Microbial biofilms: from ecology to molecular genetics

Tiny but mighty? Overview of a decade of research on nectar bacteria

An emerging focus of research at the intersection of botany, zoology, and microbiology is the study of floral nectar as a microbial habitat, referred to as the nectar microbiome, which can alter plant-pollinator interactions. Studies on these microbial communities have primarily focused on yeasts, and it was only about a decade ago that bacteria began to be studied as widespread inhabitants of floral nectar. This review aims to give an overview of the current knowledge on nectar bacteria, with emphasis on evolutionary origin, dispersal mode, effects on nectar chemistry and plant-animal interactions, community assembly, agricultural applications, and their use as model systems in ecological research. We further outline gaps in our understanding of the ecological significance of these microorganisms, their response to environmental changes, and the potential cascading effects.

A novel scaffold for biofilm formation by soil microbes using iron-cross-linked alginate gels

This study aimed to evaluate the suitability of alginate gels, specifically ferric-ion-cross-linked alginate (Fe-alginate) and calcium-ion-cross-linked alginate (Ca-alginate), as scaffolds for soil microbial attachment and biofilm formation in soil. Staining with crystal violet and observations with scanning electron microscopy showed that microorganisms formed biofilms on Fe-alginate surfaces in the soil. When the soil was incubated with Fe-alginate, microbial biomass, estimated by adenosine triphosphate content, increased not only in the Fe-alginate but also in the surrounding soil. The weight of Ca-alginate in the soil decreased with time owing to chemical dissolution. However, the weight of Fe-alginate in the soil did not decrease, likely because it was protected by the microbial biofilm that formed on its surface. These results demonstrate that the use of Fe-alginate, in contrast to Ca-alginate, as a scaffold may allow for more efficient use of soil microbial functions in agriculture and bioremediation.

Spatial population dynamics of bacterial colonies with social antibiotic resistance

Bacteria frequently inhabit surface-attached communities where rich "social" interactions can significantly alter their population-level behavior, including their response to antibiotics. Understanding these collective effects in spatially heterogeneous communities is an ongoing challenge. Here, we investigated the spatial organization that emerges from antibiotic exposure in initially randomly distributed communities containing antibiotic-resistant and -sensitive strains of Enterococcus faecalis, an opportunistic pathogen. We identified that a range of complex spatial structures emerged in the population homeland-the inoculated region that microbes inhabit prior to range expansion-which depended on initial colony composition and antibiotic concentration. We found that these arrangements were explained by cooperative interactions between resistant and sensitive subpopulations with a variable spatial scale, the result of dynamic zones of protection afforded to sensitive cells by growing populations of enzyme-producing resistant neighbors. Using a combination of experiments and mathematical models, we explored the complex spatiotemporal interaction dynamics that create these patterns, and predicted spatial arrangements of sensitive and resistant subpopulations under new conditions. We illustrated how spatial population dynamics in the homeland affect subsequent range expansion, both because they modulate the composition of the initial expanding front, and through long-range cooperation between the homeland and the expanding region. Finally, we showed that these spatial constraints resulted in populations whose size and composition differed markedly from matched populations in well-stirred (planktonic) cultures. These findings underscore the importance of spatial structure and cooperation, long-studied features in theoretical ecology, for determining the fate of bacterial communities under antibiotic exposure.

A novel Enterococcus faecalis bacteriophage Ef212: biological and genomic features

This study aimed to isolate and characterize biological and genomic features of a phage infecting Enterococcus faecalis. The phage was isolated from environmental water and temperature and pH stability, one-step growth curve, and multiplicity of infection (MOI) were determined. Whole genome sequencing (WGS) and structural and functional annotations were performed. Its antibiofilm activity was also evaluated. The optimal MOI was 0.01, the latency period was 5 min, and the burst size was 202 plaque forming unit (PFU). High phage survival rates were observed at between pH 4-10 and temperatures between 4-50 °C. WGS and Transmission electron microscopy (TEM) showed that it was an Efquatrovirus representing siphovirus morphotype respectively. It was named as Enterococcus phage Ef212 and has a linear 40,690 bp double-stranded DNA with 45.3% G + C content (GenBank accession number: OR052631). BACPHLIP tool demonstrated that Enterococcus phage Ef212 is a lytic phage (88%). A total of 80 open reading frames (ORFs) were found and there were no antibiotic resistance genes, pathogenicity, virulence genes, or tRNAs in the phage genome. It was diverged from the most similar phages (identity, 88.35%; coverage, 89%) by phylogenetic analysis. Phage Ef212 shared a large part of its genome (60/80) with several other phages, yet some unique parts were found in their genomes. Host range analysis showed that phage Ef212 showed lytic activity against vancomycin-resistant and vancomycin-susceptible E. faecalis clinical isolates. This novel phage Ef212 showed the ability to inhibit and reduce the biofilm formation by around 42% and 38%, respectively. The biological and genomic features indicate that having an effective antibacterial activity, phage Ef212 seemed a promising therapeutic and biocontrol agent.

Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy

Dispersal plays a crucial role in the development and ecology of biofilms. While extensive studies focused on elucidating the molecular mechanisms governing this process, few have characterized the associated temporal changes in composition and structure. Here, we employed solid-state nuclear magnetic resonance (NMR) techniques to achieve time-resolved characterization of Bacillus subtilis biofilms over a 5-day period. The mature biofilm, established within 48 h, undergoes significant degradation in following 72 h. The steepest decline of proteins precedes that of exopolysaccharides, likely reflecting their distinct spatial distribution. Exopolysaccharide sugar units display clustered temporal patterns, suggesting the presence of distinct polysaccharide types. A sharp rise in aliphatic carbon signals on day 4 probably corresponds to a surge in biosurfactant production. Different dynamic regimes respond differently to dispersal: the mobile domain exhibits increased rigidity, while the rigid domain remains stable. These findings provide novel insights and perspectives on the complex process of biofilm dispersal.

Carvacrol, a monoterpenoid, binds quorum sensing proteins (LasI and LasR) and swarming motility protein BswR of Pseudomonas aeruginosa, resulting in loss of pathogenicity: an in silico approach

The pathogenic Pseudomonas aeruginosa utilizes a quorum-sensing pathway for biofilm formation. The quorum-sensing proteins LasI and LasR of the Las system, alongside the swarming motility protein BswR, play a crucial role in the biofilm-mediated antibiotic resistance phenomenon. In this in silico study, LasI, LasR, and BswR were the prime targets for binding studies by promising drug candidates like linalool, ferutinin, citronellal, and carvacrol. These monoterpenoid compounds are carefully considered for this study due to their reported anti-microbial activity. Among all, carvacrol exhibited the highest binding energies with LasI (-5.932 kcal/mol), LasR (-7.469 kcal/mol), and BswR (-4.42 kcal/mol). Furthermore, the MMGBSA scores between carvacrol and LasI, LasR, and BswR individually are -33.14, -54.22, and -41.86 kcal/mol, which further corroborated the strong binding. During 100 ns of simulation, the ligand binds to the active sites of these proteins through the H-bonds at Ile107 of LasI, Tyr47 of LasR, and Leu57 of BswR. In addition, the root-mean-square deviation values of the ligand-protein complex are within the appropriate range of less than 5 Å. Absorption, Distribution, Metabolism, Excretion, and Toxicity analysis confirmed that carvacrol has the most negligible toxicity to mammalian cells. Hence, this finding is the first report to show that carvacrol can inhibit the Pseudomonas aeruginosa biofilms.

Prebiotic property of tamarind seed kernel on Bifidobacterium animalis growth and biofilm formation

This research explored the prebiotic potential of tamarind seed kernel powder (RTS), focusing on yield, nutritional composition, physicochemical properties using ATR-FTIR spectroscopy and colorimetric methods, effects on Bifidobacterium animalis in promoting the growth and biofilm formation compared to inulin using bacterial enumeration and crystal violet staining techniques, and the biofilm biomolecular composition characterization. The multi-nutrient composition RTS yielded 65.65 % (w/w), which significantly exhibited prebiotic activity in a dose-dependent manner with effective concentrations at 2.5 and 5 % RTS, stimulated B. animalis growth (rate 22 % • h-1) and enhanced biofilm formation (BFI = 256.71) exceeding the inulin. Moreover, ATR-FTIR spectroscopy and PCA analysis revealed the RTS-induced alteration of the biofilm's biomolecular composition, with a notable increase in amide A and a decrease in carboxylic hydroxyl groups. The study highlights RTS as a promising prebiotic agent with the potential for improving gut health, with further validation in the in vivo models being advisable.

Selective response of soil bacterial and fungal taxa to biodegradable polymers

Biodegradable mulching films offer an eco-friendly alternative to petroleum-based plastics in agriculture, but their effects on soil parameters are not well understood. A microcosm experiment (20 °C, 75% field capacity) investigated the impact of two doses (0.021% and 1% w/w) of a biodegradable polymer on soil chemical and microbiological properties over a year. The 1% dose significantly (p < 0.05) increased CO2 emissions, water-extractable organic C, and hydrolytic activity. A significant (p < 0.05) effect on microbial alpha- and beta-diversity was noted only during short- and medium-term incubations. In contrast, a taxon-related response was found for both bacterial and fungal taxa affecting the abundance of the genera Aquicella, Cellvibrio, Bacillus, Ramlibacter, and Saccharibacteria genera incertae sedis among bacteria, and Malassezia, Orbilia, and Rhodotorula among fungi (including both yeast and filamentous lifestyles). Microbial functions revealed a greater impact on fungal communities compared to bacterial ones. However, after one year of exposition, only a marginal effect on the abundance of both bacterial and fungal functional groups was found in the microcosms. A significantly higher concentration of tightly bound exopolysaccharides in the presence of 1% biodegradable polymer at the start of the experiment suggested their key role in microbial degradation of bioplastics via biofilm formation.

Human Herpesviruses, Bacteria, and Fungi in Gingivitis and Periodontitis Pediatric Subjects: A Systematic Review

Objectives: This systematic review assesses and compares the presence and relative abundance of periodontal pathogens, human herpesviruses (HHVs), and fungi in subgingival and/or saliva samples from pediatric subjects (≤18 years of age) with periodontally healthy status and with gingivitis and/or periodontitis. Methods: The study protocol was conducted under the PRISMA statement and registered on PROSPERO (CRD42024593007). Data from seven studies were descriptively analyzed and qualitatively assessed through the ROBINS-1 and JBI tools. Results: Pediatric subjects with clinically healthy periodontium exhibited a balanced microbiome, with early colonizers (Streptococcus species) supporting biofilm development and late colonizers like Fusobacterium nucleatum, Treponema denticola (82.35%), and Porphyromonas gingivalis (29.7%) present at low levels, suggesting subclinical dysbiosis. Viruses such as HSV-I (100%), CMV (17.8%), and EBV-I (22.09%) coexisted in a likely latent state, maintained by effective immune responses. In pediatric periodontitis, biofilms were more diverse and pathogenic, with increased prevalence of A. actinomycetemcomitans (56.09%), P. gingivalis (55.4%), and T. forsythia (35.9%). Generalized periodontitis showed higher CMV (36.36%) and EBV-I (36.24%) prevalence than gingivitis (HSV-I 18.75%). Coinfections were frequent in periodontitis, suggesting bacterial-viral synergy in exacerbating inflammation and tissue destruction. Fungi, although not studied, may also contribute under specific conditions. Conclusions: These findings highlight the role of microbial interactions in periodontal health and disease progression.

Garlic-Derived Quorum Sensing Inhibitors: A Novel Strategy Against Fungal Resistance

In recent years, the incidence of fungal infections has been rising annually, especially among immunocompromised populations, posing a significant challenge to public health. Although antifungal medications provide some relief, the escalating problem of resistance sharply curtails their effectiveness, presenting an urgent clinical dilemma that demands immediate attention. Research has shown that fungal resistance is closely related to quorum sensing (QS), and QS inhibitors (QSIs) are considered an effective solution to this issue. Garlic, as a natural QSI, has demonstrated significant effects in inhibiting fungal growth, preventing biofilm formation, enhancing immunity, and combating resistance. This study explores the potential of garlic in mitigating fungal drug resistance and identifies its key role in inhibiting the QS mechanism, these findings offer a new perspective for the treatment of fungal infections, especially in addressing the increasingly severe problem of resistance. However, the clinical application of garlic still faces several challenges, such as ensuring the standardization of active ingredient extraction, as well as issues of safety and stability. Future research should focus on the QS mechanism and promote interdisciplinary collaboration to develop more natural, effective, and safe QSI drugs like garlic, while actively conducting clinical trials to validate their efficacy and safety. Additionally, incorporating advanced technologies such as nanotechnology to enhance drug stability and targeting, provide a more comprehensive strategy for the treatment of fungal infections. Overall, Our study provides scientific evidence supporting the potential of garlic as a novel antifungal treatment and lays the groundwork for the development of future natural QSIs for therapeutic use. It offers new insights, particularly for the treatment of immunocompromised populations and drug-resistant fungal strains.

Role of bacterial quorum sensing in plant growth promotion

Quorum sensing (QS) also known as bacterial cell-cell communication or bacterial crosstalk is a phenomenon regulating various bacterial traits that can affect plant growth and defence. Similarities in the structure of root exudates and bacterial signalling molecules have tremendous implications governing the plant heath. The rhizosphere ecosystem being an excellent example of plant-microbe and microbe-microbe interactions harbours a variety of microorganisms exhibiting quorum sensing. Phytochemicals present in plant root exudates and QS signal molecules as well as volatile organic compounds (VOCs) produced by microorganisms work in coordination to establish intra- and inter-species communications. Interestingly, a number of plant growth promoting rhziobacterial (PGPR) activities like effective/enhanced root colonization, nutrient uptake, nodulation, nitrogen fixation, production of plant hormones, antimicrobial compounds and induction of plant defences can be attributed directly or indirectly to their quorum sensing and quenching abilities. Although not completely understood, root development, stress tolerance and defence against phytopathogens are some of the implications of such abilities which might prove beneficial for sustainable agriculture. Deciphering the mechanism of these interactions would be instrumental in improving crop health. Plant beneficial microorganisms employing QS and QS inhibition (QSI) strategies have been discussed in this review.

Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing

Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption. GroEL-SIP's main advantages are that (1) it can be performed with a sample-independent database and (2) sample complexity can be reduced by enriching GroEL proteins, increasing sensitivity and reducing instrument time. We applied GroEL-SIP to pure cultures, synthetic bicultures, and a human gut model using 2H-, 18O-, and 13C-labeled substrates. While 2H and 18O allowed assessing general activity, 13C enabled differentiation of substrate source and utilized metabolic pathways. GroEL-SIP offers fast and straightforward protein-SIP analyses of highly abundant families in mixed bacterial communities, but further work is needed to improve sensitivity, resolution, and database coverage.

Urinary tract infections and catheter-associated urinary tract infections caused by Pseudomonas aeruginosa

SUMMARYUrinary tract infection (UTI) is one of the most common infections in otherwise healthy individuals. UTI is also common in healthcare settings where patients often require urinary catheters to alleviate urinary retention. The placement of a urinary catheter often leads to catheter-associated urinary tract infection (CAUTI) caused by a broad range of opportunistic pathogens, commonly referred to as ESKAPE (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, and Enterobacter) pathogens. Our understanding of CAUTI is complicated by the differences in pathogens, in initial microbial load, changes that occur due to the duration of catheterization, and the relationship between infection (colonization) and disease symptoms. To advance our understanding of CAUTI, we reviewed UTI and CAUTI caused by Pseudomonas aeruginosa which is unique in that it is not commonly found associated with human microbiomes. For this reason, the ability of P. aeruginosa to cause UTI and CAUTI requires the introduction of the bacteria to the bladder from catheterization. Once in the host, the virulence factors used by P. aeruginosa in these infections remain an area of ongoing research. In this review, we will discuss studies that focus on P. aeruginosa UTI and CAUTI to better understand the infection dynamics and outcome in clinical settings, virulence factors associated with P. aeruginosa isolated from the urinary tract, and animal studies to test which bacterial factors are required for this infection. Understanding how P. aeruginosa can cause UTI and CAUTI can provide an understanding of how these infections initiate and progress and may provide possible strategies to limit these infections.

Growing bacterial colonies harness emergent genealogical demixing to regulate organizational entropy

Spatiotemporal organization of individuals within growing bacterial colonies is a key determinant of intraspecific interactions and colony-scale heterogeneities. The evolving cellular distribution, in relation to the genealogical lineage, is thus central to our understanding of bacterial fate across scales. Yet, how bacteria self-organize genealogically as a colony expands has remained unknown. Here, by developing a custom-built label-free algorithm, we track and study the genesis and evolution of emergent self-similar genealogical enclaves, whose dynamics are governed by biological activity. Topological defects at enclave boundaries tune finger-like morphologies of the active interfaces. The Shannon entropy of cell arrangements reduce over time; with faster-dividing cells possessing higher spatial affinity to genealogical relatives, at the cost of a well-mixed, entropically favorable state. Our coarse-grained lattice model demonstrates that genealogical enclaves emerge due to an interplay of division-mediated dispersal, stochasticity of division events, and cell-cell interactions. The study reports so-far hidden emergent self-organizing features arising due to entropic suppression, ultimately modulating intraspecific genealogical distances within bacterial colonies.

Essential Oils as Alternative Green Broad-Spectrum Biocides

Natural compounds from plants represent suitable options to replace synthetic biocides when employed against microorganisms in various applications. Essential oils (EOs) have attracted increased interest due to their biocompatible and rather innocuous nature, and complex biological activity (fungicide, biocide and anti-inflammatory, antioxidant, immunomodulatory action, etc.). EOs are complex mixtures of derived metabolites with high volatility obtained from various vegetal parts and employed to a great extent in different healthcare (natural cures, nutrition, phyto- and aromatherapy, spices) and cosmetics applications (perfumery, personal and beauty care), as well as in cleaning products, agriculture and pest control, food conservation and active packaging, or even for restauration and preservation of cultural artifacts. EOs can act in synergy with other compounds, organic and synthetic as well, when employed in different complex formulations. This review will illustrate the employment of EOs in different applications based on some of the most recent reports in a systematic and comprehensive, though not exhaustive, manner. Some critical assessments will also be included, as well as some perspectives in this regard.

Engineering bacterium for biofilm formation and L-lysine production in continuous fermentation

Microbial biofilms provide advantages in fermentation processes. However, Corynebacterium glutamicum (C. glutamicum) usually exhibits relatively poor biofilm formation compared to other industrial strains. To develop a biofilm-enhanced fermentation process for C. glutamicum, seven genes potentially related to biofilm formation in C. glutamicum were systematically investigated, which include ppk2B, glgC, virB11, cslA, NCgl2909, NCgl0350 and exeR. Deletion of the NCgl0350, NCgl2909 genes and heterologous expression of the cslA gene were found to increase biofilm amounts by 16.9%, 21.2% and 135%, respectively, compared to the wild-type strain. Meanwhile, the production of L-lysine by engineered strains was assessed in biofilm-based continuous fermentation. The most notable result was observed for the cslA-expressing strain, which produced an average of 26.1% higher L-lysine compared with that of wild-type strain in 6-L bioreactors. In conclusion, this study offers valuable insights into the biofilm formation in C. glutamicum and its application in continuous fermentation processes.

Aquatic macrophytes as a source of antifouling non-toxic against bacterial biofilms and golden mussel attachment: a possible role of quorum-sensing interference

Biofouling in freshwater and marine environments developed on man-made aquatic surfaces causes significant economic losses. Still, this problem is magnified when it comes to invasive species, such as the golden mussel. One of the alternatives to combat it is the use of antifouling solutions; however, the vast majority focus on solutions for the marine environment. In this same context, natural antifouling solutions from macrophytes have been reported as promising to combat estuarine biofouling; however, trials with freshwater organisms are still incipient. Thus, this study evaluated the performance of 25 macrophyte extracts in inhibiting the formation and/or eradication of bacterial biofilms, settlement of the golden mussel (Limnoperna fortunei), as well as its toxicity effect on three different non-target model organisms of three trophic levels. Among the 25 extracts, nine demonstrated ≥ 60% inhibition of biofilm formation, with only the extracts of Typha domingensis and Eichhornia crassipes having a biofilm inhibitory effect of ≥ 70% for bacterial isolates and ≥ 60% for multispecies biofilms. Planktonic growth had distinct responses, ranging from induction, inhibition, and no effect on growth. The T. domingensis extract showed quorum sensing inhibition (QSI) with a dose-dependent relationship, while the E. crassipes extract showed QSI only at a dilution of 1.2%. These same extracts prevented the golden mussel from attaching and showed safe concentrations of 35.35% for Pseudopediastrum boryanum and Daphnia magna and 70.71% for Pimephales promelas. This study highlights the biotechnological potential of macrophyte extracts as a sustainable and environmentally harmless alternative for the control of micro and macrofouling in freshwater environments.

Comparison of Taxonomic Resolutions of Various Typing Methods for Clostridium and Paraclostridium Species Isolated from Landfill Leachate

Anaerobic bacteria and methanogenic archaea at municipal landfill dumping sites play a vital role in the landfill ecology, waste degradation, global warming and climate change. Although landfill works as a cheap way of solid waste management, unmanaged landfill plays a significant role in spreading pollutants and pathogens in natural ecosystems. The genera Clostridium and Paraclostridium are important groups of anaerobic microbes from a public and environmental health perspective. In the present study, we have isolated different species of Clostridium and Paraclostridium from landfill leachate and performed a comparative analysis to understand their role in landfill ecology and public health. Our data indicate that the anoxic zone of landfills acts as a breeding ground for different species of Clostridium and Paraclostridium, including pathogenic species like C. sporogenes and C. argentinense and leachate, plays a crucial role in the spread of Clostridium in soil and water ecosystem and acts as one of the primary sources of a cause of infection in field workers. We also reported that VITEK and MALDI-TOF/MS are not ideal ways to identify Clostridium at the species level, and 16S rRNA gene sequencing should be the method of choice. In the current study, we also demonstrated that members of the genus Clostridium showed better growth response on Brain Heart Infusion (BHI) and Gifu Anaerobic Medium (GAM), and they can be one of the alternatives to existing media for cultivation and physiological studies of Clostridium.

Spatial population dynamics of bacterial colonies with social antibiotic resistance

Bacteria frequently inhabit surface-attached communities where rich "social" interactions can significantly alter their population-level behavior, including their response to antibiotics. Understanding these collective effects in spatially heterogeneous communities is an ongoing challenge. Here, we investigated the spatial organization that emerges from antibiotic exposure in initially randomly distributed communities containing antibiotic-resistant and -sensitive strains of E. faecalis , an opportunistic pathogen. We identified that a range of complex spatial structures emerged in the population homeland-the inoculated region that microbes inhabit prior to range expansion-, which depended on initial colony composition and antibiotic concentration. We found that these arrangements were explained by cooperative interactions between resistant and sensitive subpopulations with a variable spatial scale, the result of dynamic zones of protection afforded to sensitive cells by growing populations of enzyme-producing resistant neighbors. Using a combination of experiments and mathematical models, we explored the complex spatiotemporal interaction dynamics that create these patterns, and predicted spatial arrangements of sensitive and resistant subpopulations under new conditions. We illustrated how spatial population dynamics in the homeland affect subsequent range expansion, both because they modulate the composition of the initial expanding front, and through long-range cooperation between the homeland and the expanding region. Finally, we showed that these spatial constraints resulted in populations whose size and composition differed markedly from matched populations in well-stirred (planktonic) cultures. These findings underscore the importance of spatial structure and cooperation, long-studied features in theoretical ecology, for determining the fate of bacterial communities under antibiotic exposure.

Significance

Interactions between bacteria are common, particularly in the crowded surface-associated communities that occur anywhere from natural ecosystems to the human body to medical devices. Antibiotic resistance can be influenced by these "social" interactions, making it difficult to predict how spatial communities respond to antibiotic. Here, we show that complex spatial arrangements emerge when initially randomly distributed populations of antibiotic-resistant and -sensitive E. faecalis , a microbial pathogen, are exposed to antibiotic. Using mathematical models and experiments, we show how local competition and dynamic-range cross-protection drive pattern formation. As a result, these spatially structured populations respond differently to antibiotics than well-mixed communities. Our findings elucidate how "social" antibiotic resistance affects spatially structured bacterial communities, a step towards predicting and controlling resistance.

The mechanisms of environmental stress tolerance in Gluconobacter oxydans: progress and perspectives

Gluconobacter oxydans have been widely used in industrial compound production for their incomplete oxidation ability. However, they are often subjected to a wide variety of severe environmental stresses, such as extreme pH, high temperature, osmotic pressure, and organic solvents, which greatly repress microbial growth viability and productivity. As typical biocatalysis chassis cells with a high tolerance to external environmental stresses, it is extremely important to construct highly tolerant chassis cells and understand the tolerance mechanisms of G. oxydans and how different stresses interact with the cell: membranes, phospholipid bilayers, transporters, and chaperone proteins. In this review, we discuss and summarize the mechanisms of environmental stress tolerance in G. oxydans, and the promising strategies that can be used to further construct tolerant strains are prospected.

Differential expression of the yfj operon in a Bacillus subtilis biofilm

Type VII protein secretion systems play an important role in the survival and virulence of pathogens and in the competition among some microbes. Potential polymorphic toxin substrates of the type VII secretion system (T7SS) in Bacillus subtilis are important for competition in the context of biofilm communities. Within a biofilm, there is significant physiological heterogeneity as cells within the population take on differential cell fates. Which cells express and deploy the various T7SS substrates is still unknown. To identify which cells express at least one of the T7SS substrates, we investigated the yfj operon. The yfjABCDEF operon encodes at least one predicted T7SS substrate. Starting with an in silico analysis of the yfj operon promoter region, we identified potential regulatory sequences. Using a yfj promoter-reporter fusion, we then identified several regulators that impact expression of the operon, including a regulator of biofilm formation, DegU. In a degU deletion mutant, yfj expression is completely abolished. Mutation of predicted DegU binding sites also results in a significant reduction in yfj reporter levels. Further analysis of yfj regulation reveals that deletion of spo0A has the opposite effect of the degU deletion. Following the yfj reporter by microscopy of cells harvested from biofilms, we find that the yfj operon is expressed specifically in the subset of cells undergoing sporulation. Together, our results define cells entering sporulation as the subpopulation most likely to express products of the yfj operon in B. subtilis.IMPORTANCEDifferential expression of genes in a bacterial community allows for the division of labor among cells in the community. The toxin substrates of the type VII secretions system (T7SS) are known to be active in Bacillus subtilis biofilm communities. This work describes the expression of one of the T7SS-associated operons, the yfj operon, which encodes the YFJ toxin, in the sporulating subpopulation within a biofilm. The evidence that the YFJ toxin may be deployed specifically in cells at the early stages of sporulation provides a potential role for deployment of T7SS in community-associated activities, such as cannibalism.

Analysis of nasopharyngeal microbiota revealing microbial disturbance associated with ovine respiratory complex

The ovine respiratory complex (ORC) is a complex respiratory disease process in ovine causing a significant health concern with substantial morbidity and mortality. It poses a significant threat of impacting animal health, leading to severe health consequences and considerable economic loss. Research on the upper respiratory tract (URT) microbiota is critical for offering insights into pathogenesis, prevention, and treatment strategies of ORC. The goal of this study is to compare the nasopharyngeal microbiota of clinically healthy Hu sheep (Group H) and sheep with ORC (Group P). The 16S rDNA gene amplicon high-throughput sequencing technique was applied to identify the microbial composition in the nasopharyngeal samples. The results showed that there was no significant difference in the microbiota diversity and richness between ORC and healthy sheep. However, there were significant differences in microbial composition, such as the relative abundance of Enterobacteriaceae, Moraxellaceae, Pasteurellaceae, and Streptococcaceae between the two groups. The abundance of aerobes in sheep with ORC increased significantly, while the abundance of anaerobes and facultative anaerobes decreased significantly. There were also differences in the taxa phenotypes associated with biofilm forming, mobile element-containing, oxidative stress-tolerance, and potential pathogens between the two groups. Our study showed the nasopharyngeal microbiota composition and its associated shifts between clinically healthy sheep and ORC sheep in China. These findings suggest that shifts in the nasopharyngeal microbiota could be a contributing factor to the pathogenesis of ORC, offering a potential avenue for the development of targeted interventions and treatments for this condition in sheep.

Type IV pili are involved in phenotypes associated with Clostridioides difficile pathogenesis

Clostridioides difficile is a Gram-positive, spore-forming, rod-shaped, obligate anaerobe that is the leading cause of antibiotic-associated diarrhea. Type IV pili (T4P) are elongated appendages on the surface of C. difficile that are polymerized from many pilin proteins. T4P play an important role in C. difficile adherence and particularly in its persistence in the host intestine. Recent studies have shown that T4P promote C. difficile aggregation, surface motility, and biofilm formation, which may enhance its pathogenicity. Additionally, the second messenger cyclic diguanylate increases pilA1 transcript abundance, indirectly promoting T4P-mediated aggregation, surface motility, and biofilm formation of C. difficile. This review summarizes recent advances in C. difficile T4P research and the physiological activities of T4P in the context of C. difficile pathogenesis.

Alterations in structural components of extracellular polymeric substance of epilithic bacteria Brevundimonas faecalis BC1 growing on monumental rock under thermal stress

In this study, a comparison of biofilm formation, extracellular polymeric substances (EPS) production, protein and polysaccharides estimation, and protein profiling through SDS-PAGE, FTIR, GC-MS, ESI-MS, SEM, and AFM analysis were done for EPS from epilithic bacteria Brevundimonas faecalis BC1 obtained from monumental rock under normal room temperature and heat stressed condition. Heat stress (60 ± 2 °C) that simulates hot monumental rock surfaces during the summer season caused  bacteria BC1 to produce more EPS (8.56 g/L), biofilm, protein and polysaccharides, extra SDS-PAGE protein bands of different molecular weight than their control counterpart. FTIR and GC-MS analysis showed extra polysaccharide formation in the EPS under heat stress and ESI-MS analysis clearly showed differences in structural components of EPS from two different sources. Consistently, SEM and AFM showed more branching structural components with dentate spikes in the EPS obtained from a heat-stressed source than from its counterpart, suggesting their protective role toward heat stress and adhesive potential for biofilm.

Mass transfer in heterogeneous biofilms: Key issues in biofilm reactors and AI-driven performance prediction

Biofilm reactors, known for utilizing biofilm formation for cell immobilization, offer enhanced biomass concentration and operational stability over traditional planktonic systems. However, the dense nature of biofilms poses challenges for substrate accessibility to cells and the efficient release of products, making mass transfer efficiency a critical issue in these systems. Recent advancements have unveiled the intricate, heterogeneous architecture of biofilms, contradicting the earlier view of them as uniform, porous structures with consistent mass transfer properties. In this review, we explore six biofilm reactor configurations and their potential combinations, emphasizing how the spatial arrangement of biofilms within reactors influences mass transfer efficiency and overall reactor performance. Furthermore, we discuss how to apply artificial intelligence in processing biofilm measurement data and predicting reactor performance. This review highlights the role of biofilm reactors in environmental and energy sectors, paving the way for future innovations in biofilm-based technologies and their broader applications.

Unveiling the impact of antibiotic stress on biofilm formation and expression of toxin-antitoxin system genes in Clostridium difficile clinical isolates

OBJECTIVES

The study investigates how antibiotics affect biofilm formation and toxin gene expression in Clostridium difficile, which is essential for its survival and persistence.

METHODS

The study confirmed 25 strains of C. difficile and assessed biofilm formation. The MIC of metronidazole and vancomycin was determined through agar dilution, and the impact of sub-MIC levels on biofilm formation and eradication was investigated. Additionally, Real-time PCR was used to analyze the expression levels of target genes related to antibiotic treatment.

RESULTS

We found that certain genes, such as the ImmA/IrrE system, were associated with increased biofilm formation in isolates. Sub-MIC antibiotic levels influenced gene expression related to biofilm activities, particularly emphasizing the importance of toxin-antitoxin systems. The results suggest that antibiotics at sub-MIC levels may play a signaling role in promoting biofilm formation and gene expression in C. difficile.

CONCLUSION

Our study suggests that toxin and antitoxin genes may impact C. difficile biofilm formation, while antibiotics could signal biofilm strengthening and gene expression increase.

The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a mechanism independent of hfiA transcription

During its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the transition from the motile to the sessile lifestyle. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and promotes the motile lifestyle: HmrA (holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that form a putative phosphorelay pathway with HmrA. We postulate that the Hmr pathway acts as a rheostat to control the proportion of cells harboring a flagellum or a holdfast in the population. Further genetic analysis suggests that the Hmr pathway impacts c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Our results also indicate that the Hmr pathway is involved in the regulation of motile to sessile lifestyle transition as a function of various environmental factors: biofilm formation is repressed when excess copper is present and derepressed under non-optimal temperatures. Finally, we provide evidence that the Hmr pathway regulates motility and adhesion without modulating the transcription of the holdfast synthesis regulator HfiA.

IMPORTANCE

Complex communities attached to a surface, or biofilms, represent the major lifestyle of bacteria in the environment. Such a sessile state enables the inhabitants to be more resistant to adverse environmental conditions. Thus, having a deeper understanding of the underlying mechanisms that regulate the transition between the motile and the sessile states could help design strategies to improve biofilms when they are beneficial or impede them when they are detrimental. For Caulobacter crescentus motile cells, the transition to the sessile lifestyle is irreversible, and this decision is regulated at several levels. In this work, we describe a putative phosphorelay that promotes the motile lifestyle and inhibits biofilm formation, providing new insights into the control of adhesin production that leads to the formation of biofilms.

Mixed species biofilm: Structure, challenge and its intricate involvement in hospital associated infections

Hospital associated infections or healthcare associated infections (HAIs) are a major threat to healthcare and medical management, mostly because of their recalcitrant nature. The primary cause of these HAIs is bacterial associations, especially the interspecies interactions. In interspecies interactions, more than one species co-exists in a common platform of extracellular polymeric substances (EPS), establishing a strong interspecies crosstalk and thereby lead to the formation of mixed species biofilms. In this process, the internal microenvironment and the surrounding EPS matrix of the biofilms ensure the protection of the microorganisms and allow them to survive under antagonistic conditions. The communications between the biofilm members as well as the interactions between the bacterial cells and the matrix polymers, also aid in the rigidity of the biofilm structure and allow the microorganisms to evade both the host immune response and a wide range of anti-microbials. Therefore, to design a treatment protocol for HAIs is difficult and it has become a growing point of concern. This review therefore first aims to discuss the role of microenvironment, molecular structure, cell-cell communication, and metabolism of mixed species biofilms in manifestation of HAIs. In addition, we discuss the electrochemical properties of mixed-species biofilms and their mechanism in developing drug resistance. Then we focus on the most dreaded bacterial HAI including oral and gut multi-species infections, catheter-associated urinary tract infections, surgical site infections, and ventilator-associated pneumonia. Further, we highlight the challenges to eradication of the mixed species biofilms and the current and prospective future strategies for the treatment of mixed species-associated HAI. Together, the review presents a comprehensive understanding of mixed species biofilm-mediated infections in clinical scenario, and summarizes the current challenge and prospect of therapeutic strategies against HAI.

The role of aroA and ppk1 in Aeromonas veronii pathogenicity and the efficacy evaluation of mutant strain AV-ΔaroA/ppk1 as a live attenuated vaccine

Aeromonas veronii is an opportunistic pathogen that poses great threat to aquaculture and human health, so there is an urgent need for green and efficient methods to deal with its infection. In this study, single and double gene deletion strains (AV-ΔaroA, AV-Δppk1 and AV-ΔaroA/ppk1) that can be stably inherited were constructed. Pathogenicity test showed that the toxicity of AV-ΔaroA and AV-ΔaroA/ppk1 was significantly lower compared to wild-type A. veronii. Biological characterization analysis revealed that the decrease in pathogenicity might be due to the declined growth, motility, biofilm formation abilities and the expression of virulence-related genes in mutants. Subsequently, we evaluated the efficacy of AV-ΔaroA/ppk1 as a live attenuated vaccine (LAV). Safety assessment experiments showed that AV-ΔaroA/ppk1 injected at a concentration of 3 × 107 CFU/mL was safe for C. carassius. The relative percentage survival of AV-ΔaroA/ppk1 was 67.85 %, significantly higher than that of the inactivated A. veronii, which had an RPS of 54.84 %. This improved protective effect was mainly attributed to the increased levels of A. veronii specific IgM antibody, enhanced alkaline phosphatase, lysozyme and superoxide dismutase activities, as well as higher expression levels of several immune related genes. Together, these findings deepen our understanding of the functional roles of aroA and ppk1 in A. veronii pathogenicity, provide a good candidate of LAV for A. veronii.

The biophysical basis of bacterial colony growth

Bacteria often attach to surfaces and grow densely-packed communities called biofilms. As biofilms grow, they expand across the surface, increasing their surface area and access to nutrients. Thus, the overall growth rate of a biofilm is directly dependent on its "range expansion" rate. One factor that limits the range expansion rate is vertical growth; at the biofilm edge there is a direct trade-off between horizontal and vertical growth-the more a biofilm grows up, the less it can grow out. Thus, the balance of horizontal and vertical growth impacts the range expansion rate and, crucially, the overall biofilm growth rate. However, the biophysical connection between horizontal and vertical growth remains poorly understood, due in large part to difficulty in resolving biofilm shape with sufficient spatial and temporal resolution from small length scales to macroscopic sizes. Here, we experimentally show that the horizontal expansion rate of bacterial colonies is strongly coupled to vertical expansion via the contact angle at the biofilm edge. Using white light interferometry, we measure the three-dimensional surface morphology of growing colonies, and find that small colonies are surprisingly well-described as spherical caps. At later times, nutrient diffusion and uptake prevent the tall colony center from growing exponentially. However, the colony edge always has a region short enough to grow exponentially; the size and shape of this region, characterized by its contact angle, along with cellular doubling time, determines the range expansion rate. We found that the geometry of the exponentially growing biofilm edge is well-described as a spherical-cap-napkin-ring, i.e., a spherical cap with a cylindrical hole in its center (where the biofilm is too tall to grow exponentially). We derive an exact expression for the spherical-cap-napkin-ring-based range expansion rate; further, to first order, the expansion rate only depends on the colony contact angle, the thickness of the exponentially growing region, and the cellular doubling time. We experimentally validate both of these expressions. In line with our theoretical predictions, we find that biofilms with long cellular doubling times and small contact angles do in fact grow faster than biofilms with short cellular doubling times and large contact angles. Accordingly, sensitivity analysis shows that biofilm growth rates are more sensitive to their contact angles than to their cellular growth rates. Finally, we show that a simple biophysical model connecting vertical and horizontal growth dynamics can reproduce the above phenomena, suggesting that the spherical cap and spherical cap napkin ring shapes emerge due to the biophysical consequences of diffusion-limited growth. Thus, to understand the fitness of a growing biofilm, one must account for its shape, not just its cellular doubling time.

Origin of biogeographically distinct ecotypes during laboratory evolution

Resource partitioning is central to the incredible productivity of microbial communities, including gigatons in annual methane emissions through syntrophic interactions. Previous work revealed how a sulfate reducer (Desulfovibrio vulgaris, Dv) and a methanogen (Methanococcus maripaludis, Mm) underwent evolutionary diversification in a planktonic context, improving stability, cooperativity, and productivity within 300-1000 generations. Here, we show that mutations in just 15 Dv and 7 Mm genes within a minimal assemblage of this evolved community gave rise to co-existing ecotypes that were spatially enriched within a few days of culturing in a fluidized bed reactor. The spatially segregated communities partitioned resources in the simulated subsurface environment, with greater lactate utilization by attached Dv but partial utilization of resulting H2 by low affinity hydrogenases of Mm in the same phase. The unutilized H2 was scavenged by high affinity hydrogenases of planktonic Mm, producing copious amounts of methane. Our findings show how a few mutations can drive resource partitioning amongst niche-differentiated ecotypes, whose interplay synergistically improves productivity of the entire mutualistic community.

Peptide-based strategies for overcoming biofilm-associated infections: a comprehensive review

Biofilms represent resilient microbial communities responsible for inducing chronic infections in human subjects. Given the escalating challenges associated with antibiotic therapy failures in clinical infections linked to biofilm formation, a peptide-based approach emerges as a promising alternative to effectively combat these notoriously resistant biofilms. Contrary to conventional antimicrobial peptides, which predominantly target cellular membranes, antibiofilm peptides necessitate a multifaceted approach, addressing various "biofilm-specific factors." These factors encompass Extracellular Polymeric Substance (EPS) degradation, membrane targeting, cell signaling, and regulatory mechanisms. Recent research endeavors have been directed toward assessing the potential of peptides as potent antibiofilm agents. However, to translate these peptides into viable clinical applications, several critical considerations must be meticulously evaluated during the peptide design process. This review serves to furnish an all-encompassing summary of the pivotal factors and parameters that necessitate contemplation for the successful development of an efficacious antibiofilm peptide.

Carbon Source and Substrate Surface Affect Biofilm Formation by the Plant-Associated Bacterium Pseudomonas donghuensis P482

The ability of bacteria to colonize diverse environmental niches is often linked to their competence in biofilm formation. It depends on the individual characteristics of a strain, the nature of the colonized surface (abiotic or biotic), or the availability of certain nutrients. Pseudomonas donghuensis P482 efficiently colonizes the rhizosphere of various plant hosts, but a connection between plant tissue colonization and the biofilm formation ability of this strain has not yet been established. We demonstrate here that the potential of P482 to form biofilms on abiotic surfaces and the structural characteristics of the biofilm are influenced by the carbon source available to the bacterium, with glycerol promoting the process. Also, the type of substratum, polystyrene or glass, impacts the ability of P482 to attach to the surface. Moreover, P482 mutants in genes associated with motility or chemotaxis, the synthesis of polysaccharides, and encoding proteases or regulatory factors, which affect biofilm formation on glass, were fully capable of colonizing the root tissue of both tomato and maize hosts. Investigating the role of cellular factors in biofilm formation using these plant-associated bacteria shows that the ability of bacteria to form biofilm on abiotic surfaces does not necessarily mirror its ability to colonize plant tissues. Our research provides a broader perspective on the adaptation of these bacteria to various environments.

Impact of urban pollution on freshwater biofilms: Oxidative stress, photosynthesis and lipid responses

Urban ecosystems are subjected to multiple anthropogenic stresses, which impact aquatic communities. Artificial light at night (ALAN) for instance can significantly alter the composition of algal communities as well as the photosynthetic cycles of autotrophic organisms, possibly leading to cellular oxidative stress. The combined effects of ALAN and chemical contamination could increase oxidative impacts in aquatic primary producers, although such combined effects remain insufficiently explored. To address this knowledge gap, a one-month experimental approach was implemented under controlled conditions to elucidate effects of ALAN and dodecylbenzyldimethylammonium chloride (DDBAC) on aquatic biofilms. DDBAC is a biocide commonly used in virucidal products, and is found in urban aquatic ecosystems. The bioaccumulation of DDBAC in biofilms exposed or not to ALAN was analyzed. The responses of taxonomic composition, photosynthetic activity, and fatty acid composition of biofilms were examined. The results indicate that ALAN negatively affects photosynthetic yield and chlorophyll production of biofilms. Additionally, exposure to DDBAC at environmental concentrations induces lipid peroxidation, with an increase of oxylipins. This experimental study provides first insights on the consequences of ALAN and DDBAC for aquatic ecosystems. It also opens avenues for the identification of new biomarkers that could be used to monitor urban pollution impacts in natural environments.

The role and mechanism of Bacillus megaterium strain A14 in inhibiting the cadmium uptake by peanut plants in acidic red soil

AIMS

This study explores the potential of cadmium (Cd)-resistant bacteria, specifically Bacillus megaterium A14, to decrease Cd accumulation in peanuts, a crop susceptible to metal uptake from contaminated soils, by understanding the bacterium's impact on plant Cd absorption mechanisms.

METHODS AND RESULTS

Through pot experiments, we observed that A14 inoculation significantly increased peanut biomass under Cd stress conditions, primarily by immobilizing the metal and reducing its bioavailability. The bacterium effectively changed the distribution of Cd, with a notable 46.53% reduction in the exchangeable fraction, which in turn limited the expression of genes related to Cd transport in peanuts. Additionally, A14 enhanced the plant's antioxidant response, improving its tolerance to stress. Microbial analysis through 16S sequencing demonstrated that A14 inoculation altered the peanut rhizosphere, particularly by increasing populations of Firmicutes and Proteobacteria, which play crucial roles in soil remediation from heavy metals.

CONCLUSION

The A14 strain effectively counters Cd toxicity in peanuts, promoting growth through soil Cd sequestration, root barrier biofilm formation, antioxidant system enhancement, suppression of Cd transport genes, and facilitation of Cd-remediating microorganisms.

Nanomaterial in controlling biofilms and virulence of microbial pathogens

The escalating threat of antimicrobial resistance (AMR) poses a grave concern to global public health, exacerbated by the alarming shortage of effective antibiotics in the pipeline. Biofilms, intricate populations of bacteria encased in self-produced matrices, pose a significant challenge to treatment, as they enhance resistance to antibiotics and contribute to the persistence of organisms. Amid these challenges, nanotechnology emerges as a promising domain in the fight against biofilms. Nanomaterials, with their unique properties at the nanoscale, offer innovative antibacterial modalities not present in traditional defensive mechanisms. This comprehensive review focuses on the potential of nanotechnology in combating biofilms, focusing on green-synthesized nanoparticles and their associated anti-biofilm potential. The review encompasses various aspects of nanoparticle-mediated biofilm inhibition, including mechanisms of action. The diverse mechanisms of action of green-synthesized nanoparticles offer valuable insights into their potential applications in addressing AMR and improving treatment outcomes, highlighting novel strategies in the ongoing battle against infectious diseases.

Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems

Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g-1; Protein mean 65 μg g-1) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g-1; Protein mean 26 μg g-1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.

Pseudomonas aeruginosa Bacteriophages and Their Clinical Applications

Antimicrobial resistance poses a serious risk to contemporary healthcare since it reduces the number of bacterial illnesses that may be treated with antibiotics, particularly for patients with long-term conditions like cystic fibrosis (CF). People with a genetic predisposition to CF often have recurrent bacterial infections in their lungs due to a buildup of sticky mucus, necessitating long-term antibiotic treatment. Pseudomonas aeruginosa infections are a major cause of CF lung illness, and P. aeruginosa airway isolates are frequently resistant to many antibiotics. Bacteriophages (also known as phages), viruses that infect bacteria, are a viable substitute for antimicrobials to treat P. aeruginosa infections in individuals with CF. Here, we reviewed the utilization of P. aeruginosa bacteriophages both in vivo and in vitro, as well as in the treatment of illnesses and diseases, and the outcomes of the latter.

Long-Chain Alkylthio Cyclodextrin Derivatives for Modulation of Quorum-Sensing-Based Bioluminescence in Aliivibrio fischeri Model System

Quorum sensing (QS) allows bacteria to coordinate their activities by producing and detecting low-molecular-weight signal molecules based on population density, thereby controlling the infectivity of bacteria through various virulence factors. Quorum-sensing inhibition is a promising approach to tackle bacterial communication. Cyclodextrins (CDs) are a class of cyclic oligosaccharides that reversibly encapsulate the acyl chain of the signal molecules, thereby preventing their binding to receptors and interrupting bacterial communication. This results in the inhibition of the expression of various properties, including different virulence factors. To examine the potential quorum-quenching (QQ) ability of newly prepared cyclodextrin derivatives, we conducted short-term tests using Aliivibrio fischeri, a heterotrophic marine bacterium capable of bioluminescence controlled by quorum sensing. α- and β-cyclodextrins monosubstituted with alkylthio moieties and further derivatized with quaternary ammonium groups were used as the test agents. The effect of these cyclodextrins on the quorum-sensing system of A. fischeri was investigated by adding them to an exponential growth phase of the culture and then measuring bioluminescence intensity, population growth, and cell viability. Our results demonstrate that the tested cyclodextrins have an inhibitory effect on the quorum-sensing system of A. fischeri. The inhibitory effect varies based on the length of the alkyl chain, with alkylthio substitution enhancing it and the presence of quaternary ammonium groups decreasing it. Our findings suggest that cyclodextrins can be a promising therapeutic agent for the treatment of bacterial infections.

A machine learning-based strategy to elucidate the identification of antibiotic resistance in bacteria

Microorganisms, crucial for environmental equilibrium, could be destructive, resulting in detrimental pathophysiology to the human host. Moreover, with the emergence of antibiotic resistance (ABR), the microbial communities pose the century's largest public health challenges in terms of effective treatment strategies. Furthermore, given the large diversity and number of known bacterial strains, describing treatment choices for infected patients using experimental methodologies is time-consuming. An alternative technique, gaining popularity as sequencing prices fall and technology advances, is to use bacterial genotype rather than phenotype to determine ABR. Complementing machine learning into clinical practice provides a data-driven platform for categorization and interpretation of bacterial datasets. In the present study, k-mers were generated from nucleotide sequences of pathogenic bacteria resistant to antibiotics. Subsequently, they were clustered into groups of bacteria sharing similar genomic features using the Affinity propagation algorithm with a Silhouette coefficient of 0.82. Thereafter, a prediction model based on Random Forest algorithm was developed to explore the prediction capability of the k-mers. It yielded an overall specificity of 0.99 and a sensitivity of 0.98. Additionally, the genes and ABR drivers related to the k-mers were identified to explore their biological relevance. Furthermore, a multilayer perceptron model with a hamming loss of 0.05 was built to classify the bacterial strains into resistant and non-resistant strains against various antibiotics. Segregating pathogenic bacteria based on genomic similarities could be a valuable approach for assessing the severity of diseases caused by new bacterial strains. Utilization of this strategy could aid in enhancing our understanding of ABR patterns, paving the way for more informed and effective treatment options.

Isolation and Characterization of Plant-Growth-Promoting, Drought-Tolerant Rhizobacteria for Improved Maize Productivity

Drought is one of the main abiotic factors affecting global agricultural productivity. However, the application of bioinocula containing plant-growth-promoting rhizobacteria (PGPR) has been seen as a potential environmentally friendly technology for increasing plants' resistance to water stress. In this study, rhizobacteria strains were isolated from maize (Zea mays L.) and subjected to drought tolerance tests at varying concentrations using polyethylene glycol (PEG)-8000 and screened for plant-growth-promoting activities. From this study, 11 bacterial isolates were characterized and identified molecularly, which include Bacillus licheniformis A5-1, Aeromonas caviae A1-2, A. veronii C7_8, B. cereus B8-3, P. endophytica A10-11, B. halotolerans A9-10, B. licheniformis B9-5, B. simplex B15-6, Priestia flexa B12-4, Priestia flexa C6-7, and Priestia aryabhattai C1-9. All isolates were positive for indole-3-acetic acid (IAA), siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, ammonia production, nitrogen fixation, and phosphate solubilization, but negative for hydrogen cyanide production. Aeromonas strains A1-2 and C7_8, showing the highest drought tolerance of 0.71 and 0.77, respectively, were selected for bioinoculation, singularly and combined. An increase in the above- and below-ground biomass of the maize plants at 100, 50, and 25% water-holding capacity (WHC) was recorded. Bacterial inoculants, which showed an increase in the aerial biomass of plants subjected to moderate water deficiency by up to 89%, suggested that they can be suitable candidates to enhance drought tolerance and nutrient acquisition and mitigate the impacts of water stress on plants.

The role of shear rates on amyloid formation from biofilm peptide phenol-soluble modulins

Biofilms, microbial communities enclosed in the self-produced extracellular matrix, have a significant impact on human health, environment, and industry. The pathogen Staphylococcus aureus (S. aureus) is recognized as one of the most frequent causes of biofilm-related infections. Phenol-soluble modulins (PSMs) serve as a crucial component, fortifying S. aureus biofilm matrix through self-assembly into amyloid fibrils, which enhances S. aureus colonization and resistance to antibiotics. However, the role of shear rate, one of the critical physiological factors within blood vessels, on the formation of PSM amyloids remains poorly understood. In this work, using a combination of thioflavin T fluorescence kinetic studies, circular dichroism spectrometry, and electron microscopy, we demonstrated that shear rates ranging from 150 to 300 s-1 accelerate fibrillation of PSMα1, α3, and α4 into amyloids, resulting in elongated amyloid structures. Furthermore, PSMα1, α3, and α4 predominantly self-assembled into amyloid fibers with a cross-α structure under shear conditions, deviating from the typical β-sheet configuration of PSM amyloids. These findings imply the role of shear rates within the bloodstream on enhancing PSM self-assembly that is associated with S. aureus biofilm formation.

Plant-derived bioactive compounds for the inhibition of biofilm formation: a comprehensive review

Biofilm formation is a widespread phenomenon that impacts different fields, including the food industry, agriculture, health care and the environment. Accordingly, there is a serious need for new methods of managing the problem of biofilm formation. Natural products have historically been a rich source of varied compounds with a wide variety of biological functions, including antibiofilm agents. In this review, we critically highlight and discuss the recent progress in understanding the antibiofilm effects of several bioactive compounds isolated from different plants, and in elucidating the underlying mechanisms of action and the factors influencing their adhesion. The literature shows that bioactive compounds have promising antibiofilm potential against both Gram-negative and Gram-positive bacterial and fungal strains, via several mechanisms of action, such as suppressing the formation of the polymer matrix, limiting O2 consumption, inhibiting microbial DNA replication, decreasing hydrophobicity of cell surfaces and blocking the quorum sensing network. This antibiofilm activity is influenced by several environmental factors, such as nutritional cues, pH values, O2 availability and temperature. This review demonstrates that several bioactive compounds could mitigate the problem of biofilm production. However, toxicological assessment and pharmacokinetic investigations of these molecules are strongly required to validate their safety.

Effect of surface roughness and biofilm formation on the color properties of resin-infiltrated ceramic and lithium disilicate glass-ceramic CAD-CAM materials

STATEMENT OF PROBLEM

Computer-aided design and computer-aided manufacturing (CAD-CAM) materials have become popular for dental restorations; however, which materials should be preferred in terms of surface properties after biofilm formation is unclear.

PURPOSE

The purpose of this in vitro study was to investigate the effect of biofilm formation on the discoloration properties of resin-infiltrated ceramic and glass-ceramic CAD-CAM materials and human teeth and to examine the effect of the brushing procedure on color change.

MATERIAL AND METHODS

One hundred and six 2-mm-thick specimens were prepared from IPS e.max CAD and Cerasmart, and a total of 53 intact human teeth were used. Five specimens from each group were used to measure the amount of live biomass in the biofilm. The remaining 48 specimens in each group were divided into 4 subgroups: kept in distilled water without the formation of dental biofilm (DW), kept in tea without the formation of dental biofilm (T), kept in distilled water after the formation of dental biofilm (DWB), and kept in tea after the formation of dental biofilm (TB) (n=12). After finishing and polishing the materials, initial color measurements were made using a spectrophotometer, and surface roughness measurements were made using noncontact profilometer. After creating a biofilm layer in DWB and TB, all specimens were kept in their solutions at 37 °C for 24 hours, and the color measurements were repeated. After the biofilm layer had been removed by brushing, a third color measurement was made. The data were statistically analyzed with one-way analysis of variance (ANOVA) and two-way ANOVA (α=.05).

RESULTS

The lowest roughness value was observed in Cerasmart. Tooth-IPS e.max CAD gave similar results. The Cerasmart material had the most viable biomass, whereas the IPS e.max CAD material had the least. TB had the highest ΔE1 value for all materials and DW had the lowest (P<.05). The brushing procedure caused the materials to return to their initial colors or reduce the color change in most groups.

CONCLUSIONS

The presence of biofilm on CAD-CAM materials immersed in distilled water caused an unacceptable degree of discoloration (ΔE>1.8), and immersion in tea led to greater color change. The adhesion of biofilm to restorative dental materials plays an important role in the coloring of these dental materials.

Antifungal drug resistance in Candida: a special emphasis on amphotericin B

Invasive fungal infections in humans caused by several Candida species, increased considerably in immunocompromised or critically ill patients, resulting in substantial morbidity and mortality. Candida albicans is the most prevalent species, although the frequency of these organisms varies greatly according to geographic region. Infections with C. albicans and non-albicans Candida species have become more common, especially in the past 20 years, as a result of aging, immunosuppressive medication use, endocrine disorders, malnourishment, extended use of medical equipment, and an increase in immunogenic diseases. Despite C. albicans being the species most frequently associated with human infections, C. glabrata, C. parapsilosis, C. tropicalis, and C. krusei also have been identified. Several antifungal drugs with different modes of action are approved for use in clinical settings to treat fungal infections. However, due to the common eukaryotic structure of humans and fungi, only a limited number of antifungal drugs are available for therapeutic use. Furthermore, drug resistance in Candida species has emerged as a result of the growing use of currently available antifungal drugs against fungal infections. Amphotericin B (AmB), a polyene class of antifungal drugs, is mainly used for the treatment of serious systemic fungal infections. AmB interacts with fungal plasma membrane ergosterol, triggering cellular ion leakage via pore formation, or extracting the ergosterol from the plasma membrane inducing cellular death. AmB resistance is primarily caused by changes in the content or structure of ergosterol. This review summarizes the antifungal drug resistance exhibited by Candida species, with a special focus on AmB.

Identification of the Microbiota in Coconut Water, Kefir, Coconut Water Kefir and Coconut Water Kefir-Fermented Sourdough Using Culture-Dependent Techniques and Illumina-MiSeq Sequencing

The principal objective of this study was to isolate and identify the microorganisms present in commercial kefir grains, a novel kefir-fermented coconut water (CWK) and a novel coconut water kefir-fermented sourdough using phenotypic identification and Sanger sequencing and examine the microbial diversity of CWK and CWK-fermented sourdough throughout the fermentation process using the MiSeq Illumina sequencing method. The phenotypic characterisation based on morphology identified ten isolates of LAB, five AAB and seven yeasts from kefir (K), CWK and CWK-fermented sourdough (CWKS). The results confirm the presence of the LAB species Limosilactobacillus fermentum, Lactobacillus. plantarum, L. fusant, L. reuteri and L. kunkeei; the AAB species Acetobacter aceti, A. lovaniensis and A. pasteurianus; and the yeast species Candida kefyr, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, C. guilliermondii and C. colliculosa. To the best of our knowledge, the identification of Rhodotorula from kefir is being reported for the first time. This study provides important insights into the relative abundances of the microorganisms in CWKS. A decrease in pH and an increase in the titratable acidity for CWK- and CWK-fermented sourdough corresponded to the increase in D- and L-lactic acid production after 96 h of fermentation. Significant reductions in the pHs of CWK and CWKS were observed between 48 and 96 h of fermentation, indicating that the kefir microorganisms were able to sustain highly acidic environments. There was also increased production of L-lactic acid with fermentation, which was almost twice that of D-lactic acid in CWK.

Multitasking functions of bacterial extracellular DNA in biofilms

Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.

Occurrence of coliforms and biofilm-forming bacteria in raw, treated, and distributed water from two waterwork systems in Osun State, Southwestern Nigeria

This study assessed the bacteriological quality of raw, treated, and distributed water from Ede-Erinle and Opa reservoirs in Osun State, Nigeria. This was to determine the potability of water from these waterwork stations. Eighteen sampling points were established across the two reservoir networks for this study. Samples were collected bi-monthly for two annual cycles. Serial dilution and pour plate methods were employed for the enumeration of bacterial load. Total heterotrophic bacteria count (THBC) and total coliform bacteria count (TCBC) were enumerated on nutrient and MacConkey agar at 37 °C, respectively. Bacterial isolates were characterized using biochemical identification methods with reference to Bergey's Manual of Determinative Bacteriology. Bacterial isolates and biofilm formation were further identified molecularly through the PCR method using specific universal primers. Mean values of THBC and TCBC in distributed water from Ede-Erinle (9.61 × 104 ± 1.50 × 104 CFU/mL; 69.56 ± 26.81 CFU/mL) and Opa waterworks (9.58 × 104 ± 2.55 × 104 CFU/mL; 142.94 ± 44.41 CFU/mL) exceeded permissible limits for drinking water. Paenibacillus lautus, Bacillus pseudomycoides, Pseudomonas aeruginosa, and Pseudomonas stutzeri showed biofilm-forming capacity. The study concluded that the presence of coliforms and biofilm-forming bacteria in distributed water implies that the water is unfit for consumption without further treatment.

Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms

Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.

Transformation and migration of Hg in a polluted alkaline paddy soil during flooding and drainage processes

Mercury (Hg) contamination in paddy soils poses a health risk to rice consumers and the environmental behavior of Hg determines its toxicity. Thus, the variations of Hg speciation are worthy of exploring. In this study, microcosm and pot experiments were conducted to elucidate Hg transformation, methylation, bioaccumulation, and risk coupled with biogeochemical cycling of key elements in a Hg-polluted alkaline paddy soil. In microcosm and pot experiments, organic- and sulfide-bound and residual Hg accounted for more than 98% of total Hg, and total contents of dissolved, exchangeable, specifically adsorbed, and fulvic acid-bound Hg were less than 2% of total Hg, indicating a low mobility and environmental risk of Hg. The decrease of pH aroused from Fe(III), SO42-, and NO3- reduction promoted Hg mobility, whereas the increase of pH caused by Fe(II), S2-, and NH4+ oxidation reduced available Hg contents. Moreover, Fe-bearing minerals reduction and organic matter consumption promoted Hg mobility, whereas the produced HgS and Fe(II) oxidation increased Hg stability. During flooding, a fraction of inorganic Hg (IHg) could be transported into methylmercury (MeHg), and during drainage, MeHg would be converted back into IHg. After planting rice in an alkaline paddy soil, available Hg was below 0.3 mg kg-1. During rice growth, a portion of available Hg transport from paddy soil to rice, promoting Hg accumulation in rice grains. After rice ripening, IHg levels in rice tissues followed the trend: root > leaf > stem > grain, and IHg content in rice grain exceed 0.02 mg kg-1, but MeHg content in rice grain meets daily intake limit (37.45 μg kg-1). These results provide a basis for assessing the environmental risks and developing remediation strategies for Hg-contaminated redox-changing paddy fields as well as guaranteeing the safe production of rice grains.