The Great Oxygenation Event as a consequence of ecological dynamics modulated by planetary change

Analogs of Precambrian microbial communities formed de novo in Caucasian mineral water aquifers

The microbiome of deep continental aquifers is considered the most slowly evolving part of the biosphere. The Yessentukskoye Mineral Water Basin (YMWB), located in the pre-Caucasus region, contains three closely spaced but distinct aquifers, the Upper Cretaceous, the Lower Cretaceous, and the Upper Jurassic, which represent unique objects for subsurface biosphere research due to gas-hydrogeochemical and thermal anomalies of the area. We analyzed the geological and hydrogeochemical parameters of the three aquifers and a recharge area of the YMWB and investigated their microbial communities using metagenomic and cultivation-based approaches within a long-term survey. Correlation analysis of the obtained data revealed stable and highly stratified microbial communities inhabiting four distinct ecosystems. Their structure and the metabolic traits of their prokaryotic populations were similar to those presumed to have dominated the Earth's biosphere during several critical periods of its evolutionary history, that is, the Early Archean, the period of banded iron formations accumulation, and the Great Oxidation Event. Among the YMWB strata, the Upper Jurassic aquifer, supersaturated with CO2, influenced by magmatic activity, and highly enriched with thermophilic autotrophic hydrogenotrophic acetogens, turned out to be the first described modern ecosystem based on the primary production by a process predicted to support the Last Universal Common Ancestor (LUCA). The characterization of the YMWB microbial communities reveals a contemporary model environment of the early stages of Earth's development and thus contributes to the understanding of the evolutionary traits in microbial populations that may have played a critical role in the formation of the modern biosphere.IMPORTANCEContinental subsurface environments are estimated to harbor up to one-fifth of the planet's total biomass, representing the most stable and slowly evolving part of the biosphere. Among the deep subsurface inhabitants, the microbial communities of drinking mineral waters remain the least studied. Our interdisciplinary study of the Yessentukskoye Mineral Water Basin shows how hydrochemical and hydrodynamic factors shape different subsurface ecosystems, whose microbial populations influence the composition of mineral waters. A comprehensive analysis reveals the similarity of these ecosystems to those predicted for the early Earth. The deepest of the studied aquifers is the first described modern ecosystem with the most probable primary producer performing hydrogenotrophic acetogenesis. Thus, our results contribute to the understanding of the genesis of modern drinking water resources and expand the knowledge of the evolutionary traits that may have played a critical role in the formation of the Earth's biosphere.

Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology

Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.

New records on toxic cyanobacteria from Brazil: Exploring their occurrence and geography

Cyanobacterial Harmful Algal Blooms (CyanoHABs) pose a significant threat to communities globally, impacting ecosystems and public health. This study provides an in-depth review of the current state of cyanotoxins and the distribution of CyanoHABs species in Brazil, while also detailing the methods used for their detection. Four hundred and twenty-one incidents were analyzed from 1993 to 2021, compiling cyanotoxin records and toxic CyanoHABs occurrences. The investigation begins with the first detection of microcystins in 1994 and highlights pivotal moments, like the 1996 "Caruaru Syndrome" outbreak. This event encouraged research and updated cyanotoxin-monitoring guidelines. The Brazilian drought period of 2015-2016 exacerbated cyanobacterial growth and saxitoxin levels, coinciding with Zika-related microcephaly. This study delves into methods used for cyanotoxin analysis, including ELISA, bioassays, HPLC, and LC-MS. Additionally, we investigated the toxicity of 37 cyanobacterial strains isolated from various Brazilian environments. Extracts were tested against Artemia salina and analyzed by LC-MS. Results revealed toxicity in extracts from 49 % of cyanobacterial strains. LC-MS results were analyzed using GNPS MS/MS molecular networking for comparing experimental spectra with those of cyanotoxin standards against in-house databases and the existing literature. Our research underscores the variability in cyanotoxin production among species and over time, extending beyond microcystins. LC-MS results, interpreted through the GNPS platform, revealed six cyanotoxin groups in Brazilian strains. Yet, compounds present in 75 % of the toxic extracts remained unidentified. Further research is crucial for fully comprehending the impact of potentially harmful organisms on water quality and public health management strategies. The study highlights the urgent need for continuously monitoring cyanobacteria and the cyanotoxin inclusion of management in public health policies.

The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise

Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Tryptophan extends the life of cytochrome P450

Powerfully oxidizing enzymes need protective mechanisms to prevent self-destruction. The flavocytochrome P450 BM3 from Priestia megaterium (P450BM3) is a self-sufficient monooxygenase that hydroxylates fatty acid substrates using O2 and NADPH as co-substrates. Hydroxylation of long-chain fatty acids (≥C14) is well coupled to O2 and NADPH consumption, but shorter chains (≤C12) are more poorly coupled. Hydroxylation of p-nitrophenoxydodecanoic acid by P450BM3 produces a spectrophotometrically detectable product wherein the coupling of NADPH consumption to product formation is just 10%. Moreover, the rate of NADPH consumption is 1.8 times that of O2 consumption, indicating that an oxidase uncoupling pathway is operative. Measurements of the total number of enzyme turnovers before inactivation (TTN) indicate that higher NADPH concentrations increase TTN. At lower NADPH levels, added ascorbate increases TTN, while a W96H mutation leads to a decrease. The W96 residue is about 7 Å from the P450BM3 heme and serves as a gateway residue in a tryptophan/tyrosine (W/Y) hole transport chain from the heme to a surface tyrosine residue. The data indicate that two oxidase pathways protect the enzyme from damage by intercepting the powerfully oxidizing enzyme intermediate (Compound I) and returning it to its resting state. At high NADPH concentrations, reducing equivalents from the flavoprotein are delivered to Compound I by the usual reductase pathway. When NADPH is not abundant, however, oxidizing equivalents from Compound I can traverse a W/Y chain, arriving at the enzyme surface where they are scavenged by reductants. Ubiquitous tryptophan/tyrosine chains in highly oxidizing enzymes likely perform similar protective functions.

Coenzyme Q10 and nicotinamide nucleotide transhydrogenase: Sentinels for mitochondrial hydrogen peroxide signaling

Mitochondria use hydrogen peroxide (H2O2) as a mitokine for cell communication. H2O2 output for signaling depends on its rate of production and degradation, both of which are strongly affected by the redox state of the coenzyme Q10 (CoQ) pool and NADPH availability. Here, we propose the CoQ pool and nicotinamide nucleotide transhydrogenase (NNT) have evolved to be central modalities for mitochondrial H2O2 signaling. Both factors play opposing yet equally important roles in dictating H2O2 availability because they are connected to one another by two central parameters in bioenergetics: electron supply and Δp. The CoQ pool is the central point of convergence for electrons from various dehydrogenases and the electron transport chain (ETC). The increase in Δp creates a significant amount of protonic backpressure on mitochondria to promote H2O2 genesis through CoQ pool reduction. These same factors also drive the activity of NNT, which uses electrons and the Δp to eliminate H2O2. In this way, electron supply and the magnitude of the Δp manifests as a redox connection between the two sentinels, CoQ and NNT, which serve as opposing yet equally important forces required for budgeting H2O2. Taken together, CoQ and NNT are sentinels linked through mitochondrial bioenergetics to manage H2O2 availability for interorganelle and intercellular redox signaling.

Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity

Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co-evolution of life and Earth.

Intracellular energy production and distribution in hypoxia

The hydrolysis of ATP is the primary source of metabolic energy for eukaryotic cells. Under physiological conditions, cells generally produce more than sufficient levels of ATP to fuel the active biological processes necessary to maintain homeostasis. However, mechanisms underpinning the distribution of ATP to subcellular microenvironments with high local demand remain poorly understood. Intracellular distribution of ATP in normal physiological conditions has been proposed to rely on passive diffusion across concentration gradients generated by ATP producing systems such as the mitochondria and the glycolytic pathway. However, subcellular microenvironments can develop with ATP deficiency due to increases in local ATP consumption. Alternatively, ATP production can be reduced during bioenergetic stress during hypoxia. Mammalian cells therefore need to have the capacity to alter their metabolism and energy distribution strategies to compensate for local ATP deficits while also controlling ATP production. It is highly likely that satisfying the bioenergetic requirements of the cell involves the regulated distribution of ATP producing systems to areas of high ATP demand within the cell. Recently, the distribution (both spatially and temporally) of ATP-producing systems has become an area of intense investigation. Here, we review what is known (and unknown) about intracellular energy production and distribution and explore potential mechanisms through which this targeted distribution can be altered in hypoxia, with the aim of stimulating investigation in this important, yet poorly understood field of research.

SO2 Photodissociation at 193 nm Directly Forms S(3P) + O2(3Σg-): Implications for the Archean Atmosphere on Earth

It is well-documented that photodissociation of SO₂ at λ = 193 nm produces O(³P_j) + SO X(³Σ^-). We provide experimental evidence of a new product channel from one-photon absorption producing S(³P_j) + O₂ X(³Σ_g^-) in 2-4% yield. We probe the reactant and all products with time-resolved photoelectron photoion coincidence spectroscopy. High-level ab initio calculations suggest that the new product channel can only occur on the ground-state potential energy surface through internal conversion from the excited state, followed by isomerization to a transient SOO intermediate. Classical trajectories on the ground-state potential energy surface with random initial conditions qualitatively reproduce the experimental yields. This unexpected photodissociation pathway may help reconcile discrepancies in sulfur mass-independent fractionation mechanisms in Earth's geologic history, which shape our understanding of the Archean atmosphere and the Great Oxygenation Event in Earth's evolution.

A New Ecological and Evolutionary Perspective on the Emergence of Oxygenic Photosynthesis

In this hypothesis article, we propose that the timing of the evolution of oxygenic photosynthesis and the diversification of cyanobacteria is firmly tied to the geological evolution of Earth in the Mesoarchean to Neoarchean. Specifically, the diversification of species capable of oxygenic photosynthesis is tied to the growth of subaerial (above sea-level/terrestrial) continental crust, which provided niches for their diversification. Moreover, we suggest that some formerly aerobic bacterial lineages evolved to become anoxygenic photosynthetic as a result of changes in selection following the reintroduction of ferruginous conditions in the oceans at 1.88 GYa. Both conclusions are fully compatible with phylogenetic evidence. The hypothesis carries with it a predictive component-at least for terrestrial organisms-that the development and expansion of photosynthesis species was dependent on the geological evolution of Earth.

A Short Tale of the Origin of Proteins and Ribosome Evolution

Proteins are the workhorses of the cell and have been key players throughout the evolution of all organisms, from the origin of life to the present era. How might life have originated from the prebiotic chemistry of early Earth? This is one of the most intriguing unsolved questions in biology. Currently, however, it is generally accepted that amino acids, the building blocks of proteins, were abiotically available on primitive Earth, which would have made the formation of early peptides in a similar fashion possible. Peptides are likely to have coevolved with ancestral forms of RNA. The ribosome is the most evident product of this coevolution process, a sophisticated nanomachine that performs the synthesis of proteins codified in genomes. In this general review, we explore the evolution of proteins from their peptide origins to their folding and regulation based on the example of superoxide dismutase (SOD1), a key enzyme in oxygen metabolism on modern Earth.

Long-distance facilitation of coastal ecosystem structure and resilience

“Red Beach” ecosystems along the Yellow Sea coastline are biodiversity hotspots critical for migratory shorebirds of the East Asian–Australasian Flyway. Satellite images show that these ecosystems have been shrinking markedly in recent decades. The reasons for this loss are unknown. Here, we reveal a landscape-scale biotic interaction driven by the destructive effect of invasive cordgrass on native coastal saltmarsh ecosystems that has progressively emerged over the past four decades. In contrast to previous studies showing positive effects of long-distance interactions, our study demonstrates that this negative interaction operating over 10 km is leading to the extinction of the “Red Beach” ecosystem and will dramatically impact ecosystem resilience to sea-level rise in the coming decades.

Biotic interactions that hierarchically organize ecosystems by driving ecological and evolutionary processes across spatial scales are ubiquitous in our biosphere. Biotic interactions have been extensively studied at local and global scales, but how long-distance, cross-ecosystem interactions at intermediate landscape scales influence the structure, function, and resilience of ecological systems remains poorly understood. We used remote sensing, modeling, and field data to test the hypothesis that the long-distance impact of an invasive species dramatically affects one of the largest tidal flat ecosystems in East Asia. We found that the invasion of exotic cordgrass Spartina alterniflora can produce long-distance effects on native species up to 10 km away, driving decadal coastal ecosystem transitions. The invasive cordgrass at low elevations facilitated the expansion of the native reed Phragmites australis at high elevations, leading to the massive loss and reduced resilience of the iconic Suaeda salsa “Red Beach” marshes at intermediate elevations, largely as a consequence of reduced soil salinity across the landscape. Our results illustrate the complex role that long-distance interactions can play in shaping landscape structure and ecosystem resilience and in bridging the gap between local and global biotic interactions.

From manganese oxidation to water oxidation: assembly and evolution of the water-splitting complex in photosystem II

The manganese cluster of photosystem II has been the focus of intense research aiming to understand the mechanism of H₂O-oxidation. Great effort has also been applied to investigating its oxidative photoassembly process, termed photoactivation that involves the light-driven incorporation of metal ions into the active Mn₄CaO₅ cluster. The knowledge gained on these topics has fundamental scientific significance, but may also provide the blueprints for the development of biomimetic devices capable of splitting water for solar energy applications. Accordingly, synthetic chemical approaches inspired by the native Mn cluster are actively being explored, for which the native catalyst is a useful benchmark. For both the natural and artificial catalysts, the assembly process of incorporating Mn ions into catalytically active Mn oxide complexes is an oxidative process. In both cases this process appears to share certain chemical features, such as producing an optimal fraction of open coordination sites on the metals to facilitate the binding of substrate water, as well as the involvement of alkali metals (e.g., Ca²⁺) to facilitate assembly and activate water-splitting catalysis. This review discusses the structure and formation of the metal cluster of the PSII H₂O-oxidizing complex in the context of what is known about the formation and chemical properties of different Mn oxides. Additionally, the evolutionary origin of the Mn₄CaO₅ is considered in light of hypotheses that soluble Mn²⁺ was an ancient source of reductant for some early photosynthetic reaction centers ('photomanganotrophy'), and recent evidence that PSII can form Mn oxides with structural resemblance to the geologically abundant birnessite class of minerals. A new functional role for Ca²⁺ to facilitate sustained Mn²⁺ oxidation during photomanganotrophy is proposed, which may explain proposed physiological intermediates during the likely evolutionary transition from anoxygenic to oxygenic photosynthesis.

The strange history of atmospheric oxygen

Many of us think a lot about oxygen. This includes how the normal body handles oxygen in health, but particularly how this is complicated by lung disease. Few of us are aware that as human inhabitants of the earth, we have a unique privilege. This is that as air breathers, we and most other animals on Earth, are the only living creatures in the known universe that have unlimited supply of oxygen. This situation came about through one of the greatest miracles of nature, that is photosynthesis, the ability to release oxygen from water using the energy of sunlight. One consequence of this was that the first atmospheric oxygen came from the metabolism of microorganisms, the cyanobacteria, that used photosynthesis, but for which oxygen was an unwanted by-product. In fact, the oxygen had to be discarded for the organisms to thrive. When a major increase of oxygen concentration in the atmosphere occurred some 2 billion years ago, and the partial pressure of oxygen in the air rose to perhaps 200 mmHg, this Great Oxidation Event as it was called, was a death sentence for the large population of anaerobic animals for whom oxygen was toxic. Today much of the oxygen in the atmosphere comes from photosynthesis in microorganisms, including the cyanobacteria, and the recently discovered Prochlorococcus, that discard this unwanted by-product. The result is that the PO2 in our atmosphere at sea level remains nearly constant at about 150 mm Hg, although the factors responsible for this are not understood.

Autophagy and longevity: Evolutionary hints from hyper-longevous mammals

Autophagy is a fundamental multi-tasking adaptive cellular degradation and recycling strategy. Following its causal implication in age-related decline, autophagy is currently among the most broadly studied and challenged mechanisms within aging research. Thanks to these efforts, new cellular nodes interconnected with this phylogenetically ancestral pathway and unexpected roles of autophagy-associated genetic products are unveiled daily, yet the history of functional adaptations of autophagy along its evolutive trail is poorly understood and documented. Autophagy is traditionally studied in canonical and research-wise convenient model organisms such as yeast and mice. However, unconventional animal models endowed with extended longevity and exemption from age-related diseases offer a privileged perspective to inquire into the role of autophagy in the evolution of longevity. In this mini review we retrace the appearance and functions evolved by autophagy in eukaryotic cells and its protective contribution in the pathophysiology of aging.