting dynamics that characterize the relationship between human cells and their microbial counterparts, microbiology is pointing to a new vision of the human body; a hybrid entity that has been shaped by microbial relationships and co-evolutions. Yet, the epistemic culture of microbiology remains stable and dependent a disconnected and disembodied objectivity that reinforces the view of microbes as passive, mechanical objects primed for exploitation. Yet, “indigenous microbiology” practices, such as composting and artisanal cheese making, show how humans and microbes have built collaborative relationships outside of the body. Underscoring the communal nature of microbes and humans provides an opportunity for the epistemic culture of microbiology to shift by underscoring the communal nature of microbes and humans, and moving away from reductionism.

Working at another scale and resulting from questions rising from my experience as a microbiologist, graduate student and academic scientist, Chapter 4 narrates the results of my efforts to establish a Science Shop at UC Berkeley. Science Shops are organizations that coordinate and execute community-engaged research projects. Community-engaged research has been shown to better the scientific enterprise by improving its methodological rigor as well as its public relevance and policy reach. By bringing together university researchers, students, and community organizations science shops facilitate scientific research that responds to the needs and interests of all stakeholders. It is imperative that universities explore and actualize models of knowledge production that empower the communities that support them. Inspired by the co-learning and co-productive relationships between learners and teachers and by the results of the European Science Shop movement, the UC Berkeley Science Shop was established in 2013 and was successfully funded and run for two years. Grounded in the theoretical frameworks of situated knowledge, local and generalized knowledges and epistemic injustice, I proposed that Science Shops have an important role in democratizing the practice of, and access to, scientific research and knowledge production. The UC Berkeley Science Shop itself, and the three pilot projects completed provide a precedent and a model for the creation of these types of organizations in American universities.