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Open Access Publications from the University of California

Molecular Signatures of Microbial Metabolism in the Marine Water Column

  • Author(s): Kharbush, Jenan J.
  • Advisor(s): Aluwihare, Lihini I
  • et al.

Lipid biomarkers are valuable tools in studies of microbial metabolic diversity and function in both past and present marine ecosystems, but the distribution and biological sources of many of these biomarkers in the modern ocean have yet to be sufficiently defined. This dissertation examines two major classes of lipid biomarker compounds that are widely distributed in marine environments: hopanoids, biomarkers for bacteria, and intact polar diacylglycerols (IP-DAGs), potential biological tracers of recent carbon and nutrient cycling. The distribution and structural diversity of these lipid compounds is analyzed in tandem with genetic and metagenomic data, both expanding the knowledge related to the structural distribution of these lipids in the marine environment, and illuminating key aspects of the ecology of the producing organisms. This work is detailed in six chapters, consisting of an introduction, four research-oriented chapters, and concluding remarks. Chapters 2, 3, and 4 focus on the bacterial hopanoids. First, analysis of hopanoid structural diversity and abundance across oxygen gradients in the Santa Barbara Basin was complemented by a genetic survey, identifying a potential connection between hopanoid production and metabolic strategies associated with low oxygen environments. Next, this connection was further investigated using qPCR and surveys of existing metagenomes to quantify the relative abundance of groups of hopanoid producers in low oxygen regions of the Eastern North Pacific and Eastern Tropical Pacific oxygen minimum zones. Results revealed that dominant hopanoid producers in these regions are not Proteobacteria as previously hypothesized but instead are nitrite-utilizing organisms such as nitrite-oxidizing and anaerobic ammonia-oxidizing bacteria. Finally, a survey of an extensive metagenomic dataset from the Red Sea illuminated the distribution of hopanoid producers in a biogeochemically-distinct environment relative to those previously analyzed, and confirming that hopanoid producers may also play roles in marine nitrogen cycling. Chapter 5 details an exploratory investigation of the structural distribution of various classes of IP-DAGs, in the oligotrophic Tonga Trench. Results provide new insight into potential biological sources of IP-DAGs, and identify structures that may be useful as indicators of the contribution of groups of picophytoplankton to export production, or of in situ heterotrophic production at depth.

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