Visualization and quantification of the cellular and extracellular components of Salmonella Agona biofilms at different stages of development

Salmonella in black pepper (Piper nigrum): From farm to processing

Contamination of black pepper (Piper nigrum) with Salmonella is a frequent problem in retail and imported shipments. However, there is scarce information about the prevalence of the pathogen in the initial stages of black pepper production chain. This study sought to bridge this gap in research by determining the prevalence, as well as quantifying, and identifying the main Salmonella serovars present during black pepper primary production and processing. Black pepper (233) and environmental (175) samples were collected from farms (354) and processing plants (54) in Espirito Santo, Brazil. The pathogen was detected in soil (16.7 %), drying waste (20.4 %), fallen berries (3.7 %), threshed berries (14.3 %), and dried peppercorns (22.2 %) collected from farms. Salmonella was also detected in samples of raw material (11.1 %), export products (16.7 %), and processing waste (16.7 %) collected from processing plants. A total of 12 serotypes were identified, and Salmonella Javiana showed the highest prevalence (38.8 %). According to the results, contamination occurring in the post-harvest phase is not eliminated or reduced during processing. Therefore, the adoption of good agricultural and manufacturing practices, supported by hazard analysis and critical control points (HACCP), is crucial to mitigate this kind of contamination. These practices should be combined with decontamination treatments to ensure the safety of the final product.

Characterization and long-read sequencing of biofilms formed by the microbiota present on inert surfaces in poultry slaughterhouses

Cross-contamination from inert slaughterhouse surfaces is among the main sources of contamination of poultry. The objective of the research reported here was to characterize the biofilms formed by the microbiota present on various surfaces in two poultry slaughterhouses in north-western Spain. Forty-four samples (22 from each slaughterhouse) were taken by swab rubbing at different points along the processing line (from stunning to cutting). The microbiota on all surfaces was able to form biofilms, which were studied by scanning confocal laser microscopy. The total biovolume in the observation field of 16,078.24 μm2 ranged from 22,106.8 ± 5544.3 μm3 to 414,229.6 ± 1621.0 μm3. Average values were higher in abattoir A than in abattoir B, with significant differences (P < 0.05) between surfaces. The percentage of biovolume of Gram-positive bacteria ranged between 0.02 % and 5.38 %. The highest percentages of Gram-positive bacteria were detected towards the beginning of the processing line. The microbiota of the biofilms was identified using long-read sequencing techniques (Oxford Nanopore). The predominant genera (found in >50.0 % of the biofilms) were Pseudomonas, Citrobacter, Klebsiella, Serratia, Escherichia, Enterobacter, Stenotrophomonas, Salmonella, Shewanella, Acinetobacter and Aeromonas. In addition, some pathogenic bacteria were detected, including Salmonella (31 surfaces), Yersinia enterocolitica (12), Escherichia coli O157:H7 (6), Campylobacter spp. (4) and Listeria monocytogenes (3). This research work has permitted identification of the most contaminated surfaces in poultry abattoirs and can serve as a starting point for the design of more effective cleaning and disinfection protocols.

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.

Influence of Copper on Oleidesulfovibrio alaskensis G20 Biofilm Formation

Copper is known to have toxic effects on bacterial growth. This study aimed to determine the influence of copper ions on Oleidesulfovibrio alaskensis G20 biofilm formation in a lactate-C medium supplemented with variable copper ion concentrations. OA G20, when grown in media supplemented with high copper ion concentrations of 5, 15, and 30 µM, exhibited inhibited growth in its planktonic state. Conversely, under similar copper concentrations, OA G20 demonstrated enhanced biofilm formation on glass coupons. Microscopic studies revealed that biofilms exposed to copper stress demonstrated a change in cellular morphology and more accumulation of carbohydrates and proteins than controls. Consistent with these findings, sulfur (dsrA, dsrB, sat, aprA) and electron transport (NiFeSe, NiFe, ldh, cyt3) genes, polysaccharide synthesis (poI), and genes involved in stress response (sodB) were significantly upregulated in copper-induced biofilms, while genes (ftsZ, ftsA, ftsQ) related to cellular division were negatively regulated compared to controls. These results indicate that the presence of copper ions triggers alterations in cellular morphology and gene expression levels in OA G20, impacting cell attachment and EPS production. This adaptation, characterized by increased biofilm formation, represents a crucial strategy employed by OA G20 to resist metal ion stress.

Staphylococcus epidermidis biofilm assembly and self-dispersion: bacteria and matrix dynamics

Staphylococcus epidermidis, despite being a commensal of human skin and mucosa, is a major nosocomial pathogen implicated in device-associated infections. The dissemination of infection to other body sites is related to biofilm dispersal. This study focused on the dispersion stage of S. epidermidis CIP 444 biofilm, with the assessment of biofilm matrix composition in a time-dependent experiment (7 days extended) with 3 independent repetitions, using confocal laser scanning microcopy (CLSM) in association with ZEN 3.4 blue edition, COMSTAT, and ImageJ software. SYTO-9, propidium iodide (PI), DID'OIL, FITC, and calcofluor white M2R (CFW) were used to stain biofilm components. The results indicated that the biomass of dead cells increased from 15.18 ± 1.81 µm3/µm2 (day 3) to 23.15 ± 6.075 µm3/µm2 (day 4), along with a decrease in alive cells' biomass from 22.75 ± 2.968 µm3/µm2 (day 3) to 18.95 ± 5.713 µm3/µm2 (day 4). When the intensities were measured after marking the biofilm components, in a 24-h-old biofilm, polysaccharide made up the majority of the investigated components (52%), followed by protein (18.9%). Lipids make up just 11.6% of the mature biofilm. Protein makes up the largest portion (48%) of a 4-day-old biofilm, followed by polysaccharides (37.8%) and lipids (7.27%). According to our findings, S. epidermidis CIP 444 dispersion occurred on day 4 of incubation, and new establishment of the biofilm occurred on day 7. Remarkable changes in biofilm composition will pave the way for a new approach to understanding bacterial strategies inside biofilms and finding solutions to their impacts in the medical field.

Characterization of Salmonella enterica Biofilms and Antibiofilm Effect of Carvacrol and 2-Aminobenzimidazole

Biofilm-associated foodborne Salmonella infections in poultry have become increasingly challenging for veterinarians, particularly in developing countries, and warrant thorough investigation. We assessed the biofilm-forming tendency of poultry isolates of Salmonella enterica, namely Salmonella Typhimurium (n = 23), Salmonella Infantis (n = 28), and Salmonella Heidelberg (n = 18), in nutrient-rich Rappaport-Vassiliadis Soya (RVS) peptone broth and nutrient-deficient diluted Tryptone Soya Broth (TSB). Seven of the tested isolates exhibited moderate biofilm formation in diluted TSB, whereas two showed such formation in RVS. In addition, the Congo red agar assay revealed curli and cellulose production in seven isolates. Fourteen specific biofilm-associated genes were analyzed identifying sdiA and seqA to be the most prevalent (100%), and glyA the least prevalent (69.5%). The prevalence of the genes bcsA and csgA was significantly lower in moderate and weak biofilm formers, respectively, as compared with nonbiofilm formers in RVS peptone broth. Furthermore, the compounds carvacrol and 2-aminobenzimidazole (2-ABI) effectively inhibited biofilm formation by Salmonella serovars in RVS peptone and TSB media, respectively. Whereas the antibiofilm activity of 2-ABI against Salmonella has not been reported previously, we determined its most effective concentration at 1.5 mM among tested antibiofilm treatments. These findings indicate that Salmonella strains prevalent in poultry farms have the potential to form biofilms, and the tested compounds should be further explored as supportive or alternative antimicrobials.

Associations of motility and auto-aggregation with biofilm-formation capacity levels in Clostridioidesdifficile

Clostridioides difficile (C. difficile) is responsible for one of the most common nosocomial infections worldwide. This work assessed associations between biofilm-formation capacity levels of C. difficile and cell viability, motility, flagella, motility and auto-aggregation in 118 clinical isolates. Biofilm production was assessed by the crystal violet method. Cell viability was determined by BacTiter-Glo™ Microbial Cell Viability Assay and live-imaging microscopy. Expression levels of LuxS, Cwp84, Spo0A, PilA, and FliC were measured by real-time PCR. Motility was visually assessed in agar tubes. Auto-aggregation levels were determined by OD600 measurements. Out of 118 isolates, 66 (56 %) were biofilm producers, with most being strong or moderate producers. Cell viability, motility and auto-aggregation positively correlated with biofilm-production capacity (p = 0.0001, p = 0.036 and p < 0.0001, respectively). Positive associations were found between pilA, fliC and luxS expression levels and biofilm-production capacity (p = 0.04, p = 0.01, p = 0.036, respectively). This is the first report of associations between biofilm-formation capacity and cell viability, pilA, fliC, and luxS gene expression, auto-aggregation and motility. These correlations should be further explored to expand knowledge on the regulation of C. difficile biofilm formation, and pathogenesis, which will have notable implications on treatment options.

New insights into multi-strategies of sludge granulation in up-flow anaerobic sludge blanket reactors from community succession and interaction

This study aimed to elucidate the multiple strategies employed by anaerobes during granulation in a laboratory upflow anaerobic sludge blanket reactor, based on microbial succession and interactions. The anaerobic granulation process featured staged dominance of microbial genera, corresponding well with the environmental traits. Across the stages (selection, seeding, expansion, and maturation), chemotaxis attraction of nitrogen and/or carbon sources and flagellar motion were the primary strategy of microbial assembly. The second messengers - cyclic adenosine and guanosine monophosphates - partially regulated the agglomeration of filamentous Euryachaeota and Chloroflexi as the inner cores, while quorum sensing mediated the expansion of granules prior to maturation. Antagonism or competition governed the interactions within the phylogenetic molecular ecological network during sludge granulation, which were largely driven by the low-abundance (<1%) taxa. These new insights suggest that better engineering solutions to enhance chemotaxis attraction and species selection could achieve more efficient anaerobic granular sludge processes.

Illuminating the oral microbiome and its host interactions: tools and approaches for molecular ecological studies

A more comprehensive understanding of oral diseases like caries and periodontitis is dependent on an intimate understanding of the microbial ecological processes that are responsible for disease development. With this review, we provide a comprehensive overview of relevant molecular ecology techniques that have played critical roles in the current understanding of human oral biofilm development, interspecies interactions, and microbiome biogeography. The primary focus is on relevant technologies and examples available in the oral microbiology literature. However, most, if not all, of the described technologies should be readily adaptable for studies of microbiomes from other mucosal sites in the body. Therefore, this review is intended to serve as a reference guide used by microbiome researchers as they inevitably transition into molecular mechanistic studies of the many significant phenotypes observed clinically.

Responses of Salmonella biofilms to oxidizing biocides: Evidence of spatial clustering

The spatial organization of biofilm bacterial communities can be influenced by several factors, including growth conditions and challenge with antimicrobials. Differential survival of clusters of cells within biofilms has been observed. In this work, we present a variety of methods to identify, quantify and statistically analyse clusters of live cells from images of two Salmonella strains with differential biofilm forming capacity exposed to three oxidizing biocides. With a support vector machine approach, we showed spatial separation between the two strains, and, using statistical testing and high-performance computing (HPC), we determined conditions which possess an inherent cluster structure. Our results indicate that there is a relationship between biocide potency and inherent biofilm formation capacity with the tendency to select for spatial clusters of survivors. There was no relationship between positions of clusters of live or dead cells within stressed biofilms. This work identifies an approach to robustly quantify clusters of physiologically distinct cells within biofilms and suggests work to understand how clusters form and survive is needed. SIGNIFICANCE STATEMENT: Control of biofilm growth remains a major challenge and there is considerable uncertainty about how bacteria respond to disinfection within a biofilm and how clustering of cells impacts survival. We have developed a methodological approach to identify and statistically analyse clusters of surviving cells in biofilms after biocide challenge. This approach can be used to understand bacterial behaviour within biofilms under stress and is widely applicable.

Periodic fouling control strategies in gravity-driven membrane bioreactors (GD-MBRs): Impact on treatment performance and membrane fouling properties

This study aims to assess the effects of periodic membrane fouling control strategies in Gravity-Driven Membrane Bioreactor (GD-MBR) treating primary wastewater. The impact of each control strategy on the reactor performance (permeate flux and water quality), biomass morphology, and fouling composition were evaluated. The application of air scouring coupled with intermittent filtration resulted in the highest permeate flux (4 LMH) compared to only intermittent filtration (i.e., relaxation) (1 LMH) and air scouring under continuous filtration (2.5 LMH). Air scouring coupled with relaxation led to a thin (~50 μm) but with more porous fouling layer and low hydraulic resistance, presenting the lowest concentration of extracellular polymeric substance (EPS) in the biomass. Air scouring under continuous filtration led to a thin (~50 μm), dense, compact, and less porous fouling layer with the highest specific hydraulic resistance. The employment of only relaxation led to the highest fouling formation (~280 μm) on the membrane surface. The highest TN removal (~62%) was achieved in the reactor with only relaxation (no aeration) due to the anoxic condition in the filtration tank, while the highest COD removal (~ 60%) was achieved with air scouring under continuous filtration due to the longer aeration time and the denser fouling layer. The results highlighted the importance of performing in-depth fouling characterization to link the membrane fouling properties to the hydraulic resistance and membrane bioreactor performances (i.e., water quality and water production). Moreover, this work proven the versatility of the GD-MBR, where the choice of the appropriate operation and fouling control strategy relies on the eventual discharge or reuse of the treated effluent.

Self-locomotive, antimicrobial microrobot (SLAM) swarm for enhanced biofilm elimination

Biofilm is a major cause of infections and infrastructure deterioration, largely due to molecular diffusion restrictions that hamper the antimicrobial activity of traditional antibiotics and disinfectants. Here, we present a self-locomotive, antimicrobial microrobot (SLAM) swarm that can penetrate, fracture, and detach biofilm and, in turn, nullify bacterial resistance to antibiotics. The SLAM is assembled by loading a controlled mass of manganese oxide nanosheets on diatoms with the polydopamine binder. In hydrogen peroxide solution, SLAMs produce oxygen bubbles that generate thrust to penetrate the rigid and dense Pseudomonas aeruginosa biofilm and self-assemble into a swarm that repeatedly surrounds, expands, and bursts oxygen bubbles. The resulting cavities continue to deform and fracture extracellular polymeric substances from microgrooved silicone substrates and wounded skin explants while decreasing the number of viable bacterial cells. Additionally, SLAM allows irrigating water or antibiotics to access the residual biofilm better, thus enhancing the synergistic efficacy in killing up to 99.9% of bacterial cells.

Structural variations on Salmonella biofilm by exposition to river water

Biofilm formation, as adapting strategies, is the result of stressful conditions that Salmonella faces in hostile environments like surface water. We evaluated river water effect on Salmonella biofilm formation ability in terms of physical, morphological characteristics and chemical composition. A new morphotype SPAM (soft, pink and mucoid) was detected in Oranienburg strains S-76 and S-347 (environmental and clinical isolate). Oranienburg serotypes showed very marked behavior in adherence, pellicle liquid-air and resistance, being Oranienburg S-76 the strongest biofilm producer. All strains when exposed to river water presented an overlapping mucoid layer in the morphotype and increased their motility except Oranienburg S-347. The most motile was Typhimurium (control) and the least Infantis S-304 (clinical isolate). Mannose, glucose, galactose and ribose were the main biofilm sugar components; type and concentration of sugar suggest a morphotype/serotype dependent pattern. Strong morphotypes expressed in this study may be an effective protective strategy for Salmonella in hostile environments.

Exploring the Biofilm Formation Capacity in S. pseudintermedius and Coagulase-Negative Staphylococci Species

The ability of biofilm formation seems to play an important role in the virulence of staphylococci. However, studies reporting biofilm formation of coagulase-negative staphylococci isolated from animals are still very scarce. Thus, we aimed to evaluate the biofilm-forming capacity of CoNS and S. pseudintermedius isolated from several animal species and to investigate the effect of conventional antimicrobials on biofilm reduction. A total of 35 S. pseudintermedius and 192 CoNS were included. Biofilm formation was accessed by the microtiter plate assay and the biofilms were stained by crystal violet. Association between biofilm formation and staphylococci species and antimicrobial resistance was also performed. Biofilm susceptibility testing was performed with tetracycline and amikacin at the minimum inhibitory concentration (MIC) and 10 × MIC. The metabolic activity of the biofilm cells after antimicrobial treatment was accessed by the XTT assay. All isolates formed biofilm, with S. urealyticus producing the most biofilm biomass and S. pseudintermedius producing the least biomass. There was a positive association between biofilm formation and multidrug resistance as well as resistance to individual antimicrobials. Neither tetracycline nor amikacin were able to eradicate the biofilm, not even at the highest concentration used. This study provides new insights into biofilm formation and the effects of antimicrobials on CoNS species.

Biofilm Formation of Staphylococcus aureus from Pets, Livestock, and Wild Animals: Relationship with Clonal Lineages and Antimicrobial Resistance

This study aimed to compare the biofilm formation ability of Staphylococcus aureus isolated from a wide range of animals and study the association between biofilm formation and antimicrobial resistance and genetic lineages. A total of 214 S. aureus strains isolated from pets, livestock, and wild animals were evaluated regarding their ability to form biofilms by the microtiter biofilm assay and their structure via confocal scanning laser microscopy. Statistical analysis was used to find an association between biofilm formation and antimicrobial resistance, multidrug resistance, sequence types (STs), spa and agr-types of the isolates. The antimicrobial susceptibility of 24 h-old biofilms was assessed against minimum inhibitory concentrations (MIC) and 10× MIC of amikacin and tetracycline, and the biomass reduction was measured. The metabolic activity of biofilms after antimicrobial treatment was evaluated by the XTT assay. All isolates were had the ability to form biofilms. Yet, significant differences in biofilm biomass production were detected among animal species. Multidrug resistance had a positive association with biofilm formation as well as methicillin-resistance. Significant differences were also detected among the clonal lineages of the isolates. Both tetracycline and amikacin were able to significantly reduce the biofilm mass. However, none of the antimicrobials were able to eradicate the biofilm at the maximum concentration used. Our results provide important information on the biofilm-forming capacity of animal-adapted S. aureus isolates, which may have potential implications for the development of new biofilm-targeted therapeutics.

Control of bacterial biofilms in red meat - A systematic review

Biofilm formation is a serious threat in the meat industry, mainly since it aids food-borne pathogen survival. Biofilms are often difficult to eliminate, and it is essential to understand the best possible deployable measures to remove or inactivate biofilms. We systematically reviewed the published in vitro studies that investigated various methods for removing biofilms in red meat. Publicly available databases, including Google Scholar and PubMed, were queried for relevant studies. The search was restricted to articles published in the English language from 2010 to 2021. We mined a total of 394 studies, of which 12 articles were included in this review. In summary, the studies demonstrated the inhibitory effect of various methods, including the use of bacteriophages, dry heat, cold atmospheric pressure, ozone gas, oils, and acids, on red meat extract or red meat culture. This systematic review suggests that in addition to existing sanitation and antibiotic procedures, other methods, such as the use of phage cocktails and different oils as nanoparticles, yield positive outcomes and may be taken from the in vitro setting to industry with prior validation of the techniques.

Mucospheres produced by a mixotrophic protist impact ocean carbon cycling

Mixotrophic protists (unicellular eukaryotes) that engage in both phototrophy (photosynthesis) and phago-heterotrophy (engulfment of particles)—are predicted to contribute substantially to energy fluxes and marine biogeochemical cycles. However, their impact remains largely unquantified. Here we describe the sophisticated foraging strategy of a widespread mixotrophic dinoflagellate, involving the production of carbon-rich ‘mucospheres’ that attract, capture, and immobilise microbial prey facilitating their consumption. We provide a detailed characterisation of this previously undescribed behaviour and reveal that it represents an overlooked, yet quantitatively significant mechanism for oceanic carbon fluxes. Following feeding, the mucospheres laden with surplus prey are discarded and sink, contributing an estimated 0.17–1.24 mg m−2 d−1 of particulate organic carbon, or 0.02–0.15 Gt to the biological pump annually, which represents 0.1–0.7% of the estimated total export from the euphotic zone. These findings demonstrate how the complex foraging behaviour of a single species of mixotrophic protist can disproportionally contribute to the vertical flux of carbon in the ocean.

High-Pressure-Induced Sublethal Injuries of Food Pathogens-Microscopic Assessment

High Hydrostatic Pressure (HHP) technology is considered an alternative method of food preservation. Nevertheless, the current dogma is that HHP might be insufficient to preserve food lastingly against some pathogens. Incompletely damaged cells can resuscitate under favorable conditions, and they may proliferate in food during storage. This study was undertaken to characterize the extent of sublethal injuries induced by HHP (300-500 MPa) on Escherichia coli and Listeria inncua strains. The morphological changes were evaluated using microscopy methods such as Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), and Epifluorescence Microscopy (EFM). The overall assessment of the physiological state of tested bacteria through TEM and SEM showed that the action of pressure on the structure of the bacterial membrane was almost minor or unnoticeable, beyond the L. innocua wild-type strain. However, alterations were observed in subcellular structures such as the cytoplasm and nucleoid for both L. innocua and E. coli strains. More significant changes after the HHP of internal structures were reported in the case of wild-type strains isolated from raw juice. Extreme condensation of the cytoplasm was observed, while the outline of cells was intact. The percentage ratio between alive and injured cells in the population was assessed by fluorescent microscopy. The results of HHP-treated samples showed a heterogeneous population, and red cell aggregates were observed. The percentage ratio of live and dead cells (L/D) in the L. innocua collection strain population was higher than in the case of the wild-type strain (69%/31% and 55%/45%, respectively). In turn, E. coli populations were characterized with a similar L/D ratio. Half of the cells in the populations were distinguished as visibly fluorescing red. The results obtained in this study confirmed sublethal HHP reaction on pathogens cells.

A Streamlined Study on Chitosan-Zinc Oxide Nanomicelle Properties to Mitigate a Drug-Resistant Biofilm Protection Mechanism

The nosocomial multidrug resistant bacteria (MDR), are rapidly circulating from water surfaces to humans away from the clinical setting, forming a cyclical breeding ground of resistance, causing worldwide infections, and thus requiring urgent responses. The combination of chitosan and zinc oxide (CZNPs), with proven bactericidal effects on some MDRs, was further studied to set the stage for a broad-spectrum in vivo utilization of CZNPs. Toward ensuring CZNPs' uniformity and potency, when it faces not only biofilms but also their extracellular polymeric substances (EPS) defense mechanism, the size, zeta potential, and polydispersity index (PDI) were determined through dynamic light scattering (DLS). Furthermore, the efficacy of CZNPs was tested on the inhibition of MDR Gram-negative Escherichia coli BAA-2471 and Gram-positive Enterococcus faecium 1449 models, co-cultured in an Alvatex 3D fiber platform as a biofilm-like structure. The Biotek Synergy Neo2 fluorescent microplate reader was used to detect biofilm shrinkage. The biofilm protection mechanism was elucidated through detection of EPS using 3D confocal and transmission electronic microscopy. Results indicated that 200 μl/mL of CZNPs, made with 50 nm ZnO and 10,000 Da chitosan (N = 369.1 nm; PDI = 0.371; zeta potential = 22.8 mV), was the most promising nanocomposite for MDR biofilm reduction, when compared to CZNPs enclosing ZnO, 18 or 100 nm. This study depicts that CZNPs possess enough potency and versatility to face biofilms' defense mechanism in vivo.

Assessing the Role of Pharyngeal Cell Surface Glycans in Group A Streptococcus Biofilm Formation

Group A Streptococcus (GAS) causes 700 million infections and accounts for half a million deaths per year. Antibiotic treatment failure rates of 20–40% have been observed. The role host cell glycans play in GAS biofilm formation in the context of GAS pharyngitis and subsequent antibiotic treatment failure has not been previously investigated. GAS serotype M12 GAS biofilms were assessed for biofilm formation on Detroit 562 pharyngeal cell monolayers following enzymatic removal of all N-linked glycans from pharyngeal cells with PNGase F. Removal of N-linked glycans resulted in an increase in biofilm biomass compared to untreated controls. Further investigation into the removal of terminal mannose and sialic acid residues with α1-6 mannosidase and the broad specificity sialidase (Sialidase A) also found that biofilm biomass increased significantly when compared to untreated controls. Increases in biofilm biomass were associated with increased production of extracellular polymeric substances (EPS). Furthermore, it was found that M12 GAS biofilms grown on untreated pharyngeal monolayers exhibited a 2500-fold increase in penicillin tolerance compared to planktonic GAS. Pre-treatment of monolayers with exoglycosidases resulted in a further doubling of penicillin tolerance in resultant biofilms. Lastly, an additional eight GAS emm-types were assessed for biofilm formation in response to terminal mannose and sialic acid residue removal. As seen for M12, biofilm biomass on monolayers increased following removal of terminal mannose and sialic acid residues. Collectively, these data demonstrate that pharyngeal cell surface glycan structures directly impact GAS biofilm formation in a strain and glycan specific fashion.

Diversity, Antibiotic Resistance, and Biofilm-Forming Ability of Enterobacteria Isolated from Red Meat and Poultry Preparations

A total of 44 samples of beef, pork, and poultry preparations were tested. Average counts (log cfu/g) of enterobacteria were 1.99 ± 0.99 (beef preparations), 1.96 ± 1.44 (pork), 2.09 ± 0.92 (chicken), and 2.17 ± 1.06 (turkey) (p > 0.05). Two hundred enterobacterial strains were identified and 13 genera (21 species) were distinguished, including species that are a significant cause of infection. The most common genera were Escherichia (32.5% of strains), Serratia (17.0%), Hafnia (12.5%), and Salmonella (12.0%). Isolates were screened by disc diffusion for susceptibility to 15 antibiotics. A total of 126 strains (63% of the isolates) were multirresistant (having resistance to two or more antibiotics), 46 (23%) were resistant to one antibiotic, and 28 (14%) were sensitive to all antibiotics. The average number of resistances per strain was 2.53 ± 2.05. A higher (p < 0.05) average number of resistances was observed in strains from turkey (3.14 ± 2.55) than in strains from beef (2.15 ± 1.22), pork (2.16 ± 1.39), or chicken (2.44 ± 2.22). At least 50% of strains showed resistance or reduced susceptibility to ampicillin, cefotaxime, ceftazidime, or streptomycin, considered to be "critically important" antimicrobial agents in human medicine. Seventy-nine strains (39.5%), 60 strains (30.0%), and 46 strains (23.0%) were weak, moderate, and strong biofilm producers (crystal violet assay), respectively. This investigation provides evidence that bacteria from red meat and poultry preparations pose major potential risk to consumers.

Biovolume and spatial distribution of foodborne Gram-negative and Gram-positive pathogenic bacteria in mono- and dual-species biofilms

The objective of this study was to characterize the biofilms formed by Salmonella enterica serotype Agona, Listeria monocytogenes, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE) after 12, 48, 72, 120 and 240 h of incubation at 10 °C. Biofilms containing a single species, together with dual-species biofilms in which S. enterica and a Gram-positive bacterium existed in combination, were formed on polystyrene and evaluated by using confocal laser scanning microscopy (CLSM). All strains were able to form biofilm. The greatest biovolume in the observation field of 14,161 μm² was observed for mono-species biofilms after 72 h, where biovolumes of 94,409.0 μm³ ± 2131.0 μm³ (S. enterica), 58,418.3 μm³ ± 5944.9 μm³ (L. monocytogenes), 68,020.8 μm³ ± 5812.3 μm³ (MRSA) and 59,280.0 μm³ ± 4032.9 μm³ (VRE) were obtained. In comparison with single-species biofilms, the biovolume of S. enterica was higher in the presence of MRSA or VRE after 48, 72 and 120 h. In dual-species biofilms, the bacteria showed a double-layer distribution pattern, with S. enterica in the top layer and Gram-positive bacteria in the bottom layer. This spatial disposition should be taken into account when effective strategies to eliminate biofilms are being developed.

A bacterial polysaccharide biosynthesis-related gene inversely regulates larval settlement and metamorphosis of Mytilus coruscus

Larval settlement and metamorphosis is essential for the development of marine invertebrates. Although polysaccharides are involved in larval settlement and metamorphosis of Mytilus coruscus, the molecular basis of polysaccharides underlying this progression remains largely unknown. Here, the roles of the polysaccharide biosynthesis-related gene 01912 of Pseudoalteromonas marina ECSMB14103 in the regulation of larval settlement and metamorphosis were examined by gene-knockout technique. Compared with biofilms (BFs) of the wild-type P. marina, Δ01912 BFs with a higher colanic acid (CA) content showed a higher inducing activity on larval settlement and metamorphosis. Deletion of the 01912 gene caused an increase in c-di-GMP levels, accompanied by a decrease in the motility, an increase in cell aggregation, and overproduction of CA. Thus, the bacterial polysaccharide biosynthesis-related gene 01912 may regulate mussel settlement by producing CA via the coordination of c-di-GMP. This work provides a deeper insight into the molecular mechanism of polysaccharides in modulating mussel settlement.

Identification of a reliable fixative solution to preserve the complex architecture of bacterial biofilms for scanning electron microscopy evaluation

Bacterial biofilms are organized sessile communities of bacteria enclosed in extracellular polymeric substances (EPS). To analyze organization of bacteria and EPS in high resolution and high magnification by scanning electron microscopy (SEM), it is important to preserve the complex architecture of biofilms. Therefore, fixation abilities of formalin, glutaraldehyde, and Methacarn (methanol/chloroform/acetic acid-6:3:1) fixatives were evaluated to identify which fixative would best preserve the complex structure of bacterial biofilms. Economically important Gram-negative Mannheimia haemolytica, the major pathogen associated with bovine respiratory disease complex, and Gram-positive Staphylococcus aureus, the major cause of chronic mastitis in cattle, bacteria were selected since both form biofilms on solid-liquid interface. For SEM analysis, round glass coverslips were placed into the wells of 24-well plates and diluted M. haemolytica or S. aureus cultures were added, and incubated at 37°C for 48–72 h under static growth conditions. Culture media were aspirated and biofilms were fixed with an individual fixative for 48 h. SEM examination revealed that all three fixatives were effective preserving the bacterial cell morphology, however only Methacarn fixative could consistently preserve the complex structure of biofilms. EPS layers were clearly visible on the top, in the middle, and in the bottom of the biofilms with Methacarn fixative. Biomass and three-dimensional structure of the biofilms were further confirmed spectrophotometrically following crystal violet staining and by confocal microscopy after viability staining. These findings demonstrate that Methacarn fixative solution is superior to the other fixatives evaluated to preserve the complex architecture of biofilms grown on glass coverslips for SEM evaluation.

Monospecific Biofilms of Pseudoalteromonas Promote Larval Settlement and Metamorphosis of Mytilus coruscus

As a stage of life cycle, larval settlement and metamorphosis are critical processes for persistence of many marine invertebrate populations. Bacterial biofilms (BFs) could induce larval settlement and metamorphosis. Pseudoalteromonas, a widely distributed genus of marine bacteria, showed inductive effects on several invertebrates. However, how Pseudoalteromonas BFs induce settlement and metamorphosis of Mytilus coruscus remains unclear. Pseudoalteromonas marina BFs with the highest inducing activity were further investigated to define inductive cues. Surface-bound products of P. marina BFs could induce larval settlement and metamorphosis. P. marina BFs treated with formalin, antibiotics, ultraviolet irradiation, heat and ethanol significantly reduced inductive effects and cell survival rates. The confocal laser scanning microscopy and the biovolume analysis showed the dominance of α-polysaccharides on P. marina BFs. Treatment of BFs with amylases, proteases and lipase led to the decrease of inducing activity, suggesting that inductive cues of P. marina BFs may comprise of molecular domains of polysaccharides, proteins, and lipids. Finding inductive cues of BFs could put forward further studies about the mechanism of larval settlement and metamorphosis of marine invertebrates.

Visualizing Microbial Community Dynamics via a Controllable Soil Environment

Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil.

IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

The Flagellar Gene Regulates Biofilm Formation and Mussel Larval Settlement and Metamorphosis

Biofilms are critical components of most marine systems and provide biochemical cues that can significantly impact overall community composition. Although progress has been made in the bacteria–animal interaction, the molecular basis of modulation of settlement and metamorphosis in most marine animals by bacteria is poorly understood. Here, Pseudoalteromonas marina showing inducing activity on mussel settlement and metamorphosis was chosen as a model to clarify the mechanism that regulates the bacteria–mussel interaction. We constructed a flagellin synthetic protein gene fliP deletion mutant of P. marina and checked whether deficiency of fliP gene will impact inducing activity, motility, and extracellular polymeric substances of biofilms. Furthermore, we examined the effect of flagellar proteins extracted from bacteria on larval settlement and metamorphosis. The deletion of the fliP gene caused the loss of the flagella structure and motility of the ΔfliP strain. Deficiency of the fliP gene promoted the biofilm formation and changed biofilm matrix by reducing β-polysaccharides and increasing extracellular proteins and finally reduced biofilm-inducing activities. Flagellar protein extract promoted mussel metamorphosis, and ΔfliP biofilms combined with additional flagellar proteins induced similar settlement and metamorphosis rate compared to that of the wild-type strain. These findings provide novel insight on the molecular interactions between bacteria and mussels.

Architecture and Viability of the Biofilms Formed by Nine Listeria Strains on Various Hydrophobic and Hydrophilic Materials

Biofilms are a key factor in the persistence of Listeria in food processing plants, representing a potential source of foodstuff contamination. Nine Listeria strains (eight Listeria monocytogenes and one Listeria ivanovii) were studied by confocal laser scanning microscopy (CLSM) for their ability to form biofilm on glass, polystyrene, graphene and resin after 120 h of incubation at 12 °C. The relationship between cell surface hydrophobicity and biofilm formation was also investigated. On comparing the data for all the strains, similar (P > 0.05) biovolume values were obtained on glass (average 3.39 ± 1.69 µm3/µm2) and graphene (2.93 ± 1.14 µm3/µm2), while higher (P < 0.05) values were observed for polystyrene (4.39 ± 4.14 µm3/µm2). The highest (P < 0.01) biovolume levels were found in the biofilms formed on resin (7.35 ± 1.45 µm3/µm2), which also had the smallest biomass of inactivated cells (0.38 ± 0.37 µm3/µm2 vs. 1.20 ± 1.12 µm3/µm2 on the remaining surfaces; P < 0.001). No relationship was noted between cell surface hydrophobicity and biofilm-forming ability.

Persistent Listeria monocytogenes Isolates from a Poultry-Processing Facility Form more Biofilm but Do Not Have a Greater Resistance to Disinfectants Than Sporadic Strains

Some strains of Listeria monocytogenes can persist in food-processing environments, increasing the likelihood of the contamination of foodstuffs. To identify traits that contribute to bacterial persistence, a selection of persistent and sporadic L. monocytogenes isolates from a poultry-processing facility was investigated for biofilm-forming ability (crystal violet assay). The susceptibility of sessile cells to treatments (five minutes) with sodium hypochlorite having 10% active chlorine (SHY: 10,000 ppm, 25,000 ppm, and 50,000 ppm) and benzalkonium chloride (BZK: 2500 ppm, 10,000 ppm, and 25,000 ppm) was also studied. All isolates exhibited biofilm formation on polystyrene. Persistent strains showed larger (p < 0.001) biofilm formation (OD580 = 0.301 ± 0.097) than sporadic strains (OD580 = 0.188 ± 0.082). A greater susceptibility to disinfectants was observed for biofilms of persistent strains than for those of sporadic strains. The application of SHY reduced biofilms only for persistent strains. BZK increased OD580 in persistent strains (2500 ppm) and in sporadic strains (all concentrations). These results indicate that the use of BZK at the concentrations tested could represent a public health risk. Findings in this work suggest a link between persistence and biofilm formation, but do not support a relationship between persistence and the resistance of sessile cells to disinfectants.

Prevalence, Molecular Typing, and Determination of the Biofilm-Forming Ability of Listeria monocytogenes Serotypes from Poultry Meat and Poultry Preparations in Spain

A study was undertaken of the presence of Listeria monocytogenes in 260 samples of poultry meat obtained from retail outlets in northwestern Spain. L. monocytogenes was detected in 20 samples (7.7%). Twenty strains (one strain per positive sample) were characterized. The strains belonged to 10 serotypes: 1/2a (2 strains), 1/2b (2), 1/2c (2), 3a (1), 3b (2), 3c (2), 4a (2), 4b (4), 4c (1), and 4d (2). Cluster analysis (ribotyping; EcoRI) showed a strong genetic relationship between strains isolated from samples coming from different outlets. Ribotyping permitted some isolates of the same serotype to be differentiated, which points to the possible usefulness of this technique in the epidemiological surveillance of L. monocytogenes. All strains formed biofilm on polystyrene, as shown by confocal laser scanning microscopy. The biovolume (between 621.7 ± 36.0 µm3 and 62,984.0 ± 14,888.2 µm3 in the observational field of 14,161 μm2), percentage of surface coverage (from 2.17 ± 0.84% to 94.43 ± 3.97%), roughness (between 0.399 ± 0.052 and 0.830 ± 0.022), and maximum thickness (between 9.00 ± 0.00 µm and 24.00 ± 14.93 µm) of biofilms varied between strains (p < 0.05). These results expand knowledge of the characteristics of L. monocytogenes isolates from poultry.

Effect of low doses of biocides on the antimicrobial resistance and the biofilms of Cronobacter sakazakii and Yersinia enterocolitica

The susceptibility of Cronobacter sakazakii ATCC 29544 (CS) and Yersinia enterocolitica ATCC 9610 (YE) to sodium hypochlorite (10% of active chlorine; SHY), peracetic acid (39% solution of peracetic acid in acetic acid; PAA) and benzalkonium chloride (BZK) was tested. Minimum inhibitory concentration (MIC) values (planktonic cells; microdilution broth method) of 3,800 ppm (SHY), 1,200 ppm (PAA) and 15 ppm (BZK) for CS, and 2,500 ppm (SHY), 1,275 ppm (PAA) and 20 ppm (BZK) for YE, were found. In some instances, an increase in growth rate was observed in presence of sub-MICs (0.25MIC, 0.50MIC or 0.75MIC) of biocides relative to the samples without biocides. The cultures exhibited an acquired tolerance to biocides and an increase in antibiotic resistance after exposure to sub-MICs of such disinfectants. Strains were able to form strong biofilms on polystyrene after 48 hours (confocal laser scanning microscopy), with average biovolumes in the observation field (14,161 µm2) of 242,201.0 ± 86,570.9 µm3 (CS) and 190,184.5 ± 40,860.3 µm3 (YE). Treatment of biofilms for 10 minutes with disinfectants at 1MIC or 2MIC reduced the biovolume of live cells. PAA (YE) and BZK (CS and YE) at 1MIC did not alter the percentage of dead cells relative to non-exposed biofilms, and their effect of countering biofilm was due principally to the detachment of cells. These results suggest that doses of PAA and BZK close to MICs might lead to the dissemination of live bacteria from biofilms with consequent hazards for public health.

Effect of Sodium Hypochlorite and Benzalkonium Chloride on the Structural Parameters of the Biofilms Formed by Ten Salmonella enterica Serotypes

The influence of the strain on the ability of Salmonella enterica to form biofilms on polystyrene was investigated by confocal laser scanning microscopy. The effects of sodium hypochlorite with 10% active chlorine (SHY; 25,000, 50,000, or 100,000 ppm), and benzalkonium chloride (BZK; 1000, 5000, or 10,000 ppm) on twenty-four-hour-old biofilms was also determined. The biofilms of ten Salmonella enterica isolates from poultry (S. Agona, S. Anatum, S. Enteritidis, S. Hadar, S. Infantis, S. Kentucky, S. Thompson, S. Typhimurium, monophasic variant of S. Typhimurium 1,4,(5),12:i:-, and S. Virchow) were studied. Biofilms produced by S. Anatum, S. Hadar, S. Kentucky, and S. Typhimurium showed a trend to have the largest biovolume and the greatest surface coverage and thickness. The smallest biofilms (P < 0.01) in the observation field (14.2 × 103 µm2) were produced by S. Enteritidis and S. 1,4,(5),12:i:- (average 12.9 × 103 ± 9.3 × 103 µm3) compared to the rest of the serotypes (44.4 × 103 ± 24.7 × 103 µm3). Biovolume and surface coverage decreased after exposure for ten minutes to SHY at 50,000 or 100,000 ppm and to BZK at 5000 or 10,000 ppm. However, the lowest concentrations of disinfectants increased biovolume and surface coverage in biofilms of several strains (markedly so in the case of BZK). The results from this study suggest that the use of biocides at low concentrations could represent a public health risk. Further research studies under practical field conditions should be appropriate to confirm these findings.

Susceptibility of Listeria monocytogenes planktonic cultures and biofilms to sodium hypochlorite and benzalkonium chloride

The susceptibility of four L. monocytogenes isolates from pork to sodium hypochlorite (SHY) and benzalkonium chloride (BZK) was tested. Minimum inhibitory concentration (MIC) values of 3500 ppm (SHY), or between 3 ppm and 13 ppm (BZK), were found. Minimum bactericidal concentration (MBC) values ranged from 3500 ppm to 4500 ppm (SHY), and from 3 ppm to 14 ppm (BZK). The effect of SHY and BZK on the architecture and cellular viability of 24-h-old biofilms formed by such strains on polystyrene was determined through confocal laser scanning microscopy (CLSM) in conjunction with fluorescent dyes for live cells (SYTO 9) and dead cells (propidium iodide). Strains were able to form biofilm (biovolume values in the observation field of 14,161 μm² ranged between 103,928.3 ± 6730.2 μm³ and 276,030.9 ± 42,291.9 μm³). Treatment of biofilms for 10 min with SHY (1MIC or 1.5MIC) or BZK (0.5MIC, 1MIC or 1.5MIC) decreased the biovolume of live (potentially dangerous) cells. SHY reduced the cellular viability of biofilms by more than 90%. On the other hand, BZK was able to remove most biofilm mass (live and dead cells), but decreased cellular viability only to a lesser extent, this suggesting strong biofilm detachment and dissemination of live cells.

Characterization of Biofilms Formed by Foodborne Methicillin-Resistant Staphylococcus aureus

The objective of this study was to evaluate the capacity of 49 methicillin resistant Staphylococcus aureus (MRSA) from foods of animal origin (42 from dairy products and 7 from meat and meat products) to form biofilms. Overall, a higher biofilm biomass was observed for those MRSA strains harboring SCCmec type IV, while 8 MRSA strains (5 from dairy products and 3 from meat and meat products) were classified as strong biofilm formers in standard Tryptic Soy Broth medium. When a prolonged incubation period (48 h) was applied for those 8 MRSA strains, an increased biofilm biomass accumulation was observed during the time course, whereas the number of viable cells within the biofilms decreased as the biomass increased. The capacity of biofilm production correlated pretty well between the experiments using polystyrene microtiter plates and stainless steel micro-well plates, and significant higher values were observed in stainless steel when glucose was added to TSB during the enrichment. Biofilms were further characterized by confocal laser scanning microscope (CLSM), confirming that proteins and α-polysaccharides were the predominant components inside the extracellular polymeric matrix of biofilms formed by MRSA strains. In conclusion, our results confirm that MRSA isolates from foods of animal origin have significant capacity for forming biofilms with a high protein content, which can play a key role for the successful dissemination of MRSA lineages via food. Knowledge of the capacity of MRSA strains to produce biofilms, as well as characterization of the main MRSA biofilms matrix components, can help both to counteract the mechanisms involved in biofilm formation and resistance and to define more rational control strategies by using tailor-made cleaning agents.