The Evolution of Biological Carbon and Nitrogen Cycling--a Genomic Perspective

Abstract

Carbon and nitrogen are essential to all living organisms, owing to their abundance and remarkable characteristics when participating in chemical bonds. Their essentiality dates back to the very origin of life, where current theories hypothesize either a prebiotic abundance of organic compounds rich in carbon and nitrogen, or an ability to assimilate them inorganically through abiotic reactions that might have been catalyzed on ancient mineral surfaces. This chapter details the core reactions essential to the assimilation of these elements in biologically useful forms—the so-called fixation of carbon and nitrogen—focusing on recent literature and insights from comparative genomics and phylogenetics. Though considerable debate continues on the antiquity of these pathways, especially whether or not they might have been present in the last common ancestor (LCA) of modern organisms, it is clear that carbon and nitrogen fixation pathways were of crucial importance to the primitive ancestors of extant life. Furthermore, the biological assimilation of inorganic carbon (autotrophy) and atmospheric nitrogen (diazotrophy) represent pivotal juxtapositions of biological and geological cycles. It is thought that atmospheric CO2 concentrations have decreased substantially since the proposed origin of life some 3.8 billion years ago, due in large part to either primary (fixation) or secondary (e.g., weathering) influence by biota (Hayes 1994; Rye et al. 1995; Des Marais 1997; Lowe and Tice 2004). Though the biosphere accounts for a relatively small fraction of the total carbon on Earth, the rate of carbon flux through the biosphere far exceeds that through any geological reservoirs (Des Marais 1997). Biological carbon fixation is closely balanced to carbon recycling through biological oxidation, and the future stability of this and other CO2 reservoirs (and our ability to influence or understand them) depends critically on these biological underpinnings (e.g., Falkowski et al. 2000). Conversely, nitrogen, especially the …