UC Berkeley

Chlorine participates in a biogeochemical cycle that rivals that of elements like nitrogen and sulfur in chemical diversity. Nature produces a variety of organic and inorganic chlorine-containing molecules that participate in different biological, chemical, and geological processes. The most defining feature of chlorine is its high electronegativity, perhaps best illustrated by the very high reduction potential of molecules in which chlorine is at a higher oxidation state, such as hypochlorous acid (HOCl), chlorite (ClO2-), chlorate (ClO3-), and perchlorate (ClO4-).

Compared to research on the biogeochemical cycles for other elements, the mechanisms by which oxidized chlorine molecules are produced and consumed are relatively understudied. One reason is that descriptions of the biogeochemical chlorine cycle have been incomplete, omitting important processes involving inorganic chlorine molecules. Another reason is that the microbiology of oxidized chlorine has been studied almost exclusively through a reductionist approach that can preclude the discovery of ecological interactions. Yet another reason is that the genes known to be involved in the metabolism of oxidized chlorine have yet to be used to find new organisms and processes that metabolize oxidized chlorine. Here, a more holistic approach, enabled by improvements in genome sequencing, is used to better describe the biology of oxidized chlorine across several research projects.

The first chapter of this dissertation provides the first review of the entire biogeochemical chlorine cycle, emphasizing connections between the various biological, chemical, and geological processes that interconvert chlorine between different chemical forms.

The second chapter of this dissertation is a published research article describing the reduction of perchlorate in microbial communities for the first time by using bioinformatics techniques to obtain genomes from metagenomes. Instead of being dominated by the specific bacteria known to respire perchlorate, perchlorate-reducing communities contain diverse organisms that interact via the chemical intermediates of dissimilatory perchlorate reduction.

The third chapter of this dissertation is a published research article investigating the mechanism of one such interaction between perchlorate-reducing bacteria and chlorate-reducing bacteria. A combination of genomics, strain isolation, genetics, metabolite measurements, and theoretical modeling are used to learn that these two metabolisms, which have been studied separately for several decades, have a conserved interaction due to the accumulation of chlorate by perchlorate-reducing bacteria.

The fourth chapter of this dissertation is a brief report characterizing a possible perchlorate reductase or chlorate reductase first identified in perchlorate-reducing communities. An organism with this reductase, which is always found in genomes adjacent to the chlorite-degrading enzyme chlorite dismutase (Cld), is capable of chlorate reduction but not perchlorate reduction, indicating the enzyme is a chlorate reductase.

The fifth chapter of this dissertation extends the above comparative genomics analysis to identify any gene or organism linked to the enzyme Cld. Because Cld is biomarker for chlorite and other chlorine oxyanions, this approach was able to expand the environments, organisms, and processes known to participate in oxidized chlorine biology beyond the organisms and genes described above. Specifically, more was learned about the reduction of perchlorate and chlorate in the environment; the potential oxidation of chloride beyond hypochlorous acid by chemical or biological activity; and the connection between chlorite and reactive chlorine stress response.

Together, this research has answered important questions about the reduction of chlorine while opening new questions about the oxidation of chlorine and the role of oxidized chlorine species in the environment.