As the name of the genus Pantoea (“of all sorts and sources”) suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

Ice nucleation activity (INA) is the capacity of certain particles to catalyze ice formation at temperatures higher than the temperature at which pure water freezes. INA impacts the ratio of liquid to frozen cloud droplets and, therefore, the formation of precipitation and Earth’s radiative balance. Some Fusarium strains secrete ice-nucleating particles (INPs); they travel through the atmosphere and may thus contribute to these atmospheric processes. Fusarium INPs were previously found to consist of proteinaceous aggregates. Here, we determined that in F. avenaceum, the proteins forming these aggregates are smaller than 5 nm and INA is higher after growth at low temperatures and varies among strains. Leveraging these findings, we used comparative genomics and transcriptomics to identify candidate INA genes. Ten candidate INA genes that were predicted to encode secreted proteins were present only in the strains that produced the highest number of INPs. In total, 203 candidate INA genes coding for secreted proteins were induced at low temperatures. Among them, two genes predicted to encode hydrophobins stood out because hydrophobins are small, secreted proteins that form aggregates with amphipathic properties. We discuss the potential of the candidate genes to encode INA proteins and the next steps necessary to identify the molecular basis of INA in F. avenaceum.

Ice-nucleating proteins (INpros) catalyze ice formation at high subzero temperatures, with major biological and environmental implications. While bacterial INpros have been structurally characterized, their counterparts in other organisms have remained largely unknown. Here, we identify membrane-independent proteins in fungi of the Mortierellaceae family that promote ice formation with high efficiency. These proteins are predicted to adopt β-solenoid folds and multimerize to form extended ice-binding surfaces, exhibiting mechanistic parallels with bacterial INpros. Structural modeling, phylogenetic analysis, and heterologous gene expression leading to ice nucleation in Escherichia coli and Saccharomyces cerevisiae show that the fungal INpros are encoded by orthologs of the bacterial InaZ gene, which was likely acquired by a fungal ancestor through horizontal gene transfer. The discovery of cell-free fungal INpros provides tools for innovative freezing applications and reveals biophysical constraints on ice nucleation across life.

From extracellular freezing to cloud glaciation, the crystallization of water is ubiquitous and shapes life as we know it. Efficient biological ice nucleators (INs) are crucial for organism survival in cold environments and, when aerosolized, serve as a significant source of atmospheric ice nuclei. Several lichen species have been identified as potent INs capable of inducing freezing at high subzero temperatures. Despite their importance, the abundance and diversity of lichen INs are still not well understood. Here, we investigate ice nucleation activity in the cyanolichen-forming genus Peltigera from across a range of ecosystems in the Arctic, the northwestern United States, and Central and South America. We find strong IN activity in all tested Peltigera species, with ice nucleation temperatures above −12 °C and 35 % of the samples initiating freezing at temperatures at or above −6.2 °C. The Peltigera INs in aqueous extract appear to be resistant to freeze–thaw cycles, suggesting that they can survive dispersal through the atmosphere and thereby potentially influence precipitation patterns. An axenic fungal culture termed L01-tf-B03, from the lichen Peltigera britannica JNU22, displays an ice nucleation temperature of −5.6 °C at 1 mg mL⁻¹ and retains remarkably high IN activity at concentrations as low as 0.1 ng mL⁻¹. Our analysis suggests that the INs released from this fungus in culture are 1000 times more potent than the most active bacterial INs from Pseudomonas syringae. The global distribution of Peltigera lichens, in combination with the IN activity, emphasizes their potential to act as powerful ice-nucleating agents in the atmosphere.

Pantoea allii , one of four Pantoea species known to cause onion centre rot, is infrequently isolated from onion compared to its closely related onion-pathogenic species in the same genus. To better understand the genomic diversity and genetic determinants of pathogenicity in this species, we analysed a collection of 38 P . allii strains isolated from 2 primary ecological niches, plants and rainwater, across North and South American and African continents using comparative genomics and phylogenetic approaches. Core-genome phylogeny, average nucleotide identity and gene presence–absence analyses revealed three genetically distinct lineages. All strains harboured conserved biosynthetic gene clusters (BGCs) for quorum sensing, carotenoid production, siderophores and thiopeptides. In contrast, two phosphonate BGCs, key determinants of onion pathogenicity, exhibited lineage-specific distributions. Onion-associated strains from lineages 1 and 2 carried the Halophos BGC responsible for onion tissue necrosis and also encoded the alt gene cluster that confers tolerance to thiosulfinates. Lineage 3 strains, isolated from both onion and rainwater, either lacked a phosphonate BGC entirely or possessed the HiVir phosphonate BGC. In addition, lineage 3 strains lacked the alt cluster altogether. The localization of these virulence genes in the genome varied, with Halophos integrated in the chromosome, HiVir encoded on the conserved Large Pantoea Plasmid, and alt located on small, variable plasmids (plasmid B). The type IV secretion system (T4SS) and type VI secretion system (T6SS) showed variable genomic architectures, with plasmid-borne T4SSs and two chromosomal T6SS loci differing in conservation and gene content. Additionally, conserved Pantailocin phage islands were detected in most genomes. Overall, this study reveals that while core metabolic and competitive traits are conserved across P. allii , virulence-associated loci display lineage-specific distribution, reflecting ecological differentiation and evolutionary plasticity within the species.

Ice-nucleating proteins (INPs) catalyze ice formation at high subzero temperatures, with major biological and environmental implications. While bacterial INPs have been structurally characterized, their counterparts in other organisms remain unknown. Here, we identify a new class of efficient INPs in fungi. These proteins are membrane-free, adopt β-solenoid folds, and multimerize to form large ice-binding surfaces, showing mechanistic parallels with bacterial INPs. Structural modeling, sequence analysis, and functional assays show they are encoded by orthologs of the bacterial InaZ gene, likely acquired via horizontal gene transfer. Our results demonstrate that distinct lineages have independently converged on a common molecular strategy to overcome the energetic barriers of ice formation. The discovery of cell-free INPs provides tools for freezing applications and reveals biophysical constraints on nucleation across life.