Biology subjects

Stueeken, E. E.

Publications and source records attributed to Stueeken, E. E..

4 recordsLinked to original sources

bioRxiv2025

Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

The co-evolution of life and Earth has profoundly transformed global biogeochemical cycles over the past 3.5 billion years. These cycles, in turn, have dictated the availability of essential nutrients like phosphorus, nitrogen, and iron, thereby affecting primary productivity and the scale of the Earths biosphere. Despite the critical role of nutrient limitation in shaping the size and scope of the biosphere, significant uncertainties persist about which nutrients were globally limiting at various points in Earth history. Here, we use a phylogenomic approach to trace the origin and spread of genes associated with nutrient limitation over time. We show that genes associated with phosphorus limitation emerged relatively early in lifes history, whereas genes associated with nitrogen limitation emerged later, closer to the Great Oxidation Event. In terms of iron limitation, we present novel evidence that siderophores, compounds that facilitate iron uptake, may have arisen as early as the Archean. Overall, our results have important implications for understanding how the geosphere has influenced the scale and extent of life on Earth for the past 4 billion years.

bioinformatics↗

bioRxiv2025

Biological molybdenum usage stems back to 3.4 billion years ago

Molybdenum (Mo) is an essential nutrient for most living organisms, serving as a cofactor in a diverse array of molybdoenzymes that catalyze key reactions in several elemental cycles. However, geochemical data suggest that dissolved Mo concentrations in the Archean ocean (before 2.5 billion years ago) were 1-2 orders of magnitude lower than today, raising questions about its bioavailability to early life. Here, we apply a phylogenomic approach to chart the modern biological and environmental distribution of Mo-related enzymes and use phylogenetic reconciliations to reconstruct the evolutionary history of biological Mo usage. Our results reveal the ubiquity of molybdoenzymes across contemporary organisms inhabiting diverse environments. Furthermore, phylogenetic evidence indicates that the earliest molybdoenzymes stem back to the Paleo/Mesoarchean (~3.5-3.0 Gya), facilitating critical energy-harnessing reactions in some of Earths most ancient life forms. Taken together, our findings challenge the prevailing view of limited Mo bioavailability on the anoxic early Earth.

evolutionary biology↗

bioRxiv2022

The evolution and spread of sulfur-cycling enzymes reflect volcanic sulfur sources and the redox state of the early Earth

The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earths redox state, and impacting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. Here, we use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism, but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth. Teaser: Phylogenomics analyses reveal that the evolution of microbial sulfur metabolisms co-evolved with the redox state of the early Earth.

evolutionary biology↗

bioRxiv2020

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 biology↗