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PubMed2026

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.

BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear. RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles. CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.

Flavobacteriaceae↗

PubMed2026

Flavobacteria consume nitrous oxide produced by partial denitrifiers in coastal sediments.

Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed that diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling showed that both clade II nosZ flavobacterial isolates and whole sand communities exhibited a low apparent affinity for N2O under the tested experimental conditions, expanding the currently limited kinetic data available for N2O reducing microorganisms from coastal permeable sediments, including flavobacterial clade II N2O reducers. Collectively, these findings indicate that abundant N₂O reducing communities can substantially consume N2O within permeable sediments, thus limiting N2O accumulation despite active N2O production. Together with previous hydrodynamic models predicting low N2O release from permeable sediments, our results highlight the important role of specialized microbial communities in regulating N2O cycling under increasing nutrient pollution.

Nitrous Oxide↗

PubMed2026

Metagenomic insights into mechanisms of coral larval settlement induction and inhibition by marine biofilms.

BACKGROUND: Biofilms are essential to larval settlement in many marine invertebrates, yet the mechanisms driving settlement induction or inhibition in corals remain poorly resolved. This challenge lies in the vast taxonomic and functional diversity of marine biofilms, making it difficult to identify cues associated with settlement. To address this, we analysed the metagenomes of biofilms used to induce settlement (attachment and metamorphosis) of four broadcast-spawning non-acroporid coral species: Dipsastrea favus, Platygyra sinensis, Echinophyllia aspera and Porites lobata. Biofilms were developed for one or two months, under light or dark treatments, with light biofilms inducing significantly higher settlement than dark biofilms. RESULTS: Gene composition varied strongly among treatments, with light biofilms enriched in genes encoding carotenoid biosynthesis and nitrate reduction, while dark biofilms encoded more genes for denitrification and nitric oxide production. Modelling revealed the abundance of genes encoding GABA biosynthesis and the type III secretion system (SS) were positively associated with settlement, while genes encoding the type II secretion system, flagellar and lipopolysaccharides were negatively associated. Genes predicted to promote settlement were concentrated in metagenome assembled genomes (MAGs) assigned to Flavobacteriaceae, Rhodobacteraceae and Pirellulaceae, consistent with previous research identifying these lineages as potential inducers. While we detected homologues of some biosynthesis genes for the settlement-inducing compounds cycloprodigiosin and tetrabromopyrrole in the MAGs, pathways were incomplete suggesting additional compounds promote settlement on these biofilms. CONCLUSIONS: These findings link biofilm metagenomics to coral larval settlement for the first time, suggesting carotenoids may attract larvae to biofilm surfaces, while GABA may promote searching and attachment. Additional compounds, for example cycloprodigiosin, tetrabromopyrrole or effector proteins, may be required to complete metamorphosis, however the specific compounds responsible likely vary across biofilm communities and suggest multiple mechanisms can lead to settlement. Simultaneously, elevated levels of nitric oxide, type II SS exudates or an abundance of flagellar potentially inhibit the settlement process. This study advances our understanding of the complex microbial processes underpinning coral larval settlement.

Biofilm↗

PubMed2025

In vitro and in vivo efficacy of vancomycin against Elizabethkingia species and the impact of increased vancomycin MICs.

UNLABELLED: This study aimed to evaluate the concordance of vancomycin susceptibility testing methods, its in vivo and in vitro efficacy, and the mechanisms underlying elevated MICs in Elizabethkingia spp. Vancomycin susceptibilities of 18 E. anophelis isolates were determined using multiple assays. The efficacy of vancomycin against five clinical isolates and one laboratory-induced mutant with an elevated vancomycin MIC was evaluated using time-kill assays and Galleria mellonella and murine models. Vancomycin MICs (16-32 mg/L) determined by broth microdilution were consistent with agar dilution, Etest, and MBC assay results. All isolates had zone diameters < 17 mm and were, thus, categorized as non-susceptible according to the CLSI criteria for Enterococcus spp. Time-kill assays of five clinical isolates demonstrated that vancomycin at a clinically relevant concentration (4 mg/L) exhibited poor bactericidal activity similar to that of teicoplanin. Vancomycin improved Galleria mellonella survival in a dose-dependent manner, whereas teicoplanin, dalbavancin, oritavancin, and daptomycin were ineffective. Murine models revealed that vancomycin at a human-equivalent dose (25 mg/kg twice daily) prolonged survival in most infections and modestly reduced bacterial load, while teicoplanin remained ineffective. Vancomycin efficacy was significantly reduced in G. mellonella and mice infected with a mutant strain exhibiting an elevated MIC (128 mg/L), which was attributable to spontaneous mutations in pbp4. In conclusion, E. anophelis were consistently non-susceptible to vancomycin as determined by multiple in vitro assays. However, vancomycin demonstrated unique in vivo activity among glycopeptides although this effect was abrogated by spontaneous mutations leading to elevated MICs. IMPORTANCE: Elizabethkingia anophelis is a multidrug-resistant pathogen associated with limited treatment options and high mortality. Most commonly considered agents, including fluoroquinolones, piperacillin/tazobactam, and trimethoprim/sulfamethoxazole, are increasingly compromised by resistance, toxicity, or inconsistent efficacy. Although vancomycin is not routinely used for Gram-negative infections due to limited outer membrane permeability, case reports have suggested potential benefit in Elizabethkingia infections under critical conditions. In this study, we show that E. anophelis isolates are uniformly non-susceptible to vancomycin in vitro and exhibit minimal bactericidal activity. However, vancomycin conferred a modest but statistically significant survival benefit in two independent animal models. Importantly, this effect was lost in strains with vancomycin-induced MIC elevation, and genome analysis identified pbp4 mutations as a potential underlying mechanism. These findings suggest vancomycin may offer therapeutic benefit when no preferred options are available. They support cautious use in selected cases and highlight the need for continued monitoring of susceptibility and resistance development.

Vancomycin↗