Genomic insights from a long-read assembly of a deep-sea Chromohalobacter israelensis strain from Santos Basin pockmarks field

Complete genome sequence of psychrotolerant Lacisediminihabitans sp. FW035 isolated from freshwater in Antarctica

Microorganisms inhabiting cold and oligotrophic aquatic environments experience persistent physiological stress, necessitating genomic characterization to understand their survival strategies. Psychrotolerant strains have evolved diverse metabolic adaptations, including secondary metabolite biosynthesis, which may contribute to environmental fitness and offer potential for low-temperature biotechnological applications. However, the genus Lacisediminihabitans remains poorly represented at the genomic level, limiting our understanding of its ecological roles and metabolic potential. To address this gap, we generated a high-quality complete genome of a psychrotolerant Lacisediminihabitans strain isolated from Antarctic freshwater. Lacisediminihabitans sp. FW035 grew at 2 − 25 °C with an optimum at 20 °C. The genome of strain FW035 is 3,842,169 bp in size with a G+C content of 66.4%, encoding 3,592 protein-coding genes. Genome analysis revealed a complete C5–C20 isoprenoid biosynthesis pathway and multiple biosynthetic gene clusters, including terpene-associated clusters with low similarity to previously characterized pathways. These features indicate the presence of biosynthetic potential distinct from previously characterized pathways, particularly terpene-associated clusters, and highlight the dataset as a resource for future comparative genomic and functional analyses.

Genomic and Metabolomic Insights into Amazonian Oyster-Associated Cyanobacteria Reveal the First Record of Thainema in South America

Oyster-associated microbiomes represent a dynamic interface between marine hosts and their environment, yet the diversity, evolution, and functional potential of their associated cyanobacteria remain poorly understood. For microbial organisms, such as cyanobacteria, survival requires adaptation to several environmental pressures, including higher metal concentrations and osmotic stress. To investigate these adaptations, two cyanobacterial strains, CENA647 and CENA648, were isolated from oyster surfaces sampled along the Amazon coast. Genomic analysis and untargeted metabolomics were conducted to investigate the taxonomy and functional potential of these strains. Both genomes exhibited high completeness (>99.2%) and low contamination (<2.2%). The total lengths differed, with 8.3 Mbp for CENA647 and 6.5 Mbp for CENA648. The genome size correlated with the number of identified coding regions: 7593 for CENA647 and 5541 for CENA648. Phylogenetic analysis highlights their taxonomic relationships within cyanobacteria adapted to fluctuating salinity, including the first description of the genus Thainema in South America. Comparative genome mining revealed extensive genetic repertoires associated with osmoregulation and metal resistance, consistent with adaptation to oyster-associated environments. Both strains shared predicted metabolites annotated in the metabolomes, with a wide range of compound classes, including amino acids, terpenes, fatty acids, and peptides, as well as several unannotated molecular features. Overall, our findings expand current knowledge of oyster-associated cyanobacteria and highlight their metabolic diversity in the Amazon region, as well as genomic traits that may be associated with adaptation to dynamic estuarine environments.

Rich mobilomes and a conserved adaptive core in bacteria from an intensifying Mexican soda lake

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, “Candidatus Abyssoplasma scotoplanesicola”, within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. “Candidatus Abyssoplasma scotoplanesicola” occupied 76.4–98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.

Experimental, Genomic, and Structural Evidence Supporting Putative PET‐Hydrolases in Thermophilic Bacteria Isolated From Hot Springs in Cajamarca, Peru

ABSTRACT Polyethylene terephthalate (PET) waste represents a major environmental challenge due to limited recycling solutions. Thermophilic bacteria from geothermal environments harbor diverse enzymatic machinery adapted to extreme conditions, offering promising biocatalysts for plastic degradation; however, biological resources from Peru and other South American countries remain scarce. We characterized four bacterial strains isolated from two geothermal sites in Cajamarca, Peru, screened for PET hydrolysis at 50°C. Whole‐genome sequencing using hybrid assembly achieved near‐complete circular genomes. GTDB‐Tk classification identified three species: Neobacillus thermocopriae (strain 19A), Bacillus licheniformis (strains 16P and BI2), and Brevibacillus agri (strain BI8). Quantitative assays revealed that strain 16P achieved the highest mass loss (0.598%), followed by strain BI8 (0.449%). ATR‐FTIR analysis of the incubated sheets showed a significant reduction of the ester carbonyl index in strains 16P, 19A, and BI8 relative to both non‐incubated PET and an abiotic control, whereas strain BI2 did not differ from the controls, indicating preferential modification of ester bonds at the sheet surface. Genome mining and structure‐based homology searches identified multiple candidate enzymes similar to validated PETases and carboxylesterases, including PETase46‐like homologs in strains BI8 and 16P and a terephthalate‐active carboxylesterase homolog in strain 16P. Molecular docking supported the conservation of catalytic geometry and substrate‐binding sites in these candidates. This work represents one of the first systematic genomic and structural characterizations of putative PET‐hydrolases in Peruvian geothermal bacteria, expanding knowledge of extremophile diversity and advancing thermostable enzymes for sustainable plastic waste management.

Genome-resolved discovery of Candidatus Vitaminotrophota reveals carbon fixation and multi-vitamin biosynthetic potential in hot springs.

Geothermal environments harbor abundant microbial diversity, yet rare lineages remain poorly resolved, limiting understanding of ecosystem function and evolutionary innovation under energy limitation. Here, we describe Candidatus Vitaminotrophota, a previously unrecognized bacterial phylum represented by 35 metagenome-assembled genomes (MAGs) from Tengchong hot spring sediments, China. Phylogenomic analyses support a coherent internal taxonomy comprising one order, two families and four candidate genera. Metabolic reconstruction indicates a predominantly anaerobic, mixotrophic lifestyle, with widespread carbon fixation potential via the Wood-Ljungdahl pathway and a noncanonical CODH/ACS architecture featuring divergent acsA paralogs. Nitrogenase structural genes (nifHDK) occur in two genera, suggesting diazotrophic potential in part of the lineage. All MAGs encode complete or near-complete cobalamin and pantothenate biosynthesis pathways, and most retain conserved thiamine pathway components, alongside transport systems consistent with corrinoid and metal acquisition. Ca. Vitaminotrophota dominated community-level cobalamin biosynthetic potential in several samples, reaching 99.11% and accounting for >50% in nearly half of the samples. Conserved flagellar and chemotaxis gene sets suggest capacity to navigate steep physicochemical gradients. These findings expand the phylogenetic and functional landscape of geothermal bacteria and identify Ca. Vitaminotrophota as a candidate contributor to carbon fixation and vitamin-mediated metabolic interactions in nutrient-limited hot springs.