Recent lbnl_bs_jgi items

Deployable high-fidelity metagenome binning at scale with QuickBin

Fri, 6 Nov 2026 00:00:00 +0000

Reconstructing genomes from metagenomic assemblies is foundational to microbiome research, yet binning faces a persistent trade-off between fidelity and throughput. Many high-accuracy methods rely on GPU-intensive workflows, marker-gene postprocessing, or heavy computational resources, limiting reproducible use at scale. Here, we present QuickBin, a CPU-native, marker-free binning algorithm designed to recover near-complete, ultra-low-contamination metagenome-assembled genomes (MAGs) efficiently. QuickBin pairs a GC-coverage spatial index (BinMap) with an early-exit Oracle cascade of similarity tests (scalar composition/coverage filters and SIMD-accelerated k-mer comparisons), reserving a compact neural network exclusively for ambiguous merges. Across synthetic communities, evaluated by marker-based and contig-origin ground truth, QuickBin maximizes high-fidelity sequence recovery. In benchmarking 297 diverse real metagenomes, QuickBin completed all runs, recovering more high-quality...

Trichoderma sp. strain AM6 whole-genome guided untargeted metabolomics: Terpenoid backbone synthesis and modulation of VOCs in tea (Camellia sinensis L.)

Thu, 29 Oct 2026 00:00:00 +0000

Industrial cash crop tea is a cherished drink for its bioactive components like terpenoids and flavonoids shaping its flavor and health benefits. Trichoderma species are potent biocontrol agents and plant growth regulators, with unexplored potential in modulation of C. sinensis terpenoid biosynthesis. Genome sequencing of a tea root-associated Trichoderma sp. strain AM6 revealed a genome size of 39.91 Mbp, comprising 446 contigs organized into 406 scaffolds, with 98.8 % completeness. Single scaffold mitochondrial genome assembly of 34,430 bp in length with a GC content of 28.03 % encodes a total of 49 genes including 27 tRNA, 2 rRNA, and 20 protein-coding genes. Metabolic pathway analysis indicates exclusive reliance on the mevalonate pathway for terpenoid biosynthesis in Trichoderma, unlike C. sinensis, which utilizes both the mevalonate and non-mevalonate (MEP/DOXP) pathways. Untargeted LC-ESI-MS/MS analysis of Trichoderma identified 11,841 secondary metabolites, including 34...

Intra‐species genetic variability drives carbon metabolism and symbiotic host interactions in the ectomycorrhizal fungus Pisolithus microcarpus

Thu, 29 Oct 2026 00:00:00 +0000

Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood. Here, we explore the extent of intra-species variation between four isolates of the ECM fungus Pisolithus microcarpus, in terms of gene regulation, carbon metabolism and growth, and interactions with a host, Eucalyptus grandis. We demonstrate that, while a core response to the host is maintained by all of the isolates tested, they have distinct patterns of gene expression and carbon metabolism, resulting in the differential expression of isolate-specific response pathways in the host plant. Together, these results highlight the importance of using a wider range of individuals within a species to understand the broader ecological roles...

Analysis of the genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi reveals two major evolutionary lineages

Thu, 29 Oct 2026 00:00:00 +0000

Phakopsora pachyrhizi, an obligate biotrophic rust fungus, is the causal agent of Asian Soybean Rust (ASR) disease. Here, we utilized whole-genome data to explore the evolutionary patterns and population structure across 45 P. pachyrhizi isolates collected from 1972 to 2017 from diverse geographic regions worldwide. We also characterized in-silico mating-type (MAT) genes of P. pachyrhizi, in the predicted proteome of three isolates, to investigate the sexual compatibility system. Our molecular phylogenetic analysis in P. pachyrhizi inferred two distinct evolutionary lineages structured on a temporal scale, with lineage Pp1 grouping isolates obtained from 1972 to 1994, while more recently collected isolates formed a second lineage, Pp2. We found higher levels of genetic diversity in lineage Pp1, whereas lineage Pp2 exhibited a strong clonal genetic structure, with a significant lower diversity. The widespread propagation of P. pachyrhizi clonal spores across soybean-growing regions...

A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to genome-guided machine learning prediction in Klebsiella pneumoniae

Tue, 27 Oct 2026 00:00:00 +0000

Klebsiella pneumoniae is a WHO critical-priority pathogen for which strain-specific bacteriophages are being explored as precision antimicrobials, yet rapid phage-host matching remains a major barrier to therapeutic deployment. We constructed a comprehensive interaction atlas comprising 84 taxonomically diverse phages and 101 globally sourced, clinically representative K. pneumoniae strains, including multidrug-resistant isolates. Systematic pairwise profiling produced 8,484 interaction measurements, of which 2,656 (31.3%) scored positive for bacterial clearance. Genus was the dominant phage-side determinant of host range, while capsule K-serotype was the strongest host-side determinant of susceptibility; aggregate defense, prophage, plasmid, and antimicrobial-resistance features contributed comparatively little. A genome-guided machine learning model predicted interactions without curated host annotations (AUROC, 0.882; AUPR, 0.765), outperforming a model based...

Catalog of metagenome-assembled genomes of prokaryotic communities from the Red Sea hydrothermal vents

Mon, 26 Oct 2026 00:00:00 +0000

This study presents medium- and high-quality prokaryotic metagenome-assembled genomes (MAGs) from microbial mats and sediments at Hatiba Mons, a Red Sea hydrothermal system. We recovered 1,217 bacterial and archaeal MAGs across 75 phyla, dominated by Planctomycetota and Thermoproteota. Approximately 70% of these genomes likely represent previously uncharacterized taxa.

A geothermal amoeba sets a new upper temperature limit for eukaryotes

Mon, 19 Oct 2026 00:00:00 +0000

The study of temperature limits has transformed our understanding of life's boundaries but has focused on bacteria and archaea. For decades after their discovery, no eukaryote was shown to replicate above 60°C. We isolated a geothermal amoeba, Incendiamoeba cascadensis, that divides at 63°C and is motile up to 64°C. We identified an enrichment of genes related to proteostasis and environmental sensing relative to mesophilic amoebae. Comparative RNA sequencing of I. cascadensis revealed upregulation of pathways related to proteostasis, DNA repair, and membrane trafficking at high temperatures. Predicted proteins of I. cascadensis have distinct biophysical properties, including enrichment of positively charged surface residues similar to bacterial and archaeal hyperthermophiles, which suggests a convergent mechanism for protein stability under temperature stress. Together, our findings expand our understanding of where and how life can persist.

“Quadrupling” the protein family space with global metagenomics

Mon, 19 Oct 2026 00:00:00 +0000

The known universe of protein families represents only a small fraction of nature's molecular diversity. From 40.3 billion predicted open reading frames across 40 446 metagenomes, 9540 metatranscriptomes, and 539 million proteins from 167 415 reference genomes, we identified 608 258 previously uncharacterized putative protein families with ≥100 members and 6.5 million families with ≥25 members, none matching known Pfam domains or reference proteins. This effort doubles the known repertoire of large families and quadruples that of smaller families. Integration of AlphaFold2-based structural predictions with gene-neighborhood and taxonomic analyses enables the characterization of these previously unannotated proteins, revealing candidates for both novel and known biological functions in understudied microbial lineages and biomes. This expanded repertoire provides insights into microbial adaptation and broadens the molecular toolkit available for biotechnology, highlighting the power...

A genomic catalog of Earth’s bacterial and archaeal symbionts

Wed, 14 Oct 2026 00:00:00 +0000

Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth yet remains underexplored because of culturing challenges. This study used machine learning (ML) to predict symbiotic lifestyles in more than a hundred thousand microbial genomes from diverse environmental metagenome samples and reference genomes. Predictions were performed using symclatron, an ML framework developed to identify genomic signatures of symbionts. Predictions were deposited in a catalog we established called Symbiont Genomes (SymGs). The results indicate that 15–23% of uncultivated microorganisms likely engage in symbiotic relationships with other organisms, categorized as host-associated or obligate intracellular lifestyles, and are present in half of all known bacterial and archaeal phyla. We also identify genomic signatures of symbiotic lifestyles, including the loss of certain metabolic functions and the differential presence of metabolic modules that may enable host-dependent...

Correlated evolution of fish host length and parasite spore size: a tale from myxosporeans inhabiting elasmobranchs

Tue, 13 Oct 2026 00:00:00 +0000

Myxozoa represent a diverse group of microscopic cnidarian endoparasites alternating between invertebrate and vertebrate hosts. Of the approximately 2,600 species described predominantly from teleost fish, only 1.8% have been reported from cartilaginous fishes (Elasmobranchii). As ancestral vertebrate hosts of myxozoans, elasmobranchs may have played an important role in myxozoan evolution, however, they are also some of the largest vertebrate hosts known for this group of parasites. We screened 50 elasmobranchs belonging to nine species and seven families, from various geographical areas, for myxozoan infection. We found a 22% overall prevalence of myxozoans in elasmobranchs and describe five species new to science. We investigated, for the first known time, the evolution of spore size within three phylogenetic clades, Ceratomyxa, Sphaerospora sensu stricto and Parvicapsula. We found that spores from elasmobranch-infecting myxozoans were on average 4.8× (Ceratomyxa), 2.2× (Parvicapsula...

A diversity of amoebae colonise the gills of farmed Atlantic salmon (Salmo salar) with amoebic gill disease (AGD)

Tue, 13 Oct 2026 00:00:00 +0000

Neoparamoeba perurans is the aetiological agent of amoebic gill disease (AGD) in salmonids, however multiple other amoeba species colonise the gills and their role in AGD is unknown. Taxonomic assessments of these accompanying amoebae on AGD-affected salmon have previously been based on gross morphology alone. The aim of the present study was to document the diversity of amoebae colonising the gills of AGD-affected farmed Atlantic salmon using a combination of morphological and sequence-based taxonomic methods. Amoebae were characterised morphologically via light microscopy and transmission electron microscopy, and by phylogenetic analyses based on the 18S rRNA gene and cytochrome oxidase subunit I (COI) gene. In addition to N. perurans, 11 other amoebozoans were isolated from the gills, and were classified within the genera Neoparamoeba, Paramoeba, Vexillifera, Pseudoparamoeba, Vannella and Nolandella. In some cases, such as Paramoeba eilhardi, this is the first time this species...

Viral genetic diversity and functional potential in polar and subarctic sea ice

Tue, 13 Oct 2026 00:00:00 +0000

Sea ice plays a critical role in regulating the global climate and serves as a unique habitat for diverse microbial communities. Still, our understanding of viruses in these communities remains limited. To further uncover the diversity and functional potential of viruses in polar and subarctic sea ice, we explored the viral component of Arctic, Baltic Sea, and Antarctic sea ice metagenomes. Altogether, 550 viral operational taxonomic units (vOTUs) were recovered, most of which were putatively classified within the class Caudoviricetes, which comprises bacterial and archaeal tailed double-stranded DNA viruses. Hosts were predicted for 187 vOTUs, with Gammaproteobacteria and Bacteroidia being the most prevalent viral host groups. Potential functions were assigned for 56% of predicted viral gene products, including putative auxiliary metabolic genes (AMGs) involved in oxidative metabolism, photosynthesis, and metabolism regulation under stress conditions. Related viral genomes...

Single-cell genomics, metagenomics, and transcriptomics of Rhizophydium megarrhizum, an obligate fungal parasite of Planktothrix agardhii

Tue, 13 Oct 2026 00:00:00 +0000

Chytrids (phylum Chytridiomycota) are zoosporic fungi that play key roles as parasites of aquatic microorganisms, yet they are understudied and genomic resources for algal-infecting chytrids remain scarce. Here, we present the first comparative genomic analysis of multiple isolates of a single chytrid species (order Rhizophydiales) infecting the cyanobacterium Planktothrix agardhii. Isolates were collected from Sandusky Bay, Lake Erie, across two bloom years (2018 and 2019). Using single cell sequencing and metagenomic assembly, we generated individual genomes averaging 15.36 ± 0.12 Mbp in size with ~ 75% completeness, and a pangenome. Gene ontology analyses highlighted the presence of categories related to cellular structure, biosynthetic regulation, and interspecies interactions. As a preliminary exploration of gene expression during infection, we also performed RNA sequencing on a subset of size-sorted samples. These data suggest that chytrids consistently express high...

The dynamics of introgression and parallel adaptation across North American Vitis species

Tue, 13 Oct 2026 00:00:00 +0000

Hybridization between species can contribute to parallel adaptive events. However, the prevalence of introgression is rarely measured across multiple species, meaning that it is rarely integrated with landscape-scale processes or connected to adaptive repeatability. Here we analyzed whole-genome resequencing data from 639 accessions representing 48 Vitis species. Vitis is notable for the domesticated grapevine (Vitis vinifera), multiple economically important North American species, and as an example of a temperate adaptive radiation. We reconstructed individual- and species-level phylogenetic frameworks for the genus and performed population genetic analyses for 19 species. The analyses uncovered widespread evidence of introgression, comprising ~14% of the average Vitis genome. Introgression was associated with the geographic distribution between species, and highly admixed individuals were more frequently found near ecological niche margins. Genetic...

Genome sequence and annotation of Myroides phaeus DSM 23313T isolated from a human oral cavity

Tue, 13 Oct 2026 00:00:00 +0000

We present the genome sequence of Myroides phaeus DSM 23313^T, a type strain isolated from a human oral cavity. The genome comprises 2.97 Mbp and contains 2,661 predicted genes. This genome analysis will provide insight into the multiple antibiotic resistance capabilities of this opportunistic pathogen.

Parasitic flatworms infecting thorny skate, Amblyraja radiata: Infection by the monogeneans Acanthocotyle verrilli and Rajonchocotyle emarginata in Svalbard

Tue, 13 Oct 2026 00:00:00 +0000

Parasite diversity above the Arctic circle remains understudied even for commercially valuable host taxa. Thorny skate, Amblyraja radiata, is a common bycatch species with a growing commercial value. Its natural range covers both sides of the North Atlantic including the Arctic zone. Svalbard is a Norwegian archipelago located on the northwest corner of the Barents Shelf which sustains a spectacular species diversity. So far, several monogenean species have been reported infecting thorny skate across the Atlantic Ocean. In the present study, we intend to fill in the knowledge gap on monogenean parasites infecting thorny skate in the northern part of its range and thus indirectly assess the connectivity between the thorny skate populations off the Svalbard coast and from previously studied locations. 46 monogenean individuals were recovered from 11 specimens of thorny skate. Following morphological and molecular assessment, two species of monogeneans, Acanthocotyle verrilli and...

Boron excess in Alternanthera tenella Colla under in vitro conditions: tolerance and potential for supplementation in plants

Tue, 29 Sep 2026 00:00:00 +0000

Boron (B) plays a crucial role in plant physiological processes, and imbalances in its supply can markedly affect plant morphophysiology. This study evaluated the effects of a B concentration gradient on the growth and morphophysiological responses of Alternanthera tenella under in vitro conditions. Stem segments were cultured on media supplemented with different B concentrations (0, 125, 250, 500, 750, 1000, and 2000 µM) for 30 days. Growth traits, anatomical features, nutrient accumulation, photosynthetic pigment content, and photosystem II (PSII) performance were assessed. Increasing B availability enhanced Mg and S accumulation, while the thickness of root vessel elements increased progressively up to 750 µM B. Tissues associated with nutrient transport exhibited improved functionality, indicating more efficient translocation from roots to shoots under adequate B supply. Photosynthetic pigment content and PSII parameters were also highest at 750 µM B. The tolerance index remained...

Genotypic diversity of Coffea canephora cv. Conilon identified through leaf morpho- and eco-physiological traits

Tue, 29 Sep 2026 00:00:00 +0000

The knowledge about the genetic variability of a population is essential to increase the selection efficiency of promising genotypes to breeding programs. This study evaluated the genetic diversity among nine Coffea canephora genotypes based on leaf morphophysiological traits, e.g., dry mass (DM), leaf mass per unit area (LMA) and the relative water content (RWC%), as well as the performance of the photosynthetic apparatus, through PSII functioning and electron transport, performed in summer and winter in three periods of the day. Three distinct groups were formed based on chlorophyll a fluorescence (ChlaF) parameters, demonstrating the heterogeneity of the genetic constitution of the evaluated population, what is quite relevant for the analysis of genetic divergence and breeding purposes, having the potential to identify superior genotypes. In summer and winter, the initial fluorescence (F0) tended to increase in the morning and noon, while the quantum yield of the primary photochemistry...

3D epigenome of glial cell types in developing human cortex

Thu, 24 Sep 2026 00:00:00 +0000

The human cortex is complex and heterogeneous, undergoing extensive expansion during development1,2. Our prior study of neurogenesis, including radial glia (RG), intermediate progenitor cells, excitatory neurons and interneurons demonstrated that chromatin looping underlies transcriptional regulation for lineage-specific genes, shedding light on how non-coding genetic variants contribute to neuropsychiatric disorders by means of cell-type-specific gene regulation3. RG have a crucial role in generating cellular diversity through both neurogenesis and gliogenesis and can be further classified into ventricular RG (vRG) and outer RG (oRG)4,5. Given their significance in cortical development, we conducted a comprehensive three-dimensional (3D) epigenomic analysis of four main glial populations, including vRG, oRG, oligodendrocyte precursor cells and microglia, from the mid-gestational human neocortex. By integrating gene expression, chromatin accessibility, DNA methylation and...

Judicial Opinions 133 and 134

Mon, 21 Sep 2026 00:00:00 +0000

Opinion 133 addresses the unusual situation of two genus names that are homonyms and are also considered heterotypic synonyms. Furthermore, it clarifies the meaning of the term 'homonym' in the International Code of Nomenclature of Prokaryotes, as well as the implications of the absence of the term 'isonym' from that code. Isonyms are homotypic synonyms with the same spelling and as such are adequately regulated by the code. The Judicial Commission agrees that the names Methylacidiphilum caldifontis Awala et al. 2023, Methylacidiphilum Awala et al. 2023, Methylacidiphilaceae Awala et al. 2023 and Methylacidiphilales Awala et al. 2023 are illegitimate. The possible actions to resolve this illegitimacy are outlined. The request to conserve Methylacidiphilum Awala et al. 2023 over Methylacidiphilum Ratnadevi et al. 2023 is not granted. However, Methylacidiphilaceae Awala et al. 2023...

Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes

Fri, 18 Sep 2026 00:00:00 +0000

Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential...

Rhythmic Mechanisms Governing CAM Photosynthesis in Kalanchoe fedtschenkoi: High-Resolution Temporal Transcriptomics

Mon, 31 Aug 2026 00:00:00 +0000

Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO₂ uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for the CAM model Kalanchoe fedtschenkoi under both 12 h/12 h light/dark (LD) cycles and continuous light (LL). A rhythmicity analysis revealed that diel light cues are the dominant driver of transcript oscillations: 16,810 genes (54.3% of annotated genes) exhibited rhythmic expression only under LD, whereas just 399 genes (1.3%) remained rhythmic under LL. A smaller set of 3009 genes (9.7%) oscillated in both conditions, indicating that the intrinsic circadian clock sustains rhythmicity for a limited subset of the transcriptome. A gene co-expression network analysis revealed extensive integration between circadian clock components,...

A sorghum pangenome reference improves global crop trait discovery

Mon, 31 Aug 2026 00:00:00 +0000

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops1, like that of the grain and bioenergy crop sorghum2, 3, 4–5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets6. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established...

Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter

Mon, 31 Aug 2026 00:00:00 +0000

The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include...

High-throughput characterization of Mycobacterium tuberculosis gene function across diverse conditions

Fri, 28 Aug 2026 00:00:00 +0000

Mycobacterium tuberculosis (Mtb) is a human bacterial pathogen that establishes chronic infection in the lung. Although the genome of Mtb was sequenced nearly 25 years ago, the genetic basis of Mtb's success as a human pathogen remains to be fully elucidated. Large-scale mutation-based genetic approaches to understanding gene function are hindered by the limited throughput of traditional transposon sequencing strategies used in mycobacteria. To create a resource for determining the function of genes, we generated a pooled random barcode transposon-site sequencing (RB-TnSeq) library in Mtb. A unique 20-nucleotide barcode in the transposon allows for rapid, high-throughput genetic screening without the laborious protocol of standard bacterial TnSeq screens. We performed 95 RB-TnSeq screens on an array of carbon sources, nitrogen sources, stressors, and antibiotics. Using the resulting dataset, we examined phenotypes of pe and ppe genes, a mycobacterial gene family whose function...

Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome

Thu, 20 Aug 2026 00:00:00 +0000

Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single...

Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem

Wed, 19 Aug 2026 00:00:00 +0000

Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant...

Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment

Wed, 19 Aug 2026 00:00:00 +0000

The FOXG1 transcription factor is a crucial regulator of embryonic brain development. Pathogenic FOXG1 variants cause FOXG1 syndrome. Although structural variants in the non-coding region downstream of FOXG1 have been reported in 38 individuals with similar characteristics, the regulatory pathomechanisms remain unknown. Here, we identify two non-coding structural variants in individuals with FOXG1 syndrome-like features, allowing us to delineate a ~ 124 kb commonly affected regulatory region. Using epigenomic profiling and in vivo enhancer assays, we characterize and validate regulatory elements within the commonly affected regulatory region and wider FOXG1 TAD. We see strong activation of previously validated forebrain enhancers, and identify an enhancer cluster and progenitor-specific enhancer region that are strongly activated during forebrain-directed neural progenitor cell differentiation, a process in which FOXG1 is an important regulator. Perturbation of these elements...

Global population structures and demographic history of Suillus luteus, a pine co‐introduced ectomycorrhizal fungus associated with exotic forestry and invasion

Tue, 18 Aug 2026 00:00:00 +0000

Human colonization since the 19th century has resulted in the global spread of pines beyond their original northern boreal distribution. Although the introduction history of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal (ECM) fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, whole genomes of 208 individuals collected across native and introduced ranges were sequenced to reveal the introduction history of pine co-introduced ECM fungi. Population genomics analyses showed that all introductions originated from Europe. With the exception of North America, introduced populations were genetically differentiated from the European population, with varying magnitudes of population expansion in different introduced regions. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting...

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Tue, 18 Aug 2026 00:00:00 +0000

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework...

Mapping the soil microbiome functions shaping wetland methane emissions

Tue, 4 Aug 2026 00:00:00 +0000

Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover,...

In search of phage tail-like particles: nature’s versatile nanomachines

Tue, 4 Aug 2026 00:00:00 +0000

This Genome Watch article highlights the importance of predictive models for identifying and characterizing the roles of phage tail-like particles as a tool for bioengineering and biocontrol.

Increased aluminum exposure induces widespread changes in silicon, carbon, and nitrogen metabolism in Entomoneis vertebralis

Tue, 28 Jul 2026 00:00:00 +0000

BackgroundDiatoms are a class of algae that play an essential role in global ecology and produce valuable chemicals. They are known for forming intricate nanostructured silica cell walls (frustules). The introduction of non-siliceous elements like aluminum into diatoms induces properties such as a lower dissolution rate of the frustule, increasing the specific surface area of the frustule and enhancing metabolism. Previous studies have focused primarily on characterizing physiological impacts, leaving the genetic response(s) to non-siliceous elements largely unexplored.ResultsThis study investigates the transcriptional response of the pennate diatom, Entomoneis vertebralis to dissolved aluminum. Our findings reveal that in the presence of added 10 µM aluminum, biogenic silica content of the cell wall increases approximately twofold along with significant changes to core metabolism. An increase in transcription of genes encoding nitrate transporters has been observed despite...

Genome assembly and annotation of microalga Nannochloropsis oceanica C018

Tue, 28 Jul 2026 00:00:00 +0000

The microalga Nannochloropsis is an important organism for algae-based biocommodity production of food, feed, and fuel, among other products. Using PacBio Revio, we sequenced, assembled, and annotated a 26.41 Mbp Nannochloropsis oceanica C018 genome.

Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation

Tue, 28 Jul 2026 00:00:00 +0000

The interrogation of data across biological and environmental systems has become increasingly complex. Fortunately, communities are adopting the FAIR (Findable, Accessible, Interoperable, Reusable) data principles for individual datasets, and continue to develop domain-specific, machine-actionable standards. However, integrating FAIR data for meta-analysis across data resources is still challenging. Understanding how disparate datasets are organized remains a manual, time-consuming process. Updating FAIR databases to reflect changes in knowledge is slow, allowing stale annotations and incorrect relationships to propagate, amplified by Artificial Intelligence (AI) systems that harvest data. Building on FAIR, we argue that data should be iteratively updated and improved. FAIR + COPE (Comparable, Organized, Predictive, Engaged) takes FAIR data and makes it Comparable, rapidly Organized (applying / updating standards) for Predictive models, which can be validated and improved by an...

Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca

Wed, 22 Jul 2026 00:00:00 +0000

Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, as its emergence may depend on simple regulatory changes to deeply conserved metabolic pathways. Modern CAM research relies heavily on interpretation of transcriptomic data, though regulation occurs at multiple levels following transcription. Additionally, while most research to date has focused on a handful of genes and metabolites in the core CAM pathway, the co-option of conserved regulatory and functional genes is bound to have wide-ranging effects on other aspects of primary metabolism. In this study, we integrate transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C3 species, Y. filamentosa. We observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional...

Probing the limits of genetic recoding using multi-omics-guided evolution

Wed, 22 Jul 2026 00:00:00 +0000

Engineering the genetic code—by reassigning multiple of the 64 natural codons—enables making organisms resistant to all viruses, preventing genetic information exchange, and allowing the biosynthesis of genetically encoded unnatural polymers. However, synonymous codon replacement—recoding—is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using genome synthesis, directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple synthetic Escherichia coli genomes. We construct six partially recoded E. coli strains bearing up to 45.8% of a synthetic genome with a deleterious 57-codon genetic code. As our analyses revealed widespread defects—including unassigned codons in Syn61 and Syn57—we apply multi-omics to revise our genome design and mitigate defects. Using multi-omics, we show that recoding induces transcriptional and translational changes leading to fitness defects under hundreds of conditions....

Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition

Wed, 22 Jul 2026 00:00:00 +0000

Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon–atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients. We address this gap using a continental-scale dataset pairing shotgun metagenomes with high-resolution SOM chemistry, assembling 0.76 Tbp of prokaryotic MAGs (828 genomes) and identifying 66,727 SOM molecules from 47 standardized U.S. soil cores selected using respiration rates from 106 soils. Integrating these datasets reveals widespread microbial potential for depolymerizing chemically-recalcitrant SOM previously considered stable. We uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels,...

Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics

Thu, 16 Jul 2026 00:00:00 +0000

Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H₂¹⁸O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant ¹⁸O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10¹⁰ to 6.59 × 10¹⁰ virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome...

Enhancers that direct gene expression to central nervous system vascular endothelial cells in vivo

Thu, 16 Jul 2026 00:00:00 +0000

CNS vascular endothelial cells (ECs) exhibit a distinctive gene expression program that is foundational for the blood-brain barrier (BBB). Previous research identified candidate cis-regulatory elements (CREs) that were hypothesized to control this program. In this work, transgenic mice and recombinant adeno-associated virus (rAAV) vectors have been used to interrogate these candidate CREs in vivo. These experiments show that an 850 bp genomic DNA segment ∼60 kb 5' of Slc2a1 possesses enhancer activity that is (1) specific for BBB+ CNS ECs and (2) both necessary and sufficient for BBB+ EC gene expression. A screen of >8,000 genomic DNA segments from CNS EC-specific CRE candidates reveals several hundred with enhancer activity. Transcription factors ERG and LEF1 are shown to occupy sites in brain ECs that are highly enriched in candidate and experimentally validated CREs, lending strong support to a model in which canonical Wnt signaling activates the BBB program via LEF1.

CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization

Mon, 29 Jun 2026 00:00:00 +0000

Plant roots release a wide array of metabolites into the rhizosphere, shaping microbial communities and their functions. While metagenomics has expanded our understanding of these communities, little is known about the physiology of their members in host environments. Transcriptome analysis via RNA sequencing is a common approach to learning more, but its use has been challenging because of low bacterial biomass and interference from plant RNA. To overcome this, we developed a randomly-barcoded promoter-library insertion sequencing (RB-PI-seq) combined with chassis-independent recombinase-assisted genome engineering (CRAGE). Using Pseudomonas simiae WCS417 as a model rhizobacterium, this method enabled targeted amplification of barcoded transcripts, bypassing plant RNA interference and allowing measurement of thousands of promoter activities during Arabidopsis root colonization. Our analysis revealed temporally resolved transcriptional regulation, including those associated with...

Plastome evolution in annual Brachypodium species reveals widespread heteroplasmy and chloroplast capture, lineage-specific codon usage bias, and low positive selection

Fri, 26 Jun 2026 00:00:00 +0000

BackgroundComparative genomics and plastome phylogenomics have advanced significantly in recent years, highlighting the diversity, possible admixture, and non-neutral evolution of the predominantly considered non-recombinant chloroplast genomes in angiosperms. The grass genus Brachypodium serves as a powerful model for studying evolutionary processes in monocots.ResultsWe analyzed 287 plastomes across the native circum-Mediterranean range of the three annual Brachypodium species (B. distachyon, B. stacei, B. hybridum), focusing on their structural variation, selection patterns and phylogenomic relationships. Our analyses confirmed the differentiation of the S and D plastomes, inherited respectively from the diploid progenitor species B. stacei and B. distachyon. We identified novel structural rearrangements and indels, and unique repeat motifs, along with widespread heteroplasmy, particularly in ancestral B. hybridum-D plastotypes. SNP diversity varied among plastotypes, reflecting...

Genomic fingerprint of polyethylene-degrading bacteria

Tue, 16 Jun 2026 00:00:00 +0000

Polyethylene (PE) is ubiquitous in modern environments yet remains highly recalcitrant, accumulating due to inefficient and poorly understood microbial degradation. Here, we used a comparative genomics framework to identify genetic features associated with the PE-degrading phenotype by analyzing 97 bacterial genomes with experimental evidence of PE degradation alongside 87 phylogenetically balanced control genomes lacking documented activity. Genome-wide functional annotation and orthology inference revealed a coherent set of gene families, significantly enriched in PE-degraders, including extracellular proteins, oxidoreductases, membrane transport systems, regulatory and stress-response functions consistent with growth at hydrophobic, high-molecular-weight carbon source. To assess whether a minimal genomic signature could discriminate degraders from controls, we applied an integer linear programming (ILP) approach to presence/absence and copy-number-thresholded orthogroup matrices....

Author Correction: A roadmap for equitable reuse of public microbiome data

Fri, 5 Jun 2026 00:00:00 +0000

Correction to: Nature Microbiologyhttps://doi.org/10.1038/s41564-025-02116-2, published online 26 September 2025. In the version of this article initially published, in the first paragraph of the “Survey on data reuse” section, a note on participant consent, confidentiality and institutional review was missing and has now been inserted in the HTML and PDF versions of the article.

Quantitative DNA Stable Isotope Probing Identifies Active Microorganisms Assimilating Volatile Fatty Acids in Full-Scale Enhanced Biological Phosphorus Removal Processes

Thu, 4 Jun 2026 00:00:00 +0000

Enhanced biological phosphorus removal (EBPR) systems often rely on exogenous carbon sources, such as volatile fatty acids (VFAs), to achieve higher P removal. Here, we employed DNA quantitative stable isotope probing (qSIP) using two VFAs, acetate and propionate, in cyclic anaerobic/aerobic incubations to assess their effects on P cycling and microbial activity with biomass from two full-scale EBPR water resource-recovery facilities that utilize VFA addition. We found that anaerobic VFA uptake preferences differed within known groups of PAOs, such as Candidatus Accumulibacter and Tetrasphaera-affiliated members (e.g., Ca. Phosphoribacter), between the two biomasses. The combination of qSIP with metagenomics identified isotopically labeled phages that were linked to active PAOs, highlighting their potential roles in modulating EBPR community composition and activity. The highest levels of anaerobic labeling from acetate were in genomes belonging to Saccharimonadales...

Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course “Evolutionary and Comparative Genomics”

Mon, 18 May 2026 00:00:00 +0000

This perspective outlines emerging trends, key challenges, and future opportunities in evolutionary and comparative genomics. Our starting point are the topics presented at the 2024 EMBO Early Career Lecture Course "Evolutionary and Comparative Genomics", which highlighted recent conceptual and methodological advances in areas ranging from microbial pangenomes, protein evolution, hybrid speciation, novel gene origination and transposon dynamics. Here, we emphasize the role of computational and molecular approaches, providing a forward-looking view on where the field is headed and how it is being reshaped by new technologies and approaches.

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

Fri, 15 May 2026 00:00:00 +0000

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning...

Ecological and genomic variation in ectomycorrhizal fungal exploration types

Fri, 15 May 2026 00:00:00 +0000

Ectomycorrhizal fungi (EMF) produce mycelia with variable extension and complexity, which can be classified according to soil 'exploration types' (ETs). ETs have received attention as one of the few mycorrhizal trait frameworks, but without an empirical classification of ET functional diversity and environmental preferences, understanding and interpreting EMF biogeographic patterns has been difficult. We conducted a synthesis combining: comparative EMF genomics to describe functional divergence in decomposition and nutrient cycling genes across ETs; and EMF trait distribution modeling across continental Europe, pairing soil and root EMF surveys to establish biogeographic ET niche profiles. We demonstrate a signature of ETs encoded in EMF genomes, which is independent from phylogeny and linked to biomass production strategies. EMF ET relative abundances were separated by soil, root, and dominant tree leaf type habitats and exhibited unique correlations with forest biotic (e.g....

Multiomics and deep learning dissect regulatory syntax in human development

Thu, 14 May 2026 00:00:00 +0000

Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression1. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs or single modalities2. Here we present the Human Development Multiomic Atlas, a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and more than 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs that influence accessibility, including composite motifs exhibiting distinct syntactic constraints that are predicted to mediate transcription factor cooperativity....

Comparative genomics provides insights into the cold adaptation of endophytic fungi associated with Deschampsia antarctica

Wed, 13 May 2026 00:00:00 +0000

Endophytic fungi from Deschampsia antarctica, the southernmost flowering plant, provide insights into the cold adaptation mechanisms of plant-associated fungi in extreme environments. This study presents the genome sequences and comparative analysis of eight fungal isolates from D. antarctica leaves. These Antarctic fungal isolates were analyzed alongside 121 plant-associated fungal genomes to uncover signatures of adaptation and endophytic specialization. Antarctic endophytes show striking patterns, including reduced genome size (∼26.3 Mb on average), streamlined gene content (∼8844 genes), and notably small secretomes (∼288 proteins). Despite this reduced gene repertoire, they maintain a robust set of genes encoding carbohydrate-active enzymes (CAZymes) but lack those for lignin and bacterial cell wall degradation, indicating a symbiotic lifestyle that avoids host damage and predation. One isolate, Alternaria sp. UNIPAMPA017 stood out, with 26% of its genome occupied by...

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

Wed, 6 May 2026 00:00:00 +0000

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate...

A roadmap for equitable reuse of public microbiome data

Mon, 27 Apr 2026 00:00:00 +0000

Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates...

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Fri, 24 Apr 2026 00:00:00 +0000

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here, we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes program. Originating from a clone of Auburn University's historic "Toomer's Oak," this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana...

Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy

Wed, 22 Apr 2026 00:00:00 +0000

Benzylisoquinoline alkaloids (BIAs) represent a vast group of specialized plant metabolites with diverse pharmaceutical applications, synthesized by a variety of gene families. Among the multiple plant lineages that produce BIAs, the most notable is the poppy family (Papaveraceae), with California poppy (Eschscholzia californica) emerging as a model organism. Here, we report a haplotype-resolved genome assembly, in combination with a high-density expression atlas, for California poppy. Genome analyses reveal recent diversification of BIA biosynthesis genes in poppy through localized duplications. Furthermore, we demonstrate that the degree of phylogenetic relatedness among paralogs within BIA biosynthesis-associated gene families correlates with similarities in gene expression. In contrast, gene families involved in carotenoid biosynthesis, which contributes to the intense orange petal pigmentation, are not phylogenetically clustered, and floral developmental regulators exhibit...

DAP-seq Reveals Cluster-Situated Regulator Control of Numerous Streptomyces Natural Product Biosynthetic Genes

Wed, 22 Apr 2026 00:00:00 +0000

Natural products (NPs) are a rich source of therapeutic and agricultural compounds. Unfortunately, many promising metabolites are not expressed under standard laboratory conditions. Deepening our understanding of the regulatory networks governing NP biosynthetic genes is essential for unlocking this hidden chemical diversity. Cluster-situated regulators (CSRs) are transcription factors involved in the regulation of NPs, but their full regulatory range has remained elusive due to limited genome-wide data. Using DNA Affinity Purification Sequencing (DAP-seq), we defined the predicted regulons for 84 CSR homologs across 78 Streptomyces strains. CSRs in this cohort exerted influence across multiple cellular processes, with particularly strong impacts on other transcription factors throughout the genome. Approximately 30% of predicted NP biosynthetic gene clusters (BGCs) contained CSR-regulated genes. In strains encoding multiple CSR homologs, we observed substantial overlap...

systemPipeR: a multipurpose workflow management system for reproducible data analysis

Tue, 21 Apr 2026 00:00:00 +0000

Workflow management systems (WMS) are essential for creating and automating multi-step data analyses and ensuring the reproducibility of biological insights. Although numerous WMS solutions exist, few provide deep integration of command-line software with the R and Bioconductor ecosystems, where a substantial portion of statistical modeling and downstream scientific analysis is performed by a large user base. systemPipeR addresses this gap by offering a unified environment that links R-based analytical steps with command-line tools through a standardized workflow specification. It enables the design and execution of reproducible workflows on both local and high-performance computing systems, while allowing users to select the most appropriate R or command-line tool for each analysis step. The latest version introduces a fully redesigned architecture that streamlines workflow construction, execution, monitoring, and reporting. Key enhancements include a flexible workflow management...

Correction: A microbial survey of the International Space Station (ISS)

Tue, 21 Apr 2026 00:00:00 +0000

[This corrects the article DOI: 10.7717/peerj.4029.].

CAZome comparison in relation to host plant for selected Sordariomycete and Dothidiomycete plant pathogenic fungi

Tue, 21 Apr 2026 00:00:00 +0000

Introduction: While most studies focus on the effectors involved in plant infection, another important aspect is the degradation of the plant cell wall, as this is the main physical barrier protecting the plant from pathogens. The plant cell wall mainly consists of polysaccharides, proteins and the aromatic polymer lignin, but the type of polysaccharide differs significantly between plant types, species and tissues. It can therefore be expected that pathogens of specific plants have evolved to produce those plant polysaccharide degrading enzymes that match the polysaccharides in the cell wall of their host plant. Methods: In this study, we compared the plant polysaccharide degradation potential of 56 Dothideomycetes and 42 Sordariomycetes species to identify evolutionary patterns related to either host plant or phylogenomic classification of the fungal species. Results and discussion: Our results show that the CAZy content of these fungi does not correlate with their...

Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome-specificity

Tue, 21 Apr 2026 00:00:00 +0000

Abstract Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have convergently evolved multiple times from phylogenetically distant organisms into eight classes that are structurally unrelated, but share physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57,218 α-, β-, and γ-CA sequences from 24,184 metagenomes and genomes, including the first detection of α-CA from an archaeal species. CA sequences formed 3,859 protein clusters (1,188 with ≥ 3 sequences)...

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture

Mon, 20 Apr 2026 00:00:00 +0000

Trichoderma fungi support sustainable agriculture by suppressing plant diseases and improving crop performance. However, emerging pathogenicity of Trichoderma warrants further ecological and genetic characterization. Here we used machine learning to correlate genomic data from 37 Trichoderma strains with over 140 phenotypic traits, spanning metabolic versatility, biotic interactions, stress tolerance and reproductive strategies. We determined Trichoderma to be an ancient, genetically cohesive and physiologically diverse genus with spores capable of germination in water and dispersal via air and water droplets. Metabolic preferences indicate universal adaptation to mycoparasitism and to niches like arboreal microbial mats, alongside broader saprotrophic versatility. Our analyses are consistent with character displacement among close relatives and convergent evolution in distant lineages, with both processes shaping ecological plasticity and traits including dispersal modes, terrestrialization...

Global metagenomics reveals plastid diversity and unexplored algal lineages

Fri, 17 Apr 2026 00:00:00 +0000

Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights...

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Fri, 17 Apr 2026 00:00:00 +0000

Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity...

Ecology of methyl-coenzyme M reductase encoding Thermoproteota

Mon, 13 Apr 2026 00:00:00 +0000

The recent demonstration that members of at least three classes of archaea affiliated with the Thermoproteota superphylum are involved in the production of the climate-active gas methane has sparked discussions about how well we understand the diversity of methanogens. Here, we show that members of all three of these lineages, as well as several other, yet uncultured and physiologically uncharacterized groups within the Thermoproteota that encode the key enzyme of anaerobic methane cycling, methyl-coenzyme M reductase (MCR), are widely distributed in anoxic ecosystems. We postulate that the taxonomic, metabolic, and ecological diversity of methanogenic and MCR-encoding Thermoproteota are poorly understood, and that the contribution of methylotrophic and thermoproteotal methanogenesis to methane production is largely unknown. We hypothesize that thermoproteotal methanogens could contribute, potentially substantially, to methane emissions in many anoxic environments that harbor...

Complex viral interactions revealed for the harmful bloom-forming dinoflagellate Karenia brevis.

Thu, 9 Apr 2026 00:00:00 +0000

Karenia brevis regularly forms harmful blooms along the West Florida Shelf that negatively affect marine and terrestrial organisms through toxin production. These blooms impose economic and environmental hardship, driving the need for research to understand the factors influencing their dynamics and to mitigate their impacts. A mostly unresolved issue is the potential role of viruses in bloom termination. We conducted an experiment incubating K. brevis cultures with size-fractionated bloom water samples. Flow cytometry revealed giant virus-like populations (VLPs) in replicate cultures with <1 μm-filtered and <0.2 μm-filtered bloom water. The VLPs abundance was paralleled by declines in photoefficiency and culture lysis. Metagenomic analyses of the lysates revealed 11 giant virus genomes (35%-100% complete) representing 7 viral operational taxonomic units (vOTUs) within the order Imitervirales (Nucleocytoviricota). Ten of these vOTUs...

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

Mon, 6 Apr 2026 00:00:00 +0000

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein...

A genomic perspective on fungal diversity and evolution

Thu, 2 Apr 2026 00:00:00 +0000

Originating from aquatic unicellular ancestors, over the course of ~1 billion years, the fungi have evolved to occupy nearly all aerobic environments on the planet, diversified into millions of different ‘species’ and have developed complex multicellular structures. Their relatively small, simple genomes have facilitated massive-scale sequencing and allowed us to explore genome evolution across an ancient eukaryotic kingdom. With thousands of genomes from diverse lineages now available, this Review will discuss insights into fungal biology and evolution gleaned with genomics and other multi-omics approaches. Using published genomes available through GenBank and the Joint Genome Institute’s MycoCosm platform, we generated kingdom-wide phylogenies and used them to highlight how fungal genomes have changed over time. With this phylogeny as a guide, we also discuss major evolutionary transitions that occurred across the fungal kingdom. Although progress has been made, these efforts...

Agnostic capture of pathogens for the detection and diagnostics of emerging threats

Thu, 2 Apr 2026 00:00:00 +0000

The continued emergence of pathogens, whether novel, re-emerging, or engineered, poses a persistent global biosecurity and public health challenge. Recent outbreaks, including COVID-19, Lassa fever, Marburg virus, mpox, and avian influenza, underscore the urgent need for robust systems that enable rapid surveillance, early diagnosis, and timely countermeasures before widespread human transmission occurs. In this article, we focus on early detection technologies and systematically evaluate current diagnostic and sensing modalities. We highlight sequencing and spectroscopy as two complementary approaches capable of providing broad, agnostic detection and rich biological insight. Our analysis emphasizes that scientific innovation alone is insufficient: effective preparedness also requires improved data curation, integration, and sharing to build AI-ready resources that accelerate future responses. We argue for coordinated advances in both technological capabilities and supporting...

Three pairs of fungal Trametes strains isolated from distinct geographic origins show conserved genomic features and adaptive response to plant biomass

Wed, 1 Apr 2026 00:00:00 +0000

The genomes of white-rot fungi hold extended repertoires of enzymes active on virtually all the chemical bonds that intertwine lignocellulose polymers, and several Trametes species have been identified as powerful tools for biorefinery or bioremediation. However, only few studies have addressed the intra-species polymorphism one would expect from fungal strains collected in contrasted environments. We compared the genome sequence of pairs of strains collected in different geographic areas, for each of three fungal species. Using an updated list of the predicted functions for fungal ligno- and cellulolytic enzymes (CAZymes), we observed a high conservation of the gene repertoires among the six strains. We compared the adaptative response of the fungi grown on crystalline cellulose, wheat straw, aspen or pine sawdust by transcriptomics and secretomics. The gene regulation profiles were determined by the species and the substrates, rather than the strain. The secretomes did not show...

Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism

Tue, 31 Mar 2026 00:00:00 +0000

Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug...

Multi‐season analysis reveals hundreds of drought‐responsive genes in sorghum

Tue, 31 Mar 2026 00:00:00 +0000

Persistent drought affects global crop production and is becoming more severe in many parts of the world in recent decades. Deciphering how plants respond to drought will facilitate the development of flexible mitigation strategies. Sorghum bicolor L. Moench (sorghum), a major cereal crop and an emerging bioenergy crop, exhibits remarkable resilience to drought. To better understand the molecular traits that underlie sorghum's remarkable drought tolerance, we undertook a large-scale sorghum gene expression profiling effort, totaling nearly 1500 transcriptome profiles, across a 3-year field study with replicated plots in California's Central Valley. This study included time-resolved gene expression data from roots and leaves of two sorghum genotypes, BTx642 and RTx430, with different pre-flowering and post-flowering drought-tolerance adaptations under control and drought conditions. Quantification of genotype-specific drought tolerance effects was enabled by de novo sequencing,...

Salt supplementation-induced metabolic reprogramming in Streptomyces coelicolor

Wed, 25 Mar 2026 00:00:00 +0000

Members of the genus Streptomyces are major producers of a wide variety of secondary metabolites that serve as bioactive compounds. Many secondary metabolites are produced in response to environmental signals such as biotic and abiotic stresses. In this study, we identified salt supplementation as one of the stimuli activating secondary metabolism in the model Streptomyces species, Streptomyces coelicolor. Comparative metabolomics revealed overproduction of several known secondary metabolites, most notably undecylprodigiosin and coelimycin P1, in addition to their biosynthetic intermediates and derivatives, as well as many unknown metabolites. Transcriptomic analysis revealed activation of diverse biological processes including cation uptake, compatible solute production, and the phosphate limitation stress response through conserved and species-specific mechanisms, presumably to overcome the increased salinity. This response leads to activation of a variety...

Identification and Classification of Fungal GPCR Gene Families

Tue, 24 Mar 2026 00:00:00 +0000

G protein-coupled receptors (GPCRs) are transmembrane proteins crucial for signal transduction in eukaryotes, responding to diverse extracellular signals. Researchers have found and systematically summarized 14 distinct types of GPCRs in fungi but their distribution among numerous fungal species remained largely unexamined. Additionally, three families of mammalian homologs (Rhodopsin, Glutamate, and Frizzled) have been found in previous studies, but they are not included in the systematic classification of fungal GPCRs. Our study establishes a unified classification of 17 GPCR classes in fungi, combining 14 fungal and 3 mammalian previously recognized groups, and classifies 28,294 GPCRs across 1357 fungal species, significantly expanding the scale of GPCRs in fungi and demonstrating their broader distribution. We found that mammalian homologs are notably more prevalent in Early Diverging Fungi (EDF), whereas the previous 14 classes are predominantly found in Ascomycota and Basidiomycota....

Editorial: Proceedings of the first RdRp Summit

Tue, 17 Mar 2026 00:00:00 +0000

Editorial: Proceedings of the first RdRp Summit

Hydrophobins from Aspergillus Mediate Fungal Interactions with Microplastics

Fri, 13 Mar 2026 00:00:00 +0000

Microplastics cause negative environmental consequences such as the release of toxic additive leachates, increased greenhouse gas emissions during degradation, and threaten food chains. Microplastic particles are known to serve as a vector for the transport of microbes (fungi and bacteria) to new environments, threatening biodiversity. Robust biofilm formation makes fungi candidates for collecting and remediating environmental microplastics. However, fungal-microplastic colonization mechanisms have not yet been explored. In this work, we aim to understand which fungal molecules mediate microplastic binding. We examine the common fungal genus Aspergillus, which we found binds microplastics tightly, removing particles from suspension. Upon inoculation of Aspergilli with microplastic particles, up to 3.85 ± 1.48 g of microplastics were flocculated per gram of dry fungal biomass; this phenomenon was observed across various plastics ranging in size from 0.05 to 5 mm....

An expanded registry of candidate cis-regulatory elements

Mon, 9 Mar 2026 00:00:00 +0000

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression1. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions2. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq3, massively parallel reporter assay4, CRISPR perturbation5,6 and transgenic mouse assays7 have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their...

An expanded registry of candidate cis-regulatory elements

Wed, 4 Mar 2026 00:00:00 +0000

An expanded registry of candidate cis-regulatory elements

Wed, 4 Mar 2026 00:00:00 +0000

An expanded registry of candidate cis-regulatory elements

Tue, 17 Feb 2026 00:00:00 +0000

Comparative mitogenomics of kingdom Fungi – evolutionary insights and metagenomic applications

Tue, 17 Feb 2026 00:00:00 +0000

Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns...

SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesis

Tue, 10 Feb 2026 00:00:00 +0000

Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides neural competence remains poorly understood. In this study, we present integrated transcriptional, genetic and genomic analyses to uncover the regulatory mechanisms of SOX2, a key factor in establishing neural identity in RPCs. We show that SOX2 is preferentially enriched in the RPC-specific enhancer landscape associated with essential regulators of retinogenesis. Disruption of SOX2 expression impairs retinogenesis, marked by a selective loss of enhancer activity near genes essential for RPC proliferation and lineage specification. We identified the RPC transcription factor VSX2 as a binding partner for SOX2 and, together, SOX2 and VSX2 co-target a core, retina-specific chromatin repertoire characterized by enhanced TF binding and robust chromatin accessibility....

Evaluating physiological traits of Coffea canephora clones intercropped with Hevea brasiliensis

Tue, 10 Feb 2026 00:00:00 +0000

In this study, we evaluated the physiological response of the photosynthetic apparatus [using chlorophyll a fluorescence (ChlaF) measurements], changes in leaf nutrient contents, and productivity of 16 Coffea canephora clones grown alone (NC, full sunlight) or intercropped with Hevea brasiliensis (IC, shaded). Shade from H. brasiliensis trees influenced the physiological performance of coffee plants. Some of these coffee clones achieved clear responses to shading by rubber trees, indicating that the responses of coffee plants to intercropping are genotype-specific. The PSII complex of the NC plants was more susceptible to photoinhibition, especially clones 02, 73, 143, and 109A, which had increased minimal fluorescence, specific energy fluxes per reaction centers, maximum photochemical quantum yield, quantum efficiency of electron transfer from Q_A ^- to the electron transport chain beyond Q_A ^-,...

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population

Tue, 10 Feb 2026 00:00:00 +0000

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.

Ten Pressing Questions (and Answers) About Marine Fungi and Opportunities for Collaborations in the Ocean Sciences

Tue, 10 Feb 2026 00:00:00 +0000

Nearly 200 years have passed since the first marine fungus, collected from the shores of North Africa, was described. In that time, marine mycologists have continued to observe, describe, and study fungi in every marine ecosystem examined. Nevertheless, fungi remain functionally “dark matter” of the ocean, presenting a grand opportunity to unravel their roles in ecosystem processes. This report outlines the discussion among participants of the second occasional meeting of marine mycologists at Asilomar, California, in March 2024, in which a diverse and interdisciplinary consortium of researchers enumerated the most pressing, and often basic, unanswered questions in marine fungi. We report on the questions facing the field of marine mycology, identify challenges in addressing those questions, and propose concrete and practical solutions for obtaining their answers. A common thread is the need for increasing cross talk and collaboration between mycologists and oceanographers that...

A Simple and Versatile Cell-Free Expression Method for Producing Secondary Metabolites.

Thu, 29 Jan 2026 00:00:00 +0000

Secondary metabolites are a major source of natural products with industrially relevant bioactivities. Lysate-based cell-free expression (CFE) is an emerging platform for accelerating the discovery and engineering of these natural products. While Escherichia coli cell extracts are widely used for CFE, Streptomyces extracts are likely to offer a more biochemically compatible environment for their expression. However, current Streptomyces-based CFE systems remain underdeveloped, with protocols that are either strain-specific or not readily scalable. To address these limitations and enable broader access to cell-free natural product biosynthesis, we present a generalizable and simple set of reaction conditions that support high-yield protein expression (180-230 μg/mL) in lysates derived from Streptomyces venezuelae NRRL B-65422 and Streptomyces lividans TK24. Like E. coli-based systems, these extracts enable iterative and pathway-level biosynthesis,...

Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient