Pablo Cruz-Morales

Laetiporus sulphureus is an edible wood-decaying basidiomycete whose fruiting body is valued for its characteristic chicken-like texture and flavor. Although the species has been investigated for various biotechnological applications, information on the submerged fermentation physiology remains limited. In this study, two newly isolated Danish L. sulphureus strains (NFICC9002 and NFICC9004) were evaluated with respect to cultivation conditions and potential mycotoxin production. The effect of incubation temperature, initial pH, carbon source, nitrogen sources, and agitation was investigated in liquid cultivations. Both strains exhibited greater biomass production at 25–30 °C than at 35–37 °C and at low pH. Carbon and nitrogen sources exerted strain-specific influence on biomass production. HPLC analysis demonstrated that substrate consumption was not always proportional to biomass formation, with glycerol supporting high biomass production despite only moderate substrate utilization. Whole-genome sequencing and untargeted metabolomics were used to support strain characterization and to screen for evidence of known mycotoxins. Whole-genome sequencing confirmed the taxonomic identity of the two strains as L. sulphureus and revealed no evidence of known toxin- or mycotoxin-associated genes. Untargeted metabolomics detected no known mycotoxins under the cultivation, extraction and detection methods used. These findings provide physiological and genomic information that may support the future development of L. sulphureus for submerged cultivation and food-related applications.

Plastics derived from fossil feedstocks pose major recycling challenges, particularly crosslinked thermosets used in electronics, construction and composites. Polydiketoenamines (PDKs) are recyclable alternatives; however, monomers such as dimedone are petrochemical-derived and offer limited tunability. We computationally screened 144 β-keto-δ-lactones (BKDLs), identifying solvation free energy as the primary determinant of depolymerization temperature across a 20–60 °C range. We engineered hybrid type I polyketide synthases (PKSs) in Escherichia coli and Streptomyces hosts to biosynthesize BKDLs with diverse substituents and defined stereochemistry, reaching titers of 1.84 g L ⁻¹ in bioreactors. Polymerization of chemically synthesized BKDLs identical to PKS products confirmed tunable glass transition temperatures (53–98 °C) and temperature-gated depolymerization. Different BKDLs yielded PDKs with thermal, mechanical, solvent-resistance and optical properties governed by substituent and chirality. Technoeconomic and life-cycle analyses indicate that corn-stover-derived BKDLs can outperform petrochemical dimedone on cost and greenhouse gas emissions. This study demonstrates that engineered PKSs can produce monomers for recyclable plastics with programmable depolymerization behavior.

Reducing carbon emissions from aviation and long-distance transportation sectors requires the development of sustainable biofuels with suitable energy density, freezing point, and other physical properties. We previously demonstrated biological production of high energy polycyclopropanated fatty acids (POP-FAs, class I) using an iterative polyketide synthase (iPKS) pathway in a Streptomyces host. Here, we used a computational model of fuel properties to identify chain length and cyclopropanation control as critical steps to engineer this iPKS for biofuel applications. We next explored the natural diversity of POP biosynthesis by investigating homologous pathways. Then, by in vivo gene exchange, we determined cyclopropanase (CP) catalysis to be key for POP-FA engineering. Leveraging both natural and engineered pathway product diversity, we demonstrate targeted production of improved POP-FAs, namely shortened POP-FAs with predicted superior freezing point properties for aviation, as well as fully cyclopropane-saturated POP-FAs which should have superior energy-density. These precise and controllable modifications to POP-FA structure open the door for bioproduction of designer POP fuels.

Pests cause up to 40% of global crops losses. Pesticide overuse drives resistance and poses notable risks to public health and the environment. Many hypocrealean fungi form symbiotic relationships with plants while antagonizing pests, making them valuable sources of biocontrol agents and biopesticides. However, little is known about their biosynthetic capabilities. Here we use phylogenomics, metabolomics and heterologous expression to catalog the biosynthetic repertoire of 82 plant-associated and insect-associated Hypocreales species. Annotation of 5,221 biosynthetic gene clusters reveals that ~80% of them encode unknown products. By linking biosynthetic gene clusters to molecules, we investigate the biosynthesis of several natural products, including pyridones, dethiosecoemestrin and efrapeptin. Additionally, by combining our metabologenomics workflow with synthetic biology, we characterize four nonribosomal peptide synthetase-like synthetases involved in the biosynthesis of hitherto unknown products. We believe that this work lays the groundwork for future efforts toward sustainable pest control in agriculture. The alt text for this image may have been generated using AI.

Polyketide synthases (PKSs) are essential enzymatic systems that produce a wide range of natural products.

Ensuring a stable and nutritious food supply requires sustainable agricultural practices, with soil fungi emerging as promising bio-fertilizers that can enhance crop health. In this study, we assess how the fungal microbiome mediates the relationship between environmental factors and crop health in wheat fields. Using a structural equation model, we analyzed fungal genera together with abiotic variables (weather, soil nutrients, and field type), while crop health was estimated via NDVI values from satellite imagery, providing a cost-effective approach for field monitoring. Our findings from both conventional and ecological wheat fields confirm our hypothesis that the fungal microbiome mediates the effects of environmental factors, such as soil nutrients, seasonality, and weather, on crop health. Notably, we observe a consistent positive association between the fungal genus Mortierella and crop health. Positive associations were also found for Candida, Leucothecium, and Phialemonium, while Thermomyces and Trichocladium correlated negatively. Mortierella had the greatest impact, highlighting its potential as a key biofertilizer.

Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in microbial interactions and soil health, but are also crucial for the development of pharmaceuticals or agrochemicals. Over the past decades, advancements in genome sequencing have enabled the identification of large numbers of biosynthetic gene clusters directly from microbial genomes. Since its inception in 2011, antiSMASH (https://antismash.secondarymetabolites.org/), has become the leading tool for detecting and characterizing these gene clusters in bacteria and fungi. This paper introduces version 8 of antiSMASH, which has increased the number of detectable cluster types from 81 to 101, and has improved analysis support for terpenoids and tailoring enzymes, as well as improvements in the analysis of modular enzymes like polyketide synthases and nonribosomal peptide synthetases. These modifications keep antiSMASH up-to-date with developments in the field and extend its overall predictive capabilities for natural product genome mining.