Environmental Microbiology Reports

During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host‐associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.

Harmful algal blooms (HABs) pose a significant global threat to water ecosystems, prompting extensive research into their inhibition and control strategies. This study presents genomic and bioinformatic analyses to investigate the algicidal potential and elucidate the survival mechanisms in harsh conditions of newly identified Halobacillus species three strains (SSTM10‐2T, SSBR10‐3T, and SSHM10‐5T) isolated from saline environments. Moreover, genomic and bioinformatic analyses were conducted to elucidate their survival mechanisms in harsh conditions. Moreover, comparative genomic analysis revealed a diverse set of orthologous genes, with a core genome primarily associated with metabolism and information processing. Pangenome analysis highlighted accessory and unique genes potentially involved in environmental adaptation and stress response. Functional annotation using KEGG pathways identified genes linked to xenobiotic compound degradation, stress tolerance, and salt adaptation. Additionally, the study elucidated potential mechanisms underlying algicidal activity, implicating Carbohydrate‐Active enZYmes (CAZymes), cytochrome P450 oxidases (CYP), and quorum sensing (QS) systems. Finally, analysis of KEGG pathways related to microcystin degradation suggested the strains' capacity to mitigate HABs. Thus, this research enhances understanding of the genomic diversity, phylogeny, and functional characteristics of Halobacillus species, offering insights into their ecological roles and potential applications in biotechnology and environmental management.

Parageobacillus thermoglucosidasius is a thermophilic facultative anaerobe capable of hydrogenogenic carbon monoxide (CO) oxidation utilising nickel‐containing CO dehydrogenase (Ni‐CODH) and energy‐converting hydrogenase (ECH). Nitrates have been reported to exert promoting or inhibitory effects on the growth of CO oxidizers and acetogens, and these contradictory outcomes obscure the relationship between nitrate and CO oxidation. In this study, we analysed the effects of nitrate on hydrogenogenic CO oxidation and growth in P. thermoglucosidasius NBRC 107763T using wild‐type and codh‐ and/or ech‐disrupted strains. The results demonstrated that the addition of 50 mM nitrate suppressed hydrogenogenic CO oxidation while promoting hydrogen‐oxidising nitrate reduction and rapid cell growth, resulting in a 2.3‐fold higher OD600 than the control. Assays using cell lysates showed that 10 μM nitrate suppressed CO oxidation below the detection limit without affecting hydrogen production, indicating that nitrate affects the CO‐oxidising function. These findings imply that CO oxidation in P. thermoglucosidasius is primarily coupled to proton reduction, and deactivated during nitrate respiration. Therefore, hydrogenogenic CO oxidation serves as an auxiliary energy‐obtaining mechanism, functioning in the absence of alternative electron acceptors such as nitrate. This study enhances our understanding of CO‐dependent energy generation and highlights the supplemental use of CO in P. thermoglucosidasius.

The growing demand for sustainable alternatives to chemical fungicides has driven the development of microbial‐based biocontrol strategies. In this study, the native strain Trichoderma koningiopsis LBM116 (Misiones, Argentina) was optimised for the production of mycolytic enzymes (chitinases, β‐1,3‐glucanases, and proteases) using factorial and response surface experimental designs. Enzyme secretion was increased by more than 250% compared to initial conditions by selecting specific carbon and nitrogen sources and adjusting inoculum and pH parameters. The optimised enzyme formulation improved lettuce seed germination to 86.66% in the presence of the phytopathogen Fusarium sp., under controlled conditions. In seedling trials, it also reduced disease severity and improved growth parameters. These results confirm the dual effect of the enzyme formulation, acting as a biocontrol agent and plant growth promoter. This work highlights the potential of enzyme formulations derived from T. koningiopsis LBM116 as an effective, low‐cost, and sustainable alternative for managing phytopathogens in agriculture.

Symbiosis with bacteria is essential for the survival of animals with an obligate blood‐feeding lifestyle. In ticks, two distinct bacterial lineages, Coxiella‐like and Francisella‐like endosymbionts, have independently evolved into nutritional symbionts, converging on a key biochemical function for the tick's survival and growth: the production of three B vitamins. In this study, we carried out comparative analyses across multiple tick species and characterised remarkable similarities in their tissue localisation, particularly in organs important for nutrient metabolism and maternal transmission to progeny. In these organs, both symbionts colonise similar intracellular niches, residing within membrane‐bound, replicative vacuoles that occupy a substantial part of the cytoplasm of tick cells. Despite extensive genomic reduction, both symbionts have retained pathways for the biosynthesis of B vitamins and, in some cases, chorismate, a precursor used for the production of serotonin by ticks. However, differences exist: while Coxiella‐like endosymbionts lack the ability to synthesise heme, Francisella‐like endosymbionts possess a complete heme biosynthesis pathway and may potentially provide ticks with this essential cofactor. Overall, these phenotypic and genomic characteristics reveal a broad convergence among symbiotic interactions across major tick families, highlighting the essential role of symbiosis in tick nutrition, feeding behaviour, blood intake and subsequently in pathogen transmission.

Steel corrosion is an extensive problem worldwide, substantially impacting marine infrastructures. In this study, the influence of steel on bacterial succession and corrosion was investigated by culturing marine water samples with and without steel coupons for 14 days. Compared to abiotic controls, oxygen levels were rapidly depleted in biotic cultures. Fe levels increased in controls compared to biotic cultures, potentially due to anoxic conditions and the incorporation of Fe in the biofilm. Proteobacteria dominated the initial cultures, but over 14 days the number of phylogenetic groups decreased overall in abundance. Taxons that increased in abundance included Clostridiaceae, Fusobacteriaceae, Flavobacteriaceae and Prolixibacteraceae, some members of which can utilise Fe. While initially in low abundance, Arcobacteraceae, Pseudoalteromonadaceae, Rhodobacteraceae and Rhizobiaceae numbers increased over time. Sites 1 and 2 cultures displayed localised deep pitting corrosion on coupon surfaces, consistent with microbial action, with an increase in Bacteroidetes, suggesting this phylum facilitates corrosion. In contrast, Site 3 cultures displayed uniform, superficial corrosion, with Clostridiaceae being the dominating family by Day 14, suggesting corrosion inhibition through biofilm formation. By identifying bacteria associated with corrosion, targeted approaches to corrosion reduction may be developed through identifying significant metabolic pathways by transcriptomics and the application of metabolic inhibitors.

Host‐associated microbial communities play an important role in regulating many aspects of insect biology, but changes in this microbiota during diapause and overwintering are still largely unknown. Halyomorpha halys is an invasive agricultural pest characterised by a unique overwintering strategy where individuals aggregate and enter a state of dormancy, making it an excellent model to study the relationship between microbiota and diapause. We investigated the bacterial diversity of wild H. halys specimens before and after dormancy using 16S rRNA gene amplicon‐sequencing. We found that microbiota varies between geographically neighbouring sampling locations, but there were no significant differences in microbial diversity or composition between populations sampled before and after diapause, despite stressful overwintering conditions. Such stability may relate to the highly specific taxa that dominate the stinkbug‐associated microbial community. In addition, we did not detect any strong association of stink bugs with phytopathogens, but we found that two populations harboured Nosema maddoxi, a microsporidian pathogen of stink bugs. Our results are relevant to the assessment of accidental spillovers of microorganisms in newly invaded areas and to the implementation of the sterile insect technique based on mass trapping, irradiation, shipping and release after diapause of wild individuals.

Plant‐associated yeasts modulate host immunity to promote or prevent disease. Mechanisms of yeast perception by the plant innate immune system remain unknown, with progress hindered by lack of a model system with the model plant Arabidopsis thaliana (Arabidopsis). A yeast strain of Taphrina tormentillae, named M11, was previously isolated from wild Arabidopsis. Taphrina have been found on many non‐host plants, and their complex ecology remains understudied. Here, the interaction of M11 with Arabidopsis was characterised. Infection of Arabidopsis with the birch pathogen T. betulina, used as a non‐host control, triggered typical defence activation features but did not multiply, demonstrating Arabidopsis had immunity against a non‐adapted yeast. M11 triggered attenuated defence activation features, grew in planta, and caused subtle but clear leaf deformation symptoms, demonstrating it is pathogenic. M11 was widely distributed in environmental sequencing data and found on multiple non‐host plants, suggesting Taphrina play previously unrecognised ecological roles on multiple plant species. M11 genome features involved in host interaction were analysed, and potential immune stimulatory molecules in chitin‐free cell walls were identified. A pilot screen demonstrated the utility of reverse genetics with Arabidopsis and identified that the BAK1 co‐receptor is involved in the perception of M11 Taphrina cell walls.

This study investigates how Phacidium infestans acquires nutrients on Pinus sylvestris needles, which possess antimicrobial properties. P. infestans was evaluated for its growth and enzyme production on various substrates, alongside genomic and metabolomic analysis. Direct‐infusion high‐resolution mass spectrometry (DI‐HRMS) was performed on methanol extracts obtained from P. infestans cultivated on needles and malt extract media. DI‐HRMS analysis identified 21 compounds from the malt extract and 112 from the needle samples. The resin components increased in the needle samples post‐cultivation, suggesting terpenoid release from resin ducts due to fungal degradation of plant cell walls. P. infestans fully consumed sugars and antifungal compounds, including taxiresinol and salicylic acid, with control‐to‐sample ratios (CTR/SA) of 289.76 and 47.24, respectively. Moreover, lariciresinol and pinoresinol were reduced to undetectable levels. The genomic analysis identified 421 secreted proteins, including 128 carbohydrate‐active enzymes, 3 cutinases, and 49 lipases that aid host penetration and wax degradation. Several multi‐drug efflux pumps and two acyclic terpene utilisation proteins were identified as well. These proteins support the cellular integrity of P. infestans by expelling toxic compounds. Our findings provide valuable insights into the metabolic strategies of P. infestans for nutrient assimilation on pine needles.

Plant‐associated fungi can host unique bacterial microbiota to provide multiple benefits to their fungal hosts. Here it was characterised the bacterial microbiota associated with an Epichloë fungal endophyte (strain AR135) isolated from perennial ryegrass (Lolium perenne) via both 16S rRNA gene sequencing and direct microbial isolation and investigated the microbe‐microbe interactions between these bacteria and the fungus. The bacterial microbiota of AR135 was dominated by members within the genus Paenibacillus, with 99% of abundance (on average); although bacteria within genera Delftia and Bradyrhizobium were also present. Paenibacillus cells were located on the surface of hyphae of AR135 fungus in vitro on synthetic media and in planta within perennial ryegrass leaves. Two bacterial strains, E100 and E300, identified as Paenibacillus, were isolated from the AR135 mycelium. E300 drastically altered the abundance of both the whole bacterial microbiota (increased by 63%) and E100 (reduced to 0%). None of the variations observed in the abundance of total bacterial microbiota and E100 and E300 were associated with changes in the fungal biomass of Epichloë. The findings show that Epichloë fungal endophytes can host bacterial communities, the structure of which was regulated by key members of the bacterial community.

Candidatus Altiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of two Ca. Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high‐CO2 groundwater system in the USA, Ca. Altiarchaeum crystalense co‐occurs with the symbiont Ca. Huberiarchaeum crystalense, while in the Muehlbacher sulfidic spring in Germany, an artesian spring high in sulfide concentration, Ca. A. hamiconexum is heavily infected with viruses. We here mapped metatranscriptome reads against their genomes to analyse the in situ expression profile of their core genomes. Out of 537 shared gene clusters, 331 were functionally annotated and 130 differed significantly in expression between the two sites. Main differences were related to genes involved in cell defence like CRISPR‐Cas, virus defence, replication, transcription and energy and carbon metabolism. Our results demonstrate that altiarchaeal populations in the subsurface are likely adapted to their environment while influenced by other biological entities that tamper with their core metabolism. We consequently posit that viruses and symbiotic interactions can be major energy sinks for organisms in the deep biosphere.

This study aimed to understand the genetic and molecular mechanisms enabling Alcanivorax borkumensis SK2, a hydrocarbonoclastic marine bacterium, to thrive under iron‐limited conditions. Using SMRT PacBio whole‐genome sequencing, Illumina total RNA sequencing, and proteomics analysis, we examined the strain's response to iron‐rich and iron‐depleted media. Despite minimal impact on growth, significant changes in gene expression were observed when using n‐tetradecane or acetate under iron limitation. Iron scarcity, depending on the carbon source, affects energy metabolism, membrane transport, lipid metabolism, stress‐adaptive responses, and siderophore synthesis. We identified several methyltransferases (MTases) in the studied genome, including RS14230, which is a part of a fully functional restriction‐modification (RM) system causing bipartite cytosine methylation and DNA cleavage at AgGCcT sites. Another MTase, RS09425, controls bipartite adenine methylation at GaTNNNNNGtGG motifs; however, no restriction activity at these motifs has been detected. Many epigenetically modified nucleotides lacked canonical motifs, possibly due to MTase byproducts. Notably, non‐canonical modifications were statistically associated with transcriptional start sites and gene regulation, suggesting an indirect role in transcription via DNA conformation changes and its accessibility to MTases near actively transcribed genes.

Phosphorus (P) dynamics at the sediment–water interface of aquatic ecosystems are receiving increasing attention due to their implications for water quality. P uptake by microbial biofilms can serve as a mechanism to control and mitigate the risk of eutrophication. Microbial biofilms capture P both intracellularly and extracellularly. While the significance of extracellular P entrapment in biofilms in engineered systems has recently been established, little is known about its dynamics in aquatic ecosystems. Current research on eutrophication control predominantly emphasises nitrogen, phosphorus or nitrogen‐phosphorus ratio‐based approaches, often overlooking the potential indirect influence of bioavailable dissolved organic carbon (DOC) on P uptake by heterotrophic microorganisms. In this study, we tested the effect of bioavailable DOC on P entrapment patterns in biofilms and in biofilm P‐regulation mechanisms such as polyphosphate accumulation and alkaline phosphatase activity in semi‐natural flow‐through experimental flumes. Our results show that intracellular P entrapment is limited by bioavailable DOC, while extracellular P entrapment is independent of bioavailable DOC and has the potential to offset intracellular P saturation. We further demonstrate that DOC bioavailability influences benthic P cycling and that its implications extend into critical areas of ecosystem functioning such as river self‐purification, competitive resource utilisation and organic P cycling.

Vibrio cholerae is a water‐borne pathogen transmitted via the faecal‐oral route, with water being a major vehicle for infection. The pathogen has caused seven pandemics in history, with contaminated water identified as the infection source. Seasonal outbreaks, claiming approximately 21,000–143,000 lives yearly, are facilitated by contaminated water environments. This systematic review, therefore, determined the prevalence of V. cholerae in water environments. A comprehensive literature search was conducted in PubMed, Web of Science, and SCOPUS. After the screening process, 87 articles were included in our study. RStudio version 4.3.3 was used in conducting our meta‐analysis with the data subjected to the random‐effects model. The included articles were from 38 countries, which spanned 6 continents. The prevalences of V. cholerae in water environments were as follows: drinking water (15.69%), untreated sewage (57.26%), treated sewage (95.18%), surface water (41.95%), groundwater (26.23%), and others (20.81%). Continental prevalence revealed the following: Australia (85.00%), North America (66.60%), Africa (42.07), South America (39.32%), Asia (29.28%), and Europe (24.48%). There is a high prevalence of V. cholerae in water environments. More effective water treatment methods are needed to drastically reduce its prevalence to insignificant levels, especially in treated drinking water.

Little is known about the role of antibiotics in microbial ecosystems in the absence of clinical antibiotic pressure. The soft rot Pectobacteriaceae (SRP) species complex comprises 37 bacterial species that are collectively responsible for severe plant decay in many crops. Within this complex, Pectobacterium versatile strains harbour the BlaPEC‐1 β‐lactamase. The aim of our work was to analyse the role of BlaPEC‐1 during plant infection. To this end, two blaPEC‐1‐deleted strains were compared with their wild‐type counterparts in vitro and in mono‐ or mixed infections of potato tubers with different SRP strains. In vitro, BlaPEC‐1 enables P. versatile to resist ampicillin or the carbapenem produced by Pectobacterium brasiliense. In mono‐infections of potato tubers, blaPEC‐1‐deleted strains were not affected in virulence, fitness, or association with bacterial commensals. In mixed infections, BlaPEC‐1 was required for the coexistence of P. versatile with the carbapenem‐producing strain and was necessary to rescue carbapenem‐sensitive strains both in vitro and in planta. Protection was observed even if both the blaPEC‐1 gene was repressed and the BlaPEC1‐expressing bacteria were a minority in the symptoms. These results indicate that BlaPEC‐1 exerts a true β‐lactamase function during the infection process and acts as a public good of the SRP species complex to maintain SRP strain diversity.

Herbicides impact, particularly tebuthiuron (TBT), on agroecosystems and surrounding environments had been documented in scientific literature. This study investigated the hypothesis that areas exposed to TBT, a prevalent herbicide in Brazil's sugarcane crops, might harbour microbial consortia capable of degrading this compound, assessed through a Bayesian‐based colorimetric method. Soil samples from plant cane (pC), characterised by lower organic matter on the surface, and first‐cut ratoon cane (rC) fields, with higher organic matter due to crop residues deposition, were collected for analysis. Colorimetric assays with DCPIP (2,6‐Dichlorophenolindophenol) were performed with microorganisms isolated from these fields to evaluate their TBT‐degradation capacity. In an ELISA microplate, absorbance was measured at 600 nm as DCPIP is a redox indicator. Results confirmed the degradation potential of soil microbial consortia, particularly from rC samples, as evidenced by reduced absorbance relative to the control. The data deviated from the expected sigmoidal pattern, necessitating an alternative data interpretation method. A Bayesian factor estimation approach for kernel density curves of the logarithmic response ratio proved effective for handling non‐sigmoidal spectrophotometric data. The findings offered valuable insights into TBT‐degrading microorganisms and introduced an alternative analytical tool for interpreting variable data, potentially aiding in the development of bio‐based remediation strategies.

Fermentative yeasts play important roles in both ecological and industrial processes, but their distribution and abundance in natural environments are not well understood. We investigated the diversity of yeasts at the northern range limit of their oak tree hosts (Quercus spp.) in Sweden, and identified climatic and ecological conditions governing their distribution. Yeasts were isolated from bark samples from 28 forests and identified to the species level using DNA metabarcoding. Most communities were dominated by species in the Saccharomycetaceae family, especially by species of Saccharomyces, Kluyveromyces and Pichia. Each genus showed a distinct latitudinal and longitudinal distribution, and both temperature and precipitation metrics predicted significant variation in their abundance. Consistent with this, laboratory assays revealed significant effects of temperature on the growth of strains collected from different longitudes and latitudes. We found that older trees harbour more diverse and more balanced fermentative yeast communities with more evenly distributed species abundances. Communities across trees were more similar when sharing a common dominant species. This work provides a baseline for future studies on the impact of climate change on the fermentative yeast biodiversity of temperate forests in northern latitudes and contributes to a growing collection of wild isolates for potential biotechnological applications.

Following a 3.5‐year enrichment cultivation period, a novel ammonia‐oxidising archaeon (AOA), designated strain CL1T, was isolated from Yangshan Harbour (East China Sea). Strain CL1T demonstrates a maximum ammonia tolerance of up to 10 mM. Its optimal growth conditions include a pH range of 7–8, a salinity of 2%–3%, and a temperature range of 20°C–25°C. Under these conditions, strain CL1T achieved a maximum specific growth rate of 0.87 d⁻¹, with cell yields estimated at 3.92 × 10⁶ cells mL⁻¹ μM ammonia⁻¹. Genomic sequencing revealed that strain CL1T possesses a genome size of 1.63 megabases with a high completeness of 99.95%. Phylogenetic analysis based on the 16S rRNA gene and whole‐genome data placed strain CL1T within the genus Nitrosarchaeum. The average nucleotide identity (ANI) between the genome of strain CL1T and its closest relative was 92.01%, confirming that strain CL1T represents a novel species within Nitrosarchaeum. Metabolic pathway analysis demonstrated that strain CL1T encodes key enzymes for ammonia oxidation, including ammonia monooxygenase (amoA, amoB, amoC) and copper oxidase, indicating its capacity for ammonia oxidation. Additionally, strain CL1T likely assimilates ammonia through the GS‐GOGAT and GDH pathways. Consistent with the observation of extracellular vesicles (EVs) in strain CL1T via electron microscopy, genome annotation identified core genes associated with EVs function, such as vps4 and FtsZ. The isolation of strain CL1T provides a valuable model system for investigating its ammonia metabolism and exploring its ecological interactions with other AOA, ammonia‐oxidising bacteria (AOB) and nitrite‐oxidising bacteria (NOB), thereby contributing to a deeper understanding of nitrogen cycling mechanisms in aquatic environments.

Among potentially toxigenic cyanobacteria, Raphidiopsis raciborskii has attracted considerable attention due to its ability to produce massive blooms and its recent spread to temperate regions. In this work, we reported for the first time a taxonomic and functional assessment of a R. raciborskii strain isolated from the Mediterranean region, contributing to filling a gap in the global distribution and characteristics of this species. The strain LT_0923 was isolated from Lake Trasimeno, a large and shallow lake in central Italy. The phylogenomic analyses based on selected marker genes and the core genome obtained from a pangenomic analysis based on a selection of available high‐quality genomes showed a strong correspondence of the Lake Trasimeno strain with the North American and, at a lower average nucleotide identity, with the South American genomes. The LT_0923 genome did not show the presence of gene clusters encoding legacy cyanotoxins or emerging toxigenic compounds. The open pangenome and the large fraction of distinct gene families identified in the cloud and partly shell genome, enriched with genes specialised in environmental‐specific functions and defence mechanisms, are consistent with the development of Raphidiopsis in geographically distinct regions.

This study assessed the concentration, composition, and spatiotemporal distribution of airborne fungi in a metropolitan area, comparing urban and peri‐urban sites across rainy and dry seasons. An 8‐month fungal bioaerosol monitoring was conducted using a six‐stage Andersen cascade impactor. Data analysis involved generalised linear regression models and multifactorial ANOVA to assess the relationships between meteorological conditions, sampling sites, campaigns, fungal concentrations, and impactor stages. Additionally, a Bayesian neural network was developed to predict bioaerosol dynamics based on the analysed variables. We identified 10 viable fungal species, including Aspergillus niger, Aspergillus nidulans, Aspergillus. fumigatus, Aspergillus terreus, Aspergillus flavus, Aspergillus versicolor, Penicillium spp. and Fusarium oxysporum. Notable differences in the aerodynamic sizes of fungal particles influenced their distribution and potential impact on the respiratory system. The Bayesian neural network successfully predicted fungal bioaerosol concentrations with an accuracy of 76.87%. Our findings reveal the significant role of environmental and human‐related factors in shaping bioaerosol distribution in tropical urban contexts. This research provides essential insights into the behaviour of fungal bioaerosols, highlighting their relevance for public health, especially for immunocompromised populations, and their impact on local agriculture. Furthermore, it demonstrates the potential of fungal bioaerosols as bioindicators for environmental monitoring and predictive modelling.

Honey bees (Apis mellifera) play a crucial role in global food production through pollination services. However, their populations are threatened by various stressors, like the ectoparasitic mite Varroa destructor and associated viral pathogens. In this study, we aimed to characterise and compare the viral communities (viromes) in V. destructor‐resistant and susceptible colonies using high‐throughput sequencing. Our findings revealed differences in virome composition associated with the season and not with the resistance or susceptibility to V. destructor. Furthermore, we detected Apis mellifera filamentous virus (AmFV) and Lake Sinai virus (LSV) for the first time in Uruguay, and obtained the complete or partial genomes of both viruses, along with those of other previously described viruses, such as Acute bee paralysis virus (ABPV), Black queen cell virus (BQCV), Deformed wing virus (DWV), and Sacbrood virus (SBV). This study contributes to a deeper understanding of the virome dynamics in honey bees. It highlights the importance of this type of study for the early detection of new viral pathogens, which could help to understand the tripartite network involving V. destructor, honey bees, and viruses.

In the Boreal region, extreme seasonal variations in day–night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate‐driven shifts; yet the fixed day‐length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day‐night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.

Honey bee colonies contain thousands of individuals living in close proximity in a thermally homeostatic nest, creating ideal conditions for the thriving of numerous pathogens. Among the bacterial pathogens, Paenibacillus larvae infects larvae via the nutritive jelly that adult workers feed them, causing the highly contagious American foulbrood disease. Further Paenibacillus species were anecdotally found in association with honey bees, including when affected by another disease, European foulbrood (EFB). However, their pathogenicity remains largely unknown. Our results indicate that Paenibacillus dendritiformis, Paenibacillus thiaminolyticus and newly described Paenibacillus melissococcoides are pathogenic towards honey bee brood and that their virulence correlates with their sporulation ability, which confers them resistance to the bactericidal properties of the nutritive jelly. Our survey occasionally but increasingly detected P. melissococcoides in confirmed and idiopathic cases of EFB but never in healthy colonies, suggesting that this bacterium is an emerging pathogen of honey bee brood. Overall, our results suggest that virulence traits allowing a pathogenic or opportunistically pathogenic habit towards honey bee brood are frequent in Paenibacillus spp., but that their degree of adaptation to this host varies. Our study clarifies the ecology of this ubiquitous genus, especially when infecting honey bees.

Genetic features of host adaptation of S. aureus to ruminants have been extensively studied, but the extent to which this adaptation occurs in nature remains unknown. In New Zealand, clonal complex 1 (CC1) is among the most common lineages in humans and the dominant lineage in cattle, enabling between‐, and within‐CC genomic comparisons of epidemiologically cohesive samples of isolates. We assessed the following genomic benchmarks of host adaptation to ruminants in 277 S. aureus from cattle, small ruminants, humans, and pets: 1, phylogenetic clustering of ruminant strains; 2, abundance of homo‐specific ruminant‐adaptive factors, and 3, scarcity of heterospecific factors. The genomic comparisons were complemented by comparative analyses of the metabolism of carbon sources that abound in ruminant milk. We identified features fulfilling the three benchmarks in virtually all ruminant isolates, including CC1. Data suggest the virulomes adapt to the ruminant niche sensu lato accross CCs. CC1 forms a ruminant‐adapted clade that appears better equipped to utilise milk carbon sources than human CC1. Strain flow across the human–ruminant interface appears to only occur occasionally. Taken together, the results suggest a specialisation, rather than mere adaptation, clarifying why zoonotic and zoo‐anthroponotic S. aureus transmission between ruminants and humans has hardly ever been reported.

Although the Antarctic continent represents one of the most hostile environments on earth, microbial life has adapted to cope with these extreme conditions. Lichens are one of the most successful groups of organisms in Antarctica, where they serve as unique niches for microbial diversification. We have selected eight epilithic lichen species growing in Victoria Land (three cosmopolitan and five endemic to Antarctica) to describe with amplicon sequencing the diversity of the associated fungal and bacterial communities. The lichen mycobiota is predominantly composed of Ascomycota belonging to the classes Chaetothyriomycetes and Dothideomycetes, while a few key representative taxa were recognised as basidiomycetous yeasts. Bacteria associated with lichens were represented by Pseudomonadota, Cyanobacteria, and Bacteroidota in which psychrophilic genera were identified. The microbiota was diverse among the lichen species, and their variation was driven by the lichen species itself and their endemic or cosmopolitan distribution. There was a strong association of the microbial communities linked to the lichen itself, rather than to the specific characteristics of the collecting site. The lichen thallus, thus, plays an important role in microbial diversification and may potentially act as a selective biodiversity filter in which different fungal and bacterial communities thrive in it.