Applied and Environmental Microbiology

Global plastics pollution is a major environmental challenge, and we still have limited knowledge of marine microbiota involved in possible remediation. Our research shows that marine Flavobacteria harbor the potential for PET degradation using dienelactone hydrolases (DLHs, EC 3.1.1.45). The widespread distribution of these microorganisms and the notion that these enzymes are secreted may imply …

In January 2025, Santé publique France detected several cases of hemolytic uremic syndrome (HUS) in adults caused by a rare serotype of Shiga toxin-producing <i>Escherichia coli</i>, STEC O77g:H18. Epidemiological and traceability investigations linked the consumption of raw-milk cheese to these cases. The outbreak strain belonged to sequence type 69 (ST69) and harbored a Shiga toxin (stx) subtyp…

The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium <i>Bacillus aerius</i> acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soi…

African swine fever (ASF) is a highly fatal viral disease that poses a severe threat to the global swine industry. Developing a safe and effective vaccine remains an urgent and complex challenge. Lactobacillus plantarum (<i>L. plantarum</i>), recognized as a food-grade antigen delivery vehicle, has demonstrated great promise in vaccine development and application for various infectious diseases. …

Understanding the role of cave ecosystems in preventing disease invasion is essential, as caves where bats roost act as natural reservoirs of bacteria. This study focused on the cave walls where bats hibernate, examining the composition of bacterial communities during hibernation and identifying bacteria that inhibit the pathogen <i>Pseudogymnoascus destructans</i> (<i>Pd</i>), the pathogen respo…

Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium …

Well-characterized induction systems that offer tightly regulated, graded, and homogeneous control of gene expression are essential tools for basic and applied microbiology. Tetracycline-based induction systems are widely used non-toxic expression systems in bacteria; however, the generally recognized as safe (GRAS) and industrially relevant model organism <i>Bacillus subtilis</i> currently lacks…

Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of <i>Bacillus</i> volatile compounds as potential signaling molecule…

<i>Avibacterium paragallinarum</i> is the etiological agent of infectious coryza, a significant respiratory ailment associated with growth inhibition and diminished egg production in poultry. Given the increasing incidence of antibiotic resistance in bacteria, there is an imperative need for the development of genetically engineered vaccines; however, the lack of effective tools for genetic manip…

Bacterial biofilms dominate microbial life; however, their evolutionary genetics remain incompletely understood. Extensive replication of biofilm selection experiments by secondary school students can provide valuable insights into mechanisms of adaptation. Notably, mutations in a conserved phosphodiesterase, PFLU0185/<i>bmo</i>, dominate evolved populations without changing colony morphology. Ph…

The automatic, real-time classification of <i>Plasmopara viticola</i> spores presented in this study offers a significant advancement in disease risk forecasting. By integrating airborne spore detection, this approach reduces the likelihood of false-positive recommendations, applying fungicides when weather conditions are favorable, but disease risk is low and false negatives, when spores are pre…

Iron acquisition plays a crucial role in fungal pathogenicity. Nematode-trapping fungi (NTFs) serve as important biocontrol agents that can develop traps to capture and kill nematodes. Here, we characterize a non-ribosomal peptide synthase-independent siderophore biosynthetic gene, <i>DhSip1</i>, in NTF <i>Dactylellina haptotyla</i>, which modulates trap (adhesive knob) development and pathogenic…

<i>Vibrio vulnificus</i> is an opportunistic marine pathogen that causes severe wound-associated and systemic infections. Following entry into the host, the bacterium must rapidly adapt to host-associated stresses that differ substantially from those encountered in aquatic environments. However, the physiological functions supporting bacterial fitness during infection remain incompletely understo…

When the heterofermentative lactic acid bacterium <i>Weissella cibaria</i> JCM12495 was cultivated anaerobically in medium supplemented with 3-hydroxy-4-methoxycinnamic acid (ferulic acid), all the added ferulic acid was converted to 3-(4-hydroxy-3-methoxyphenyl)propionic acid (HMPA, dihydroferulic acid) via reduction of the propenoic acid side chain. Complete conversion to HMPA was achieved with…

Nanobubble technology has shown considerable promise in sustainable agriculture due to its ability to enhance seed germination, plant growth, and soil quality without leaving harmful residues. While benefits are often attributed to improved soil aeration and soil texture changes (e.g., permeability), nanobubbles may also influence soil microbiome, an essential driver of plant health and nutrient …

In this study, we isolated and sequenced the genomes of three lactic acid bacteria derived from Greek fermented table olives. The isolates, OLXI-1, OLXI-6, and OLXI-9, all belonged to the species <i>Lacticaseibacillus paracasei,</i> and a phylogenomic analysis revealed they clustered into three distinct clades. A pangenome analysis was performed with 220 public <i>Lc. paracasei</i> genomes and th…

Fossil fuels have negative impacts on the environment and will become limited in the next decades. Hence, alternative, sustainable energy sources need to be urgently established. Microbial fermentation of biomass for biofuel production presents a promising avenue. The gram-negative alpha-proteobacterium <i>Zymomonas mobilis</i> exhibits a superior capacity to convert sugars into ethanol, a clean,…

The genus <i>Rhodococcus</i> comprises numerous strains recognized for degradation of pollutants and production of secondary metabolites, including biosurfactants, lignin breakdown, and utilization of volatile organic compounds. Often, gene redundancies and the evolution of alternative pathways are attributed to such characteristics. <i>Rhodococcus opacus</i> 1CP, initially isolated as a chloroph…

Benzene is a widespread, persistent, and toxic pollutant that can accumulate in anoxic environments such as groundwater and sediments. Benzene can be metabolized in the absence of oxygen; however, despite decades of research, the biochemical mechanisms for benzene activation under anaerobic conditions remain unproven. This study provides strong genetic and proteomic evidence for a new suite of en…

Antimicrobial-resistant <i>Salmonella</i> poses a severe threat to food safety and public health, particularly through persistent biofilms on food-processing surfaces and animal-derived products. Traditional disinfection methods often fail against biofilms, while antibiotic overuse accelerates resistance. Bacteriophages offer a targeted, sustainable alternative, but their real-world efficacy in f…