Recent lbnl_bs_jgi items

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....

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

Tue, 16 Jun 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...

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...

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

Wed, 3 Jun 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.

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....

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

Tue, 10 Mar 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...

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

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

Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cycling taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide...

A collection of archaeal 16S rRNA Clone-FISH cultures for probe validation in fluorescence in situ hybridization experiments

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

We present a collection of 30 Escherichia coli cultures (Clone-FISH cultures), each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from 1 of 30 lineages of archaea, including 17 yet uncultured ones. We make these clones available for use as controls in fluorescence in situ hybridization experiments.

A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions

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

Viruses are key modulators of human gut microbiome composition and function. While metagenomic sequencing has enabled culture-independent discovery of gut bacteriophage diversity, existing genomic catalogues suffer from limited geographic representation, sparse taxonomic classification, and insufficient functional annotation, hindering detailed investigation into phage biology. Here, we present the Unified Human Gastrointestinal Virome (UHGV), a collection of 873,994 viral genomes from globally diverse populations that addresses these limitations. UHGV provides high-quality virome references with extensive host predictions, comprehensive functional annotations, protein structures, a classification framework for comparative analysis, and a web portal to facilitate data access. Using UHGV to profile worldwide metagenomes, we found that host range breadth is strongly associated with phage prevalence. Additionally, we identified diversity-generating retroelements and DNA methyltransferases...

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations

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

Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence assemblies. Accurate metagenome assembly is especially challenging in diverse environments, such as soil, and long-read sequencing has been shown to improve assembly. Here, we use metagenomic data with paired long-read and short-read sequences to identify specific factors that impact genome assembly and assess their relative importance in a natural soil community. Our analysis suggests that low coverage and high sequence diversity are the two main factors leading to misassemblies in short-read data, and many of these "missed" regions tend to be variable parts of the genome, such as integrated viruses or defense system islands. Taken together, our results demonstrate that short-read metagenomes can possibly underestimate the diversity of these genome...

Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)

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

The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List (https://ictv.global/msl), the Virus Metadata Resource (https://ictv.global/vmr), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm (Singelaviria), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming...

Limited consensus of marine viral diversity observed across techniques

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

BackgroundViruses are fundamental to many aspects of life influencing ecosystem functions. The `number of lenses´ we use for exploring the viral diversity has expanded, yet each has limitations that constrain our view of the uncultured virosphere. It is fundamental to evaluate the different viromic approaches and sequencing methods on their ability to recover the extant viral diversity and microdiversity present in a sample. The differences in genome recovery between technologies have downstream impacts on subsequent estimates of viral diversity and function within a sample that can limit our comprehension of natural viral assemblages and their interactions with their microbial hosts.ResultsHere, using the same surface seawater sample, we compare short- and long-read viromics (i.e., Illumina, PacBio–HiFi and MinION sequencing) along with high-throughput single-virus genomics (sequencing of 700 uncultured single-viruses) to explore the consensus between approaches to uncover the...

Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt

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

Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene...

Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development

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

Conserved non-coding sequences (CNSs) are integral elements of transcriptional regulation. Transcriptional tuning of PLETHORA (PLT) genes that encode master regulators of plant development is vital for embryogenesis and meristematic function. However, how the expression of PLT genes is modulated through CNSs remains unclear. Through motif-based mining of upstream sequences in 120 angiosperm genomes, we identified 21 conserved and lineage-specific CNSs, two of which are unusually long, similar, and colinear within eudicots. Using Arabidopsis thaliana, we demonstrate that these two deeply conserved elements, which we named BOX1 and BOX2, control PLT1 and PLT2 expression. CRISPR mutants within these elements specifically reduced PLT expression levels, and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip, affecting the ability to rescue the plt1 plt2 double mutant. We further show that the influence...

Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy

Fri, 23 Jan 2026 00:00:00 +0000

Root biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free, in situ imaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With...

AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids

Thu, 22 Jan 2026 00:00:00 +0000

BackgroundThe genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use.ResultsWe have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their...

Mining Thermophile Photosynthesis Genes: A Synthetic Operon Expressing Chloroflexota Species Reaction Center Genes in Rhodobacter sphaeroides

Wed, 21 Jan 2026 00:00:00 +0000

Photosynthesis is the foundation of the vast majority of life systems, and is therefore the most important bioenergetic process on earth. The greatest diversity of photosynthetic systems is found in microorganisms. However, our understanding of the biophysical and biochemical processes that transduce light into chemical energy is derived from a relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of predicted proteins that catalyze the initial photochemical reactions deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for the expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic...

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

Wed, 21 Jan 2026 00:00:00 +0000

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for understanding desiccation tolerance. Despite its ecological and medicinal significance, genomic and transcriptomic resources for the species are limited. We generated a chromosome-level, haplotype-resolved reference genome assembly and annotation for M. flabellifolia and conducted transcriptomic profiling across a natural dehydration-rehydration time course in the field. Genome architecture and sex determination were characterized, and co-expression network and cis-regulatory element (CRE) enrichment analyses were used to investigate dynamic responses to desiccation. The 1.28-Gb genome exhibits unusually consistent chromatin architecture with unique chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on Chromosome 8. Transcriptomic responses varied with dehydration severity, pointing...

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Wed, 21 Jan 2026 00:00:00 +0000

Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses...

Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus

Fri, 16 Jan 2026 00:00:00 +0000

Development of the DNA affinity purification and sequencing (DAP-seq) technique has allowed genome-scale studies of transcription factor (TF)-binding sites with high reproducibility. Here, we apply this technique to the human opportunistic pathogen Rhizopus microsporus, a mucoralean fungus belonging to the understudied group of early-diverging fungi. We characterize genome-wide binding sites of 58 TFs encoded by genes regulated through adenine methylation and representing major TF families. This analysis reveals their binding profiles and recognized sequences, expanding and diversifying the catalog of known fungal motifs. By integrating this data with DNA 6-methyladenine profiling, we uncover the extensive direct and indirect impact of this epigenetic modification on the regulation of gene expression. Furthermore, we use the generated data to identify TFs involved in biologically relevant processes such as zinc metabolism and light response. Our work enhances our understanding...

Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

Mon, 12 Jan 2026 00:00:00 +0000

Thanks to next-generation sequencing (NGS) technologies, the diversity of fungi can now be investigated through the analysis of their genome sequences. Naviculisporaceae is a family within the Sordariales, whose diversity is not well-known, with only one genome sequence published for this family. Here, we report on the isolation and cultivation of 20 new strains of Naviculisporaceae. Their genome sequences, as well as those of the five commercially available strains, were determined, thus providing complete genome sequences for 25 new Naviculisporaceae strains. Species delimitation was conducted using a combination of (1) ITS + LSU phylogenetic analysis of the new isolates along with other known species of the family, (2) comparisons between DNA barcode sequences of the new strains with those of the known species, and (3) average genome-wide nucleotide identity calculation. We built a phylogenomic tree and studied the organization of the mating-type...

Multi‐Omics Analyses Reveal Divergent Molecular Mechanisms Underlying Plant Biomass Conversion by Five Fungi

Mon, 12 Jan 2026 00:00:00 +0000

Fungal plant biomass conversion (FPBC) is of great importance to the global carbon cycle and has been increasingly applied for the production of biofuel and biochemicals from lignocellulose. However, the comprehensive understanding of relevant molecular mechanisms in different fungi remains challenging. Here, we comparatively analyzed the transcriptome, proteome and metabolome profile of four ascomycetes and one basidiomycete fungi during their growth on two common agricultural feedstocks (soybean hulls and corn stover). We revealed strong time-, substrate- and species-specific responses at multi-omics levels for the tested fungi, highlighting species-specific carbon utilization approaches and evolutionary adaptation to environmental niches. Notably, a remarkable expressional diversity of lignocellulose degrading enzymes, sugar transporter and metabolic genes, as well as industrially relevant metabolites were identified across different fungi and cultivation conditions. The findings...

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

Mon, 12 Jan 2026 00:00:00 +0000

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences...

The genomic footprints of wild Saccharum species trace domestication, diversification, and modern breeding of sugarcane

Mon, 12 Jan 2026 00:00:00 +0000

Sugarcane is a major crop of unclear origins due to its complex polyploid interspecific genome. We analyzed genome ancestries using whole-genome sequence data from 390 representative accessions based on repeated k-mers and chloroplast phylogeny. The results provided evidence that Saccharum officinarum was domesticated in the New Guinea region from the S. robustum wild species and revealed that its genome is a mosaic involving different S. robustum subgroups. We discovered a wild Saccharum contributor to most modern cultivars, likely originating from East Melanesia. We highlighted two early centers of sugarcane diversification associated with human transport, one in continental Asia through hybridization with different S. spontaneum subgroups and one in the Melanesian and Polynesian islands via hybridization with the discovered ancestor and Miscanthus. Finally, we revealed the genome ancestry of modern cultivars, highlighting untapped wild Saccharum diversity as a source of alleles...

The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

Wed, 17 Dec 2025 00:00:00 +0000

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with a broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of N. luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80× of coverage, and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology...

High-quality draft genome sequence of Thermobifida halotolerans DSM 44931

Tue, 16 Dec 2025 00:00:00 +0000

Here, we report the genome sequence of Thermobifida halotolerans DSM 44931, a bacterium that was originally isolated from a salt mine in the Yunnan Province of China. This genome was sequenced using Pacific Biosciences sequencing technology and was assembled into 2 contigs in 2 scaffolds. It has a total length of 5,506,851 bp and a GC content of 71.16%. Functional annotation of this genome provides further metabolic insight into this species.

Genome sequence of Streptomyces sp. DSM 42143

Tue, 16 Dec 2025 00:00:00 +0000

We report the 7.9 Mb genome sequence of Streptomyces sp. DSM 42143, which contains a 7,807,748 bp linear chromosome and a 108,164 bp circular plasmid. AntiSMASH predicted 39 diverse biosynthetic gene clusters, suggesting that this strain may be a rich resource for antibiotic discovery.

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Tue, 16 Dec 2025 00:00:00 +0000

Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative...

A multi-omic characterization of the physiological responses to salt stress in Scenedesmus obliquus UTEX393

Tue, 16 Dec 2025 00:00:00 +0000

Scenedesmus obliquus UTEX393 is a promising microalgal candidate for sustainable biomanufacturing but its limited halotolerance hinders large-scale cultivation in saline environments. To investigate the molecular basis of salt stress responses, we conducted a comprehensive multi-omic analysis integrating genomics, transcriptomics, proteomics, lipidomics, metabolomics, and DNA affinity purification sequencing (DAP-seq). An improved nuclear genome assembly and annotation yielded 19,017 gene models and a 97% BUSCO completeness score, enabling construction of a genome-scale metabolic model. Comparing 15 ppt salinity stress to 5 ppt control, growth and productivity were significantly reduced, accompanied by widespread transcriptomic and proteomic changes. Transcriptomic analysis revealed downregulation of photosynthetic machinery and energy conservation genes, and upregulation of stress-responsive elements such as expansins, flavodoxins, and osmoprotectants. Lipidomic profiling showed...

Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae

Wed, 10 Dec 2025 00:00:00 +0000

Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous...

Green genes from blue greens: challenges and solutions to unlocking the potential of cyanobacteria in drug discovery

Tue, 9 Dec 2025 00:00:00 +0000

Cyanobacteria are prolific producers of biologically active compounds that are important in influencing ecology, behavior of interacting organisms, and as leads in drug discovery efforts. Here we discuss the challenges faced by all natural product researchers, especially those that focus on cyanobacteria, and then describe progress that has been made in these areas. We also propose some solutions, paths forward, and thoughts for consideration on these challenges.

Draft genome sequence of Gleimia europaea DSM 26657

Fri, 5 Dec 2025 00:00:00 +0000

Here, we report the draft genome sequence of Gleimia europaea DSM 26657, a pathogenic gram-positive bacillus, isolated from a patient with a subcutaneous fistula in 2007 in Germany. The genome is 2.0 Mb in size with 1,813 predicted genes, having only one putative antibiotic resistance gene.

Draft genome assembly and annotation of Haematococcus lacustris strain Liv1, an industrial astaxanthin-producing microalga

Fri, 5 Dec 2025 00:00:00 +0000

Haematococcus lacustris is a ubiquitous unicellular green alga with industrial bioproduct applications, namely, as feedstock for natural astaxanthin. We report the annotated 291.5 Mbp genome for H. lacustris Liv1 to support future algal research in the areas of carotenoid biosynthesis and crop protection.

Draft genome of the switchgrass head smut pathogen Tilletia maclaganii

Fri, 5 Dec 2025 00:00:00 +0000

Tilletia maclaganii is a smut fungal pathogen that causes significant biomass reduction of switchgrass (Panicum virgatum) used for animal forage and biofuel production. Here we present the annotated genome of T. maclaganii, strain Tm001-NY21, estimated at 42.79 Mb in size, in 53 assembled contigs and encoding 10,235 predicted genes. This genome will be important for future comparative studies of Ustilaginales across its geographic and host range.

Draft genome sequence of Clostridium tetanomorphum DSM 4474T isolated from a septic wound

Fri, 5 Dec 2025 00:00:00 +0000

We report the genome sequence of Clostridium tetanomorphum DSM 4474^T isolated from a septic wound. In addition to its potential as a human pathogen, this species may be useful in biofuel production due to its ability to synthesize butanol without the byproduct acetone. The genome is 4,374,054 bp.

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism

Tue, 2 Dec 2025 00:00:00 +0000

Syntrophic microbial consortia can contribute substantially to the activity of anoxic ecosystems but are often too rare to allow the study of their in situ physiologies using traditional molecular methods. Here we combined bioorthogonal non-canonical amino acid tagging (BONCAT), stable isotope probing and metaproteomics to improve the recovery of proteins from active members and track isotope incorporation in an anaerobic digestion community. Click-chemistry-enabled cell sorting and direct protein pull-down coupled to metaproteomics improved recovery of isotopically labelled proteins during anaerobic acetate oxidation. BONCAT-enabled protein profiles revealed elevated activity and labelling of a rare and so-far uncharacterized syntrophic bacterium belonging to the family Natronincolaceae that expressed a previously hypothesized oxidative glycine pathway for syntrophic acetate oxidation. Stable-isotope-probing-informed metabolic modelling predicted that this organism accounted...

Correction: Myco-Ed: Mycological curriculum for education and discovery

Mon, 1 Dec 2025 00:00:00 +0000

[This corrects the article DOI: 10.1371/journal.ppat.1013303.].

Comparative transcriptomics of CAZy enzymes in white- and brown-rot agaricomycetes: Evolutionary insights into lignocellulose degradation and the relevance of GH16 glycoside hydrolase functional divergence

Mon, 1 Dec 2025 00:00:00 +0000

White-rot and brown-rot fungi (WRF and BRF, respectively) decompose lignocellulose, the main structural component of plant biomass, through distinct mechanisms. This study examines the transcriptomic responses of three WRF species (Pleurotus ostreatus, Phanerochaete chrysosporium, and Heterobasidion irregulare) and two BRF species (Fomitopsis schrenkii and Rhodonia placenta) grown on poplar wood (W) and glucose (G) as sole carbon sources. RNA-seq analysis revealed upregulation of carbohydrate-active enzymes (CAZymes) linked to lignocellulose degradation. WRF displayed a broader enzymatic repertoire, whereas BRF employed a more selective approach. Among these responses, GH16 glycoside hydrolases were consistently upregulated across all species, including BRF. Since GH16 enzymes are involved in both plant hemicellulose modification and cell wall remodeling, their wood-induced expression may reflect multiple processes rather than a single conserved wood-decay mechanism. Structural...

Speciation across depth gradients in reef corals

Wed, 26 Nov 2025 00:00:00 +0000

Ecological speciation through adaptation to different habitats can readily occur without strong geographic isolation when the same traits underlie both ecological divergence and reproductive isolation. In light-dependent corals with environment-mediated spawning, adaptation to varying light regimes across depths provides opportunities for such speciation. We show that depth-related distributions are common among sister lineages of corals within the photic zone. We then investigated molecular drivers of depth-associated adaptive divergence by analyzing sequence variation in proteins related to environmental sensing in depth-segregated and light-dependent lineages in the Orbicella species complex. Specifically, we analyzed 1) two genetically divergent ecotypes of Orbicella faveolata across a depth gradient, and 2) two depth-segregated sister species, O. annularis and O. franksi, with different spawning times following sunset. Genome-wide analyses indicate divergence across depths...

A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes

Thu, 20 Nov 2025 00:00:00 +0000

Plasmids play significant roles in microbial adaptation to ecosystems, yet their dynamics remain poorly understood due to identification challenges. We present the Global Soil Plasmidome Resource (GSPR), a comprehensive dataset of 98,728 plasmid sequences amassed from 6860 terrestrial microbial communities and isolates. We explore this resource through various computational approaches, including phylogenetic diversity analysis, host prediction, and extensive functional annotation, to understand the contribution of plasmids to the genetic and functional diversity in soil, correlating these findings with sample type, as well as the soil habitat they were retrieved from. Our analysis reveals insights into plasmid-encoded functions such as effector modules, quorum sensing, and stress resistance, which may contribute to their persistence and microbial adaptation in soil. Furthermore, CRISPR analysis suggests a prevalent role of these elements related to intra-plasmid competition....

A multifunctional sesquiterpene synthase integrates with cytochrome P450s to reinforce the terpenoid defense network in maize

Thu, 20 Nov 2025 00:00:00 +0000

Terpenoids, the largest and most structurally diverse class of plant natural products, play essential roles in maize defense and ecological interactions. In this study, we identified and functionally characterized a sesquiterpenoid-based defense pathway in maize centered on α-santalenoic acid, a pathogen-inducible sesquiterpenoid antibiotic. Using a combination of metabolite-based genome-wide association studies (mGWAS), linkage mapping, and heterologous expression assays, we identified ZmTPS9 as a multiproduct terpene synthase that primarily produces α-santalene and β-bisabolene. Sequence analysis and site-directed mutagenesis revealed that threonine at position 413 is critical for enzyme activity, with its deletion resulting in a complete loss of enzyme activity. The sesquiterpene hydrocarbons produced by ZmTPS9 are further oxidized by three cytochrome P450 monooxygenases, ZmCYP71Z16, ZmCYP71Z18, and ZmCYP71Z19, to yield antimicrobial metabolites including α-santalenoic acid,...

Siderophores and secondary metabolites produced by Ganoderma adspersum.

Wed, 19 Nov 2025 00:00:00 +0000

Ganoderma adspersum is a white-rot wood-degrading basidiomycete of ecological, biotechnological and medicinal interest. In addition to its role in lignin degradation, it produces bioactive metabolites with reported antimicrobial and antioxidant activities. However, the mechanisms of iron acquisition, including siderophore-mediated pathways, remain poorly characterized in Ganoderma species. Improved understanding of these systems is essential to elucidate their contributions to fungal physiology, secondary metabolism and ecological adaptation. In this study, the genome of G. adspersum was sequenced for the first time and screened for genes that may be involved in the production of secondary metabolites. A gene cluster was identified as potentially involved in iron uptake. In particular, genes related to non-ribosomal peptide synthetases were detected next to a gene encoding a monooxygenase and indicated a potential hydroxamate-family siderophore. Liquid chromatography...

Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in Pseudomonas putida

Tue, 18 Nov 2025 00:00:00 +0000

Synthetic biology generates vast combinatorial designs, yet high-throughput analytical methods to screen them are poorly matched to interrogate this search space. We address this challenge by developing a biosensor-driven, growth-coupled selection strategy in Pseudomonas putida for isoprenol, a potential aviation fuel precursor. We found and characterized a noncanonical signaling pathway, revealing a functional and physical complex between a hybrid histidine kinase and an alcohol dehydrogenase, whose activity is tuned by heterodimerization. Leveraging this biosensor in a pooled CRISPRi library selection, we identified key host limitations. Iterative combinatorial strain engineering derived from these hits yielded a 36-fold titer increase to ~900 milligrams per liter. Integrated omics analysis revealed that metabolic rewiring toward amino acid catabolism was crucial for this improvement. This observation was found to be beneficial by technoeconomic analysis. Our modular...

Author Correction: Comparative and demographic analysis of orang-utan genomes

Wed, 22 Oct 2025 00:00:00 +0000

In this Article, we reported genome sequencing data from five Sumatran and five Bornean orang-utans. In re-analysing these data, Banes et al.1 found that eight of the ten samples were mislabelled, and we wish to correct the original publication according to their findings. In addition, Banes et al.1 find that one of the orang-utans that we had labelled as a male Sumatran is in fact a female Tapanuli orang-utan (an orang-utan species that was unknown at the time of publication of our original Article and that was first reported in 2017 (ref. 2)). While we here correct the original tables to display the correct names and IDs of the individuals studied, we do not correct the analyses in the original paper since the Tapanuli species was discovered only after we had concluded our study. We refer the reader to Banes et al.1 for further information. In the main text, the sentence “We also sequenced the genomes of 10 additional unrelated wild-caught orang-utans, five Sumatran and five...

Quorum-driven microbial consortium for Bioplastic production from agro-waste

Mon, 13 Oct 2025 00:00:00 +0000

Microbial consortia have high relevance in natural environments. Here we present the production of polyhydroxyalkanoates (PHA) from agro-industrial residues by a synthetic interkingdom consortium formed by the saprotrophic fungus Ophiostoma piceae CECT 20146, which encodes a wide range of lignocellulolytic enzymes, and a natural PHA producer, Pseudomonas putida KT2440. Two agro-industrial residues were utilized: Brewer's Spent Grain (BSG) as a carbon/nitrogen source and biofilm scaffold and waste cooking oil (WCO) as a carbon source for PHA synthesis. Through biochemistry, microscopy, and omics analyses, it is shown that P. putida accumulates up to 40.2% of intracellular PHA when the quorum sensing molecule, farnesol (naturally produced by O. piceae) is added, thanks to the increased proliferation of P. putida cells. An interactive Shiny application has also been developed for an easy visualization and comprehension of all the transcriptomics...

A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

Tue, 7 Oct 2025 00:00:00 +0000

Cells must accurately sense and respond to nutrients to compete for resources and establish growth. Phosphate is a critical nutrient source necessary for signaling, energy metabolism, and synthesis of nucleic acids, phospholipids, and cellular metabolites. During phosphate limitation, fungi import phosphate from the environment and liberate phosphate from phosphate-containing molecules in the cell. In the model filamentous fungus Neurospora crassa, the phosphate starvation response is regulated by the conserved transcription factor NUC-1. The activity of NUC-1 is repressed by a complex of the cyclin-dependent kinase MDK-1 and the cyclin PREG when phosphate is plentiful. When phosphate is limiting, NUC-1 repression by MDK-1/PREG is relieved by the cyclin-dependent kinase inhibitor NUC-2. We investigated the global response of N. crassa to phosphate starvation. During phosphate starvation, NUC-1 directly activated the expression of genes encoding phosphatases, nucleases,...

Characterization of the thermophilic xylanase Fsa02490Xyn from the hyperthermophile Fervidibacter sacchari belonging to glycoside hydrolase family 10

Tue, 7 Oct 2025 00:00:00 +0000

Fervidibacter sacchari is an aerobic hyperthermophile belonging to the phylum Armatimonadota that degrades a variety of polysaccharides. Its genome encodes 117 enzymes with one or more annotated glycoside hydrolase (GH) domain, but the roles of these putative GHs in polysaccharide catabolism are poorly defined. Here, we describe one F. sacchari enzyme encoding a GH10 domain, Fsa02490Xyn, that was previously shown to be active on Miscanthus, oat β-glucan, and beech-wood xylan, with optimal activity at 90-100 °C. We show that Fsa02490Xyn is also active on birch-wood xylan and gellan gum. The pH range on beech-wood xylan was 4.5 to 9.5 (pH_opt 7.0-8.0). Fsa024940Xyn had a K_m of 2.375 mm, V_max of 1250 μm·min^-1, and k_cat/K_m of 1.259 × 10⁴ s^-1·m^-1 when using a para-nitrophenyl-?-xylobioside assay. A phylogenetic analysis of GH10 family enzymes revealed a large clade of enzymes from diverse...

metagRoot: a comprehensive database of protein families associated with plant root microbiomes

Tue, 7 Oct 2025 00:00:00 +0000

The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.me...

Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in Pseudomonas putida

Thu, 25 Sep 2025 00:00:00 +0000

ABSTRACT

Synthetic biology tools have accelerated the generation of simple mutants, but combinatorial testing remains challenging. High-throughput methods struggle translating from proof-of-principle molecules to advanced bioproducts. We address this challenge with a biosensor-driven strategy for enhanced isoprenol production in Pseudomonas putida , a key precursor for sustainable aviation fuel and platform chemicals. This biosensor leverages P. putida ’s native response to short-chain alcohols via a previously uncharacterized hybrid histidine kinase signaling cascade. Refactoring the biosensor for a conditional growth-based selection enabled identification of competing cellular processes with a ∼16,500-member CRISPRi-library. An iterative combinatorial strain engineering approach yielded an integrated P. putida strain producing ∼900 mg/L isoprenol in glucose minimal medium, a 36-fold increase. Ensemble -omics analysis revealed metabolic rewiring, including amino acid...

Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake

Tue, 23 Sep 2025 00:00:00 +0000

The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation...

Superfacility: The Convergence of Data, Compute, Networking, Analytics and Software

Mon, 22 Sep 2025 00:00:00 +0000

Superfacility: The Convergence of Data, Compute, Networking, Analytics and Software

Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Thu, 11 Sep 2025 00:00:00 +0000

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was...

Eucalyptus grandis MYB‐Like and RAN‐Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis Pathways

Fri, 5 Sep 2025 00:00:00 +0000

Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending...

Astrovirology: Expanding the Search for Life