The present essay attempts to stimulate interest and provide insight into the dynamics of internal conflicts, kin selection, and ecological interactions in multicellular, metabolically gifted microorganisms and how these processes may affect biosynthetic gene cluster (BGC) diversity. The multicellular antibiotic-producing soil bacterium Streptomyces provides a useful model for exploring how internal conflicts emerge and are resolved in biology. These organisms must balance two resource-intensive processes that can create internal conflicts-natural product biosynthesis and sporulation. In Streptomyces, there is potential to mitigate these internal conflicts through division of labour, phenotypic specialisation, and extensive gene duplication and diversification, enabling colonies to optimise both natural product production and reproductive success. Horizontal gene transfer further expands gene families and BGCs, introducing new metabolic capabilities while generating opportunities for functional divergence to reduce internal conflict and potentially promote kin selection. Natural product BGCs also possess features that could identify them as 'greenbeards' (kin selection by trait), promoting cooperation among producers and harming non-producers. The coexistence of multiple natural product BGCs and resistance mechanisms in Streptomyces is discussed in the context of the diverse eco-evolutionary processes occurring in structured natural environments, competition among close relatives, recurrent BGC acquisition, and regulatory compatibility encountered by Streptomyces.

Marine plastisphere expands the ecological niche and evolutionary dynamics of nrfA-dependent nitrite ammonifying bacteria.

Insights into Fe0, Fe2O3, and Fe3O4-Mediated reduction of antibiotic resistance genes and horizontal gene transfer via reactive oxygen species during composting.

The removal mechanisms and novel strategies of antibiotic resistance genes in anaerobic sludge digestion: Insight into microbial metabolic regulation.

Temperature-dependent biofilm and sublancin production arrest soil arsenic and antibiotic resistance gene mobility.

The Intensive Care Unit (ICU) is an environment where multiple factors that predispose to the transmission of Antimicrobial Resistance (AMR) coexist. Genomic sequencing is a technology that enables a better understanding of how AMR genes are transmitted within the ICU environment. To evaluate the genomic dynamics of the transmission of antimicrobial resistance genes between bacteria from ICU surfaces and bacteria from critically ill patients. A cross-sectional analytical study. Surface swab samples were collected from the ICU, including suction units, infusion pumps, stethoscopes, dialysis machines, monitors, ventilators and gas valves, as well as samples from critically ill patients with infections. Species were identified using microbiological microplate panels; antibiotic susceptibility testing was carried out to assess AMR; and whole-genome sequencing was performed on isolates that were multidrug-resistant (MDR). The sequencing was carried out using a nanopore long-read sequencer and the results were analysed using specialised bioinformatics tools. A total of 130 positive isolates were identified, of which 96 (73.85%) were from environmental samples and 34 (26.15%) from patient samples. Forty (30.76%) MDR species were identified. The most common MDR species were Klebsiella pneumoniae and Acinetobacter baumannii. The most frequently detected AMR genes were blaNDM-5 and blaOXA-23. The most common plasmids were IncFIB(K)_1_Kpn3, Col440I and IncL/M(pMU407)_1_pMU407. A clonal outbreak of Acinetobacter baumannii ST 2 was detected on the dialysis machine, stethoscopes and patient samples. Evidence of horizontal transfer of resistance genes via plasmids conjugation was found in samples taken from suction units, oxygen valves and tracheal secretion in three cases. The findings of this research show that antimicrobial resistance genes are transferred between bacteria on surfaces and bacteria in critically ill patients, and that this transfer occurs in both directions.

A Constructal Law interpretation of species variability: Insights from microalgae.

Genomic expansion of efflux pumps is associated with metal-antibiotic super-resistance in bacteria from mining environments.

Fungal biotechnology is crucial for generating high-value enzymes and fermentation products. Despite its industrial importance, major knowledge gaps in understanding fungal genomic variation, phenotypic diversity, and protein function prediction constrain biological innovation. While advancements in sequencing technologies have established data science as an integral component in driving developments in industrial fungal biotechnology, the inherent complexity of fungal genomes and incompatible repositories continue to limit comprehensive characterization of biological relationships and their translation into industrial applications. This review examines recent progress in non-graph methodologies applied to fungal biology. Genome annotation tools uncover genetic variation through homology-based approaches and enable functional annotation of sequence variants. Metric-based methods identify horizontal gene transfer events, while multivariate techniques characterize phenotypic variation across conditions. However, the increasing diversity, scale, and multimodal nature of fungal datasets require more integrative frameworks. Graph data science, a multivariate approach to model complex relationships as networks, offers opportunities to overcome these challenges. We discuss how graph-based methods enhance the detection of genomic structural variation and enable the modeling of molecular interactions. Furthermore, we outline how these approaches facilitate the exploration of complex fungal systems through multi-taxon, reference-free analyses, that integrate evolutionary signals, functional associations, and curated knowledgebases. By surveying available fungal resources and their taxonomic and ecological representations, we identify well-characterized genera, highlight underexplored taxa requiring further data generation, and pinpoint the ecological biases inherent in current sequencing efforts. Collectively, these advancements demonstrate how graph data science can accelerate fungal research and bridge fundamental discoveries and biotechnological applications.

Evidence for the connectivity of antibiotic resistance genes between seamount and coastal environments.

Unraveling the arsenite response mechanisms in the facultative anaerobe Aromatoleum sp. CIB.

Masked ecological risk: Stable anammox performance conceals resistance genes propagation under short-term non-antibiotic antimicrobials stress.

We isolated a novel halophilic archaeon, strain DSL9, representing the proposed new species Haloliberatus hailidukes gen. nov., sp. nov., from Dishui Lake, China. Unlike most obligate halophiles, DSL9 survives in low salinity, even distilled water, without lysis. Genomic analysis revealed dual salinity adaptation strategies: salt-in and compatible solutes, including a complete trehalose biosynthesis pathway. The strain harbors multiple plasmids, notably a 111,311 bp large plasmid (pHdsl9-3) encoding replication (Orc1/Cdc6, SSB), transcription (TFIIB), transmission (T4SS cluster, ArdC-like protein), and recombination (XerA) modules. pHdsl9-3 provides auxiliary functions such as defense, genome diversification, ion detoxification, and suggests active horizontal gene transfer. Similar elements are widespread in Halobacteriales, highlighting their role in haloarchaeal genetic diversity and plasticity. The encoded XerA hinted at a function beyond DNA dimer resolution, suggesting it may have been adapted by other archaeal mobile genetic elements. These findings underscore the need to investigate plasmid-driven evolution and environmental adaptation mechanisms in haloarchaea.IMPORTANCEThis study reports the isolation and characterization of DSL9, a novel halophilic archaeon from a freshwater lake. Remarkably, DSL9 defies the typical obligate halophilic lifestyle by surviving in low-salinity environments, including distilled water, without cell lysis. A key discovery is the identification of a 111,311 bp large plasmid harboring essential modules for replication, transcription, transmission, and integration. Widespread distribution of similar elements across Halobacteriales suggests their crucial role in haloarchaeal genetic diversity and plasticity, warranting further study of plasmid-mediated evolution and adaptation strategies.

Persistence and dynamics of antibiotic resistance genes in livestock manure during anaerobic digestion.

Antimicrobial resistance (AMR) among Gram-negative bacteria, particularly those producing extended-spectrum β-lactamase (ESBLs), represents a significant global healthcare challenge. CTX-M enzymes have achieved global dominance, often disseminated through plasmid-mediated horizontal gene transfer, complicating treatment in resource-limited settings. This study aimed to determine prevalence, antimicrobial resistance patterns and ESBL-associated gene profiles in clinical Gram-negative isolates. A hospital-based cross-sectional study was conducted at Mahakali Provincial Hospital from November 2024 to February 2026. Using a consecutive sampling technique, 1485 clinical specimens (including urine, pus, blood, wound swabs, throat swabs and tissues) were processed for bacterial culture, identification, antimicrobial susceptibility testing and ESBL detection following CLSI 2024 guidelines. ESBL-associated genes (blaCTX-M, blaTEM and blaSHV) were detected by PCR. Of 1485 specimens, 478 (32.3%) were culture-positive, yielding 411 (86.0%) Gram-negative bacteria. Urine samples accounted for 88.3% of isolates. E. coli (71.8%) and K. pneumoniae (15.6%) were the most common pathogens. Overall, 54.7% of isolates were multidrug-resistant (MDR). Among ESBL-screened Enterobacterales (n = 385), 108 (28.1%) were confirmed ESBL producers. Molecular analysis of 108 ESBL- producing MDR isolates revealed blaCTX-M (56.5%) as the most prevalent gene followed by blaTEM (44.4%) and blaSHV (32.4%). Co-occurrence of multiple genes was observed in 56 (51.9%) isolates, with 6 (5.6%) harboring all three genes. To the best of our knowledge, this is the first report from Far-Western Nepal documenting the co-carriage of triple ESBL-associated genes in clinical Enterobacterales. These findings highlight a high regional burden of community-level resistance and emphasize the urgent need for continuous molecular surveillance, targeted antimicrobial stewardship and region-specific treatment guidelines.

The World Health Organization classifies extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing Klebsiella pneumoniae as critical-priority pathogens due to their high incidence, mortality, transmissibility, rapid resistance acquisition, and limited treatment options. Beyond clinical settings, their detection in wastewater treatment plants (WWTPs) provides an opportunity to assess their prevalence, persistence, and circulation within wastewater systems. This study characterized 37 antibiotic-resistant K. pneumoniae-related species strains isolated from two WWTPs in the metropolitan area of Barcelona, analyzing their antimicrobial resistance (AMR) profiles, antimicrobial resistance genes (ARGs), biocide and heavy metal tolerance genes (HMTGs), virulence factor genes (VFGs), biofilm-forming capacity, and conjugation ability. Among them, 70.3% were multidrug-resistant (MDR), and 16.2% were extensively drug-resistant. Whole-genome sequencing revealed diverse ARGs; all strains carried β-lactam resistance genes (14 ESBL and 12 carbapenemase producers), nearly all (96.9%) carried biocide or HMTGs, 64.9% harbored integrases, and all carried VFGs. Core-genome SNP analysis identified closely related strains across sampling periods and treatment stages, suggesting long-term persistence within the wastewater treatment system, despite biological and chemical processes in secondary treatment. Most strains (67.6%) displayed biofilm-forming capacity, and conjugation assays confirmed horizontal gene transfer in five of the seven ESBL-producing strains tested. High-risk clones were predominantly detected in the IFAS secondary treatment stage of the Gavà-Viladecans WWTP. The three strains recovered from the reclaimed water of the Baix Llobregat WWTP were ESBL or carbapenemase producers. Altogether, these results provide genomic and phenotypic evidence of the persistence and circulation of antibiotic-resistant K. pneumoniae-related species within wastewater treatment systems.IMPORTANCEWWTPs are essential for urban sanitation and environmental protection. Understanding how clinically relevant pathogens, such as ESBL and carbapenemase-producing K. pneumoniae-related species strains, behave in these settings may inform public health considerations. Investigating the presence and persistence of high-risk MDR pathogens in WWTPs helps identify circulation of AMR, assess the risk of gene transfer, and evaluate the potential for co-selection with other contaminants. This knowledge supports efforts to improve wastewater treatments, strengthen environmental surveillance, and develop integrated One Health strategies to limit the spread of AMR across human, animal, and environmental sectors.

Latilactobacillus curvatus is a lactic acid bacterium with a remarkable ability to persist in diverse niches, including fermented foods and gut. Despite its industrial and potential probiotic relevance, the genomic underpinnings of its cross-niche adaptability remain poorly characterized. We conducted a species-contextualized comparative genomic analysis of 53 L. curvatus strains from food and gut isolates. This analysis integrated pangenome structure, metabolic repertoire, CRISPR-Cas immunity profiles, and mobilome analysis. Additionally, binding mode predictions and dynamics simulations were used to evaluate the theoretical binding energies of bacteriocins to the BamA target. Phylogenomics revealed a polyphyletic population structure, indicating that long-term evolution is not strictly niche-specific. In contrast, genome-wide similarity showed clustering by isolation source, highlighting horizontal gene transfer (HGT) as a plausible contributor to niche adaptation. We identified a highly active mobilome, encompassing diverse plasmids, IS elements, and multiple intact prophages, reflecting high genomic plasticity characteristic of a multihabitat lifestyle. CRISPR-Cas systems were widespread, and analysis of 2,029 spacers revealed a broad immune repertoire targeting mobile genetic elements represented in fermented food, gut, and environmental datasets. We also identified spacer matches to phage-plasmid hybrid-like elements, highlighting the diversity of mobile genetic elements associated with the L. curvatus spacerome. Our study reveals genomic features consistent with ecological flexibility in L. curvatus, including high genomic plasticity and a broad CRISPR spacer repertoire. Rather than demonstrating strict niche-specific evolution or a causal mechanism for cross-niche persistence, these findings support the hypothesis that this species has experienced diverse interactions with mobile genetic elements across multiple ecological contexts.

Like a roll of dice, unraveling the antimicrobial resistance to ESKAPE pathogens against various drugs is a perilous challenge in coeval healthcare due to their swift acquisition of resistant genes and drastic spreading of antimicrobial resistance. These pathogens manifest both innate and adopted resistance machineries against manifold antibiotic categories, consisting of -lactams, glycopeptides, fluoroquinolones, aminoglycosides, tetracyclines, macrolides, and salvage therapy agents - linezolid and colistin. The machineries underlying resistance include enzymatic drug alteration, as seen with -lactamases, aminoglycoside-altering or methylating enzymes, carbapenemase, chloramphenicol acetyltransferase; biofilm formation, target site mutations, resistance determinants lateral gene transfer, and overexpression of efflux pumping. The frequency of incidence of multidrug-resistant strains as well as extensively drugresistant, and also pan-drug-resistant strains appreciably intricates infection management, and furthermore pitches into amplified morbidity, mortality, and ultimately affects global healthcare expenditures. This overview provides an ample review of the antimicrobial resistance contours, elementary molecular mechanisms, and clinical consequences of ESKAPE pathogens, accentuating emerging waves and potential approaches to counter these menacible nosocomial pathogens.

Achromobacter xylosoxidans is an emerging opportunistic pathogen associated with a wide range of infections in humans. This species is widely distributed in the environment due to its high adaptability. Isolates of A. xylosoxidans have intrinsic resistance to several antibiotics and the potential to acquire genetic resistance determinants. Despite its growing frequency of isolation, little is known about the genomic characteristics of this pathogen. In this study, we conducted a comprehensive genomic analysis of assemblies from the NCBI RefSeq database, along with a newly sequenced respiratory isolate from a patient with cystic fibrosis. Through pangenome analysis, we identified genes and functions associated with specific isolation sources, suggesting niche-specific adaptation. Resistance-associated mutations in the AxyZ efflux pump regulator, along with bla AXC-1, were exclusively detected in genomes of clinical origin. Furthermore, while the resistome is limited, non-core antimicrobial resistance genes were detected to be primarily associated with the mobilome, underscoring the potential for horizontal gene transfer to further shape resistance in this species.

Targeted pollutant exposure is widely used to acclimate microbial communities for enhanced biodegradation of recalcitrant contaminants, yet the evolutionary mechanisms underlying functional reinforcement remain poorly understood. Here, we acclimated a methanotrophic consortium achieving efficient removal of 3-amino-5-methyl-isoxazole (3A5MI) (>90%, >5 mg/L/d) and elucidated the adaptive evolutionary processes behind it. Analyses of mobile genetic elements (MGEs) and horizontal gene transfer (HGT) revealed that dominant Methylococcaceae members served as genetic exchange hubs in the acclimation bioreactor. Integrated metagenomic and metatranscriptomic analyses showed that prolonged 3A5MI exposure activated their MGEs and promoted extensive HGT of genes related to energy generation, oxidative stress defense, and biosynthesis. This adaptive evolution enabled community-level metabolic rewiring, including optimized carbon metabolism to relieve energy limitation, niche differentiation, and specialized transcription of C-N bond catalytic functions. Furthermore, batch experiments and transformation product analyses confirmed that 3A5MI-induced functional traits (e.g., heterocycle hydroxylation and C-N bond catalysis) facilitated complete sulfamethoxazole (SMX) biodegradation. Overall, this study demonstrates the evolutionary plasticity of methanotrophic consortia under targeted acclimation and highlights MGE-driven genetic exchange and metabolic adaptation as key mechanisms that both underpin functional enhancement and support the development of methanotroph-based strategies for the biodegradation of recalcitrant isoxazole-based pollutants.