See also nitrogenase.

CHEMICAL EVOLUTION

Geobiological feedbacks, oxygen, and the evolution of nitrogenase

Biological nitrogen fixation via the activity of nitrogenase is arguably one of the most important biological innovations, allowing for an increase in global productivity that eventually permitted the emergence of complex forms of life. The complex metalloenzyme termed nitrogenase contains complex iron-sulfur cofactors. Three versions of nitrogenase exist that differ mainly by the presence or absence of a heterometal at the active site metal cluster (either  Mo or V).  Mo-dependent nitrogenase is the most common while V-dependent or heterometal independent (Fe-only) are often termed alternative nitrogenases since they have lower activities and are expressed in the absence of  Mo. Phylogenetic evidence indicates that biological nitrogen fixation emerged in an anaerobic, thermophilic ancestor of hydrogenotrophic methanogens and later diversified via lateral gene transfer into anaerobic bacteria, and eventually aerobic bacteria. Isotopic evidence indicates that nitrogenase activity existed at 3.2Ga prior to the advent of oxygenic photosynthesis and rise of oxygen in the atmosphere, implying the presence of favorable environmental conditions for oxygen-sensitive nitrogenase to evolve. Following the proliferation of oxygenic phototrophs, diazotrophic organisms had to develop strategies to protect nitrogenase from oxygen inactivation and generate the right balance of low potential reducing equivalents and cellular energy for growth and nitrogen fixation activity. Here we review the fundamental advances in our understanding of biological nitrogen fixation in the context of the emergence, evolution, and distribution of nitrogenase, with an emphasis placed on key events associated with its emergence and diversification from anoxic into oxic environmental conditions.

F. Mus, D. R. Colman, J. W. Peters, and E. S. Boyd,Geobiological feedbacks, oxygen, and the evolution of nitrogenase, Free radical biology & medicine, 2019. https://doi.org/10.1016/j.freeradbiomed.2019.01.050

Oxygenation of the Earth's atmosphere is thought to have proceeded in two broad steps near the beginning of the Proterozoic eon (2,500 million years ago) and its end (542 million years ago). The oxidation state of the Proterozoic ocean between its beginning and its end and the timing of deep-ocean oxygenation have important implications for the evolutionary course of life on Earth. A new perspective on ocean oxygenation based on the authigenic accumulation of molybdenum in sulfidic black shales is presented.

By 2,650 Myr ago accumulation of authigenic molybdenum from sea water is already seen in shales. The small magnitudes of these enrichments reflect weak or transient sources of dissolved molybdenum before about 2,200 Myr ago, consistent with minimal oxidative weathering of the continents.

At roughly 2,150 Myr ago, more than 200 million years after the initial rise in atmospheric oxygen, in deposited shales enrichments appear which are indicative of persistent and vigorous oxidative weathering.

After about 1,800 Myr ago expansion of sulfidic conditions maintained a mid- Proterozoic molybdenum reservoir at below 20 per cent of the modern concentration, which in turn may have acted as a nutrient feedback limiting the spatiotemporal distribution of euxinic ( sulfidic) bottom waters and perhaps the evolutionary and ecological expansion of eukaryotic organisms(10).

By 551 Myr ago, molybdenum contents reflect a greatly expanded oceanic reservoir due to oxygenation of the deep ocean and corresponding decrease in sulfidic conditions in the sediments and water column.

Scott, C., Lyons, T. W., Bekker, A., Shen, Y., Poulton, S. W., Chu, X., and Anbar, A. D., Tracing the, Nature, 2008, 452, 456-4U5.

See also

Pearce, C. R., Cohen, A. S., Coe, A. L., and Burton, K. W., Molybdenum isotope evidence for global ocean anoxia coupled with perturbations to the carbon cycle during the early Jurassic, Geology, 2008, 36, 231-234.

The nitrogen cycle provides essential nutrients to the biosphere, but its antiquity in modern form is unclear. In a drill core though homogeneous organic- rich shale in the 2.5- billion- year- old Mount McRae Shale, Australia, nitrogen isotope values vary from +1.0 to +7.5 per mil (parts per thousand) and back to +2.5 parts per thousand over similar to 30 meters. These changes evidently record a transient departure from a largely anaerobic to an aerobic nitrogen cycle complete with nitrification and denitrification. Complementary molybdenum abundance and sulfur isotopic values suggest that nitrification occurred in response to a small increase in surface- ocean oxygenation. These data imply that nitrifying and denitrifying microbes had already evolved by the late Archean and were present before oxygen first began to accumulate in the atmosphere

Garvin, J., Buick, R., Anbar, A. D., Arnold, G. L., and Kaufman, A. J., Isotopic Evidence for an Aerobic Nitrogen Cycle in the Latest Archean, Science, 2009, 323, 1045-1048.
Rehder, D., Is vanadium a more versatile target in the activity of primordial life forms than hitherto anticipated?, Organic & Biomolecular Chemistry, 2008, 6, 957-964.

PREBIOTIC EVOLUTION

Green rust: The simple organizing 'seed' of all life?

Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 degrees C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 degrees C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence Fe(II)/Fe(III) oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.

M. J. Russell, Green rust: The simple organizing 'seed' of all life?, Life (Basel), 2018, 8.

An evolutionary tree of key enzymes from the Complex-Iron-Sulfur-Molybdoenzyme (CISM) superfamily distinguishes "ancient" members, i.e. enzymes in the last universal common ancestor (LUCA) of prokaryotes, from more recently evolved subfamilies. The molybdo-enzyme superfamily existed in LUCA. The results are discussed with respect to the nature of bioenergetic substrates available to early life and to problems arising from the low solubility of molybdenum under conditions of the primordial Earth.

Schoepp-Cothenet, B., van Lis, R., Philippot, P.,Magalon, A., Russell, M.J., Nitschke, W., Scientific Reports, 2012, 2, 263. The ineluctable requirement for the trans-iron elements molybdenum and/or tungsten in the origin of life