The evolving redox chemistry and bioavailability of vanadium in deep time

Enigmatic evolution of microbial nitrogen fixation: insights from Earth's past

The evolution of nitrogen fixation undoubtedly altered nearly all corners of the biosphere, given the essential role of nitrogen in the synthesis of biomass. To date, there is no unified view on what planetary conditions gave rise to nitrogen fixation or how these conditions have sustained it evolutionarily. Intriguingly, the concentrations of metals that nitrogenases require to function have changed throughout Earth's history. In this review, we describe the interconnection of the metal and nitrogen cycles with nitrogenase evolution and the importance of ancient ecology in the formation of the modern nitrogen cycle. We argue that exploration of the nitrogen cycle's deep past will provide insights into humanity's immediate environmental challenges centered on nitrogen availability.

Emergence of an Orphan Nitrogenase Protein Following Atmospheric Oxygenation

Molecular innovations within key metabolisms can have profound impacts on element cycling and ecological distribution. Yet, much of the molecular foundations of early evolved enzymes and metabolisms are unknown. Here, we bring one such mystery to relief by probing the birth and evolution of the G-subunit protein, an integral component of certain members of the nitrogenase family, the only enzymes capable of biological nitrogen fixation. The G-subunit is a Paleoproterozoic-age orphan protein that appears more than 1 billion years after the origin of nitrogenases. We show that the G-subunit arose with novel nitrogenase metal dependence and the ecological expansion of nitrogen-fixing microbes following the transition in environmental metal availabilities and atmospheric oxygenation that began ∼2.5 billion years ago. We identify molecular features that suggest early G-subunit proteins mediated cofactor or protein interactions required for novel metal dependency, priming ancient nitrogenases and their hosts to exploit these newly diversified geochemical environments. We further examined the degree of functional specialization in G-subunit evolution with extant and ancestral homologs using laboratory reconstruction experiments. Our results indicate that permanent recruitment of the orphan protein depended on the prior establishment of conserved molecular features and showcase how contingent evolutionary novelties might shape ecologically important microbial innovations.

Vanadium in the Environment: Biogeochemistry and Bioremediation

Vanadium(V) is a highly toxic multivalent, redox-sensitive element. It is widely distributed in the environment and employed in various industrial applications. Interactions between V and (micro)organisms have recently garnered considerable attention. This Review discusses the biogeochemical cycling of V and its corresponding bioremediation strategies. Anthropogenic activities have resulted in elevated environmental V concentrations compared to natural emissions. The global distributions of V in the atmosphere, soils, water bodies, and sediments are outlined here, with notable prevalence in Europe. Soluble V(V) predominantly exists in the environment and exhibits high mobility and chemical reactivity. The transport of V within environmental media and across food chains is also discussed. Microbially mediated V transformation is evaluated to shed light on the primary mechanisms underlying microbial V(V) reduction, namely electron transfer and enzymatic catalysis. Additionally, this Review highlights bioremediation strategies by exploring their geochemical influences and technical implementation methods. The identified knowledge gaps include the particulate speciation of V and its associated environmental behaviors as well as the biogeochemical processes of V in marine environments. Finally, challenges for future research are reported, including the screening of V hyperaccumulators and V(V)-reducing microbes and field tests for bioremediation approaches.

Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation

Nitrogenase is the only known biological enzyme capable of reducing N₂ to bioavailable NH₃. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.

Mineral Element Insiders and Outliers Play Crucial Roles in Biological Evolution

The geosphere of primitive Earth was the source of life’s essential building blocks, and the geochemical interactions among chemical elements can inform the origins of biological roles of each element. Minerals provide a record of the fundamental properties that each chemical element contributes to crustal composition, evolution, and subsequent biological utilization. In this study, we investigate correlations between the mineral species and bulk crustal composition of each chemical element. There are statistically significant correlations between the number of elements that each element forms minerals with (#-mineral-elements) and the log of the number of mineral species that each element occurs in, and between #-mineral-elements and the log of the number of mineral localities of that element. There is a lesser correlation between the log of the crustal percentage of each element and #-mineral-elements. In the crustal percentage vs. #-mineral-elements plot, positive outliers have either important biological roles (S, Cu) or toxic biological impacts (Pb, As), while negative outliers have no biological importance (Sc, Ga, Br, Yb). In particular, S is an important bridge element between organic (e.g., amino acids) and inorganic (metal cofactors) biological components. While C and N rarely form minerals together, the two elements commonly form minerals with H, which coincides with the role of H as an electron donor/carrier in biological nitrogen and carbon fixation. Both abundant crustal percentage vs. #-mineral-elements insiders (elements that follow the correlation) and less abundant outsiders (positive outliers from the correlation) have important biological functions as essential structural elements and catalytic cofactors.

The expanding network of mineral chemistry throughout earth history reveals global shifts in crustal chemistry during the Proterozoic

Earth surface redox conditions are intimately linked to the co-evolution of the geosphere and biosphere. Minerals provide a record of Earth’s evolving surface and interior chemistry in geologic time due to many different processes (e.g. tectonic, volcanic, sedimentary, oxidative, etc.). Here, we show how the bipartite network of minerals and their shared constituent elements expanded and evolved over geologic time. To further investigate network expansion over time, we derive and apply a novel metric (weighted mineral element electronegativity coefficient of variation; wMEE_CV) to quantify intra-mineral electronegativity variation with respect to redox. We find that element electronegativity and hard soft acid base (HSAB) properties are central factors in mineral redox chemistry under a wide range of conditions. Global shifts in mineral element electronegativity and HSAB associations represented by wMEE_CV changes at 1.8 and 0.6 billion years ago align with decreased continental elevation followed by the transition from the intermediate ocean and glaciation eras to post-glaciation, increased atmospheric oxygen in the Phanerozoic, and enhanced continental weathering. Consequently, network analysis of mineral element electronegativity and HSAB properties reveal that orogenic activity, evolving redox state of the mantle, planetary oxygenation, and climatic transitions directly impacted the evolving chemical complexity of Earth’s crust.

Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history

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.

Evolutionary History of Bioessential Elements Can Guide the Search for Life in the Universe

Our understanding of life in the universe comes from one sample, life on Earth. Current and next-generation space missions will target exoplanets as well as planets and moons in our own solar system with the primary goal of detecting, interpreting and characterizing indications of possible biological activity. Thus, understanding life's fundamental characteristics is increasingly critical for detecting and interpreting potential biological signatures elsewhere in the universe. Astrobiologists have outlined the essential roles of carbon and water for life, but we have yet to decipher the rules governing the evolution of how living organisms use bioessential elements. Does the suite of life's essential chemical elements on Earth constitute only one possible evolutionary outcome? Are some elements so essential for biological functions that evolution will select for them despite low availability? How would this play out on other worlds that have different relative element abundances? When we look for life in the universe, or the conditions that could give rise to life, we must learn how to recognize it in extremely different chemical and environmental conditions from those on Earth. We argue that by exposing self-organizing biotic chemistries to different combinations of abiotic materials, and by mapping the evolutionary history of metalloenzyme biochemistry onto geological availabilities of metals, alternative element choices that are very different from life's present-day molecular structure might result. A greater understanding of the paleomolecular evolutionary history of life on Earth will create a predictive capacity for detecting and assessing life's existence on worlds where alternate evolutionary paths might have been taken.

On the Capability of Oxidovanadium(IV) Derivatives to Act as All-Around Catalytic Promoters Since the Prebiotic World

For a long time the biological role of vanadium was not known, while now the possibility of using its derivatives as potential therapeutic agents has given rise to investigations on their probable side effects. Vanadium compounds may inhibit different biochemical processes and lead to a variety of toxic effects and serious diseases. But, on the other hand, vanadium is an essential element for life. In recent years, increasing evidence has been acquired on the possible roles of vanadium in the higher forms of life. Despite several biochemical and physiological functions that have been suggested for vanadium and notwithstanding the amount of the knowledge so far accumulated, it still does not have a clearly defined role in the higher forms of life. What functions could vanadium or its very stable oxidovanadium(IV) derivatives have had in the prebiotic world and in the origins of life? In this review, we have briefly tried to highlight the most useful aspects that can be taken into consideration to give an answer to this still unresolved question and to show the high versatility of the oxidovanadium(IV) group to act as promoter of several oxidation reactions when coordinated with a variety of ligands, including diketones like acylpyrazolones.