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Marine microbial communities are vital to biogeochemical cycling, yet their dynamics in regions of ecological and industrial significance, such as the Santos Basin (SB), Brazil’s largest offshore oil-producing basin, remain poorly resolved. To address this gap, we combined 16S rRNA amplicon sequencing, flow cytometry, and a hybrid machine learning framework (Self-Organizing Maps and Random Forest) to analyze microbial community stratification across pelagic depths in the SB. We identified five depth-specific microbial associations predicted with 86% accuracy, driven primarily by temperature, salinity, water density, and nutrient availability. Shallow epipelagic and mesopelagic zones were dominated by temperature-driven assemblages, while deeper bathypelagic communities responded to salinity and density gradients. Temporal and spatial patterns further highlighted the influence of regional oceanographic processes, including the Cabo Frio upwelling and Rio de la Plata plume. Microbial diversity increased with depth, contrasting with higher cell abundances in nutrient-rich shallow waters. We provided new insights into the relative importance of oceanographic processes, suggesting that vertical stratification and regional hydrography may play a more central role shaping microbial communities than previously recognized. We also established a predictive framework for microbial dynamics in marine ecosystems, with direct implications for assessing anthropogenic impacts in industrially active regions like the SB.

Iron-rich minerals, such as hematite (α-Fe2O3), are prominent constituents of the Martian surface; they are considered to be potential indicators of past aqueous activity and habitability. This study investigated the interaction between the extremophilic black fungus Rhinocladiella similis LaBioMMi 1217 and hematite under simulated laboratory conditions on Mars, focusing on redox-mediated dissolution processes, metabolic adaptations, and biosignature formation. The fungus was cultivated with powdered and polished hematite substrates, and mineral alteration was monitored through physicochemical measurements and scanning electron microscopy (SEM). Genome mining was performed to identify and map genes involved in iron metabolism. The metabolic profile of the fungus under hematite treatment was assessed via untargeted metabolomics. Over 15 days, the cultures exhibited marked acidification (pH decreased from 7.0 to 4.7) and a 10-fold increase in the dissolved Fe2+ ion concentration (26–270 mg/L), indicating metabolically driven iron reduction. SEM revealed surface etching and localized roughening consistent with microbially induced weathering, whereas these changes were absent in the abiotic controls. Genes linked to siderophore biosynthesis (sidA, sidC, sidD, sidF, sidH, sidI, and sidL) and reductive iron assimilation (FET3, FTR1, and FRE1) were identified. Untargeted metabolomics confirmed the secretion of organic acids, iron-chelating siderophores (e.g., ferrichrome C), and redox-active aromatic compounds in the presence of hematite, supporting a multifaceted strategy that combines acidification, chelation, and redox mediation. Collectively, these results show that the fungus actively promotes hematite dissolution through organic molecule-mediated mechanisms. Such interactions hold astrobiological relevance, as fungal modification of hematite might lead to the production of diagnostic chemical and mineralogical biosignatures, informing future life-detection strategies on Mars.

Long-term ecosystem development includes a build-up phase followed by a decline (retrogressive) phase characterized by reduced plant productivity and belowground process rates due to reduced nutrient availability. In boreal forests, retrogression is accompanied by soil organic matter (SOM) accumulation, especially in the prolonged absence of fire. However, the role of bacterial communities in SOM dynamics during ecosystem retrogression has been little explored. Using a 5000-year post-fire boreal forest chronosequence, we investigated how long-term succession and retrogression shapes soil bacterial community structure and functional specialization. While the Actinomycetota phylum dominated communities across all chronosequence stages, a significant family-level shift within this phylum occurred in the later (retrogressive) phase, characterized by a transition from Mycobacteriaceae to Streptosporangiaceae. The recovery of metagenome-assembled genomes (MAGs) revealed distinct life-history trade-offs between these families. Streptosporangiaceae MAGs were significantly enriched in genes for degrading phenolics, cellulose, and lignin, and exhibited potential for chitin, lipid and peptide degradation. This positions them as potential decomposers of the primary constituents of stored soil carbon, including plant-derived complex carbohydrates and fungal necromass, during retrogression when fungal activity declines. In contrast, Mycobacteriaceae MAGs are likely to prioritize inorganic phosphate (Pi) uptake-by pstS gene enrichment, reflecting adaptation to P availability changes during ecosystem development. Collectively, our results demonstrate that long-term ecosystem retrogression drives shifts in the bacterial communities and functions within the Actinomycetota. These shifts may indicate possible divergent strategies, i.e. recalcitrant carbon turnover versus nutrient scavenging, which could explain shifts in the microbial community as the ecosystem transitions toward retrogressive, nutrient-limited states.

Members of the bacterial family Endozoicomonadaceae are ubiquitous marine symbionts associated with diverse hosts, including corals, sponges, molluscs, and fishes. Despite their ecological pervasiveness, inhabiting hosts in deep-sea vents and sunlit coral reefs, their taxonomy remains inconsistent, largely due to reliance on 16S rRNA gene phylogenies that fail to fully resolve evolutionary relationships. Here, we integrate phylogenomics, comparative genomics, and overall genome relatedness indices across 63 high-quality genomes to re-define genus boundaries within the Endozoicomonadaceae family. Among the metrics, the core-proteome average amino acid identity proved the most robust for genus-level resolution, with a proposed identity cutoff of 76%, aligning with phylogenomic structure and maintaining taxonomic robustness across the family. Phylogenomic reconstructions further revealed that the taxon Endozoicomonas is paraphyletic, forming two well-supported but distinct clades. This prompts a taxonomic revision, dividing Endozoicomonas into Endozoicomonas sensu stricto and Neoendozoicomonas gen. nov., with Neoendozoicomonas montiporae designated as the type species. Furthermore, the sister clade to Endozoicomonas sensu stricto—comprising the genera Endonucleibacter and Sororendozoicomonas—is characterized by genomic streamlining, including reduced genome size, lower GC content, reduced number of orthogroups, and potential functional divergences consistent with host specialization. Functional annotations highlighted secretion and conjugation systems as key differentiators between genera, emphasizing potential distinct host-interaction strategies. This genome-based framework refines the taxonomy of the Endozoicomonadaceae, provides additional criteria for genus delimitation, and strengthens the evolutionary and ecological interpretation of these widespread marine bacterial symbionts.