Microbial exopolysaccharides (EPSs) serve multiple industrial and environmental purposes operating as complex biopolymers produced by bacteria and fungus, as well as by yeast and microalgae. The structural diversity of microbial EPS enables the biofilm formation, the stress resistance and the nutrient storage, comprising homopolysaccharides and heteropolysaccharides. Soil structure receives substantial improvement through EPS because the polymers help aggregate particles, retaining more water and trapping heavy metals, that results in enhanced soil fertility useful in sustainable agricultural practices. Moreover, through the presence of EPS-producing bacteria, plants can establish beneficial connections with microorganisms that improve their tolerance to environmental factors, including salt exposure, drought conditions and extreme temperature changes. Such polymers find applications in the bioremediation and pharmaceutical fields because they present significant pharmacological properties, such as antibacterial, anti-inflammatory activities and antioxidant behavior. Their biodegradable nature and eco-friendly properties make it eligible as a sustainable choice to replace synthetic polymers. This paper broaches the multiple ways how EPS improves plant wellness and enhances soil quality. Potential solutions emerge from microbial EPS research to address global challenges in agricultural sectors, biotechnological fields, and environmental management domains.

Aflatoxin B1 (AFB1) is a highly toxic mycotoxin that threatens global food and feed safety. While enzymatic detoxification is a promising strategy, robust and efficient enzymes remain scarce. This study identified that the multicopper oxidase CueO from E. coli CG1061 transforms AFB1 into the less toxic aflatoxin Q1, exhibiting optimal activity at pH 8 and 60 °C. The CueO-2,2′-azino-bis (3-ethylbenzothazoline-6-sulfonic acid) (ABTS) mediator system achieved >90% of AFB1 transformation in 10 min and complete transformation in 20 min, significantly outperforming CueO alone (51% in 60 min). Mechanistically, CueO oxidizes ABTS to form the ABTṠ+ radical, which subsequently oxidizes AFB1. Mutants (Met510Leu, Asp439Ala, and Pro444Ala) exhibited enhanced enzymatic activity toward ABTS but showed no improvement in the catalytic efficiency for AFB1 transformation. Molecular docking suggests this is because AFB1 binds to surface-exposed residue Ser243, distal to the active site. These findings highlight E. coli CueO’s a promising candidate for managing AFB1 contamination.

Transposons are among the most abundant and diverse mobile genetic elements in nature. A unique class termed IStrons encodes a transposase for transposon mobility, an RNA-guided nuclease for maintenance, and a self-splicing group I intron for element removal from host mRNA. However, it is unclear how a single polynucleotide sequence balances these distinct biochemical functions. Here we employed pooled library mutagenesis coupled with high-throughput sequencing to systematically dissect the molecular determinants of IStron transposition, RNA-guided DNA cleavage, and self-splicing. We found that the terminal trinucleotide of the transposon right end is constrained by all three functions, identifying a molecular convergence point. Cross-assay comparisons revealed that most variants maintained or lost activity across multiple assays simultaneously. However, a subset selectively retained one activity while losing another, revealing antagonism between DNA cleavage and splicing governed by guide RNA structural stability. Increased GC content at the base of the guide RNA 3' terminal stem-loop abolished splicing while maintaining DNA cleavage, and the properly folded guide RNA sterically occluded alternative splice sites, ensuring splicing accuracy across variable flanking contexts. Thus, IStron transcripts overcome an inherent trade-off between guide RNA maturation and splicing, with RNA structural stability as the primary determinant of pathway choice.

Droplet sorting technology has the potential to revolutionize the biotechnology sector as it provides massive high-throughput screening capacity, but the technology remains not accessible for a wider audience yet. There is a need for more affordable droplet sorting platforms to design cell factories and screen cell libraries. In here we demonstrate our droplet cytometry/sorter platform for single-cell screening of yeast cells based on their fluorescence signal.

The availability of large-scale protein structure collections enables structure-based analysis of their function and evolution beyond what is possible from sequence alone. However, applying three-dimensional structure comparison at scale remains computationally demanding and limits practical exploration of large experimental and predicted collections. This creates a need for fast, structure-based search methods that retain biological relevance while enabling large-scale exploration. In this paper, we present AlphaFind v2, an application for finding structurally similar proteins in the AlphaFold Database https://alphafold.ebi.ac.uk/ of predicted structures. AlphaFind v2 uses fast pre-filtering via state-of-the-art protein embeddings that preserve structural information, followed by refinement with US-align. The application presents multiple complementary search modes, including (i) search over full protein chains, (ii) search aware of the AlphaFold pLDDT metric, restricting similarity computation to the most stable and structurally relevant regions, (iii) search over protein domains from the TED database https://ted.cathdb.info/ , and (iv) a multidomain search mode, combining multiple chain-level domain matches within a single score and alignment. The application accepts protein identifiers and returns similar proteins with metrics, rich metadata, and interactive superpositions. AlphaFind v2 additionally allows searching within an organism or CATH label and matches the proteins with experimental structures. AlphaFind v2 is accessible at https://alphafind.ics.muni.cz/ 

Bacteria of the genus Bacillus are widely used in agriculture due to their ability to synthesise IAA, but the metabolic pathways of IAA synthesis and the regulatory mechanisms of key genes remain unclear. In this study, the biochemical characteristics of Bacillus cereus, Bacillus subtilis and Bacillus safensis were detected. It was found that Bacillus subtilis has a higher indoles synthesis efficiency, Bacillus safensis has stronger salt tolerance and Bacillus cereus has more prominent alkali tolerance. Through whole-genome sequencing and comparative analysis, combined with the retrieval of key genes in the tryptophan metabolic pathway and the metabolic analysis of indole compounds, it is clarified that Bacillus cereus has three IAA synthesis pathways, namely TAM, IAM and IPyA; Bacillus subtilis contains IAM and IPyA pathways; and Bacillus safensis only has the IPyA pathway. This study offers new insights into Bacillus metabolism, high-quality strains for microbial agents, and matters for plant-growth bacteria application and agricultural sustainability.

Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.

Limonene is a high-value monoterpenoid used in food, pharmaceutical, and fragrance applications. To overcome limitations of conventional production, this study developed a biosynthesis platform using acetate as the sole carbon source. Acetate is an ideal nonfood substrate that can be sustainably derived from industrial waste streams, syngas, and CO2 reduction. Initially, the heterologous synthetic pathway was constructed to yield 0.13 mg/L limonene from acetate. By introducing the mutated EfMVASA110G to enhance catalytic efficiency, along with promoter engineering and substitution of the synthesis substrate, the production titer was enhanced to 49.24 mg/L. Subsequent host optimization through NADPH regeneration and pathway knockout, combined with fermentation optimization, increased the titer to 167.45 mg/L. Ultimately, whole-cell biocatalysis achieved 450.72 mg/L, establishing the highest reported acetate-based limonene titer. Overall, this study establishes a framework for biosynthesis of high-value terpenoids from nonfood feedstocks and demonstrates acetate as a promising carbon source for advanced bioproduction systems.