Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.

Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles.

Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.

Unlabelled: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.

Ultrafast Photoflash Synthesis of High-Entropy Oxide Nanoparticles.

High-entropy metal oxides (HEOs) have recently received growing attention for broad energy conversion and storage applications due to their tunable properties. HEOs typically involve the combination of multiple metal cations in a single oxide lattice, thus bringing distinctive structures, controllable elemental composition, and tunable functional properties. Many synthesis methods for HEOs have been reported, such as solid-state reactions and carbon thermal shock methods.

Global insights into the genome dynamics of associated with antimicrobial resistance, virulence, and genomic adaptations among clonal lineages.

Background: is a significant cause of healthcare-associated infections, with rising antimicrobial resistance complicating treatment. This study offers a genomic analysis of , focusing on sequence types (STs), global distribution, antibiotic resistance genes, and virulence factors in its chromosomal and plasmid DNA.

Methods: A total of 19,711 genomes were retrieved from GenBank.

Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020.

Swine influenza A viruses (swIAVs) are a major cause of respiratory disease in pigs worldwide, presenting significant economic and health risks. These viruses can reassort, creating new strains with varying pathogenicity and cross-species transmissibility. This study aimed to monitor the genetic and antigenic evolution of swIAV in France from 2019 to 2022.

Spatiotemporal variation in size-dependent growth rates in small isolated populations of Arctic charr ().

As a key life-history trait, growth rates are often used to measure individual performance and to inform parameters in demographic models. Furthermore, intraspecific trait variation generates diversity in nature. Therefore, partitioning out and understanding drivers of spatiotemporal variation in growth rate is of fundamental interest in ecology and evolution.

Directional Selection and Evolution of Polygenic Traits in Eastern Eurasia: Insights from Ancient DNA.

This study explores directional selection on physical and psychosocial phenotypes in Eastern Eurasian populations, utilizing a dataset of 1245 ancient genomes. By analyzing polygenic scores (PGS) for traits including height, educational attainment (EA), IQ, autism, schizophrenia, and others, we observed significant temporal trends spanning the Holocene era. The results suggest positive selection for cognitive-related traits such as IQ, EA and autism spectrum disorder (ASD), alongside negative selection for anxiety and depression.

Morphological and molecular phylogeny of sp. (Digenea: Clinostomidae) metacercariae, using DNA barcode from a South American freshwater fish.

Here, we present a comprehensive morphological and molecular phylogenetic analysis of sp. (Digenea: Clinostomidae) metacercariae parasitizing two freshwater fish species from Southeast Brazil: (piranha) and (tambuatá). The morphological examination revealed distinct characteristics of metacercariae in each host.

Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age.

A comprehensive understanding of the evolution of the immune landscape in humans across the entire lifespan at single-cell transcriptional and protein levels, during development, maturation and senescence is currently lacking. We recruited a total of 220 healthy volunteers from the Shanghai Pudong Cohort (NCT05206643), spanning 13 age groups from 0 to over 90 years, and profiled their peripheral immune cells through single-cell RNA-sequencing coupled with single T cell and B cell receptor sequencing, high-throughput mass cytometry, bulk RNA-sequencing and flow cytometry validation experiments. We revealed that T cells were the most strongly affected by age and experienced the most intensive rewiring in cell-cell interactions during specific age.

An evaporite sequence from ancient brine recorded in Bennu samples.

Evaporation or freezing of water-rich fluids with dilute concentrations of dissolved salts can produce brines, as observed in closed basins on Earth and detected by remote sensing on icy bodies in the outer Solar System. The mineralogical evolution of these brines is well understood in regard to terrestrial environments, but poorly constrained for extraterrestrial systems owing to a lack of direct sampling. Here we report the occurrence of salt minerals in samples of the asteroid (101955) Bennu returned by the OSIRIS-REx mission.

Global meta-analysis shows action is needed to halt genetic diversity loss.

Mitigating loss of genetic diversity is a major global biodiversity challenge. To meet recent international commitments to maintain genetic diversity within species, we need to understand relationships between threats, conservation management and genetic diversity change. Here we conduct a global analysis of genetic diversity change via meta-analysis of all available temporal measures of genetic diversity from more than three decades of research.

Genomes reveal pervasive distant hybridization in nature among cyprinid fishes.

Background: Genomic data have unveiled a fascinating aspect of the evolutionary past, showing that the mingling of different species through hybridization has left its mark on the histories of numerous life forms. However, the relationship between hybridization events and the origins of cyprinid fishes remains unclear.

Results: In this study, we generated de novo assembled genomes of 8 cyprinid fishes and conducted phylogenetic analyses on 24 species.

The developmental and genetic basis of male genitalia evolution in Drosophilids.

Reproductive organs are among the most variable and rapidly evolving structures in the animal kingdom, probably due to sexual selection. In insects, the diverse morphology of male genitalia is often one of the few visible characteristics that can reliably distinguish closely related species, making it crucial for taxonomic classification. Consistent with this, males of the model organism Drosophila melanogaster and its closely related species display remarkable variations in genital morphology.

Swarm systems as a platform for open-ended evolutionary dynamics.

Artificial swarm systems have been extensively studied and used in computer science, robotics, engineering and other technological fields, primarily as a platform for implementing robust distributed systems to achieve pre-defined objectives. However, such swarm systems, especially heterogeneous ones, can also be utilized as an ideal platform for creating open-ended evolutionary dynamics that do not converge toward pre-defined goals but keep exploring diverse possibilities and generating novel outputs indefinitely. In this article, we review Swarm Chemistry and its variants as concrete sample cases to illustrate beneficial characteristics of heterogeneous swarm systems, including the cardinality leap of design spaces, multi-scale structures/behaviours and their diversity, and robust self-organization, self-repair and ecological interactions of emergent patterns, all of which serve as the driving forces for open-ended evolutionary processes.

The rate of glucose metabolism sets the cell morphology across yeast strains and species.

Yeasts are a diverse group of unicellular fungi that have developed a wide array of phenotypes and traits over 400 million years of evolution. However, we still lack an understanding of the biological principles governing the range of cell morphologies, metabolic modes, and reproductive strategies yeasts display. In this study, we explored the relationship between cell morphology and metabolism in sixteen yeast strains across eleven species.

The first ornithocheiromorph humerus from Wuerho (Urho), China, with a new isotopic age of the Tugulu Group.

Pterosaur remains are rare from the lowermost Cretaceous, hampering our understanding of the taxonomic and morphological diversities of pterosaurs during this period. The Lower Cretaceous Tugulu Group in Wuerho, China is renowned for hosting the Wuerho Pterosaurian Fauna (WPF), which has so far yielded numerous fossil remains of two dsungaripterid pterosaurs, Dsungaripterus weii and Noripterus complicidens. Here we report a partial ornithocheiromorph humerus from the WPF, representing a deeply divergent clade from Dsungaripteridae.

Bacterial sensor evolved by decreasing complexity.

Bacterial receptors feed into multiple signal transduction pathways that regulate a variety of cellular processes including gene expression, second messenger levels, and motility. Receptors are typically activated by signal binding to ligand-binding domains (LBDs). Cache domains are omnipresent LBDs found in bacteria, archaea, and eukaryotes, including humans.

HIV-1 resistance mutations and genetic diversity among children failing antiretroviral treatment in five healthcare facilities in Benin, West Africa.

Background: Antiretroviral treatment increases the risk of accumulation of resistance mutations that negatively impact the possibilities of future treatment. This study aimed to present the frequency of HIV-1 antiretroviral resistance mutations and the genetic diversity among children with virological failure in five pediatric care facilities in Benin.

Methods: A cross-sectional study was carried out from November 20, 2020, to November 30, 2022, in children under 15 years of age who failed ongoing antiretroviral treatment at five facilities care in Benin (VL > 3log10 on two consecutive realizations three months apart).

An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the .

Members of the phylum inhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of various lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes , , and were highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classes and showed preferences to non-soil habitats.

Eco-friendly zinc oxide nanoparticle biosynthesis powered by probiotic bacteria.

The rapid advancement of nanotechnology, particularly in the realm of pharmaceutical sciences, has significantly transformed the potential for treating life-threatening diseases. A pivotal aspect of this evolution is the emergence of "green nanotechnology," which emphasizes the environmentally sustainable synthesis of raw materials through biological processes. This review focuses on the biological synthesis and application of zinc oxide (ZnO) nanoparticles (NPs) from probiotic bacteria, particularly those sourced from wastewater.

Size-Effect Enriched Phase Diagram in -Type Skutterudite Superconductor IrSb.

Pressurized IrX (X = P and As) stands out as the sole -type superconductors among dozens of filled-skutterudites that are primarily characterized by -type charge carriers. The emergence of superconductivity is proposed to be intimately related to the inharmonic rattling phonons originating from the filled atoms. Here, we explore the impact of the size effect of the rattling atoms by substituting X with Sb, whose radius is 30 and 17% larger than those of P and As, respectively.

Diversity and dynamics of multiple symbionts contribute to early development of broadcast spawning reef-building coral .

Sexual reproduction and recruitment enhance the genetic diversity and evolution of reef-building corals for population recovery and coral reef conservation under climate change. However, new recruits are vulnerable to physical changes and the mechanisms of symbiosis establishment remain poorly understood. Here, , a broadcast spawning hermaphrodite reef-building coral, was subjected to settlement and juvenile growth in flow-through seawater at 27.

Discovery of a Novel Species from Indonesian Peat Soil with Potent Anti Multidrug-Resistant Activity.

<b>Background and Objective:</b> Peatlands are unique ecosystems rich in microbial diversity, including bacteria with potential antibiotic activity. This study focuses on the isolation and characterization of bacteria from Indonesian peat soil, particularly their potential to produce antibiotics against multidrug-resistant (MDR) pathogens, including Methicillin-Resistant <i>Staphylococcus aureus</i> (MRSA). <b>Materials and Methods:</b> Bacterial isolates were rejuvenated on nutrient agar and subjected to antimicrobial activity testing using the Bauer & Kirby diffusion method against MRSA.

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity.

Background: In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).

Results: We achieved a haploid size of 940 megabase pairs (Mbp) for haplome 1 and 929 Mbp for haplome 2 with high scaffold N50 values of 36.

Molecular and functional convergences associated with complex multicellularity in Eukarya.

A key trait of Eukarya is the independent evolution of complex multicellular (CM) in animals, plants, fungi, brown algae and red algae. This phenotype is characterized by the initial exaptation of cell-cell adhesion genes followed by the emergence of mechanisms for cell-cell communication, together with the expansion of transcription factor gene families responsible for cell and tissue identity. The number of cell types (NCT) is commonly used as a quantitative proxy for biological complexity in comparative genomics studies.