Vitamin B ₁₂ -dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification

Abstract

Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth’s climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B12) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche—for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene–Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene–Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.

The occurrence of 2‐methylhopanoids in modern bacteria and the geological record

“…The high 2-MeHops' index during some of the geological events (Figure 4) could therefore (partly) be explained by an expansion of Nitrobacter that drove the high rates of nitrification. A similar hypothesis was recently proposed by Elling et al, (2020). They used cultures of Nitrobacter vulgaris AB1 and argued the high 2-MeHops' level observed during OAEs reflects an expansion of Nitrobacter in response to high rates of nitrification.…”

Linking diatom-diazotroph symbioses to nitrogen cycle perturbations and deep-water anoxia: Insights from Mediterranean sapropel events

“…This idea is supported by proto-North Atlantic OAE biomarker distributions, which show a high abundance of BHP degradation products that are methylated at the C-2 position (2Me-hopanoids) . Recent experimental results have shown that these compounds are produced in abundance by nitrite oxidizing bacteria of the genus Nitrobacter (Elling et al, 2020). This scenario is also con-sistent with model predictions and data compilations for upwelling regions during OAE-2, in which all components of the nitrogen cycle are greatly amplified in response to higher simulated phosphorous inputs (Naafs et al, 2019).…”

Marine and terrestrial nitrifying bacteria are sources of diverse bacteriohopanepolyols

“…Relative abundances of major bacteriohopanepolyols (BHPs) are shown in panels a–d (BHT: bacteriohopanetetrol; BHaminotriol: 35‐aminobacteriohopanetriol; and BHaminopentol: aminobacteriohopanepentol). Abundances of total BHPs relative to 2‐methyl BHPs and the non‐functionalized hopanoids diploptene and 2‐methyl diploptene are shown in panels e–h (data for panel h from Elling et al, 2020). Abundances of total hopanoids (BHPs + 2‐methyl BHPs + diploptene + 2‐methyl diploptene) are shown in panels i–l (vertical line: average; n.a., not available).…”