An EPR model for predicting the bearing capacity of single and double-strip foundations near earth slope crests.

It is imperative to understand how foundations behave on earthen slopes to accurately predict their allowable carrying capacity in geotechnical engineering. A comprehensive finite element (FE) simulation with PLAXIS 2D was conducted to assess the effects of various parameters on the bearing capacity (BC) of single- and double-strip foundations placed near the earth's slope crest. The specified parameters include foundation width (B) and depth (Df/B); setback distance between the slope edge and foundation (b/B); soil internal friction (ϕ) and cohesion (c); slope inclination (ß); and spacing between foundations (S/B). In addition, the numerically simulated database was used to develop simple mathematical expressions for predicting the capacities in both cases using evolutionary polynomial regression (EPR). The results revealed that the bearing capacity of single- and double-strip foundations increased with an increase in all studied parameters except slope inclination. For single-strip foundations, the outcomes demonstrated that slope inclination has no impact on BC when it is located 6B from the slope edge. However, under interference conditions, the critical center-to-center spacing between foundations is 3-4B, beyond which they behave as individual foundations. Additionally, EPR provides a robust method of predicting the BC of single- and double-strip foundations within slope crests based on the strong correlation of various statistical criteria between simulated and predicted results from training, validation, and testing. Finally, according to sensitivity analysis, in both single and double-strip foundations resting on an earthen slope crest, b/B, B, and ϕ are the most important input parameters that impact the output results.

Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics.

Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life's origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, 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 Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS; <1 µM) appeared around the same time or in the Mesoarchean depending on the reconstruction method. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life later. 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 µM. Our results thus indicate at least local regions of declining phosphate levels through the Archean, possibly linked to phosphate-scavenging Fe(III), 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 expansion of the biosphere at that time.

Space research to explore novel biochemical insights on Earth.

Travel to space has overcome unprecedent technological challenges and this has resulted in transfer of these technological results on Earth to better our lives. Health technology, medical devices, and research advancements in human biology are the first beneficiaries of this transfer. The real breakthrough came with the International Space Station, which endorsed multidisciplinary international scientific collaborations and boosted the research on pathophysiological adaptation of astronauts to life on space. These studies evidenced that life in space appeared to have exposed the astronauts to an accelerated aging-related pathophysiological dysregulation across multiple systems. In this review we emphasize the interaction between several biomarkers and their alteration in concentrations/expression/function by space stress factors. These altered interactions, suggest that different biochemical and hormonal factors, and cell signals, contribute to a complex network of pathophysiological mechanisms, orchestrating the homeostatic dysregulation of various organs/metabolic pathways. The main effects of space travel on altering cell organelles biology, ultrastructure, and cross-talk, have been observed in cell aging as well as in the disruption of metabolic pathways, which are also the causal factor of rare inherited metabolic disorders, one of the major pediatric health issue. The pathophysiologic breakthrough from space research could allow the development of precision health both on Earth and Space by promoting the validation of improved biomarker-based risk scores and the exploration of new pathophysiologic hypotheses and therapeutic targets. Nonstandard abbreviations: International Space Station (ISS), Artificial Intelligence (AI), European Space Agency (ESA), National Aeronautics and Space Agency (NASA), Low Earth Orbit (LEO), high sensitive troponin (hs-cTn), high sensitive troponin I (hs-cTn I), high sensitive troponin T, Brain Natriuretic Peptide (BNP), N terminal Brain Natriuretic Peptide (NT-BNP), cardiovascular disease (CVD), parathyroid hormone (PTH), urinary hydroxyproline (uHP), urinary C- and N-terminal telopeptides (uCTX and uNTX), pyridinoline (PYD), deoxypyridinoline (DPD), half-time (HF), serum Bone Alkaline Phosphatase (sBSAP), serum Alkaline Phosphatase (sAP), Carboxy-terminal Propeptide of Type 1 Procollagen (P1CP), serum Osteocalcin (sOC)), advanced glycation end products (AGEs), glycated hemoglobin A1c (HbA1c), Insulin-like growth factor 1 (IGF1), Growth Hormone (GH), amino acid (AA), ß-hydroxy-ß methyl butyrate (HMB), maple syrup urine disease (MSUD), non-communicable diseases (NCDs).

Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction.

Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.

Considerations for Detecting Organic Indicators of Metabolism on Enceladus.

Enceladus is of interest to astrobiology and the search for life since it is thought to host active hydrothermal activity and habitable conditions. It is also possible that the organics detected on Enceladus may indicate an active prebiotic or biotic system; in particular, the conditions on Enceladus may favor mineral-driven protometabolic reactions. When including metabolism-related biosignatures in Enceladus mission concepts, it is necessary to base these in a clearer understanding of how these signatures could also be produced prebiotically. In addition, postulating which biological metabolisms to look for on Enceladus requires a non-Earth-centric approach since the details of biological metabolic pathways are heavily shaped by adaptation to geochemical conditions over the planet's history. Creating metabolism-related organic detection objectives for Enceladus missions, therefore, requires consideration of how metabolic systems may operate differently on another world, while basing these speculations on observed Earth-specific microbial processes. In addition, advances in origin-of-life research can play a critical role in distinguishing between interpretations of any future organic detections on Enceladus, and the discovery of an extant prebiotic system would be a transformative astrobiological event in its own right.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth.

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

Chapter 9: Life as We Don't Know It.

While Earth contains the only known example of life in the universe, it is possible that life elsewhere is fundamentally different from what we are familiar with. There is an increased recognition in the astrobiology community that the search for life should steer away from terran-specific biosignatures to those that are more inclusive to all life-forms. To start exploring the space of possibilities that life could occupy, we can try to dissociate life from the chemistry that composes it on Earth by envisioning how different life elsewhere could be in composition, lifestyle, medium, and form, and by exploring how the general principles that govern living systems on Earth might be found in different forms and environments across the Solar System. Exotic life-forms could exist on Mars or Venus, or icy moons like Europa and Enceladus, or even as a shadow biosphere on Earth. New perspectives on agnostic biosignature detection have also begun to emerge, allowing for a broader and more inclusive approach to seeking exotic life with unknown chemistry that is distinct from life as we know it on Earth.

Chapter 3: The Origins and Evolution of Planetary Systems.

The materials that form the diverse chemicals and structures on Earth-from mountains to oceans and biological organisms-all originated in a universe dominated by hydrogen and helium. Over billions of years, the composition and structure of the galaxies and stars evolved, and the elements of life, CHONPS, were formed through nucleosynthesis in stellar cores. Climactic events such as supernovae and stellar collisions produced heavier elements and spread them throughout the cosmos, often to be incorporated into new, more metal-rich stars. Stars typically form in molecular clouds containing small amounts of dust through the collapse of a high-density core. The surrounding nebular material is then pulled into a protoplanetary disk, from which planets, moons, asteroids, and comets eventually accrete. During the accretion of planetary systems, turbulent mixing can expose matter to a variety of different thermal and radiative environments. Chemical and physical changes in planetary system materials occur before and throughout the process of accretion, though many factors such as distance from the star, impact history, and level of heating experienced combine to ultimately determine the final geophysical characteristics. In Earth's planetary system, called the Solar System, after the orbits of the planets had settled into their current configuration, large impacts became rare, and the composition of and relative positions of objects became largely fixed. Further evolution of the respective chemical and physical environments of the planets-geosphere, hydrosphere, and atmosphere-then became dependent on their local geochemistry, their atmospheric interactions with solar radiation, and smaller asteroid impacts. On Earth, the presence of land, air, and water, along with an abundance of important geophysical and geochemical phenomena, led to a habitable planet where conditions were right for life to thrive.

Chapter 2: What Is Life?

The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.

Chapter 8: Searching for Life Beyond Earth.

The search for life beyond Earth necessitates a rigorous and comprehensive examination of biosignatures, the types of observable imprints that life produces. These imprints and our ability to detect them with advanced instrumentation hold the key to our understanding of the presence and abundance of life in the universe. Biosignatures are the chemical or physical features associated with past or present life and may include the distribution of elements and molecules, alone or in combination, as well as changes in structural components or physical processes that would be distinct from an abiotic background. The scientific and technical strategies used to search for life on other planets include those that can be conducted in situ to planetary bodies and those that could be observed remotely. This chapter discusses numerous strategies that can be employed to look for biosignatures directly on other planetary bodies using robotic exploration including those that have been deployed to other planetary bodies, are currently being developed for flight, or will become a critical technology on future missions. Search strategies for remote observations using current and planned ground-based and space-based telescopes are also described. Evidence from spectral absorption, emission, or transmission features can be used to search for remote biosignatures and technosignatures. Improving our understanding of biosignatures, their production, transformation, and preservation on Earth can enhance our search efforts to detect life on other planets.

Chapter 6: The Breadth and Limits of Life on Earth.

Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.

RNA-catalyzed evolution of catalytic RNA.

An RNA polymerase ribozyme that was obtained by directed evolution can propagate a functional RNA through repeated rounds of replication and selection, thereby enabling Darwinian evolution. Earlier versions of the polymerase did not have sufficient copying fidelity to propagate functional information, but a new variant with improved fidelity can replicate the hammerhead ribozyme through reciprocal synthesis of both the hammerhead and its complement, with the products then being selected for RNA-cleavage activity. Two evolutionary lineages were carried out in parallel, using either the prior low-fidelity or the newer high-fidelity polymerase. The former lineage quickly lost hammerhead functionality as the population diverged toward random sequences, whereas the latter evolved new hammerhead variants with improved fitness compared to the starting RNA. The increase in fitness was attributable to specific mutations that improved the replicability of the hammerhead, counterbalanced by a small decrease in hammerhead activity. Deep sequencing analysis was used to follow the course of evolution, revealing the emergence of a succession of variants that progressively diverged from the starting hammerhead as fitness increased. This study demonstrates the critical importance of replication fidelity for maintaining heritable information in an RNA-based evolving system, such as is thought to have existed during the early history of life on Earth. Attempts to recreate RNA-based life in the laboratory must achieve further improvements in replication fidelity to enable the fully autonomous Darwinian evolution of RNA enzymes as complex as the polymerase itself.

Chapter 7: Assessing Habitability Beyond Earth.

All known life on Earth inhabits environments that maintain conditions between certain extremes of temperature, chemical composition, energy availability, and so on (Chapter 6). Life may have emerged in similar environments elsewhere in the Solar System and beyond. The ongoing search for life elsewhere mainly focuses on those environments most likely to support life, now or in the past-that is, potentially habitable environments. Discussion of habitability is necessarily based on what we know about life on Earth, as it is our only example. This chapter gives an overview of the known and presumed requirements for life on Earth and discusses how these requirements can be used to assess the potential habitability of planetary bodies across the Solar System and beyond. We first consider the chemical requirements of life and potential feedback effects that the presence of life can have on habitable conditions, and then the planetary, stellar, and temporal requirements for habitability. We then review the state of knowledge on the potential habitability of bodies across the Solar System and exoplanets, with a particular focus on Mars, Venus, Europa, and Enceladus. While reviewing the case for the potential habitability of each body, we summarize the most prominent and impactful studies that have informed the perspective on where habitable environments are likely to be found.

Gazing into the abyss: A glimpse into the diversity, distribution, and behaviour of heterotrophic protists from the deep-sea floor.

The benthic biome of the deep-sea floor, one of the largest biomes on Earth, is dominated by diverse and highly productive heterotrophic protists, second only to prokaryotes in terms of biomass. Recent evidence suggests that these protists play a significant role in ocean biogeochemistry, representing an untapped source of knowledge. DNA metabarcoding and environmental sample sequencing have revealed that deep-sea abyssal protists exhibit high levels of specificity and diversity across local regions. This review aims to provide a comprehensive summary of the known heterotrophic protists from the deep-sea floor, their geographic distribution, and their interactions in terms of parasitism and predation. We offer an overview of the most abundant groups and discuss their potential ecological roles. We argue that the exploration of the biodiversity and species-specific features of these protists should be integrated into broader deep-sea research and assessments of how benthic biomes may respond to future environmental changes.

Disentangling the variability of symbiotic nitrogen fixation rate and the controlling factors.

Symbiotic nitrogen (N) fixation (SNF), replenishing bioavailable N for terrestrial ecosystems, exerts decisive roles in N cycling and gross primary production. Nevertheless, it remains unclear what determines the variability of SNF rate, which retards the accurate prediction for global N fixation in earth system models. This study synthesized 1230 isotopic observations to elucidate the governing factors underlying the variability of SNF rate. The SNF rates varied significantly from 3.69 to 12.54 g N m-2 year-1 across host plant taxa. The traits of host plant (e.g. biomass characteristics and taxa) far outweighed soil properties and climatic factors in explaining the variations of SNF rate, accounting for 79.0% of total relative importance. Furthermore, annual SNF yield contributed to more than half of N uptake for host plants, which was consistent across different ecosystem types. This study highlights that the biotic factors, especially host plant traits (e.g. biomass characteristics and taxa), play overriding roles in determining SNF rate compared with soil properties. The suite of parameters for SNF lends support to improve N fixation module in earth system models that can provide more confidence in predicting bioavailable N changes in terrestrial ecosystems.

Hydrogeological controls on microbial activity and habitability in the Precambrian continental crust.

Earth's deep continental subsurface is a prime setting to study the limits of life's relationship with environmental conditions and habitability. In Precambrian crystalline rocks worldwide, deep ancient groundwaters in fracture networks are typically oligotrophic, highly saline, and locally inhabited by low-biomass communities in which chemolithotrophic microorganisms may dominate. Periodic opening of new fractures can lead to penetration of surface water and/or migration of fracture fluids, both of which may trigger changes in subsurface microbial composition and activity. These hydrogeological processes and their impacts on subsurface communities may play a significant role in global cycles of key elements in the crust. However, to date, considerable uncertainty remains on how subsurface microbial communities may respond to these changes in hydrogeochemical conditions. To address this uncertainty, the biogeochemistry of Thompson mine (Manitoba, Canada) was investigated. Compositional and isotopic analyses of fracture waters collected here at ~1 km below land surface revealed different extents of mixing between subsurface brine and (paleo)meteoric waters. To investigate the effects this mixing may have had on microbial communities, the Most Probable Number technique was applied to test community response for a total of 13 different metabolisms. The results showed that all fracture waters were dominated by viable heterotrophic microorganisms which can utilize organic materials associated with aerobic/facultative anaerobic processes, sulfate reduction, or fermentation. Where mixing between subsurface brines and (paleo)meteoric waters occurs, the communities demonstrate higher cell densities and increased viable functional potentials, compared to the most saline sample. This study therefore highlights the connection between hydrogeologic heterogeneity and the heterogeneity of subsurface ecosystems in the crystalline rocks, and suggests that hydrogeology can have a considerable impact on the scope and scale of subsurface microbial communities on Earth and potentially beyond.