Frontiers in Microbiology

The Southern Ocean harbors diverse marine microbial communities shaped by both local oceanographic conditions and dispersal limitations. However, this knowledge is mainly based on coastal Antarctic sites, whereas circumpolar Antarctic open sea and subantarctic ecosystems remain poorly explored. Here, we characterize marine microbial communities (using 16S rDNA high-throughput sequencing) and marine oceanographic data across two regions: the Subantarctic, involving two localities (the Magellan Strait and the Beagle Channel), and Antarctic open sea, involving two localities (Eastern Indian and Central South Pacific). We found extensive differences across regions and localities, characterized by distinct taxonomic patterns, alpha diversity, microbial composition, and enriched taxa profiles. Despite these differences, Clade Ia, Amylibacter, NS5 marine group, and NS2b marine group exhibited high prevalence across regions. Oceanographic parameters had variable relationships with microbial alpha diversity across regions: Sea surface temperature and salinity had a negative and positive correlation, respectively, in the Magellan Strait during 2024. In the Antarctic region, dissolved oxygen displayed a negative correlation in the Indian Ocean during 2024, whereas salinity displayed a more variable relationship in the Indian Ocean: positively correlated during 2024, while negatively correlated during 2025. Collectively, our results highlight a strong microbiological biogeographic structure in the Southern Ocean, both across broad scales (between Subantarctic and Antarctic regions) and within regions. Furthermore, our results show dynamic relationships between oceanographic variables and marine microbial diversity across Antarctic and Subantarctic regions.

Epichloe fungal endophytes form widespread symbioses with temperate grasses, yet the extent to which diversity within endophyte species is shaped by host association remains poorly understood. Here, we characterized naturally occurring Festuca_Epichloe symbioses across diverse Iberian ecosystems using an integrative framework combining ecological, cytogenetic, phenotypic, molecular and chemical analyses. Novel associations of Epichloe festucae with Festuca trichophylla, F. lambinonii and F. yvesii were documented, together with substantial variation in infection incidence and mating-type composition among host-associated populations. Morphological traits, vegetative growth and alkaloid profiles differentiated strains according to host identity. Furthermore, multilocus phylogenetic analyses assigned all fine-leaved Festuca host isolates to Epichloe festucae, but identified a recurrent host-associated genetic structure, along with a deeper evolutionary signal, that largely corresponds to the host phylogeny. By contrast, genome size estimates varied little among Epichloe festucae strains, with all isolates exhibiting haploid genomes. Alkaloid content across the four major classes of Epichloe compounds (pyrrolopyrazines, 1-aminopyrrolizidines, ergot alkaloids and indole-diterpenes) showed only partial concordance with the presence of biosynthetic genes, indicating that functional outcomes are influenced by regulatory and environmental factors beyond biosynthetic gene presence. Chemotypic profiles clearly differentiated Epichloe festucae from E. coenophiala while demonstrating considerable functional diversity among E. festucae strains. Collectively, these complementary datasets reveal two interconnected signatures of diversification: pervasive host-associated differentiation across multiple biological dimensions and a deeper historical signal retained in phylogenetic relationships. These findings provide a foundation for future genomic, evolutionary and systematic studies to determine whether these lineages represent ongoing fungal divergence and speciation

The rise of antimicrobial resistance has intensified interest in antimicrobial photodynamic inactivation (aPDI) and antimicrobial blue light (aBL) as alternatives or adjuvants to conventional antibiotics. However, whether chemically distinct photodynamic treatments elicit a shared bacterial response remains unclear. Here, we integrated transcriptomic profiles of Escherichia coli BW25113 exposed to five short-term, sub-lethal photodynamic treatments: antimicrobial blue light (aBL), aBL combined with 5-aminolevulinic acid (aBL+ALA), rose bengal (RB), new methylene blue (NMB), and the cationic porphyrin TMPyP. Intersection analysis identified 891 conserved core genes differentially expressed across all treatments, of which approximately 98% changed in a consistent direction despite differences in photosensitizer chemistry and activating wavelength. Random-effects meta-analysis and robust rank aggregation prioritized 88 high-confidence genes, revealing induction of envelope stress and cytoplasmic protein quality control pathways alongside repression of acid resistance, hydrogen metabolism, molybdate transport, and biofilm formation. Regulon enrichment indicated that heat-shock sigma factor {sigma}32/RpoH and the envelope-stress regulators CpxR, BaeR, {sigma}24/RpoE, and PspF were enriched among induced genes, whereas GadW/GadX/GadE, Fur, and {sigma}38/RpoS were enriched among repressed genes. Functional validation using selected single-gene Keio knockouts confirmed that deletion of conserved-core genes sensitized E. coli to photodynamic treatment and delayed post-treatment recovery in a modality-dependent manner. Moreover, RT-qPCR analysis of selected transcriptional responses confirmed the direction and overall pattern of RNA-seq-derived expression changes. Together, these findings define a unified conserved early survival program in E. coli after chemically distinct photodynamic treatments and identify stress-response modules that may serve as targets for potentiating aPDI. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/744726v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@dbbadaorg.highwire.dtl.DTLVardef@1c85538org.highwire.dtl.DTLVardef@152d699org.highwire.dtl.DTLVardef@18705a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

Anaerobic gut fungi (AGF) are central to the degradation of plant material in the digestive systems of herbivores. However, how their environment influences their colonisation and degradation of complex biomass is unclear. Here, cellulose filter paper was used as a simplified model of the plant cell wall to investigate how the presence of free sugars in the rumen can affect AGF growth and degradative responses of phylogenetically distinct AGF isolates. From this, galactose was revealed to be inhibitory to both Neocallimastix frontalis and Caecomyces communis, and mannose inhibitory to C. communis. Complete inhibition of C. communis growth was conserved when galactose and mannose were added in their polymeric forms, whereas in contrast, N. frontalis growth was unaffected. This indicates, depending on the AGF isolate, the presence of free sugars and their polymeric form may influence AGF growth through regulatory and metabolic interactions - even if the sugar cannot be utilised for growth as the sole substrate. Collectively, this work highlights the functional diversity in AGF carbohydrate responses and the need for greater understanding of their metabolic regulation for applications in lignocellulosic bioconversion and ruminant nutrition.

Microbial chain elongation enables the conversion of organic waste into higher-value products and is therefore a promising process for circular biomanufacturing. However, the microbial interactions governing chain elongation communities remain poorly understood. While quorum sensing has been extensively studied in the context of pathogens and model organisms, research on the perception of quorum-sensing molecules by non-model organisms and their effects within microbial consortia has remained limited. Here, Lactiplantibacillus plantarum and Megasphaera elsdenii were selected as representatives of two key functional guilds in chain elongation communities, namely lactic acid bacteria and chain-elongating bacteria. The effects of different exogenous quorum sensing molecules were evaluated in pure cultures and co-cultures using microtiter plates and serum bottles. Both organisms exhibited distinct molecule-dependent responses for both growth and biofilm formation. Moreover, the response of M. elsdenii was highly dependent on the supplied substrate. Despite changes in growth and/or biofilm formation, product yield and product spectra remained largely unaffected. Importantly, responses observed in pure cultures did not predict co-culture behavior, and no clear response to the tested molecules was detected in the co-culture grown in serum bottles. These findings demonstrate that responses to quorum sensing molecules are strongly dependent on the signal, substrate, microbial context, and cultivation conditions. These results highlight the limited predictive power of pure-culture assays for microbial communication in interacting communities and emphasize the importance of studying signal perception under process-relevant cultivation conditions.

Increased temperature is one of the first environmental cues encountered by bacteria upon entering a mammalian host. Here, we investigated the effects of temperature on the transcriptome and proteome of Escherichia marmotae and E. coli. Previous studies demonstrated that temperature affects motility in E. marmotae; therefore, we examined how temperature alters gene expression at 37 {degrees}C versus 28 {degrees}C and whether this response is conserved in E. coli. Strains were grown under static conditions at both temperatures, and gene expression and protein abundance were assessed by RNA transcriptome analysis and global proteomics. Temperature altered the expression of 111 genes (2.7%) in E. marmotae and 99 genes (2.5%) in E. coli (adjusted p < 0.05, [&ge;]2-fold change), with changes concentrated within specific functional pathways. In E. marmotae, flagellar and chemotaxis genes and operons involved in cellulose-dependent biofilm formation and nitrate respiration were markedly downregulated at 37 {degrees}C. In contrast, genes associated with fimbrial adhesion and immune evasion, including fimA/fimB, ompT, and prophage-associated loci, were upregulated. Proteomic analysis corroborated these trends, showing reduced flagellar and chemotaxis proteins and increased stress-adaptation and host-interaction proteins. E. coli showed a distinct response, with stronger enrichment of metabolic and amino-acid biosynthesis pathways and minimal changes in motility regulation. Together, these findings demonstrate that E. marmotae motility is temperature-dependent and may represent a mechanism for immune evasion within the host.

Amplicon-based techniques provide a rapid and cost-effective approach for profiling microbial communities. However, the observed microbial diversity is influenced by a wide range of factors, encompassing pre-analytical steps such as the choice of primers and target regions, as well as the bioinformatic pipeline, including the selection of tools, reference databases, and parameter settings. Several benchmarks are already available in the literature, but the updates to important tools and databases, namely LotuS3, the Ribosomal Database Project and GreenGenes2, prompted our investigation. In this study, we conducted a comprehensive benchmark of the main bioinformatic tools and databases. Using seven regions for three publicly available mock communities of increasing complexity, we tested 38 possible combinations of sequence resolution algorithms (DADA2 stand-alone, LotuS3 (DADA2/UPARSE)), taxonomic classifiers and search tools (Kraken2, DECIPHER, RDP, MMseqs2, Lambda, and Metaxa2), and databases (SILVA, GreenGenes2, RDP, RefSeq, and Metaxa2). The region V1-V3, coupled with DADA2+MMseqs2+SILVA, DADA2+Metaxa2, or LotuS3 (DADA2)+RDP yielded the highest-quality estimates of the true diversity according to the metrics. We also demonstrated that even certain dominant genera remain difficult to detect, and that the quantification of all genera can be substantially over- or under-estimated, even when using optimal combinations of tools and reference databases.

The coprophilous agaricomycete Coprinopsis cinerea is a model organism for antagonistic fungal-bacterial interactions. Previous studies showed that C. cinerea responds to antagonistic bacteria with strong induction of a set of genes encoding secreted antibacterial molecules. However, little is known about the elicitors of this response. Key open questions in this respect include whether individual antibacterial defence genes are induced by different bacteria and/or by specific bacterial soluble molecules. Here, we present a new C. cinerea reporter system to monitor antibacterial defence induction and address related outstanding issues with minimal hands-on time. In this system, the promoter of the endogenous bacterial-induced gene cclys1 drives the expression of cnluc, which encodes a secreted variant of the deep-sea shrimp luciferase Nluc. We show that cNluc allows to detect and quantify cclys1 induction by measuring luminescence directly in the culture medium of reporter strain colonies. Building on these features, we successfully leveraged the inducible cNluc reporter strain for the development of a novel 96-well plate assay that allows the high-throughput screening of antibacterial defence elicitors. As cNluc can be subject to degradation by secreted proteases of fungal or bacterial origin in the culture medium, we coupled this assay to confirmatory qRT-PCR. Testing this set-up by confronting the reporter strain with several different bacteria revealed that cclys1 induction occurs independently of the bacterial ecological niche. Based on these results, we also recommend qRT-PCR exclusively for validation of negative results. We conclude that cNluc offers significant advantages over cytoplasmic reporter proteins, especially for preliminary rapid screening of multiple conditions.

Aerobiological studies have largely focused on near-surface sampling and horizontal biogeographic patterns, while vertical structuring of airborne microbial communities within the atmospheric boundary layer (ABL) remains poorly understood. Here, we investigated microbial communities across the lower and upper ABL in a low-orography coastal site on the Antarctic Peninsula, representative of the Southern Ocean marine ABL and with low direct human influence. Airborne microorganisms were sampled simultaneously using ground-based and aerial platforms on five occasions. Community composition, abundance, and cell morphometry were assessed using metabarcoding and epifluorescence microscopy and interpreted alongside atmospheric observations. Airborne bacterial and eukaryotic communities showed consistent vertical stratification, although partial taxonomic overlap indicates vertical connectivity between atmospheric layers. Lower ABL communities were more diverse than upper ABL counterpart, compositionally homogeneous, and dominated by marine-associated taxa, reflecting strong influence from local sources and turbulent mixing. In contrast, upper ABL communities were less diverse but more heterogeneous among sampling events, enriched in stress-tolerant, terrestrial and plant-associated taxa, consistent with atmospheric filtering, selective upward transport, and long-range atmospheric inputs. Upper-layer samples also exhibited higher microbial abundance and greater prevalence of elongated cell morphologies, suggesting particle accumulation aloft and aerodynamic selection permanence. Together, these findings identify the Southern Ocean ABL as a vertically structured microbial habitat organized into two partially decoupled sublayers, in which atmospheric dynamics regulate microbial dispersal, ecosystem connectivity, and biogeographic patterns.

Klebsiella pneumoniae is an important cause of severe respiratory and systemic infections, and the increasing prevalence of multidrug-resistant strains has created an urgent need for alternative antibacterial strategies. In this study, nine K. pneumoniae-infecting bacteriophages isolated from diverse environmental sources were characterized genomically and functionally. Genome analyses revealed substantial genomic and proteomic diversity among the isolates. Functional screening against the clinical K. pneumoniae isolate JJD85 identified Curly as the most active phage, producing the highest plaque-forming titer and rapid suppression of bacterial growth in liquid culture. Curly was predicted to have a virulent lifestyle and encoded structural, genome-packaging, and DNA replication-associated proteins. In primary human monocyte-derived macrophage cultures, Curly markedly reduced bacterial burden in both cell-associated and cell-free fractions, while treatment of primary human neutrophil cultures produced an approximately 10^6-fold reduction in total recoverable bacterial burden. Transmission electron microscopy demonstrated phage-like particles within bacterial profiles located in both extracellular and macrophage-associated intracellular compartments. In a C57BL/6J murine pneumonia model, intranasal Curly treatment reduced pulmonary bacterial burden in a dose-associated manner, with approximately 10-fold and 100-fold reductions at the low and high doses, respectively. Curly treatment also attenuated infection-associated lung inflammation and preserved pulmonary architecture. These findings identify Curly as a promising bacteriophage candidate against K. pneumoniae and support further evaluation of its host range, resistance profile, and therapeutic potential.

Biopreservatives including nisin and its derivatives are becoming more desirable in the food processing industry because of the growing demand for naturally preserved and minimally processed foods free from artificial preservatives. However, ensuring microbiological safety while meeting these consumer preferences remains a major challenge. This has necessitated the continuous investigation of potential new antimicrobial agents produced by naturally occurring microorganisms. Hence, this study explored the synthesis, characterisation, and optimisation of a bacteriocinogenic lactic acid bacterium and its antimicrobial product, possibly novel bacteriocin (Nisin 2A) from Lactococcus lactis isolated from commercial brined cheese. The isolation was achieved by screening for wild-type bacteriocin-producing lactic acid bacteria from dairy products using MRS media. Screening was performed using antagonism assays, yielding five producer organisms. Of these, the isolate whose metabolites exhibited the most potent antimicrobial activity was identified as Lactococcus lactis, which synthesised an active antimicrobial peptide designated as Nisin 2A, with a molecular mass of approximately 3.3 kDa as determined by UHPLC-MS and SDS-PAGE. Production of Nisin 2A was scaled up through fed-batch fermentation of Lactococcus lactis in modified MRS broth following process optimisation using a Plackett-Burman experimental design and purified by ammonium sulphate precipitation and solid-phase extraction (SPE). Furthermore, the antimicrobial potential of the bacteriocin was evaluated by the agar well diffusion assay and quantified using the tube dilution method. The purified peptide demonstrated broad-spectrum antimicrobial activity, particularly against the test Gram-positive bacteria Bacillus cereus and retained its bioactivity across a wide pH range (3-9) and high thermal conditions (up to 100 {degrees}C). Furthermore, it had high sensitivity to proteolytic enzymes (Proteinase K and Trypsin). Notably, the peptide was thermostable and retained up to 90% of its initial activity after thermal treatment and maintained consistent inhibitory performance after extended storage. These findings highlight the potential application of Nisin 2A as a natural biopreservative in food systems.

Subgingival biofilms in periodontitis exhibit spatial heterogeneity, yet the organization of microbial communities across periodontal niches remains incompletely defined. Using paired sampling and 16S rRNA gene sequencing, we characterized non-attached and attached subgingival plaque from patients with periodontitis, together with non-attached plaque from periodontally healthy individuals. Across diversity metrics and ordination analyses, non-attached plaque from periodontitis patients occupied positions between healthy-associated and attached-plaque communities. Taxonomically, these communities contained both health-associated commensals and anaerobic genera commonly enriched in periodontitis. Network analysis identified differences in association-network topology among niches, with the non-attached periodontitis network containing more retained associations than the healthy network. These cross-sectional results describe niche-associated patterns of subgingival community composition and association structure. They do not establish temporal progression, direct microbial interactions, or clinical utility.

Romanian bors, a traditional fermented wheat bran beverage, is produced through spontaneous fermentation and represents a complex microbial ecosystem. Despite its cultural importance and presumed health benefits, its microbial ecology and functional potential remain poorly characterized. The present study aimed to elucidate the microbial community structure of bors and link it to functional traits relevant to fermentation performance and food functionality by integrating culture-independent sequencing with culture-dependent isolation and functional characterization. A total of 32 bors samples (12 commercial and 20 homemade) were analyzed. Amplicon-based sequencing revealed a microbiome dominated by lactic acid bacteria (LAB), with lactobacilli accounting for the majority of the bacterial communities and Lactobacillus amylolyticus being identified as the most prevalent and abundant species. The yeast communities were mainly composed of fermentative taxa, including Pichia kudriavzevii and Kluyveromyces marxianus. Lactobacillus amylolyticus and P. kudriavzevii were also the most frequently isolated species among bacteria and yeasts, respectively. These results highlighted a strong adaptation of the microbial isolates to starch-rich cereal substrates and underscored the central role of these microorganisms in wheat bran fermentation for bors production. Whereas the sequencing-based analyses showed no significant differences in overall diversity between the commercial and homemade bors samples, the cultivation-based results indicated a higher bacterial richness in the commercial products. Notably, the culture-dependent method captured substantially fewer taxa, highlighting the complementary nature of the two approaches. Of a total of 101 bacterial strains (88 LAB and 13 acetic acid bacteria) isolated, many exhibited rapid growth and strong acidification capacity, reaching pH values below 4.5 within 12 h. A functional screening revealed that 21 % of these strains displayed -amylase activity, 65 % phytase activity, and 50 % {beta}-glucosidase activity, highlighting their capacity to metabolize cereal substrates and enhance the nutrient availability of bors. All strains showed antibacterial activity against at least one indicator bacterium tested, with a universal inhibition of Listeria monocytogenes. Overall, Romanian bors harbored a lactic acid bacteria-dominated core microbiome with a significant functional diversity. These findings underscored its potential as a rich source of functional and technologically important strains for application in starter and protective culture development.

Diarrheagenic Escherichia coli (DEC) pathotypes are commonly defined by molecular detection of discrete virulence genes, yet how quickly these diagnostic genes emerge and move among co-circulating lineages remain unclear. Here, we classified 248 whole-genome-sequenced E. coli isolates from the EcoZUR case-control study in northern Ecuador into intra-species genomovar units using the recently described 99.5% ANI threshold. This framework exposed cryptic population structure, revealing that single sequence types, representing identical multilocus sequence types (MLST), can harbor multiple distinct genomovars. Within individual genomovars, we observed a few cases of different pathotypes among isolates showing ~99.7% ANI (and many such cases between genomovars). Coupled with synteny and phylogeny analyses that revealed pervasive incongruences between pathotype-diagnostic virulence genes and the core genome, these findings suggest recent horizontal gene transfer as the primary driver of pathotype evolution. Virulence gene profiling further revealed that accessory virulence repertoires are hierarchically structured by phylogroup across pathotypes, with genomovars assigned to phylogroups B2 and D exhibiting more conserved virulence architectures than those in phylogroup A and B1. Among DAEC isolates specifically, the B2- and D-associated genomovars showed elevated diarrhea-association rates relative to their phylogroup A counterparts. Rare virulence genes, including Type VI secretion systems, further distinguished diarrhea-associated from asymptomatic genomovars. These findings demonstrate that, although there seems to be within-lineage (phylogroup) conservation of virulence, pathotype identity is a labile state defined by horizontally acquired virulence genes at the genomovar level, and that the genomovar framework provides a biologically meaningful unit for linking intra-species diversity to pathogenic potential and outbreaks.

Plant growth-promoting bacterial endophytes represent a sustainable strategy for enhancing agricultural productivity while reducing reliance on synthetic fertilizers and pesticides. This study focused on the genomic and functional characterization of two endophytic bacterial strains, R11F and R19M, isolated from bean and maize roots, respectively. Comparative analyses based on 16S rRNA gene sequences, average nucleotide identity (ANI), and genome-to-genome distance calculations (GGDC) classified both isolates as Pseudomonas palleroniana. Comparative genomic analyses revealed highly conserved genomes containing genes associated with plant colonization, phosphate solubilization, stress adaptation, heavy metal resistance, and hydrocarbon degradation. Genome mining further identified 17 and 18 biosynthetic gene clusters (BGCs) in R11F and R19M, respectively, including non-ribosomal peptide synthetases (NRPS), pyoverdine, NRP-metallophores, RiPP-like compounds, arylpolyenes, {beta}-lactones, terpenes, NAGGN, and hydrogen cyanide. Strain-specific BGCs associated with syringomycin and viscosin biosynthesis were identified in R11F, whereas R19M harbored clusters related to asplenin and kolossin biosynthesis. In vitro assays confirmed indole production, phosphate solubilization, and siderophore production, as well as the ability of both strains to grow in nitrogen-free medium. Both strains significantly inhibited the growth of Fusarium oxysporum, Phytophthora cinnamomi, and Colletotrichum gloeosporioides. Furthermore, plant inoculation assays demonstrated host-dependent growth promotion, with R11F showing the most consistent improvements in plant growth parameters in tomato, wheat, and lentil. Overall, the integration of comparative genomics and experimental validation demonstrates that P. palleroniana R11F and R19M possess complementary traits associated with plant growth promotion, pathogen suppression, saline stress adaptation, and bioremediation.

ABSTRACT: The bacterial small RNA (sRNA) OxyS is expressed in Escherichia coli during oxidative stress. The sRNA OxyS enhances cell survival by controlling genes involved in the regulation of hydrogen peroxide (H2O2) and iron-sulfur (Fe-S) cluster formation. Here, we used the MS2 affinity purification coupled with RNA sequencing (MAPS) technique to identify new target mRNAs of the sRNA OxyS. Our analysis revealed a significant enrichment of mepS mRNA, which encodes a peptidoglycan endopeptidase that promotes cell growth. Our results confirm a previous report on the sRNA OxyS repressing the translation of mepS. We also found that an {Delta}oxyS background facilitates the emergence of mutations, conferring increased resistance to the last-resort antibiotics polymyxin B and E (colistin), but only in the presence of the target mepS gene. This suggests that the translation repression of mepS by OxyS could prevent mutations in bacterial DNA during H2O2-induced oxidative stress. Moreover, we show that adding the antioxidant thiourea or sequestering iron in the {Delta}oxyS background effectively reduces the emergence of resistance against both polymyxin B and colistin. These results suggest that reactive oxygen species (ROS), in conjunction with intracellular iron, play a key role in driving the emergence of antibiotic resistance. Overall, our work underlines a mechanism of antimicrobial emergence implicating oxidative stress, intracellular Fe, and cell wall remodeling in E. coli. IMPORTANCE: This study uncovers an underexplored link between peptidoglycan remodeling and oxidative stress responses during exposure to antibiotics. By elucidating how MepS and the sRNA OxyS interact in the presence of polymyxins and oxidative stress, our study suggests that MepS may exert an anti-mutator function. The repression of mepS translation by OxyS seems to limit the emergence of antibiotic resistance driven by DNA mutations. Together, these findings suggest cell wall remodeling and oxidative stress response pathways as promising targets to enhance antibiotic efficacy and limit the emergence of resistance.

Background and aimsExcess nitrate (NO3-), from fertilizer overuse and intensive agriculture, can pollute water and contribute to greenhouse gas production (nitrous oxide - N2O). Plant metabolites from pastural herbs such as Plantago lanceolata (plantain) can inhibit microbial nitrification of ammonium to NO3- (biological nitrification inhibition - BNI) and change soil nitrogen cycle dynamics (lower potential nitrification rate - PNR). The main aim was to investigate differential plant metabolite expression associated with BNI and lowered PNR in different soil types. MethodsSix plantain cultivars were tested for BNI potential and screened for metabolites that correlated with inhibition of the ammonia oxidising bacterium (AOB) Nitrosospira multiformis. PNR and microbiome change was then investigated in four different New Zealand soils under the plantain cultivar Agritonic and ryegrass cultivar One50. ResultsPNR under plantain was 11 to 41% lower than fallow soil while PNR under ryegrass was 0 to 39% lower. In addition to verbascoside and aucubin, plantain metabolites associated with lower PNR included plantamajoside, riboflavin 3- and 5-sulfate, plantagoguanidinic acid. Chlorogenic acid was associated with lowered PNR under ryegrass. PNR reductions, microbiome structure and the ratio of ammonia oxidising archaea (AOA) relative to AOB was modulated by soil type. ConclusionPlantain and ryegrass lowered the PNR in four different soils and was correlated with metabolites beyond just aucubin and verbascoside. Based on candidate BNI-associated metabolites identified, it was hypothesised that lowered PNR is likely indirect through mechanisms such as chelation and appears to be dependent on both plant physiology and soil physicochemistry.

Rhodotorula mucilaginosa is an emerging opportunistic fungal pathogen increasingly associated with catheter-related bloodstream infections. Although biofilm formation is considered a major virulence trait for R. mucilaginosa, factors contributing to biofilm persistence on medical devices remain poorly understood. Here, we characterized the thermotolerance, biofilm formation, UV resistance, and cell surface hydrophobicity profiles of eight R. mucilaginosa strains representing clinical and non-clinical (laboratory, environmental, and marine mammal) isolates. All strains grew optimally at 30C and exhibited restricted growth at 35C and 37C, although one environmental isolate maintained robust growth at 37C. All strains exhibited moderate to high cell surface hydrophobicity. We then assessed biofilm formation for each strain, including adherence to two different plastic substrates, development of biofilm biomass, comparison of biofilm metabolic activity, and the effects of temperature on biofilm formation. Under static conditions, biofilm biomass of most isolates on 96-well polystyrene plates was greatest at 24C. Clinical isolates generally maintained higher biofilm metabolic activity at 37C than nonclinical isolates, while at lower temperatures, clinical and non-clinical isolates did not differ significantly in metabolic activity. All strains readily formed biofilms on polyurethane intravenous catheters under dynamic conditions, as confirmed by scanning electron microscopy and metabolic activity. While planktonic cells already displayed substantial UV-C tolerance, biofilm-associated cells remained viable following exposure to UV-C doses up to eightfold higher than those that impaired planktonic growth. These findings document differences in thermotolerance and biofilm formation by isolate origin and identify biofilm formation as a major factor promoting persistence of R. mucilaginosa on clinically relevant materials and reduced susceptibility to UV-C sterilization.

The genus Erwinia comprises a diverse group of bacteria associated with plants, insects, and the environment, including several economically important phytopathogens. The genus has been revised taxonomically many times, yet a thorough and genome-wide assessment of its evolutionary relationships and genomic diversity has been lacking. In this research, we carried out an extensive phylogenomic and comparative genomic analyses of the genus Erwinia using 104 genomes including historically important strains. Genome-wide analyses integrating average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), core-genome phylogenomics, pan-genome analysis, and comparative genomics resolved evolutionary relationships across the genus and identified multiple taxonomic inconsistencies. The pan-genome analysis revealed a relatively small core genome alongside an extensive accessory genome, underscoring the substantial genomic plasticity and ongoing diversification within the genus. The comparative analyses further showed pronounced lineage-specific variation in secretion systems, exopolysaccharide biosynthetic loci, flagellar gene clusters, genomic islands, prophages, and iron acquisition systems, suggesting that virulence-associated determinants have evolved through differential gene gain, loss, and conservation across distinct lineages, thereby facilitating host and ecological niche adaptation. This lineage-specific variation indicates that pathogenicity in the genus is not driven by a single conserved set of virulence determinants but instead reflects distinct combinations of virulence-associated genes. These findings refine the genomic framework of the genus Erwinia, provide evidence for taxonomic revision of several lineages, and improve our understanding of the evolutionary relationships, genomic diversification, and lineage-specific adaptations associated with host interactions and ecological specialization. Impact StatementThis study provides the first comprehensive genome-wide phylogenomic framework for the genus Erwinia, integrating taxonomy, pan-genome diversity, virulence-associated determinants, and mobile genetic elements across all 18 currently recognized species. Analyses resolve evolutionary relationships, uncover multiple taxonomic inconsistencies, identify previously unrecognized species-level lineages, including a putative novel Erwinia species PL328 isolated from Cornus florida (dogwood), and reveal lineage-specific genomic features. These findings establish a valuable genomic foundation for future studies of Erwinia evolution, taxonomy, and plant-microbe interactions. Data SummaryGenomes sequenced in this study were submitted to the NCBI database under the accession numbers: JCBCPT000000000

Forest-associated Saccharomycotina occur at low relative abundance, limiting inference about their diversity and dynamics. We sampled leaf litter weekly for 47 weeks across a subtropical forest in northern Taiwan. Enrichment, isolation and ITS sequencing recovered 687 isolates, including 613 Saccharomycotina representing 56 described species and 77 putatively novel operational taxonomic units. Rarefaction indicated unsampled culturable diversity. Among litter traps, community dissimilarity was high and dominated by taxon replacement, but neither topography nor geographic distance was associated with composition, and turnover matched randomised expectations. Richness peaked during warm, wet periods and declined in winter, and minimum temperature showed the strongest statistical association. Composition was associated with maximum temperature, minimum relative humidity, precipitation and solar radiation. Selected isolates' thermal optima covaried with collection-week temperatures, and two October Magnusiomyces magnusii isolates had higher optima than four winter isolates. Together, these findings reveal substantial culturable diversity and seasonal community restructuring consistent with temperature-related filtering.