Abstract
Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen‐utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen‐cycling genes, dated with a time‐calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum‐based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid‐Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N2. Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.
Highlights
Nitrogen is a critical element to life on Earth, important as an essential building block in the synthesis of biological molecules, and for its role in redox reactions for microbial energy metabolism
Our results show that biological nitrogen fixation appears to have arisen and proliferated early in the Archaean, and that genes in the denitrification pathway and genes related to the consumption of nitrite and its downstream products began to proliferate across the tree of life following the oxygenation of Earth's atmosphere and oceans
Our results support the hypothesis that the molybdenum-based variety of nitrogenase diversified much earlier than alternative nitrogenases, which may only have become important with the increasing nitrogen demand of algae in the Neoproterozoic, implying that molybdenum was not a limiting resource in the Archean ocean
Summary
Nitrogen is a critical element to life on Earth, important as an essential building block in the synthesis of biological molecules, and for its role in redox reactions for microbial energy metabolism It is often a limiting nutrient in marine and terrestrial environments and likely had a significant influence on the evolutionary trajectory of the biosphere over Earth's history. To create the species tree, all bacterial and archaeal genomes in our database were mined for single-copy ribosomal protein sequences L2, L3, L4, L5, L6, L14, L15, L16, L18, L22, L24, S3, S8, S10, S17, and S19 using Phylosift (Darling et al, 2014), with the isolate and best hit command line flags These 16 ribosomal proteins represent the same proteins used to create a recent comprehensive tree of life (Hug et al, 2016) and, in the case of eukaryotes, ribosomal sequences were directly drawn from their dataset. The root for the species tree was placed in the Bacterial domain (Fournier & Gogarten, 2010)
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