The fish pathogen Yersinia ruckeri forms biofilms on abiotic surfaces, contributing to recurrent infections in aquaculture. Increasing evidence suggests that the RNA chaperone Hfq and small non-coding RNAs (sRNAs) are key regulators of bacterial biofilm formation. However, the regulatory mechanisms mediated by these factors remain largely unexplored in Y. ruckeri. In this study, we investigated the roles of Hfq and the Hfq-dependent sRNAs RprA, ArcZ, and RybB in the biofilm formation of Y. ruckeri. We first characterized the sRNAome of biofilm-forming cells, identifying the conserved RprA, ArcZ, and RybB, among the upregulated sRNAs. We then evaluated motility, biofilm formation, and architecture in strains lacking either hfq (Δhfq) or these sRNAs (ΔsRNA). Our results reveal that both Δhfq and ΔsRNA strains exhibit significant alterations in biofilm and motility phenotypes, including changes in bacterial morphology and extracellular matrix. Furthermore, expression analyses indicate that these sRNAs modulate the transcription of key regulatory factors, flagellar and phosphodiesterase genes, ultimately influencing intracellular cyclic di-GMP levels, a key second messenger in biofilm formation. Together, our findings demonstrate that Hfq and its associated sRNAs play critical regulatory roles in Y. ruckeri biofilm formation by controlling the expression of genes involved in motility, bacterial envelope proteins, and c-di-GMP metabolism.

Horizontal gene transfer plays a critical role in microbial genome evolution and adaptation. Integrated foreign DNA fragments encompass various types of mobile genetic elements (MGEs), ranging from small transposons to conspicuous integrative and conjugative elements. These regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain foreign sequence signatures and hallmark genes such as transposases, integrases, etc. While bioinformatic tools target specific MGE subsets using alignments, compositional signatures, or diagnostic gene mapping, no single platform offers a unified framework for comprehensive, evidence-based, MGE identification and classification. To address this challenge, we developed MOBHunter, an advanced bioinformatic pipeline that consolidates standalone tools and in-house algorithms. Unlike basic tool concatenation, MOBHunter yields consensus identifications, score-supported classifications, and enhanced web visualizations. The platform reduces end user analysis time by integrating data collection, processing, and interpretation into a unified workflow. It delivers robust classifications of MGEs into distinct families and provides a comprehensive overview of the flexible regions of any given input genome. URL: https://informatica.utem.cl/mobhunter/.

Extreme acidic environments represent natural laboratories for investigating the mechanisms of microbial community assembly, yet the ecological processes structuring these communities remain incompletely understood. Here, we investigate how spatial partitioning, hydrodynamics, and colonization history shape microbial succession in a unique sulfur-rich, acidic river of volcanic origin in northern Patagonia. We combined 16S rRNA gene profiling and shotgun metagenomics with a multi-scale experimental framework encompassing water column fractionation and colonization assays under native and controlled conditions. Microbial diversity was strongly influenced by spatial fractionation, with free-living communities exhibiting higher richness and temporal variability than particle-associated assemblages. Water flow modulated community structure, increasing evenness in free-living fractions under high-flow conditions, but had limited impact on particle-attached communities. Colonization of sulfur-beads followed a structured successional trajectory, with autotrophic sulfur oxidizers dominating early stages and heterotrophs adapted to biofilm lifestyles increasing over time. Ex situ recolonization assays revealed strong priority effects, with initial colonizers determining successional trajectories. Turnover analyses revealed that the balance among stochastic and deterministic assembly processes shifted across communities with pronounced stochasticity in the water column and flow-dependent effects in free-living communities, while biofilm associated communities on sulfur-beads exhibited stronger contribution of deterministic selection. These ecological patterns were mirrored by functional differentiation, with gene enrichment analyses revealing adaptive signatures of substrate attachment and resource acquisition. By integrating fine-scale environmental variation with colonization dynamics, this study reveals how microscale habitat structure and temporal fluxes jointly modulate microbial community assembly rules, offering a nuanced framework to dissect ecological processes in extreme systems.

The vaginal microbiota plays a critical role in maintaining reproductive health. Although Lactobacillus species often dominate the vaginal environment in healthy individuals, recent studies have shown that healthy microbiota compositions can also include Lactobacillus-depleted states, as described by the Community State Types (CSTs) framework. However, disruptions in the microbiota composition, such as those caused by sexually transmitted infections (STIs), can lead to increased diversity and instability, compromising host protection. This study investigates the association between vaginal microbiota composition and the prevalence of STIs in a cohort of incarcerated women in Chile. Using metataxonomic approaches targeting 16S and 18S rRNA genes, we characterized prokaryotic and eukaryotic components of the vaginal microbiota across healthy, dysbiotic, and pathogen-dominated subjects. Alpha diversity analysis using the Shannon index indicated that Lactobacillus-dominant communities were associated with lower microbial diversity correlates with reduced variability. Whereas communities dominated by pathogens including Trichomonas vaginalis, Gardnerella vaginalis, Treponema pallidum, and HIV, tended to exhibit higher diversity. The pathogen-dominated group displayed an increased prevalence of opportunistic microorganisms and reduced Lactobacillus abundance, which may reflect an imbalance in the microbial ecosystem, often interpreted as reduced stability. This study provides novel insights into the intricate dynamics between normal and altered vaginal microbiomes and their association with STIs. Understanding these community-level patterns and associations is crucial for designing targeted interventions aimed at restoring microbial balance and preventing infections.

The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains three genera of chemolithoautotrophs: Sulfuricaulis (2016), Sulfurifustis (2015) and Acidiferrobacter (2011). While the two former are neutrophilic sulfur oxidizers isolated from lake sediments in Japan, the latter is an extremely acidophilic, moderately osmophilic, thermotolerant iron/sulfur oxidizer known to occur in macroscopic streamers in Rio Tinto, Spain and in acid waters worldwide. The type strains of both Sulfuricaulis limnicola (HA5^T) and Sulfurifustis variabilis (skN76^T) have been sequenced, and the draft genome of the ZJ isolate of Acidiferrobacter thiooxydans (MDCF01) has recently been deposited in public databases. Despite this fact, little evidence on the genomic diversity and evolution of this group has been presented so far. Using comparative genomic analyses and phylogenetic reconstruction strategies, we explored the evolutionary information contained in the available genome sequences to shed light on the taxonomic status of a novel isolate of the genus Acidiferrobacter (SP-III/3; DSM 27195).

Biofilm formation by bacterial pathogens represents a major challenge in aquaculture, since biofilms promote persistence and increase tolerance to antimicrobial treatments. Yersinia ruckeri, the etiological agent of enteric redmouth disease in salmonids, contributes to recurrent infections in aquaculture. However, the molecular mechanisms governing biofilm development in this pathogen remain poorly understood. In this study, we investigated the role of the global transcriptional regulator Fur in the biofilm formation of Y. ruckeri. To this aim, a fur deletion mutant (Δfur) was phenotypically, structurally, and transcriptionally characterized under biofilm-forming conditions. Fur deletion resulted in impaired motility, reduced flagellar synthesis, and a marked decrease in mature biofilm formation. These changes were accompanied by alterations in three-dimensional architecture, cellular organization, and extracellular matrix production, as revealed by scanning electron and confocal microscopy analyses. Furthermore, transcriptomic profiling via RNA-seq demonstrated that the absence of Fur leads to extensive transcriptional reprogramming. Genes associated with the biosynthesis of flagella and oxidative stress response were significantly down-regulated, whereas genes associated with SOS responses, non-ribosomal peptide biosynthesis, and those related to iron acquisition and siderophore systems exhibited significant up-regulation in the absence of Fur. Interestingly, the strong up-regulation of P2-type prophage genes was also observed in the Δfur strain. Collectively, our findings identify Fur as an important contributor to the normal progression toward mature and spatially organized Y. ruckeri biofilms. Likewise, the Fur-dependent pathways and factors identified here provide candidates for future mechanistic studies and may ultimately help identify strategies to interfere with Y. ruckeri persistence in aquaculture environments.