Biology subjects

Boden, J. S.

Publications and source records attributed to Boden, J. S..

8 recordsLinked to original sources

bioRxiv2026

Tracing the evolution of microbial alkaline phosphatases and their role in phosphorus recycling through time

Phosphorus (P) recycling in seawater is critical for maintaining nutrient availability and marine primary productivity. This process is catalyzed by alkaline phosphatases enzymes, which hydrolyze dissolved organic phosphorus (DOP) compounds, releasing inorganic P for cellular assimilation. Here, we reconstructed the evolutionary history of three major alkaline phosphatase families through deep time using phylogenetic reconciliation across the tree of life. We further quantified their distribution and cellular localization across major metabolic groups using extant genomes to assess how the oceans capacity for P regeneration has changed through time. Our results demonstrate that alkaline phosphatases emerged early in the Archaean, indicating that DOP has sustained marine ecosystems for most of Earths history. A pronounced expansion and diversification of alkaline phosphatases occurred during the Neoproterozoic, coinciding with the rise and ecological diversification of algae. Across metabolic groups, extracellular alkaline phosphatases are particularly concentrated in ferric iron reducers, fermenters, and aerobic heterotrophs, but are comparatively rare in other metabolisms. This distribution suggests that the efficiency of marine P recycling has been strongly influenced by prevailing metabolic strategies and environmental redox conditions. Overall, our results provide new insights into the enzymatic drivers of marine P cycling and the mechanisms that maintained marine productivity as Earths surface became progressively oxygenated and biologically complex.

microbiology↗

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

Microbial exoenzymes catalyzed the transition to an oxygenated Earth

Microbial exoenzymes--extracellular enzymes secreted to degrade complex organic polymers-- are essential for recycling carbon and nutrients, thus sustaining primary productivity in todays oceans1. Yet, their evolutionary history and role in shaping Earths early biosphere remain entirely unexplored. Here, we trace the origins of microbial exoenzymes and reveal their previously unrecognized role in driving planetary oxygenation. Our results show that exoenzymes are more common in microorganisms utilizing high-energy metabolisms, likely reflecting the energetic costs of enzyme biosynthesis and secretion. They are especially advantageous in environments rich in particulate organic matter (POM). A refined carbon cycle model indicates that early Archean oceans offered few such habitats, as low productivity and intense UV radiation rapidly photodegraded POM. However, with a Paleoproterozoic rise of atmospheric oxygen2, increased oxidative weathering boosted marine primary productivity and POM accumulation3, creating conditions favoring exoenzyme evolution. Molecular clock analyses further indicate that alkaline phosphatase, a key phosphorus-releasing exoenzyme, had likely emerged with the permanent rise of oxygen, enabling more efficient phosphorus recycling. We propose that exoenzymes initiated a positive feedback loop: by accelerating nutrient regeneration, they fueled cyanobacterial productivity and oxygen release, which in turn favored greater exoenzyme capacity, reinforcing long-term oxygenation of the planet.

microbiology↗

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↗

bioRxiv2024

Early-branching cyanobacteria up-regulate superoxide dismutase activity under a simulated early Earth anoxic atmosphere.

The evolution of oxygenic photosynthesis during the Archean (4-2.5 Ga), required the presence of complementary reducing pathways to maintain the cellular redox balance. While the timing of the evolution of superoxide dismutases (SODs), enzymes that convert superoxide to hydrogen peroxide, within the Bacteria and Archaea is not resolved, SODs containing copper and zinc in the reaction centre (CuZnSOD) were the first SODs estimated to appear in photosynthetic cyanobacteria, [≥] 2.93 Ga. Here we analysed the SOD gene expression and activity in the deep branching strain, Pseudanabaena sp. PCC7367. It releases more O2 and exhibits significantly higher growth rates (p<0.001) and protein and glycogen contents (p<0.05) under anoxic conditions compared to control cultures grown under present oxygen rich atmospheres in low CO2 (LC) or high CO2 (HC), prompting the question as to whether this correlates to higher cellular SOD activity under anoxic Archean simulated conditions. Expression of sodB encoding an iron containing SOD (FeSOD) and sodC, encoding a CuZnSOD, strongly correlated with increased extracellular O2 levels (p<0.001), while transcription of sodA, encoding a manganese containing (MnSOD), correlated to SOD activity during the day (p=0.019), when medium O2 concentrations were the highest. Cytosolic SOD activity was significantly higher (p<0.001) in anoxic cultures, two hrs before nightfall compared to oxic growth conditions. Night-time combined sodABC transcription in stirred cultures was significantly reduced (p<0.05) under anoxic conditions at elevated CO2 levels, as were medium O2 levels (p[≤]0.001), when compared to cultures grown under present-day oxic conditions with low CO2. Total cytosolic SOD activity remained comparable, suggesting that the replacement rate of SOD is higher under modern-day conditions than on early Earth. Our data suggest that the early branching cyanobacterium Pseudanabaena sp. PCC7367 may have retained ancestral features permitting it to thrive in its ecological niche as a benthic mat in shallow water marine environments.

microbiology↗

bioRxiv2023

Evolution of Multicellularity Genes in the Lead Up to the Great Oxidation Event

Cyanobacteria are among the most morphologically diverse prokaryotic phyla on Earth. Their morphotypes range from unicellular to multicellular filaments, yet mechanisms underlying the evolution of filamentous morphologies remain unknown. Here, we implement phylogenomic, Bayesian molecular clock and gene-tree-species-tree reconciliation analyses to estimate when genes encoding cell-cell joining structures first evolved. We also characterise septal structures and measure intercellular communication rates in non-model and early-branching filamentous strains. Our results suggest that genes encoding septal proteins (namely sepJ, sepI, and fraE) and potentially pattern formation (hetR) evolved in the Neoarchaean [~]2.6-2.7 billion years (Ga) ago. Later, at the start of the Great Oxygenation Event [~]2.5 Ga, genes involved in cellular differentiation (namely hetZ, patU3 and hglK) appeared. Our results predict that early-branching lineages like Pseudanabaena were capable of intercellular communication, but further innovations in cellular differentiation were needed to drive ecological expansion on a scale large enough to permanently oxygenate Earths atmosphere.

evolutionary biology↗

bioRxiv2023

Timing the Evolution of Phosphorus-Cycling 1 Enzymes Through Geological Time

SUMMARY PARAGRAPHPhosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during lifes origin and early evolution, vary over several orders of magnitude1-10. While reduced phosphorus species may have served as alternative substrates to phosphate11, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the mid-Archean (ca. 3.2 Ga) and are consistent with phosphate concentrations above modern levels (>3 M). The first gene optimized for low phosphate levels (pstS; <1 M) appeared around 2.9 Ga. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life in the Neoarchean to Paleoproterozoic (ca. 2.6 to 1.8 Ga). This includes phosphonate-catabolising CP-lyases, phosphite-oxidising pathways and hypophosphite-oxidising pathways. CP-lyases are particularly abundant in dissolved phosphate concentrations below 0.1 M. Our results thus indicate declining phosphate levels through the Archean, possibly linked to increasing deposition of phosphate-scavenging iron oxides, which may have limited productivity. However, reduced phosphorus species did not become widely used until after the Paleoproterozoic Great Oxidation Event (2.3 Ga), possibly linked to an expansion of the biosphere at that time.

evolutionary biology↗

bioRxiv2021

Lack of Fe(II) transporters in basal Cyanobacteria complicates iron uptake in ferruginous Archean oceans.

Introductory paragraphCyanobacteria oxygenated Earths atmosphere during the Great Oxygenation Event (GOE) through oxygenic photosynthesis. Their high iron requirement was presumed met by high levels of Fe(II) in the anoxic Archean ocean. Here we show that most basal Cyanobacteria cannot synthesize the primary Fe(II) transporter, FeoB. Relaxed molecular clock analyses estimate the arrival of FeoB, as well as the Fe(III) transporters, cFTR1 and FutB, in the Cyanobacteria after the GOE. Furthermore Pseudanabaena sp. PCC7367, a basal marine, benthic strain grown under simulated Archean conditions, constitutively expressed cftr1, even after the addition of Fe(II). By utilizing gene expression studies under a simulated Archean atmosphere, as well as comparative genomics, phylogenetics and molecular clock analyses, this study identified a need to reappraise iron uptake in ancestral Cyanobacteria, as genetic profiling suggests that scavenging of siderophore bound Fe(III), rather than Fe(II), appears to have been the means of iron acquisition prior to the GOE.

evolutionary biology↗