The 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.
Abstract
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.
Analysis revealed genes for metabolizing diverse carbohydrate sources, a complete ectoine synthesis cluster essential for halophily, and genes conferring tolerance to osmotic stress, low temperatures, and pH, underscoring its polyextremophilic capacity.
Ian Ariel Barbosa Nunes, Adan Rodrigues de Oliveira, Adonney Allan de Oliveira Veras et al.· Brazilian Journal of Microbi...· 0 citations
Soda lakes represent some of the most extreme aquatic ecosystems on Earth, yet their microbial diversity and functional potential remain poorly characterized, particularly in East Africa. This study presents the first shotgun metagenomic analysis of bacterial communities inhabiting both water and sediment of Small Momela Lake, a soda lake in northern Tanzania. Samples were sequenced using Illumina NovaSeq and analyzed with MetaPhlAn4 and HUMAnN3 to resolve taxonomic composition, diversity patterns and predicted metabolic functions. Results showed 27 distinct species within Pseudomonadota, Bacteroidota, Firmicutes, Cyanobacteria and Verrucomicrobia dominated by sulfur-cycling Thioalkalivibrio denitrificans and uncultured Candidatus lineages. Notably, based on currently available literature multiple taxa were detected for the first time in soda lake environments globally, within Africa and East Africa, expanding the known biogeography of extremophiles. Functional profiling revealed a strong enrichment of nucleotide and amino acid biosynthesis pathways, alongside marker genes linked to pH homeostasis, osmotic stress tolerance, sulfur metabolism and carbon fixation. These features suggest pronounced metabolic flexibility supporting microbial persistence under extreme alkaline and saline conditions. These findings underscore Small Momela Lake as a critical reservoir of novel, functional bacterial resources with promising applications in biotechnology and bioprospecting.
A. A. Siima, Sadikiel E. Kaale, F. Mpenda et al.· Discover Life· 0 citations
Aquirufa
is a widespread and diverse bacterial genus inhabiting freshwater ecosystems. Analyses of genomes from cultured strains and metagenome-assembled genomes (MAGs) of the genus revealed four phylogenetically distinct branches that differed markedly in the proportions of cultured strains and MAGs they contained. In total, 56 species or species-like taxa were identified, including eight novel species described here. Proteorhodopsin genes were detected in many of the genomes and were found across a wide range of habitat types, but their prevalence differed considerably among the four phylogenetic branches. Detailed analyses of two branches with markedly different proteorhodopsin gene frequencies suggested differences in the occurrence, size, structure, and pangenomes of their populations. Comparative whole-genome analyses showed that proteorhodopsin genes in
Aquirufa
consistently co-occurred with two key genes involved in retinal chromophore biosynthesis. These three genes exhibited distinct evolutionary patterns, most likely reflecting differences in recombination and co-evolution. Phylogenetic analyses placed the
Aquirufa
proteorhodopsins within the proteorhodopsin-xanthorhodopsin clade, specifically in a lineage comprising proteorhodopsins from species of the phylum
Bacteroidota
. Extending the analyses to related proteorhodopsins revealed additional patterns. Thirteen distinct gene arrangement types and all three common spectral-tuning residues were identified, with variation occurring not only among genera but occasionally even among species within the same genus. Overall, our findings indicated that the evolution, acquisition, horizontal transfer, and recombination of proteorhodopsin genes and associated genes have proceeded differently across taxonomic groups.
Alexandra Pitt, Stefan Lienbacher, J. Schmidt et al.· Microbial Ecology· 0 citations
Environmental filtering is a major driver of microbial community assembly in Antarctic ecosystems, yet its influence on biosynthetic potential and antimicrobial resistance remains poorly understood. Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.
William B. Medeiros, Kelly Hidalgo-Martinez, D. D. P. S. Penna et al.· World Journal of Microbiolog...· 0 citations
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.
A comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome is provided and microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake are identified.
M. Macey, Velislava Ilieva, B. Stephens et al.· Environmental Microbiome· 0 citations
