Recent lbnl_bs items

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...

Expanding the scope of redox-balance growth coupling techniques with a carbon co-feeding strategy

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

Metabolic engineering to produce molecules not naturally synthesized by the host often requires directed evolution to improve pathway enzyme performance. Growth-coupled selection can dramatically increase directed-evolution throughput, and manipulation of redox balance has proven effective for tying reductase fitness to microbial growth. However, most redox-balance selections require feeding the reductase substrate because of stoichiometric constraints. This is impractical for many biosynthetic pathways either due to practical limitations on cost or complexity of bulk substrate synthesis, or the lack of an ability to transport substrate into cells, for example intracellular acyl-CoA/ACP intermediates. Here we define stoichiometric constraints that make substrate feeding necessary for many acetyl-CoA-derived reduction pathways in NADPH-imbalanced hosts. We overcome these constraints with a dual-feedstock strategy in which glucose provides reducing power while acetate supplies additional...

Adaptive rewiring of NADPH electron flow reveals escape routes from redox-balance-based growth coupling in Escherichia coli

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

Redox-balance-based growth coupling links oxidoreductase activity to cellular fitness and can enable high-throughput enzyme selection and strain evolution. However, because growth reflects the fitness of the whole cell, metabolic adaptation can circumvent the intended selective pressure. Here, we investigated the evolutionary stability of an aerobic NADPH redox-balance selection strain of Escherichia coli engineered to accumulate NADPH during growth on glucose. Adaptive evolution first selected mutations predicted to relax cofactor specificity in NADH-dependent quinone oxidoreductases, allowing NADPH-derived reducing equivalents to enter respiratory electron flow. Removing major NADH-to-quinone oxidoreductases did not eliminate the capacity for evolutionary escape; in one successfully evolving lineage, adaptive evolution uncovered a latent lactate-mediated route for electron transfer into the quinone pool. These results reveal strong selective pressure to reconnect soluble nicotinamide...

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.

Charge-switching ionizable lipids lower the toxicity of lipid nanoparticles

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

Lipid nanoparticles (LNPs) have great potential as nucleic acid delivery vehicles; however, they trigger the production of inflammatory cytokines, which limits their medical applications. Developing non-inflammatory LNPs is challenging because the LNP’s ionizable lipid and the process of endosomal disruption are the major sources of LNP toxicity but are also essential for delivering nucleic acids. Here we demonstrate that ionizable lipids containing a carboxylic acid and an amine (termed S-lipid) switch their charged state between the pHs of 7.4 and 4.0, allowing them to generate LNPs (termed switchable nanoparticles) that efficiently encapsulate nucleic acid and trigger endosomal release without activation of the TLR4, complement, galectin-8 and platelet activating factor signalling pathways. Finally, we demonstrate that switchable nanoparticles are better at treating lipopolysaccharide-induced acute lung injury than traditional LNPs because they do not exacerbate pre-existing...

Cobamide-based interactions between soil bacteria can be predicted based on monoculture growth.

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

Interactions between microbes shape the structure and function of microbial communities. While studying interactions is key to understanding microbial communities as a whole, gaining a detailed mechanistic view is challenging due to the number of co-occurring interactions. Here, we focus on a single class of shared nutrients, the cobalamin (vitamin B₁₂) family of enzyme cofactors known as cobamides, to study nutrient interactions in laboratory consortia of increasing complexity. Measuring cobamide-dependent growth of two soil Caulobacter isolates in monoculture revealed that each grows faster within a distinct range of cobamide concentrations. Co-culturing the two isolates demonstrated that the cobamide concentration predictably determines which isolate predominates. These results suggest that, although the two organisms appear functionally redundant, with identical metabolic capabilities predicted in their genomes, they may occupy distinct niches in their environment...

Biomanufacturing and Scale‐Up: Pathways to Biochemicals, Biofuels, and Biomaterials

Tue, 20 Oct 2026 00:00:00 +0000

Biomanufacturing and Scale‐Up: Pathways to Biochemicals, Biofuels, and Biomaterials

An additional water is introduced into the manganese cluster during the formation of the S3 state of photosystem II

Tue, 20 Oct 2026 00:00:00 +0000

During photosynthetic water oxidation, the Mn4Ca cluster in Photosystem II progresses through five intermediate Si (i = 0–4) states. X-ray crystallography studies have reported the insertion of one new O ligand during the formation of the S3 state, but recent studies question the presence of this additional ligand based on cryo-EM and earlier room-temperature crystallography data. There is also controversy about whether the O-O bond interaction already occurs in the S3 state or in the subsequent S3 to S0 transition. Here we report conventional high-resolution data for the S1, S2, and S3 states to a resolution of ~1.9 Å, and anomalous diffraction data at two energies (9.5 keV and 7 keV), that was used to model the Mn positions, followed by determination of oxygen positions using the high-resolution maps. We show that the new oxygen atom, OX (or O6), in the S3 state is observable as a distinct peak without any restraints, confirming its ligation to Mn1 and Ca. The OX-O5 distance...

Broad Stability and pH-Mediated Reversible Disassembly of In Vitro Assembled Bacterial Microcompartment Shells

Tue, 20 Oct 2026 00:00:00 +0000

Abstract Bacterial microcompartments (BMCs) are self-assembling organelles that colocalize enzymes and metabolites of various biochemical pathways. Their selectively permeable shell is made entirely of protein, and the inherent properties of these systems make them attractive templates for bioengineering synthetic nanoreactors. Understanding the extent of shell stability in an extended range of conditions broadens the scope of chemistries that can be confined in these nanocompartments. Here we analyze the stability of in vitro assembled BMC shells and find that they retain their structure at high concentrations of various solvents and detergents, at temperatures up to 75 °C, and across a pH range from 3.9 to 11. Shell disassembly is observed below pH 3.9, but shells can be reassembled upon increasing the pH back to 8. These results expand the range of reactions that can be performed inside protein-based nanoreactors and underscore the potential of modular BMC shell proteins as...

Artifact segmentation using the U-Net architecture for powder X-ray diffraction images

Tue, 20 Oct 2026 00:00:00 +0000

Modern synchrotron X-ray facilities generate X-ray diffraction (XRD) image data at rates that far exceed the capacity of manual analysis, yet critical processing steps such as artifact removal rely on human intervention. Rule-based algorithms in standard beamline software cannot reliably distinguish harmful artifacts like single-crystal diffraction spots from desirable features like preferred orientation, which leads to incorrectly processed data. We demonstrate that a U-Net convolutional neural network trained on expert-labeled experimental data can help automate artifact segmentation in time-resolved XRD measurements of battery materials. To address overfitting from redundant time-series frames, we introduce a mutual information-based pruning algorithm that selects maximally diverse training images. Our optimized model achieves an 85.1% true positive rate on a fully held-out battery dataset while reducing false positives by 34% compared with GSAS-II. Critically, the model preserves...

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